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Each folder contains a readMe document explaining the nature of each file and dataset and the results and analyses that they relate to. The same anlaysis code (but not VCF files) is also available at https://github.com/seanstankowski/Littorina_reproductive_mode"}],"type":"research_data_reference","date_published":"2023-09-05T00:00:00Z","doi":"10.5281/ZENODO.8318995","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.8318995"}],"citation":{"chicago":"Stankowski, Sean. “Data and Code for: The Genetic Architecture of a Recent Transition to Live-Bearing in Marine Snails.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8318995.","mla":"Stankowski, Sean. Data and Code for: The Genetic Architecture of a Recent Transition to Live-Bearing in Marine Snails. Zenodo, 2023, doi:10.5281/ZENODO.8318995.","short":"S. Stankowski, (2023).","ista":"Stankowski S. 2023. Data and code for: The genetic architecture of a recent transition to live-bearing in marine snails, Zenodo, 10.5281/ZENODO.8318995.","ieee":"S. Stankowski, “Data and code for: The genetic architecture of a recent transition to live-bearing in marine snails.” Zenodo, 2023.","apa":"Stankowski, S. (2023). Data and code for: The genetic architecture of a recent transition to live-bearing in marine snails. Zenodo. https://doi.org/10.5281/ZENODO.8318995","ama":"Stankowski S. Data and code for: The genetic architecture of a recent transition to live-bearing in marine snails. 2023. doi:10.5281/ZENODO.8318995"},"oa":1,"has_accepted_license":"1","article_processing_charge":"No","day":"05","month":"09"},{"month":"04","publication_identifier":{"issn":["2791-4585"]},"oa":1,"degree_awarded":"MS","supervisor":[{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"}],"language":[{"iso":"eng"}],"doi":"10.15479/at:ista:12800","file_date_updated":"2023-06-02T22:30:04Z","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"year":"2023","date_created":"2023-04-04T18:57:11Z","date_updated":"2023-06-02T22:30:05Z","author":[{"full_name":"Julseth, Mara","id":"1cf464b2-dc7d-11ea-9b2f-f9b1aa9417d1","first_name":"Mara","last_name":"Julseth"}],"day":"05","article_processing_charge":"No","has_accepted_license":"1","page":"21","citation":{"ista":"Julseth M. 2023. The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone. Institute of Science and Technology Austria.","apa":"Julseth, M. (2023). The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12800","ieee":"M. Julseth, “The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone,” Institute of Science and Technology Austria, 2023.","ama":"Julseth M. The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone. 2023. doi:10.15479/at:ista:12800","chicago":"Julseth, Mara. “The Effect of Local Population Structure on Genetic Variation at Selected Loci in the A. Majus Hybrid Zone.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12800.","mla":"Julseth, Mara. The Effect of Local Population Structure on Genetic Variation at Selected Loci in the A. Majus Hybrid Zone. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12800.","short":"M. Julseth, The Effect of Local Population Structure on Genetic Variation at Selected Loci in the A. Majus Hybrid Zone, Institute of Science and Technology Austria, 2023."},"date_published":"2023-04-05T00:00:00Z","alternative_title":["ISTA Master's Thesis"],"type":"dissertation","abstract":[{"text":"The evolutionary processes that brought about today’s plethora of living species and the many billions more ancient ones all underlie biology. Evolutionary pathways are neither directed nor deterministic, but rather an interplay between selection, migration, mutation, genetic drift and other environmental factors. Hybrid zones, as natural crossing experiments, offer a great opportunity to use cline analysis to deduce different evolutionary processes - for example, selection strength. Theoretical cline models, largely assuming uniform distribution of individuals, often lack the capability of incorporating population structure. Since in reality organisms mostly live in patchy distributions and their dispersal is hardly ever Gaussian, it is necessary to unravel the effect of these different elements of population structure on cline parameters and shape. In this thesis, I develop a simulation inspired by the A. majus hybrid zone of a single selected locus under frequency dependent selection. This simulation enables us to untangle the effects of different elements of population structure as for example a low-density center and long-range dispersal. This thesis is therefore a first step towards theoretically untangling the effects of different elements of population structure on cline parameters and shape. ","lang":"eng"}],"status":"public","ddc":["576"],"title":"The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone","_id":"12800","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","file":[{"creator":"mjulseth","content_type":"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet","file_size":52795,"access_level":"closed","file_name":"Dispersaldata.xlsx","embargo_to":"open_access","checksum":"b76cf6d69f2093d8248f6a3f9d4654a4","date_created":"2023-04-06T06:09:40Z","date_updated":"2023-06-02T22:30:04Z","file_id":"12805","relation":"supplementary_material"},{"file_id":"12806","embargo":"2023-06-01","relation":"supplementary_material","checksum":"5a13b6d204371572e249f03795bc0d04","date_created":"2023-04-06T06:11:27Z","date_updated":"2023-06-02T22:30:04Z","access_level":"open_access","file_name":"2023_MSc_ThesisMaraJulseth_Notebook.nb","creator":"mjulseth","content_type":"application/vnd.wolfram.nb","file_size":787239},{"relation":"source_file","file_id":"12812","checksum":"c3ec842839ed1e66bf2618ae33047df8","date_updated":"2023-06-02T22:30:04Z","date_created":"2023-04-06T08:26:12Z","access_level":"closed","embargo_to":"open_access","file_name":"ThesisMaraJulseth_04_23.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":1061763,"creator":"mjulseth"},{"file_name":"ThesisMaraJulseth_04_23.pdf","access_level":"open_access","creator":"mjulseth","content_type":"application/pdf","file_size":1741364,"file_id":"12813","embargo":"2023-06-01","relation":"main_file","date_created":"2023-04-06T08:26:37Z","date_updated":"2023-06-02T22:30:04Z","checksum":"3132cc998fbe3ae2a3a83c2a69367f37"}],"oa_version":"Published Version"},{"publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Proceedings of the National Academy of Sciences","acknowledgement":"I thank Laura Hayward, Jitka Polechova, and Anja Westram for discussions and comments.","year":"2022","pmid":1,"date_created":"2022-07-31T22:01:47Z","date_updated":"2022-08-01T11:00:25Z","volume":119,"author":[{"full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"article_number":"e2122147119","file_date_updated":"2022-08-01T10:58:28Z","quality_controlled":"1","external_id":{"pmid":["35858408"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1073/pnas.2122147119","month":"07","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"ddc":["570"],"title":"The \"New Synthesis\"","status":"public","intvolume":" 119","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11702","oa_version":"Published Version","file":[{"date_updated":"2022-08-01T10:58:28Z","date_created":"2022-08-01T10:58:28Z","checksum":"06c866196a8957f0c37b8a121771c885","success":1,"relation":"main_file","file_id":"11716","file_size":848511,"content_type":"application/pdf","creator":"dernst","file_name":"2022_PNAS_Barton.pdf","access_level":"open_access"}],"type":"journal_article","abstract":[{"text":"When Mendel’s work was rediscovered in 1900, and extended to establish classical genetics, it was initially seen in opposition to Darwin’s theory of evolution by natural selection on continuous variation, as represented by the biometric research program that was the foundation of quantitative genetics. As Fisher, Haldane, and Wright established a century ago, Mendelian inheritance is exactly what is needed for natural selection to work efficiently. Yet, the synthesis remains unfinished. We do not understand why sexual reproduction and a fair meiosis predominate in eukaryotes, or how far these are responsible for their diversity and complexity. Moreover, although quantitative geneticists have long known that adaptive variation is highly polygenic, and that this is essential for efficient selection, this is only now becoming appreciated by molecular biologists—and we still do not have a good framework for understanding polygenic variation or diffuse function.","lang":"eng"}],"issue":"30","article_type":"original","publication":"Proceedings of the National Academy of Sciences of the United States of America","citation":{"ieee":"N. H. Barton, “The ‘New Synthesis,’” Proceedings of the National Academy of Sciences of the United States of America, vol. 119, no. 30. Proceedings of the National Academy of Sciences, 2022.","apa":"Barton, N. H. (2022). The “New Synthesis.” Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2122147119","ista":"Barton NH. 2022. The ‘New Synthesis’. Proceedings of the National Academy of Sciences of the United States of America. 119(30), e2122147119.","ama":"Barton NH. The “New Synthesis.” Proceedings of the National Academy of Sciences of the United States of America. 2022;119(30). doi:10.1073/pnas.2122147119","chicago":"Barton, Nicholas H. “The ‘New Synthesis.’” Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences, 2022. https://doi.org/10.1073/pnas.2122147119.","short":"N.H. Barton, Proceedings of the National Academy of Sciences of the United States of America 119 (2022).","mla":"Barton, Nicholas H. “The ‘New Synthesis.’” Proceedings of the National Academy of Sciences of the United States of America, vol. 119, no. 30, e2122147119, Proceedings of the National Academy of Sciences, 2022, doi:10.1073/pnas.2122147119."},"date_published":"2022-07-18T00:00:00Z","scopus_import":"1","day":"18","article_processing_charge":"No","has_accepted_license":"1"},{"citation":{"chicago":"Matejovicova, Lenka. “Genetic Basis of Flower Colour as a Model for Adaptive Evolution.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11128.","mla":"Matejovicova, Lenka. Genetic Basis of Flower Colour as a Model for Adaptive Evolution. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11128.","short":"L. Matejovicova, Genetic Basis of Flower Colour as a Model for Adaptive Evolution, Institute of Science and Technology Austria, 2022.","ista":"Matejovicova L. 2022. Genetic basis of flower colour as a model for adaptive evolution. Institute of Science and Technology Austria.","apa":"Matejovicova, L. (2022). Genetic basis of flower colour as a model for adaptive evolution. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11128","ieee":"L. Matejovicova, “Genetic basis of flower colour as a model for adaptive evolution,” Institute of Science and Technology Austria, 2022.","ama":"Matejovicova L. Genetic basis of flower colour as a model for adaptive evolution. 2022. doi:10.15479/at:ista:11128"},"page":"112","date_published":"2022-04-06T00:00:00Z","has_accepted_license":"1","article_processing_charge":"No","day":"06","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"11128","ddc":["576","582"],"title":"Genetic basis of flower colour as a model for adaptive evolution","status":"public","oa_version":"Published Version","file":[{"creator":"cchlebak","file_size":11906472,"content_type":"application/pdf","access_level":"open_access","file_name":"LenkaPhD_Official_PDFA.pdf","checksum":"e9609bc4e8f8e20146fc1125fd4f1bf7","date_created":"2022-04-07T08:11:34Z","date_updated":"2022-04-07T08:11:34Z","file_id":"11129","relation":"main_file"},{"creator":"cchlebak","content_type":"application/x-zip-compressed","file_size":23036766,"access_level":"closed","file_name":"LenkaPhD Official_source.zip","checksum":"99d67040432fd07a225643a212ee8588","date_created":"2022-04-07T08:11:51Z","date_updated":"2022-04-07T08:11:51Z","file_id":"11130","relation":"source_file"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"text":"Although we often see studies focusing on simple or even discrete traits in studies of colouration,\r\nthe variation of “appearance” phenotypes found in nature is often more complex, continuous\r\nand high-dimensional. Therefore, we developed automated methods suitable for large datasets\r\nof genomes and images, striving to account for their complex nature, while minimising human\r\nbias. We used these methods on a dataset of more than 20, 000 plant SNP genomes and\r\ncorresponding fower images from a hybrid zone of two subspecies of Antirrhinum majus with\r\ndistinctly coloured fowers to improve our understanding of the genetic nature of the fower\r\ncolour in our study system.\r\nFirstly, we use the advantage of large numbers of genotyped plants to estimate the haplotypes in\r\nthe main fower colour regulating region. We study colour- and geography-related characteristics\r\nof the estimated haplotypes and how they connect to their relatedness. We show discrepancies\r\nfrom the expected fower colour distributions given the genotype and identify particular\r\nhaplotypes leading to unexpected phenotypes. We also confrm a signifcant defcit of the\r\ndouble recessive recombinant and quite surprisingly, we show that haplotypes of the most\r\nfrequent parental type are much less variable than others.\r\nSecondly, we introduce our pipeline capable of processing tens of thousands of full fower\r\nimages without human interaction and summarising each image into a set of informative scores.\r\nWe show the compatibility of these machine-measured fower colour scores with the previously\r\nused manual scores and study impact of external efect on the resulting scores. Finally, we use\r\nthe machine-measured fower colour scores to ft and examine a phenotype cline across the\r\nhybrid zone in Planoles using full fower images as opposed to discrete, manual scores and\r\ncompare it with the genotypic cline.","lang":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"doi":"10.15479/at:ista:11128","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"}],"degree_awarded":"PhD","supervisor":[{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton"}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-016-9"]},"month":"04","year":"2022","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","author":[{"full_name":"Matejovicova, Lenka","first_name":"Lenka","last_name":"Matejovicova","id":"2DFDEC72-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2022-04-07T08:19:54Z","date_updated":"2023-06-23T06:26:41Z","file_date_updated":"2022-04-07T08:11:51Z"},{"day":"01","article_processing_charge":"No","has_accepted_license":"1","keyword":["genetics","ecology","evolution","behavior and systematics"],"date_published":"2022-02-01T00:00:00Z","publication":"Evolution Letters","citation":{"ama":"Turelli M, Barton NH. Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics, and disease control. Evolution Letters. 2022;6(1):92-105. doi:10.1002/evl3.270","ista":"Turelli M, Barton NH. 2022. Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics, and disease control. Evolution Letters. 6(1), 92–105.","apa":"Turelli, M., & Barton, N. H. (2022). Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics, and disease control. Evolution Letters. Wiley. https://doi.org/10.1002/evl3.270","ieee":"M. Turelli and N. H. Barton, “Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics, and disease control,” Evolution Letters, vol. 6, no. 1. Wiley, pp. 92–105, 2022.","mla":"Turelli, Michael, and Nicholas H. Barton. “Why Did the Wolbachia Transinfection Cross the Road? Drift, Deterministic Dynamics, and Disease Control.” Evolution Letters, vol. 6, no. 1, Wiley, 2022, pp. 92–105, doi:10.1002/evl3.270.","short":"M. Turelli, N.H. Barton, Evolution Letters 6 (2022) 92–105.","chicago":"Turelli, Michael, and Nicholas H Barton. “Why Did the Wolbachia Transinfection Cross the Road? Drift, Deterministic Dynamics, and Disease Control.” Evolution Letters. Wiley, 2022. https://doi.org/10.1002/evl3.270."},"article_type":"original","page":"92-105","abstract":[{"text":"Maternally inherited Wolbachia transinfections are being introduced into natural mosquito populations to reduce the transmission of dengue, Zika, and other arboviruses. Wolbachia-induced cytoplasmic incompatibility provides a frequency-dependent reproductive advantage to infected females that can spread transinfections within and among populations. However, because transinfections generally reduce host fitness, they tend to spread within populations only after their frequency exceeds a critical threshold. This produces bistability with stable equilibrium frequencies at both 0 and 1, analogous to the bistability produced by underdominance between alleles or karyotypes and by population dynamics under Allee effects. Here, we analyze how stochastic frequency variation produced by finite population size can facilitate the local spread of variants with bistable dynamics into areas where invasion is unexpected from deterministic models. Our exemplar is the establishment of wMel Wolbachia in the Aedes aegypti population of Pyramid Estates (PE), a small community in far north Queensland, Australia. In 2011, wMel was stably introduced into Gordonvale, separated from PE by barriers to A. aegypti dispersal. After nearly 6 years during which wMel was observed only at low frequencies in PE, corresponding to an apparent equilibrium between immigration and selection, wMel rose to fixation by 2018. Using analytic approximations and statistical analyses, we demonstrate that the observed fixation of wMel at PE is consistent with both stochastic transition past an unstable threshold frequency and deterministic transformation produced by steady immigration at a rate just above the threshold required for deterministic invasion. The indeterminacy results from a delicate balance of parameters needed to produce the delayed transition observed. Our analyses suggest that once Wolbachia transinfections are established locally through systematic introductions, stochastic “threshold crossing” is likely to only minimally enhance spatial spread, providing a local ratchet that slightly—but systematically—aids area-wide transformation of disease-vector populations in heterogeneous landscapes.","lang":"eng"}],"issue":"1","type":"journal_article","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2022_EvolutionLetters_Turelli.pdf","file_size":2435185,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"11689","checksum":"7e9a37e3b65b480cd7014a6a4a7e460a","success":1,"date_created":"2022-07-29T06:59:10Z","date_updated":"2022-07-29T06:59:10Z"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10604","status":"public","ddc":["570"],"title":"Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics, and disease control","intvolume":" 6","month":"02","publication_identifier":{"eissn":["2056-3744"]},"doi":"10.1002/evl3.270","language":[{"iso":"eng"}],"external_id":{"isi":["000754412600008"]},"oa":1,"quality_controlled":"1","isi":1,"file_date_updated":"2022-07-29T06:59:10Z","author":[{"first_name":"Michael","last_name":"Turelli","full_name":"Turelli, Michael"},{"full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"11686","relation":"research_data","status":"public"}]},"date_updated":"2023-08-02T13:50:09Z","date_created":"2022-01-09T09:45:17Z","volume":6,"acknowledgement":"We thank S. O'Neill, C. Simmons, and the World Mosquito Project for providing access to unpublished data. S. Ritchie provided valuable insights into Aedes aegypti biology and the literature describing A. aegypti populations near Cairns. We thank B. Cooper for help with the figures and D. Shropshire, S. O'Neill, S. Ritchie, A. Hoffmann, B. Cooper, and members of the Cooper lab for comments on an earlier draft. Comments from three reviewers greatly improved our presentation.","year":"2022","publication_status":"published","publisher":"Wiley","department":[{"_id":"NiBa"}]},{"keyword":["Biological sciences"],"article_processing_charge":"No","month":"01","day":"06","citation":{"chicago":"Turelli, Michael, and Nicholas H Barton. “Wolbachia Frequency Data from: Why Did the Wolbachia Transinfection Cross the Road? Drift, Deterministic Dynamics and Disease Control.” Dryad, 2022. https://doi.org/10.25338/B81931.","mla":"Turelli, Michael, and Nicholas H. Barton. Wolbachia Frequency Data from: Why Did the Wolbachia Transinfection Cross the Road? Drift, Deterministic Dynamics and Disease Control. Dryad, 2022, doi:10.25338/B81931.","short":"M. Turelli, N.H. Barton, (2022).","ista":"Turelli M, Barton NH. 2022. Wolbachia frequency data from: Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics and disease control, Dryad, 10.25338/B81931.","apa":"Turelli, M., & Barton, N. H. (2022). Wolbachia frequency data from: Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics and disease control. Dryad. https://doi.org/10.25338/B81931","ieee":"M. Turelli and N. H. Barton, “Wolbachia frequency data from: Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics and disease control.” Dryad, 2022.","ama":"Turelli M, Barton NH. Wolbachia frequency data from: Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics and disease control. 2022. doi:10.25338/B81931"},"tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.25338/B81931"}],"doi":"10.25338/B81931","date_published":"2022-01-06T00:00:00Z","type":"research_data_reference","abstract":[{"text":"Maternally inherited Wolbachia transinfections are being introduced into natural mosquito populations to reduce the transmission of dengue, Zika and other arboviruses. Wolbachia-induced cytoplasmic incompatibility provides a frequency-dependent reproductive advantage to infected females that can spread transinfections within and among populations. However, because transinfections generally reduce host fitness, they tend to spread within populations only after their frequency exceeds a critical threshold. This produces bistability with stable equilibrium frequencies at both 0 and 1, analogous to the bistability produced by underdominance between alleles or karyotypes and by population dynamics under Allee effects. Here, we analyze how stochastic frequency variation produced by finite population size can facilitate the local spread of variants with bistable dynamics into areas where invasion is unexpected from deterministic models. Our exemplar is the establishment of wMel Wolbachia in the Aedes aegypti population of Pyramid Estates (PE), a small community in far north Queensland, Australia. In 2011, wMel was stably introduced into Gordonvale, separated from PE by barriers to Ae. aegypti dispersal. After nearly six years during which wMel was observed only at low frequencies in PE, corresponding to an apparent equilibrium between immigration and selection, wMel rose to fixation by 2018. Using analytic approximations and statistical analyses, we demonstrate that the observed fixation of wMel at PE is consistent with both stochastic transition past an unstable threshold frequency and deterministic transformation produced by steady immigration at a rate just above the threshold required for deterministic invasion. The indeterminacy results from a delicate balance of parameters needed to produce the delayed transition observed. Our analyses suggest that once Wolbachia transinfections are established locally through systematic introductions, stochastic “threshold crossing” is likely to only minimally enhance spatial spread, providing a local ratchet that slightly – but systematically – aids area-wide transformation of disease-vector populations in heterogeneous landscapes.","lang":"eng"}],"_id":"11686","year":"2022","acknowledgement":"Bill and Melinda Gates Foundation, Award: OPP1180815","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publisher":"Dryad","department":[{"_id":"NiBa"}],"title":"Wolbachia frequency data from: Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics and disease control","status":"public","ddc":["570"],"related_material":{"record":[{"id":"10604","status":"public","relation":"used_in_publication"}]},"author":[{"full_name":"Turelli, Michael","last_name":"Turelli","first_name":"Michael"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H"}],"oa_version":"Published Version","date_updated":"2023-08-02T13:50:08Z","date_created":"2022-07-29T06:45:41Z"},{"abstract":[{"lang":"eng","text":"Predicting function from sequence is a central problem of biology. Currently, this is possible only locally in a narrow mutational neighborhood around a wildtype sequence rather than globally from any sequence. Using random mutant libraries, we developed a biophysical model that accounts for multiple features of σ70 binding bacterial promoters to predict constitutive gene expression levels from any sequence. We experimentally and theoretically estimated that 10–20% of random sequences lead to expression and ~80% of non-expressing sequences are one mutation away from a functional promoter. The potential for generating expression from random sequences is so pervasive that selection acts against σ70-RNA polymerase binding sites even within inter-genic, promoter-containing regions. This pervasiveness of σ70-binding sites implies that emergence of promoters is not the limiting step in gene regulatory evolution. Ultimately, the inclusion of novel features of promoter function into a mechanistic model enabled not only more accurate predictions of gene expression levels, but also identified that promoters evolve more rapidly than previously thought."}],"type":"journal_article","file":[{"relation":"main_file","file_id":"10739","checksum":"decdcdf600ff51e9a9703b49ca114170","success":1,"date_updated":"2022-02-07T07:14:09Z","date_created":"2022-02-07T07:14:09Z","access_level":"open_access","file_name":"2022_ELife_Lagator.pdf","content_type":"application/pdf","file_size":5604343,"creator":"cchlebak"}],"oa_version":"Published Version","ddc":["576"],"status":"public","title":"Predicting bacterial promoter function and evolution from random sequences","intvolume":" 11","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10736","day":"26","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2022-01-26T00:00:00Z","article_type":"original","publication":"eLife","citation":{"chicago":"Lagator, Mato, Srdjan Sarikas, Magdalena Steinrueck, David Toledo-Aparicio, Jonathan P Bollback, Calin C Guet, and Gašper Tkačik. “Predicting Bacterial Promoter Function and Evolution from Random Sequences.” ELife. eLife Sciences Publications, 2022. https://doi.org/10.7554/eLife.64543.","short":"M. Lagator, S. Sarikas, M. Steinrueck, D. Toledo-Aparicio, J.P. Bollback, C.C. Guet, G. Tkačik, ELife 11 (2022).","mla":"Lagator, Mato, et al. “Predicting Bacterial Promoter Function and Evolution from Random Sequences.” ELife, vol. 11, e64543, eLife Sciences Publications, 2022, doi:10.7554/eLife.64543.","apa":"Lagator, M., Sarikas, S., Steinrueck, M., Toledo-Aparicio, D., Bollback, J. P., Guet, C. C., & Tkačik, G. (2022). Predicting bacterial promoter function and evolution from random sequences. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.64543","ieee":"M. Lagator et al., “Predicting bacterial promoter function and evolution from random sequences,” eLife, vol. 11. eLife Sciences Publications, 2022.","ista":"Lagator M, Sarikas S, Steinrueck M, Toledo-Aparicio D, Bollback JP, Guet CC, Tkačik G. 2022. Predicting bacterial promoter function and evolution from random sequences. eLife. 11, e64543.","ama":"Lagator M, Sarikas S, Steinrueck M, et al. Predicting bacterial promoter function and evolution from random sequences. eLife. 2022;11. doi:10.7554/eLife.64543"},"file_date_updated":"2022-02-07T07:14:09Z","ec_funded":1,"article_number":"e64543","date_created":"2022-02-06T23:01:32Z","date_updated":"2023-08-02T14:09:02Z","volume":11,"author":[{"id":"345D25EC-F248-11E8-B48F-1D18A9856A87","first_name":"Mato","last_name":"Lagator","full_name":"Lagator, Mato"},{"full_name":"Sarikas, Srdjan","last_name":"Sarikas","first_name":"Srdjan","id":"35F0286E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Steinrueck, Magdalena","first_name":"Magdalena","last_name":"Steinrueck"},{"last_name":"Toledo-Aparicio","first_name":"David","full_name":"Toledo-Aparicio, David"},{"full_name":"Bollback, Jonathan P","last_name":"Bollback","first_name":"Jonathan P","orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","first_name":"Calin C","full_name":"Guet, Calin C"},{"full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","first_name":"Gašper","last_name":"Tkačik"}],"publication_status":"published","department":[{"_id":"CaGu"},{"_id":"GaTk"},{"_id":"NiBa"}],"publisher":"eLife Sciences Publications","acknowledgement":"We thank Hande Acar, Nicholas H Barton, Rok Grah, Tiago Paixao, Maros Pleska, Anna Staron, and Murat Tugrul for insightful comments and input on the manuscript. This work was supported by: Sir Henry Dale Fellowship jointly funded by the Wellcome Trust and the Royal Society (grant number 216779/Z/19/Z) to ML; IPC Grant from IST Austria to ML and SS; European Research Council Funding Programme 7 (2007–2013, grant agreement number 648440) to JPB.","year":"2022","pmid":1,"month":"01","publication_identifier":{"eissn":["2050-084X"]},"language":[{"iso":"eng"}],"doi":"10.7554/eLife.64543","isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Selective Barriers to Horizontal Gene Transfer","grant_number":"648440","_id":"2578D616-B435-11E9-9278-68D0E5697425"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["35080492"],"isi":["000751104400001"]},"oa":1},{"issue":"5","abstract":[{"lang":"eng","text":"Hybridization is a common evolutionary process with multiple possible outcomes. In vertebrates, interspecific hybridization has repeatedly generated parthenogenetic hybrid species. However, it is unknown whether the generation of parthenogenetic hybrids is a rare outcome of frequent hybridization between sexual species within a genus or the typical outcome of rare hybridization events. Darevskia is a genus of rock lizards with both hybrid parthenogenetic and sexual species. Using capture sequencing, we estimate phylogenetic relationships and gene flow among the sexual species, to determine how introgressive hybridization relates to the origins of parthenogenetic hybrids. We find evidence for widespread hybridization with gene flow, both between recently diverged species and deep branches. Surprisingly, we find no signal of gene flow between parental species of the parthenogenetic hybrids, suggesting that the parental pairs were either reproductively or geographically isolated early in their divergence. The generation of parthenogenetic hybrids in Darevskia is, then, a rare outcome of the total occurrence of hybridization within the genus, but the typical outcome when specific species pairs hybridize. Our results question the conventional view that parthenogenetic lineages are generated by hybridization in a window of divergence. Instead, they suggest that some lineages possess specific properties that underpin successful parthenogenetic reproduction."}],"type":"journal_article","file":[{"file_id":"11729","relation":"main_file","date_created":"2022-08-05T06:19:28Z","date_updated":"2022-08-05T06:19:28Z","success":1,"checksum":"c27c025ae9afcf6c804d46a909775ee5","file_name":"2022_Evolution_Freitas.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":2855214}],"oa_version":"Published Version","_id":"11334","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 76","ddc":["570"],"status":"public","title":"Parthenogenesis in Darevskia lizards: A rare outcome of common hybridization, not a common outcome of rare hybridization","article_processing_charge":"No","has_accepted_license":"1","day":"01","scopus_import":"1","date_published":"2022-05-01T00:00:00Z","citation":{"mla":"Freitas, Susana, et al. “Parthenogenesis in Darevskia Lizards: A Rare Outcome of Common Hybridization, Not a Common Outcome of Rare Hybridization.” Evolution, vol. 76, no. 5, Wiley, 2022, pp. 899–914, doi:10.1111/evo.14462.","short":"S. Freitas, A.M. Westram, T. Schwander, M. Arakelyan, Ç. Ilgaz, Y. Kumlutas, D.J. Harris, M.A. Carretero, R.K. Butlin, Evolution 76 (2022) 899–914.","chicago":"Freitas, Susana, Anja M Westram, Tanja Schwander, Marine Arakelyan, Çetin Ilgaz, Yusuf Kumlutas, David James Harris, Miguel A. Carretero, and Roger K. Butlin. “Parthenogenesis in Darevskia Lizards: A Rare Outcome of Common Hybridization, Not a Common Outcome of Rare Hybridization.” Evolution. Wiley, 2022. https://doi.org/10.1111/evo.14462.","ama":"Freitas S, Westram AM, Schwander T, et al. Parthenogenesis in Darevskia lizards: A rare outcome of common hybridization, not a common outcome of rare hybridization. Evolution. 2022;76(5):899-914. doi:10.1111/evo.14462","ista":"Freitas S, Westram AM, Schwander T, Arakelyan M, Ilgaz Ç, Kumlutas Y, Harris DJ, Carretero MA, Butlin RK. 2022. Parthenogenesis in Darevskia lizards: A rare outcome of common hybridization, not a common outcome of rare hybridization. Evolution. 76(5), 899–914.","apa":"Freitas, S., Westram, A. M., Schwander, T., Arakelyan, M., Ilgaz, Ç., Kumlutas, Y., … Butlin, R. K. (2022). Parthenogenesis in Darevskia lizards: A rare outcome of common hybridization, not a common outcome of rare hybridization. Evolution. Wiley. https://doi.org/10.1111/evo.14462","ieee":"S. Freitas et al., “Parthenogenesis in Darevskia lizards: A rare outcome of common hybridization, not a common outcome of rare hybridization,” Evolution, vol. 76, no. 5. Wiley, pp. 899–914, 2022."},"publication":"Evolution","page":"899-914","article_type":"original","ec_funded":1,"file_date_updated":"2022-08-05T06:19:28Z","author":[{"first_name":"Susana","last_name":"Freitas","full_name":"Freitas, Susana"},{"last_name":"Westram","first_name":"Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","full_name":"Westram, Anja M"},{"full_name":"Schwander, Tanja","first_name":"Tanja","last_name":"Schwander"},{"first_name":"Marine","last_name":"Arakelyan","full_name":"Arakelyan, Marine"},{"full_name":"Ilgaz, Çetin","first_name":"Çetin","last_name":"Ilgaz"},{"first_name":"Yusuf","last_name":"Kumlutas","full_name":"Kumlutas, Yusuf"},{"full_name":"Harris, David James","last_name":"Harris","first_name":"David James"},{"last_name":"Carretero","first_name":"Miguel A.","full_name":"Carretero, Miguel A."},{"first_name":"Roger K.","last_name":"Butlin","full_name":"Butlin, Roger K."}],"volume":76,"date_updated":"2023-08-03T07:00:28Z","date_created":"2022-04-24T22:01:44Z","pmid":1,"acknowledgement":"The authors thank A. van der Meijden and F. Ahmadzadeh for providing specimens and tissue samples, and A. Vardanyan, C. Corti, F. Jorge, and S. Drovetski for support during field work. The authors also thank S. Qiu for assistance with python scripting, S. Rocha for her support in BEAST analysis, and B. Wielstra for his comments on\r\na previous version of the manuscript. SF was funded by FCT grant SFRH/BD/81483/2011 (a PhD individual grant). AMW was funded by the European Union’s Horizon 2020 research and innovation programme under Marie Skłodowska-Curie grant agreement no. 797747. TS acknowledges funding from the Swiss National Science Foundation (grants\r\nPP00P3_170627 and 31003A_182495). The work was carried out under financial support of the projects “Preserving Armenian biodiversity: Joint Portuguese – Armenian program for training in modern conservation biology” of Gulbenkian Foundation (Portugal) and PTDC/BIABEC/101256/2008 of Fundação para a Ciência e a Tecnologia (FCT, Portugal).","year":"2022","department":[{"_id":"NiBa"},{"_id":"BeVi"}],"publisher":"Wiley","publication_status":"published","publication_identifier":{"eissn":["1558-5646"],"issn":["0014-3820"]},"month":"05","doi":"10.1111/evo.14462","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"external_id":{"isi":["000781632500001"],"pmid":["35323995"]},"oa":1,"project":[{"call_identifier":"H2020","name":"Theoretical and empirical approaches to understanding Parallel Adaptation","grant_number":"797747","_id":"265B41B8-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1"},{"issue":"8","abstract":[{"text":"Empirical essays of fitness landscapes suggest that they may be rugged, that is having multiple fitness peaks. Such fitness landscapes, those that have multiple peaks, necessarily have special local structures, called reciprocal sign epistasis (Poelwijk et al. in J Theor Biol 272:141–144, 2011). Here, we investigate the quantitative relationship between the number of fitness peaks and the number of reciprocal sign epistatic interactions. Previously, it has been shown (Poelwijk et al. in J Theor Biol 272:141–144, 2011) that pairwise reciprocal sign epistasis is a necessary but not sufficient condition for the existence of multiple peaks. Applying discrete Morse theory, which to our knowledge has never been used in this context, we extend this result by giving the minimal number of reciprocal sign epistatic interactions required to create a given number of peaks.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"11455","date_created":"2022-06-20T07:51:32Z","date_updated":"2022-06-20T07:51:32Z","checksum":"05a1fe7d10914a00c2bca9b447993a65","success":1,"file_name":"2022_BulletinMathBiology_Saona.pdf","access_level":"open_access","file_size":463025,"content_type":"application/pdf","creator":"dernst"}],"_id":"11447","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 84","ddc":["510","570"],"title":"Relation between the number of peaks and the number of reciprocal sign epistatic interactions","status":"public","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"17","scopus_import":"1","keyword":["Computational Theory and Mathematics","General Agricultural and Biological Sciences","Pharmacology","General Environmental Science","General Biochemistry","Genetics and Molecular Biology","General Mathematics","Immunology","General Neuroscience"],"date_published":"2022-06-17T00:00:00Z","citation":{"short":"R.J. Saona Urmeneta, F. Kondrashov, K. Khudiakova, Bulletin of Mathematical Biology 84 (2022).","mla":"Saona Urmeneta, Raimundo J., et al. “Relation between the Number of Peaks and the Number of Reciprocal Sign Epistatic Interactions.” Bulletin of Mathematical Biology, vol. 84, no. 8, 74, Springer Nature, 2022, doi:10.1007/s11538-022-01029-z.","chicago":"Saona Urmeneta, Raimundo J, Fyodor Kondrashov, and Kseniia Khudiakova. “Relation between the Number of Peaks and the Number of Reciprocal Sign Epistatic Interactions.” Bulletin of Mathematical Biology. Springer Nature, 2022. https://doi.org/10.1007/s11538-022-01029-z.","ama":"Saona Urmeneta RJ, Kondrashov F, Khudiakova K. Relation between the number of peaks and the number of reciprocal sign epistatic interactions. Bulletin of Mathematical Biology. 2022;84(8). doi:10.1007/s11538-022-01029-z","ieee":"R. J. Saona Urmeneta, F. Kondrashov, and K. Khudiakova, “Relation between the number of peaks and the number of reciprocal sign epistatic interactions,” Bulletin of Mathematical Biology, vol. 84, no. 8. Springer Nature, 2022.","apa":"Saona Urmeneta, R. J., Kondrashov, F., & Khudiakova, K. (2022). Relation between the number of peaks and the number of reciprocal sign epistatic interactions. Bulletin of Mathematical Biology. Springer Nature. https://doi.org/10.1007/s11538-022-01029-z","ista":"Saona Urmeneta RJ, Kondrashov F, Khudiakova K. 2022. Relation between the number of peaks and the number of reciprocal sign epistatic interactions. Bulletin of Mathematical Biology. 84(8), 74."},"publication":"Bulletin of Mathematical Biology","article_type":"original","ec_funded":1,"file_date_updated":"2022-06-20T07:51:32Z","article_number":"74","related_material":{"link":[{"url":"https://doi.org/10.1007/s11538-022-01118-z","relation":"erratum"}]},"author":[{"first_name":"Raimundo J","last_name":"Saona Urmeneta","id":"BD1DF4C4-D767-11E9-B658-BC13E6697425","orcid":"0000-0001-5103-038X","full_name":"Saona Urmeneta, Raimundo J"},{"full_name":"Kondrashov, Fyodor","last_name":"Kondrashov","first_name":"Fyodor","orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Kseniia","last_name":"Khudiakova","id":"4E6DC800-AE37-11E9-AC72-31CAE5697425","orcid":"0000-0002-6246-1465","full_name":"Khudiakova, Kseniia"}],"volume":84,"date_updated":"2023-08-03T07:20:53Z","date_created":"2022-06-17T16:16:15Z","acknowledgement":"We are grateful to Herbert Edelsbrunner and Jeferson Zapata for helpful discussions. Open access funding provided by Austrian Science Fund (FWF). Partially supported by the ERC Consolidator (771209–CharFL) and the FWF Austrian Science Fund (I5127-B) grants to FAK.","year":"2022","department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"JaMa"}],"publisher":"Springer Nature","publication_status":"published","publication_identifier":{"issn":["0092-8240"],"eissn":["1522-9602"]},"month":"06","doi":"10.1007/s11538-022-01029-z","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000812509800001"]},"project":[{"grant_number":"771209","_id":"26580278-B435-11E9-9278-68D0E5697425","name":"Characterizing the fitness landscape on population and global scales","call_identifier":"H2020"},{"name":"Evolutionary analysis of gene regulation","grant_number":"I05127","_id":"c098eddd-5a5b-11eb-8a69-abe27170a68f"}],"quality_controlled":"1","isi":1},{"_id":"11546","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Inversions and parallel evolution","ddc":["570"],"status":"public","intvolume":" 377","file":[{"access_level":"open_access","file_name":"2022_PhilosophicalTransactionsB_Westram.pdf","creator":"dernst","file_size":920304,"content_type":"application/pdf","file_id":"12479","relation":"main_file","success":1,"checksum":"49f69428f3dcf5ce3ff281f7d199e9df","date_updated":"2023-02-02T08:20:29Z","date_created":"2023-02-02T08:20:29Z"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Local adaptation leads to differences between populations within a species. In many systems, similar environmental contrasts occur repeatedly, sometimes driving parallel phenotypic evolution. Understanding the genomic basis of local adaptation and parallel evolution is a major goal of evolutionary genomics. It is now known that by preventing the break-up of favourable combinations of alleles across multiple loci, genetic architectures that reduce recombination, like chromosomal inversions, can make an important contribution to local adaptation. However, little is known about whether inversions also contribute disproportionately to parallel evolution. Our aim here is to highlight this knowledge gap, to showcase existing studies, and to illustrate the differences between genomic architectures with and without inversions using simple models. We predict that by generating stronger effective selection, inversions can sometimes speed up the parallel adaptive process or enable parallel adaptation where it would be impossible otherwise, but this is highly dependent on the spatial setting. We highlight that further empirical work is needed, in particular to cover a broader taxonomic range and to understand the relative importance of inversions compared to genomic regions without inversions.","lang":"eng"}],"issue":"1856","publication":"Philosophical Transactions of the Royal Society B: Biological Sciences","citation":{"chicago":"Westram, Anja M, Rui Faria, Kerstin Johannesson, Roger Butlin, and Nicholas H Barton. “Inversions and Parallel Evolution.” Philosophical Transactions of the Royal Society B: Biological Sciences. Royal Society of London, 2022. https://doi.org/10.1098/rstb.2021.0203.","short":"A.M. Westram, R. Faria, K. Johannesson, R. Butlin, N.H. Barton, Philosophical Transactions of the Royal Society B: Biological Sciences 377 (2022).","mla":"Westram, Anja M., et al. “Inversions and Parallel Evolution.” Philosophical Transactions of the Royal Society B: Biological Sciences, vol. 377, no. 1856, 20210203, Royal Society of London, 2022, doi:10.1098/rstb.2021.0203.","ieee":"A. M. Westram, R. Faria, K. Johannesson, R. Butlin, and N. H. Barton, “Inversions and parallel evolution,” Philosophical Transactions of the Royal Society B: Biological Sciences, vol. 377, no. 1856. Royal Society of London, 2022.","apa":"Westram, A. M., Faria, R., Johannesson, K., Butlin, R., & Barton, N. H. (2022). Inversions and parallel evolution. Philosophical Transactions of the Royal Society B: Biological Sciences. Royal Society of London. https://doi.org/10.1098/rstb.2021.0203","ista":"Westram AM, Faria R, Johannesson K, Butlin R, Barton NH. 2022. Inversions and parallel evolution. Philosophical Transactions of the Royal Society B: Biological Sciences. 377(1856), 20210203.","ama":"Westram AM, Faria R, Johannesson K, Butlin R, Barton NH. Inversions and parallel evolution. Philosophical Transactions of the Royal Society B: Biological Sciences. 2022;377(1856). doi:10.1098/rstb.2021.0203"},"article_type":"original","date_published":"2022-08-01T00:00:00Z","scopus_import":"1","keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology"],"day":"01","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","year":"2022","acknowledgement":"We thank the editor and two anonymous reviewers for their helpful and interesting comments on this manuscript.","publication_status":"published","publisher":"Royal Society of London","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"author":[{"full_name":"Westram, Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","first_name":"Anja M","last_name":"Westram"},{"full_name":"Faria, Rui","last_name":"Faria","first_name":"Rui"},{"full_name":"Johannesson, Kerstin","last_name":"Johannesson","first_name":"Kerstin"},{"full_name":"Butlin, Roger","last_name":"Butlin","first_name":"Roger"},{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton"}],"date_created":"2022-07-08T11:41:56Z","date_updated":"2023-08-03T11:55:42Z","volume":377,"article_number":"20210203","file_date_updated":"2023-02-02T08:20:29Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000812317300005"]},"oa":1,"isi":1,"quality_controlled":"1","project":[{"_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","grant_number":"P32166","name":"The maintenance of alternative adaptive peaks in snapdragons"}],"doi":"10.1098/rstb.2021.0203","language":[{"iso":"eng"}],"month":"08","publication_identifier":{"issn":["0962-8436"],"eissn":["1471-2970"]}},{"ec_funded":1,"file_date_updated":"2023-02-02T08:11:23Z","author":[{"id":"485BB5A4-F248-11E8-B48F-1D18A9856A87","first_name":"Eniko","last_name":"Szep","full_name":"Szep, Eniko"},{"full_name":"Trubenova, Barbora","first_name":"Barbora","last_name":"Trubenova","id":"42302D54-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6873-2967"},{"full_name":"Csilléry, Katalin","last_name":"Csilléry","first_name":"Katalin"}],"volume":22,"date_created":"2022-07-24T22:01:43Z","date_updated":"2023-08-03T12:11:01Z","acknowledgement":"ES was supported by an IST studentship provided by IST Austria. BT was funded by the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Independent Fellowship (704172, RACE). This project received further funding awarded to KC from the Swiss National Science Foundation (SNSF CRSK-3_190288) and the Swiss Federal Research Institute WSL. We thank Nick Barton for many invaluable discussions and his comments on the thesis chapter and this manuscript. We thank Peter Ralph and Jerome Kelleher for useful discussions and Bisschop Gertjan for comments on this manuscript. We thank Fortunat Joos for providing us with the raw data from the LPX-Bern model for silver fir, and Willy Tinner for helpful insights about the demographic history of silver fir. We also thank the editor Alana Alexander for useful comments and advice on the manuscript. Open access funding provided by Eidgenossische Technische Hochschule Zurich.","year":"2022","department":[{"_id":"NiBa"}],"publisher":"Wiley","publication_status":"published","publication_identifier":{"issn":["1755-098X"],"eissn":["1755-0998"]},"month":"11","doi":"10.1111/1755-0998.13676","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"external_id":{"isi":["000825873600001"]},"project":[{"call_identifier":"H2020","name":"Rate of Adaptation in Changing Environment","grant_number":"704172","_id":"25AEDD42-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"issue":"8","abstract":[{"text":"Spatially explicit population genetic models have long been developed, yet have rarely been used to test hypotheses about the spatial distribution of genetic diversity or the genetic divergence between populations. Here, we use spatially explicit coalescence simulations to explore the properties of the island and the two-dimensional stepping stone models under a wide range of scenarios with spatio-temporal variation in deme size. We avoid the simulation of genetic data, using the fact that under the studied models, summary statistics of genetic diversity and divergence can be approximated from coalescence times. We perform the simulations using gridCoal, a flexible spatial wrapper for the software msprime (Kelleher et al., 2016, Theoretical Population Biology, 95, 13) developed herein. In gridCoal, deme sizes can change arbitrarily across space and time, as well as migration rates between individual demes. We identify different factors that can cause a deviation from theoretical expectations, such as the simulation time in comparison to the effective deme size and the spatio-temporal autocorrelation across the grid. Our results highlight that FST, a measure of the strength of population structure, principally depends on recent demography, which makes it robust to temporal variation in deme size. In contrast, the amount of genetic diversity is dependent on the distant past when Ne is large, therefore longer run times are needed to estimate Ne than FST. Finally, we illustrate the use of gridCoal on a real-world example, the range expansion of silver fir (Abies alba Mill.) since the last glacial maximum, using different degrees of spatio-temporal variation in deme size.","lang":"eng"}],"type":"journal_article","file":[{"date_created":"2023-02-02T08:11:23Z","date_updated":"2023-02-02T08:11:23Z","success":1,"checksum":"3102e203e77b884bffffdbe8e548da88","file_id":"12477","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":6431779,"file_name":"2022_MolecularEcologyRes_Szep.pdf","access_level":"open_access"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"11640","intvolume":" 22","ddc":["570"],"title":"Using gridCoal to assess whether standard population genetic theory holds in the presence of spatio-temporal heterogeneity in population size","status":"public","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"01","scopus_import":"1","date_published":"2022-11-01T00:00:00Z","citation":{"mla":"Szep, Eniko, et al. “Using GridCoal to Assess Whether Standard Population Genetic Theory Holds in the Presence of Spatio-Temporal Heterogeneity in Population Size.” Molecular Ecology Resources, vol. 22, no. 8, Wiley, 2022, pp. 2941–55, doi:10.1111/1755-0998.13676.","short":"E. Szep, B. Trubenova, K. Csilléry, Molecular Ecology Resources 22 (2022) 2941–2955.","chicago":"Szep, Eniko, Barbora Trubenova, and Katalin Csilléry. “Using GridCoal to Assess Whether Standard Population Genetic Theory Holds in the Presence of Spatio-Temporal Heterogeneity in Population Size.” Molecular Ecology Resources. Wiley, 2022. https://doi.org/10.1111/1755-0998.13676.","ama":"Szep E, Trubenova B, Csilléry K. Using gridCoal to assess whether standard population genetic theory holds in the presence of spatio-temporal heterogeneity in population size. Molecular Ecology Resources. 2022;22(8):2941-2955. doi:10.1111/1755-0998.13676","ista":"Szep E, Trubenova B, Csilléry K. 2022. Using gridCoal to assess whether standard population genetic theory holds in the presence of spatio-temporal heterogeneity in population size. Molecular Ecology Resources. 22(8), 2941–2955.","ieee":"E. Szep, B. Trubenova, and K. Csilléry, “Using gridCoal to assess whether standard population genetic theory holds in the presence of spatio-temporal heterogeneity in population size,” Molecular Ecology Resources, vol. 22, no. 8. Wiley, pp. 2941–2955, 2022.","apa":"Szep, E., Trubenova, B., & Csilléry, K. (2022). Using gridCoal to assess whether standard population genetic theory holds in the presence of spatio-temporal heterogeneity in population size. Molecular Ecology Resources. Wiley. https://doi.org/10.1111/1755-0998.13676"},"publication":"Molecular Ecology Resources","page":"2941-2955","article_type":"original"},{"file_date_updated":"2023-02-27T07:17:42Z","publication_status":"published","publisher":"Oxford Academic","department":[{"_id":"NiBa"}],"year":"2022","acknowledgement":"We thank A. Wright and four anonymous reviewers for valuable comments on an earlier draft of this manuscript and all members of the Littorina group for helpful discussions. This work was supported by a European Research Council grant to RKB and by a Natural Environment Research Council studentship to KEH through the ACCE doctoral training program. KJ acknowledges support from the Swedish Science Research Council VR (Vetenskaprådet) (2017-03798). RF was supported by an FCT CEEC (Fundação para a Ciênca e a Tecnologia, Concurso Estímulo ao Emprego Científico) contract (2020.00275.CEECIND).","date_created":"2022-08-28T22:02:02Z","date_updated":"2023-08-03T13:18:17Z","volume":6,"author":[{"full_name":"Hearn, Katherine E.","last_name":"Hearn","first_name":"Katherine E."},{"full_name":"Koch, Eva L.","last_name":"Koch","first_name":"Eva L."},{"first_name":"Sean","last_name":"Stankowski","id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean"},{"full_name":"Butlin, Roger K.","last_name":"Butlin","first_name":"Roger K."},{"last_name":"Faria","first_name":"Rui","full_name":"Faria, Rui"},{"first_name":"Kerstin","last_name":"Johannesson","full_name":"Johannesson, Kerstin"},{"full_name":"Westram, Anja M","last_name":"Westram","first_name":"Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87"}],"month":"10","publication_identifier":{"eissn":["2056-3744"]},"quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000839621100001"]},"language":[{"iso":"eng"}],"doi":"10.1002/evl3.295","type":"journal_article","abstract":[{"lang":"eng","text":"Sexual antagonism is a common hypothesis for driving the evolution of sex chromosomes, whereby recombination suppression is favored between sexually antagonistic loci and the sex-determining locus to maintain beneficial combinations of alleles. This results in the formation of a sex-determining region. Chromosomal inversions may contribute to recombination suppression but their precise role in sex chromosome evolution remains unclear. Because local adaptation is frequently facilitated through the suppression of recombination between adaptive loci by chromosomal inversions, there is potential for inversions that cover sex-determining regions to be involved in local adaptation as well, particularly if habitat variation creates environment-dependent sexual antagonism. With these processes in mind, we investigated sex determination in a well-studied example of local adaptation within a species: the intertidal snail, Littorina saxatilis. Using SNP data from a Swedish hybrid zone, we find novel evidence for a female-heterogametic sex determination system that is restricted to one ecotype. Our results suggest that four putative chromosomal inversions, two previously described and two newly discovered, span the putative sex chromosome pair. We determine their differing associations with sex, which suggest distinct strata of differing ages. The same inversions are found in the second ecotype but do not show any sex association. The striking disparity in inversion-sex associations between ecotypes that are connected by gene flow across a habitat transition that is just a few meters wide indicates a difference in selective regime that has produced a distinct barrier to the spread of the newly discovered sex-determining region between ecotypes. Such sex chromosome-environment interactions have not previously been uncovered in L. saxatilis and are known in few other organisms. A combination of both sex-specific selection and divergent natural selection is required to explain these highly unusual patterns."}],"issue":"5","status":"public","title":"Differing associations between sex determination and sex-linked inversions in two ecotypes of Littorina saxatilis","ddc":["570"],"intvolume":" 6","_id":"12001","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"checksum":"2dcd06186a11b7d1be4cddc6b189f8fb","success":1,"date_created":"2023-02-27T07:17:42Z","date_updated":"2023-02-27T07:17:42Z","relation":"main_file","file_id":"12686","file_size":2368965,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2022_EvolutionLetters_Hearn.pdf"}],"oa_version":"Published Version","scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"Yes","article_type":"original","page":"358-374","publication":"Evolution Letters","citation":{"ama":"Hearn KE, Koch EL, Stankowski S, et al. Differing associations between sex determination and sex-linked inversions in two ecotypes of Littorina saxatilis. Evolution Letters. 2022;6(5):358-374. doi:10.1002/evl3.295","ista":"Hearn KE, Koch EL, Stankowski S, Butlin RK, Faria R, Johannesson K, Westram AM. 2022. Differing associations between sex determination and sex-linked inversions in two ecotypes of Littorina saxatilis. Evolution Letters. 6(5), 358–374.","ieee":"K. E. Hearn et al., “Differing associations between sex determination and sex-linked inversions in two ecotypes of Littorina saxatilis,” Evolution Letters, vol. 6, no. 5. Oxford Academic, pp. 358–374, 2022.","apa":"Hearn, K. E., Koch, E. L., Stankowski, S., Butlin, R. K., Faria, R., Johannesson, K., & Westram, A. M. (2022). Differing associations between sex determination and sex-linked inversions in two ecotypes of Littorina saxatilis. Evolution Letters. Oxford Academic. https://doi.org/10.1002/evl3.295","mla":"Hearn, Katherine E., et al. “Differing Associations between Sex Determination and Sex-Linked Inversions in Two Ecotypes of Littorina Saxatilis.” Evolution Letters, vol. 6, no. 5, Oxford Academic, 2022, pp. 358–74, doi:10.1002/evl3.295.","short":"K.E. Hearn, E.L. Koch, S. Stankowski, R.K. Butlin, R. Faria, K. Johannesson, A.M. Westram, Evolution Letters 6 (2022) 358–374.","chicago":"Hearn, Katherine E., Eva L. Koch, Sean Stankowski, Roger K. Butlin, Rui Faria, Kerstin Johannesson, and Anja M Westram. “Differing Associations between Sex Determination and Sex-Linked Inversions in Two Ecotypes of Littorina Saxatilis.” Evolution Letters. Oxford Academic, 2022. https://doi.org/10.1002/evl3.295."},"date_published":"2022-10-01T00:00:00Z"},{"author":[{"full_name":"Hayward, Laura","id":"fc885ee5-24bf-11eb-ad7b-bcc5104c0c1b","first_name":"Laura","last_name":"Hayward"},{"full_name":"Sella, Guy","first_name":"Guy","last_name":"Sella"}],"date_created":"2023-01-12T12:09:00Z","date_updated":"2023-08-04T09:04:58Z","volume":11,"acknowledgement":"We thank Guy Amster, Jeremy Berg, Nick Barton, Yuval Simons and Molly Przeworski for many helpful discussions, and Jeremy Berg, Graham Coop, Joachim Hermisson, Guillaume Martin, Will Milligan, Peter Ralph, Yuval Simons, Leo Speidel and Molly Przeworski for comments on the manuscript.\r\nNational Institutes of Health GM115889 Laura Katharine Hayward Guy Sella \r\nNational Institutes of Health GM121372 Laura Katharine Hayward","year":"2022","publication_status":"published","publisher":"eLife Sciences Publications","department":[{"_id":"NiBa"}],"file_date_updated":"2023-01-24T12:21:32Z","article_number":"66697","doi":"10.7554/elife.66697","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000890735600001"]},"isi":1,"quality_controlled":"1","month":"09","publication_identifier":{"eissn":["2050-084X"]},"file":[{"file_id":"12363","relation":"main_file","date_updated":"2023-01-24T12:21:32Z","date_created":"2023-01-24T12:21:32Z","success":1,"checksum":"28de155b231ac1c8d4501c98b2fb359a","file_name":"2022_eLife_Hayward.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":18935612}],"oa_version":"Published Version","_id":"12157","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Polygenic adaptation after a sudden change in environment","status":"public","ddc":["570"],"intvolume":" 11","abstract":[{"text":"Polygenic adaptation is thought to be ubiquitous, yet remains poorly understood. Here, we model this process analytically, in the plausible setting of a highly polygenic, quantitative trait that experiences a sudden shift in the fitness optimum. We show how the mean phenotype changes over time, depending on the effect sizes of loci that contribute to variance in the trait, and characterize the allele dynamics at these loci. Notably, we describe the two phases of the allele dynamics: The first is a rapid phase, in which directional selection introduces small frequency differences between alleles whose effects are aligned with or opposed to the shift, ultimately leading to small differences in their probability of fixation during a second, longer phase, governed by stabilizing selection. As we discuss, key results should hold in more general settings and have important implications for efforts to identify the genetic basis of adaptation in humans and other species.","lang":"eng"}],"type":"journal_article","date_published":"2022-09-26T00:00:00Z","publication":"eLife","citation":{"ama":"Hayward L, Sella G. Polygenic adaptation after a sudden change in environment. eLife. 2022;11. doi:10.7554/elife.66697","ieee":"L. Hayward and G. Sella, “Polygenic adaptation after a sudden change in environment,” eLife, vol. 11. eLife Sciences Publications, 2022.","apa":"Hayward, L., & Sella, G. (2022). Polygenic adaptation after a sudden change in environment. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.66697","ista":"Hayward L, Sella G. 2022. Polygenic adaptation after a sudden change in environment. eLife. 11, 66697.","short":"L. Hayward, G. Sella, ELife 11 (2022).","mla":"Hayward, Laura, and Guy Sella. “Polygenic Adaptation after a Sudden Change in Environment.” ELife, vol. 11, 66697, eLife Sciences Publications, 2022, doi:10.7554/elife.66697.","chicago":"Hayward, Laura, and Guy Sella. “Polygenic Adaptation after a Sudden Change in Environment.” ELife. eLife Sciences Publications, 2022. https://doi.org/10.7554/elife.66697."},"article_type":"original","day":"26","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"]},{"scopus_import":"1","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"article_processing_charge":"No","day":"28","citation":{"ama":"Westram AM, Butlin R. Professor Kerstin Johannesson–winner of the 2022 Molecular Ecology Prize. Molecular Ecology. 2022;32(1):26-29. doi:10.1111/mec.16779","ista":"Westram AM, Butlin R. 2022. Professor Kerstin Johannesson–winner of the 2022 Molecular Ecology Prize. Molecular Ecology. 32(1), 26–29.","apa":"Westram, A. M., & Butlin, R. (2022). Professor Kerstin Johannesson–winner of the 2022 Molecular Ecology Prize. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.16779","ieee":"A. M. Westram and R. Butlin, “Professor Kerstin Johannesson–winner of the 2022 Molecular Ecology Prize,” Molecular Ecology, vol. 32, no. 1. Wiley, pp. 26–29, 2022.","mla":"Westram, Anja M., and Roger Butlin. “Professor Kerstin Johannesson–Winner of the 2022 Molecular Ecology Prize.” Molecular Ecology, vol. 32, no. 1, Wiley, 2022, pp. 26–29, doi:10.1111/mec.16779.","short":"A.M. Westram, R. Butlin, Molecular Ecology 32 (2022) 26–29.","chicago":"Westram, Anja M, and Roger Butlin. “Professor Kerstin Johannesson–Winner of the 2022 Molecular Ecology Prize.” Molecular Ecology. Wiley, 2022. https://doi.org/10.1111/mec.16779."},"publication":"Molecular Ecology","page":"26-29","article_type":"letter_note","date_published":"2022-11-28T00:00:00Z","type":"journal_article","issue":"1","abstract":[{"text":"Kerstin Johannesson is a marine ecologist and evolutionary biologist based at the Tjärnö Marine Laboratory of the University of Gothenburg, which is situated in the beautiful Kosterhavet National Park on the Swedish west coast. Her work, using marine periwinkles (especially Littorina saxatilis and L. fabalis) as main model systems, has made a remarkable contribution to marine evolutionary biology and our understanding of local adaptation and its genetic underpinnings.","lang":"eng"}],"_id":"12166","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 32","status":"public","title":"Professor Kerstin Johannesson–winner of the 2022 Molecular Ecology Prize","oa_version":"Published Version","publication_identifier":{"issn":["0962-1083"],"eissn":["1365-294X"]},"month":"11","main_file_link":[{"url":"https://doi.org/10.1111/mec.16779","open_access":"1"}],"external_id":{"isi":["000892168800001"]},"oa":1,"isi":1,"quality_controlled":"1","doi":"10.1111/mec.16779","language":[{"iso":"eng"}],"year":"2022","department":[{"_id":"NiBa"}],"publisher":"Wiley","publication_status":"published","author":[{"full_name":"Westram, Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","first_name":"Anja M","last_name":"Westram"},{"first_name":"Roger","last_name":"Butlin","full_name":"Butlin, Roger"}],"volume":32,"date_updated":"2023-08-04T09:09:15Z","date_created":"2023-01-12T12:10:28Z"},{"date_created":"2023-01-16T09:50:48Z","date_updated":"2023-08-04T09:35:48Z","volume":76,"author":[{"full_name":"Stankowski, Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","first_name":"Sean","last_name":"Stankowski"}],"publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Wiley","year":"2022","file_date_updated":"2023-01-27T11:28:38Z","language":[{"iso":"eng"}],"doi":"10.1111/evo.14632","isi":1,"quality_controlled":"1","external_id":{"isi":["000855751600001"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"month":"11","publication_identifier":{"eissn":["1558-5646"],"issn":["0014-3820"]},"file":[{"access_level":"open_access","file_name":"2022_Evolution_Stankowski.pdf","file_size":287282,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"12425","checksum":"4c0f05083b414ac0323a1b9ee1abc275","success":1,"date_created":"2023-01-27T11:28:38Z","date_updated":"2023-01-27T11:28:38Z"}],"oa_version":"Published Version","title":"Digest: On the origin of a possible hybrid species","status":"public","ddc":["570"],"intvolume":" 76","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12234","abstract":[{"text":"Hybrid speciation—the origin of new species resulting from the hybridization of genetically divergent lineages—was once considered rare, but genomic data suggest that it may occur more often than once thought. In this study, Noguerales and Ortego found genomic evidence supporting the hybrid origin of a grasshopper that is able to exploit a broader range of host plants than either of its putative parents.","lang":"eng"}],"issue":"11","type":"journal_article","date_published":"2022-11-01T00:00:00Z","article_type":"original","page":"2784-2785","publication":"Evolution","citation":{"ista":"Stankowski S. 2022. Digest: On the origin of a possible hybrid species. Evolution. 76(11), 2784–2785.","apa":"Stankowski, S. (2022). Digest: On the origin of a possible hybrid species. Evolution. Wiley. https://doi.org/10.1111/evo.14632","ieee":"S. Stankowski, “Digest: On the origin of a possible hybrid species,” Evolution, vol. 76, no. 11. Wiley, pp. 2784–2785, 2022.","ama":"Stankowski S. Digest: On the origin of a possible hybrid species. Evolution. 2022;76(11):2784-2785. doi:10.1111/evo.14632","chicago":"Stankowski, Sean. “Digest: On the Origin of a Possible Hybrid Species.” Evolution. Wiley, 2022. https://doi.org/10.1111/evo.14632.","mla":"Stankowski, Sean. “Digest: On the Origin of a Possible Hybrid Species.” Evolution, vol. 76, no. 11, Wiley, 2022, pp. 2784–85, doi:10.1111/evo.14632.","short":"S. Stankowski, Evolution 76 (2022) 2784–2785."},"day":"01","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","keyword":["General Agricultural and Biological Sciences","Genetics","Ecology","Evolution","Behavior and Systematics"],"scopus_import":"1"},{"intvolume":" 76","ddc":["570"],"status":"public","title":"Genetic architecture of repeated phenotypic divergence in Littorina saxatilis evolution","_id":"12247","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"creator":"dernst","file_size":2990581,"content_type":"application/pdf","access_level":"open_access","file_name":"2022_Evolution_Koch.pdf","success":1,"checksum":"defd8a4bea61cf00a3c88d4a30e2728c","date_created":"2023-01-30T08:45:35Z","date_updated":"2023-01-30T08:45:35Z","file_id":"12439","relation":"main_file"}],"oa_version":"Published Version","type":"journal_article","issue":"10","abstract":[{"lang":"eng","text":"Chromosomal inversions have been shown to play a major role in a local adaptation by suppressing recombination between alternative arrangements and maintaining beneficial allele combinations. However, so far, their importance relative to the remaining genome remains largely unknown. Understanding the genetic architecture of adaptation requires better estimates of how loci of different effect sizes contribute to phenotypic variation. Here, we used three Swedish islands where the marine snail Littorina saxatilis has repeatedly evolved into two distinct ecotypes along a habitat transition. We estimated the contribution of inversion polymorphisms to phenotypic divergence while controlling for polygenic effects in the remaining genome using a quantitative genetics framework. We confirmed the importance of inversions but showed that contributions of loci outside inversions are of similar magnitude, with variable proportions dependent on the trait and the population. Some inversions showed consistent effects across all sites, whereas others exhibited site-specific effects, indicating that the genomic basis for replicated phenotypic divergence is only partly shared. The contributions of sexual dimorphism as well as environmental factors to phenotypic variation were significant but minor compared to inversions and polygenic background. Overall, this integrated approach provides insight into the multiple mechanisms contributing to parallel phenotypic divergence."}],"page":"2332-2346","article_type":"original","citation":{"ieee":"E. L. Koch, M. Ravinet, A. M. Westram, K. Johannesson, and R. K. Butlin, “Genetic architecture of repeated phenotypic divergence in Littorina saxatilis evolution,” Evolution, vol. 76, no. 10. Wiley, pp. 2332–2346, 2022.","apa":"Koch, E. L., Ravinet, M., Westram, A. M., Johannesson, K., & Butlin, R. K. (2022). Genetic architecture of repeated phenotypic divergence in Littorina saxatilis evolution. Evolution. Wiley. https://doi.org/10.1111/evo.14602","ista":"Koch EL, Ravinet M, Westram AM, Johannesson K, Butlin RK. 2022. Genetic architecture of repeated phenotypic divergence in Littorina saxatilis evolution. Evolution. 76(10), 2332–2346.","ama":"Koch EL, Ravinet M, Westram AM, Johannesson K, Butlin RK. Genetic architecture of repeated phenotypic divergence in Littorina saxatilis evolution. Evolution. 2022;76(10):2332-2346. doi:10.1111/evo.14602","chicago":"Koch, Eva L., Mark Ravinet, Anja M Westram, Kerstin Johannesson, and Roger K. Butlin. “Genetic Architecture of Repeated Phenotypic Divergence in Littorina Saxatilis Evolution.” Evolution. Wiley, 2022. https://doi.org/10.1111/evo.14602.","short":"E.L. Koch, M. Ravinet, A.M. Westram, K. Johannesson, R.K. Butlin, Evolution 76 (2022) 2332–2346.","mla":"Koch, Eva L., et al. “Genetic Architecture of Repeated Phenotypic Divergence in Littorina Saxatilis Evolution.” Evolution, vol. 76, no. 10, Wiley, 2022, pp. 2332–46, doi:10.1111/evo.14602."},"publication":"Evolution","date_published":"2022-10-01T00:00:00Z","keyword":["General Agricultural and Biological Sciences","Genetics","Ecology","Evolution","Behavior and Systematics"],"scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"01","department":[{"_id":"NiBa"}],"publisher":"Wiley","publication_status":"published","pmid":1,"year":"2022","acknowledgement":"We thank everyone who helped with fieldwork, snail processing, and DNA extractions, particularly Laura Brettell, Mårten Duvetorp, Juan Galindo, Anne-Lise Liabot, Irena Senčić, and Zuzanna Zagrodzka. We also thank Rui Faria and Jenny Larsson for their contributions, with inversions and shell shape respectively. KJ was funded by the Swedish research council Vetenskapsrådet, grant number 2017-03798. R.K.B. and E.K. were funded by the European Research Council (ERC-2015-AdG-693030-BARRIERS). R.K.B. was also funded by the Natural Environment Research Council and the Swedish Research Council Vetenskapsrådet.","volume":76,"date_created":"2023-01-16T09:54:15Z","date_updated":"2023-08-04T09:42:11Z","related_material":{"record":[{"id":"13066","relation":"research_data","status":"public"}]},"author":[{"full_name":"Koch, Eva L.","first_name":"Eva L.","last_name":"Koch"},{"last_name":"Ravinet","first_name":"Mark","full_name":"Ravinet, Mark"},{"full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","first_name":"Anja M"},{"first_name":"Kerstin","last_name":"Johannesson","full_name":"Johannesson, Kerstin"},{"last_name":"Butlin","first_name":"Roger K.","full_name":"Butlin, Roger K."}],"file_date_updated":"2023-01-30T08:45:35Z","isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000848449100001"],"pmid":["35994296"]},"language":[{"iso":"eng"}],"doi":"10.1111/evo.14602","publication_identifier":{"eissn":["1558-5646"],"issn":["0014-3820"]},"month":"10"},{"abstract":[{"text":"Chromosomal inversions have been shown to play a major role in local adaptation by suppressing recombination between alternative arrangements and maintaining beneficial allele combinations. However, so far, their importance relative to the remaining genome remains largely unknown. Understanding the genetic architecture of adaptation requires better estimates of how loci of different effect sizes contribute to phenotypic variation. Here, we used three Swedish islands where the marine snail Littorina saxatilis has repeatedly evolved into two distinct ecotypes along a habitat transition. We estimated the contribution of inversion polymorphisms to phenotypic divergence while controlling for polygenic effects in the remaining genome using a quantitative genetics framework. We confirmed the importance of inversions but showed that contributions of loci outside inversions are of similar magnitude, with variable proportions dependent on the trait and the population. Some inversions showed consistent effects across all sites, whereas others exhibited site-specific effects, indicating that the genomic basis for replicated phenotypic divergence is only partly shared. The contributions of sexual dimorphism as well as environmental factors to phenotypic variation were significant but minor compared to inversions and polygenic background. Overall, this integrated approach provides insight into the multiple mechanisms contributing to parallel phenotypic divergence.","lang":"eng"}],"type":"research_data_reference","oa_version":"Published Version","date_updated":"2023-08-04T09:42:10Z","date_created":"2023-05-23T16:33:12Z","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"12247"}]},"author":[{"first_name":"Eva","last_name":"Koch","full_name":"Koch, Eva"},{"first_name":"Mark","last_name":"Ravinet","full_name":"Ravinet, Mark"},{"orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","first_name":"Anja M","full_name":"Westram, Anja M"},{"first_name":"Kerstin","last_name":"Jonannesson","full_name":"Jonannesson, Kerstin"},{"first_name":"Roger","last_name":"Butlin","full_name":"Butlin, Roger"}],"publisher":"Dryad","department":[{"_id":"NiBa"}],"status":"public","ddc":["570"],"title":"Data from: Genetic architecture of repeated phenotypic divergence in Littorina saxatilis ecotype evolution","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13066","year":"2022","article_processing_charge":"No","month":"07","day":"28","date_published":"2022-07-28T00:00:00Z","doi":"10.5061/DRYAD.M905QFV4B","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"citation":{"ista":"Koch E, Ravinet M, Westram AM, Jonannesson K, Butlin R. 2022. Data from: Genetic architecture of repeated phenotypic divergence in Littorina saxatilis ecotype evolution, Dryad, 10.5061/DRYAD.M905QFV4B.","apa":"Koch, E., Ravinet, M., Westram, A. M., Jonannesson, K., & Butlin, R. (2022). Data from: Genetic architecture of repeated phenotypic divergence in Littorina saxatilis ecotype evolution. Dryad. https://doi.org/10.5061/DRYAD.M905QFV4B","ieee":"E. Koch, M. Ravinet, A. M. Westram, K. Jonannesson, and R. Butlin, “Data from: Genetic architecture of repeated phenotypic divergence in Littorina saxatilis ecotype evolution.” Dryad, 2022.","ama":"Koch E, Ravinet M, Westram AM, Jonannesson K, Butlin R. Data from: Genetic architecture of repeated phenotypic divergence in Littorina saxatilis ecotype evolution. 2022. doi:10.5061/DRYAD.M905QFV4B","chicago":"Koch, Eva, Mark Ravinet, Anja M Westram, Kerstin Jonannesson, and Roger Butlin. “Data from: Genetic Architecture of Repeated Phenotypic Divergence in Littorina Saxatilis Ecotype Evolution.” Dryad, 2022. https://doi.org/10.5061/DRYAD.M905QFV4B.","mla":"Koch, Eva, et al. Data from: Genetic Architecture of Repeated Phenotypic Divergence in Littorina Saxatilis Ecotype Evolution. Dryad, 2022, doi:10.5061/DRYAD.M905QFV4B.","short":"E. Koch, M. Ravinet, A.M. Westram, K. Jonannesson, R. Butlin, (2022)."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.m905qfv4b"}],"oa":1},{"publication_identifier":{"eissn":["1420-9101"],"issn":["1010-061X"]},"month":"09","doi":"10.1111/jeb.14005","language":[{"iso":"eng"}],"external_id":{"isi":["000849851100002"],"pmid":["36063156"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"name":"The maintenance of alternative adaptive peaks in snapdragons","grant_number":"P32166","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E"}],"isi":1,"quality_controlled":"1","file_date_updated":"2023-01-30T10:05:31Z","related_material":{"record":[{"id":"12265","relation":"other","status":"public"}]},"author":[{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","first_name":"Anja M","last_name":"Westram","full_name":"Westram, Anja M"},{"id":"43161670-5719-11EA-8025-FABC3DDC885E","first_name":"Sean","last_name":"Stankowski","full_name":"Stankowski, Sean"},{"id":"455235B8-F248-11E8-B48F-1D18A9856A87","last_name":"Surendranadh","first_name":"Parvathy","full_name":"Surendranadh, Parvathy"},{"last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"}],"volume":35,"date_updated":"2023-08-04T09:53:40Z","date_created":"2023-01-16T09:59:24Z","pmid":1,"year":"2022","acknowledgement":"We are grateful to the participants of the ESEB satellite symposium ‘Understanding reproductive isolation: bridging conceptual barriers in speciation research’ in 2021 for the interesting discussions that helped us clarify the thoughts presented in this article. We thank Roger Butlin, Michael Turelli and two anonymous reviewers for their thoughtful comments on this manuscript. We are also very grateful to Roger Butlin and the Barton Group for the continued conversa-tions about RI. In addition, we thank all participants of the speciation survey. Part of this work was funded by the Austrian Science Fund FWF (grant P 32166)","department":[{"_id":"NiBa"}],"publisher":"Wiley","publication_status":"published","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"01","scopus_import":"1","keyword":["Ecology","Evolution","Behavior and Systematics"],"date_published":"2022-09-01T00:00:00Z","citation":{"ama":"Westram AM, Stankowski S, Surendranadh P, Barton NH. What is reproductive isolation? Journal of Evolutionary Biology. 2022;35(9):1143-1164. doi:10.1111/jeb.14005","ieee":"A. M. Westram, S. Stankowski, P. Surendranadh, and N. H. Barton, “What is reproductive isolation?,” Journal of Evolutionary Biology, vol. 35, no. 9. Wiley, pp. 1143–1164, 2022.","apa":"Westram, A. M., Stankowski, S., Surendranadh, P., & Barton, N. H. (2022). What is reproductive isolation? Journal of Evolutionary Biology. Wiley. https://doi.org/10.1111/jeb.14005","ista":"Westram AM, Stankowski S, Surendranadh P, Barton NH. 2022. What is reproductive isolation? Journal of Evolutionary Biology. 35(9), 1143–1164.","short":"A.M. Westram, S. Stankowski, P. Surendranadh, N.H. Barton, Journal of Evolutionary Biology 35 (2022) 1143–1164.","mla":"Westram, Anja M., et al. “What Is Reproductive Isolation?” Journal of Evolutionary Biology, vol. 35, no. 9, Wiley, 2022, pp. 1143–64, doi:10.1111/jeb.14005.","chicago":"Westram, Anja M, Sean Stankowski, Parvathy Surendranadh, and Nicholas H Barton. “What Is Reproductive Isolation?” Journal of Evolutionary Biology. Wiley, 2022. https://doi.org/10.1111/jeb.14005."},"publication":"Journal of Evolutionary Biology","page":"1143-1164","article_type":"review","issue":"9","abstract":[{"lang":"eng","text":"Reproductive isolation (RI) is a core concept in evolutionary biology. It has been the central focus of speciation research since the modern synthesis and is the basis by which biological species are defined. Despite this, the term is used in seemingly different ways, and attempts to quantify RI have used very different approaches. After showing that the field lacks a clear definition of the term, we attempt to clarify key issues, including what RI is, how it can be quantified in principle, and how it can be measured in practice. Following other definitions with a genetic focus, we propose that RI is a quantitative measure of the effect that genetic differences between populations have on gene flow. Specifically, RI compares the flow of neutral alleles in the presence of these genetic differences to the flow without any such differences. RI is thus greater than zero when genetic differences between populations reduce the flow of neutral alleles between populations. We show how RI can be quantified in a range of scenarios. A key conclusion is that RI depends strongly on circumstances—including the spatial, temporal and genomic context—making it difficult to compare across systems. After reviewing methods for estimating RI from data, we conclude that it is difficult to measure in practice. We discuss our findings in light of the goals of speciation research and encourage the use of methods for estimating RI that integrate organismal and genetic approaches."}],"type":"journal_article","oa_version":"Published Version","file":[{"creator":"dernst","file_size":3146793,"content_type":"application/pdf","access_level":"open_access","file_name":"2022_JourEvoBiology_Westram.pdf","success":1,"checksum":"f08de57112330a7ee88d2e1b20576a1e","date_created":"2023-01-30T10:05:31Z","date_updated":"2023-01-30T10:05:31Z","file_id":"12448","relation":"main_file"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12264","intvolume":" 35","ddc":["570"],"status":"public","title":"What is reproductive isolation?"},{"date_published":"2022-09-01T00:00:00Z","page":"1200-1205","article_type":"letter_note","citation":{"chicago":"Westram, Anja M, Sean Stankowski, Parvathy Surendranadh, and Nicholas H Barton. “Reproductive Isolation, Speciation, and the Value of Disagreement: A Reply to the Commentaries on ‘What Is Reproductive Isolation?’” Journal of Evolutionary Biology. Wiley, 2022. https://doi.org/10.1111/jeb.14082.","short":"A.M. Westram, S. Stankowski, P. Surendranadh, N.H. Barton, Journal of Evolutionary Biology 35 (2022) 1200–1205.","mla":"Westram, Anja M., et al. “Reproductive Isolation, Speciation, and the Value of Disagreement: A Reply to the Commentaries on ‘What Is Reproductive Isolation?’” Journal of Evolutionary Biology, vol. 35, no. 9, Wiley, 2022, pp. 1200–05, doi:10.1111/jeb.14082.","apa":"Westram, A. M., Stankowski, S., Surendranadh, P., & Barton, N. H. (2022). Reproductive isolation, speciation, and the value of disagreement: A reply to the commentaries on ‘What is reproductive isolation?’ Journal of Evolutionary Biology. Wiley. https://doi.org/10.1111/jeb.14082","ieee":"A. M. Westram, S. Stankowski, P. Surendranadh, and N. H. Barton, “Reproductive isolation, speciation, and the value of disagreement: A reply to the commentaries on ‘What is reproductive isolation?,’” Journal of Evolutionary Biology, vol. 35, no. 9. Wiley, pp. 1200–1205, 2022.","ista":"Westram AM, Stankowski S, Surendranadh P, Barton NH. 2022. Reproductive isolation, speciation, and the value of disagreement: A reply to the commentaries on ‘What is reproductive isolation?’ Journal of Evolutionary Biology. 35(9), 1200–1205.","ama":"Westram AM, Stankowski S, Surendranadh P, Barton NH. Reproductive isolation, speciation, and the value of disagreement: A reply to the commentaries on ‘What is reproductive isolation?’ Journal of Evolutionary Biology. 2022;35(9):1200-1205. doi:10.1111/jeb.14082"},"publication":"Journal of Evolutionary Biology","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"01","keyword":["Ecology","Evolution","Behavior and Systematics"],"scopus_import":"1","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2022_JourEvoBiology_Westram_Response.pdf","file_size":349603,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"12449","checksum":"27268009e5eec030bc10667a4ac5ed4c","success":1,"date_created":"2023-01-30T10:14:09Z","date_updated":"2023-01-30T10:14:09Z"}],"intvolume":" 35","status":"public","ddc":["570"],"title":"Reproductive isolation, speciation, and the value of disagreement: A reply to the commentaries on ‘What is reproductive isolation?’","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12265","issue":"9","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1111/jeb.14082","project":[{"name":"The maintenance of alternative adaptive peaks in snapdragons","grant_number":"P32166","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000849851100009"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"publication_identifier":{"eissn":["1420-9101"],"issn":["1010-061X"]},"month":"09","volume":35,"date_created":"2023-01-16T09:59:37Z","date_updated":"2023-08-04T09:53:41Z","related_material":{"record":[{"id":"12264","relation":"other","status":"public"}]},"author":[{"last_name":"Westram","first_name":"Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","full_name":"Westram, Anja M"},{"first_name":"Sean","last_name":"Stankowski","id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean"},{"full_name":"Surendranadh, Parvathy","first_name":"Parvathy","last_name":"Surendranadh","id":"455235B8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"}],"publisher":"Wiley","department":[{"_id":"NiBa"}],"publication_status":"published","year":"2022","acknowledgement":"We are very grateful to the authors of the commentaries for the interesting discussion and to Luke Holman for handling this set of manuscripts. Part of this work was funded by the Austrian Science Fund FWF (grant P 32166).","file_date_updated":"2023-01-30T10:14:09Z"},{"day":"11","article_processing_charge":"No","has_accepted_license":"1","keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology"],"scopus_import":"1","date_published":"2022-04-11T00:00:00Z","article_type":"original","publication":"Philosophical Transactions of the Royal Society B: Biological Sciences","citation":{"chicago":"Barton, Nicholas H, and Oluwafunmilola O Olusanya. “The Response of a Metapopulation to a Changing Environment.” Philosophical Transactions of the Royal Society B: Biological Sciences. The Royal Society, 2022. https://doi.org/10.1098/rstb.2021.0009.","mla":"Barton, Nicholas H., and Oluwafunmilola O. Olusanya. “The Response of a Metapopulation to a Changing Environment.” Philosophical Transactions of the Royal Society B: Biological Sciences, vol. 377, no. 1848, The Royal Society, 2022, doi:10.1098/rstb.2021.0009.","short":"N.H. Barton, O.O. Olusanya, Philosophical Transactions of the Royal Society B: Biological Sciences 377 (2022).","ista":"Barton NH, Olusanya OO. 2022. The response of a metapopulation to a changing environment. Philosophical Transactions of the Royal Society B: Biological Sciences. 377(1848).","apa":"Barton, N. H., & Olusanya, O. O. (2022). The response of a metapopulation to a changing environment. Philosophical Transactions of the Royal Society B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rstb.2021.0009","ieee":"N. H. Barton and O. O. Olusanya, “The response of a metapopulation to a changing environment,” Philosophical Transactions of the Royal Society B: Biological Sciences, vol. 377, no. 1848. The Royal Society, 2022.","ama":"Barton NH, Olusanya OO. The response of a metapopulation to a changing environment. Philosophical Transactions of the Royal Society B: Biological Sciences. 2022;377(1848). doi:10.1098/rstb.2021.0009"},"abstract":[{"text":"A species distributed across diverse environments may adapt to local conditions. We ask how quickly such a species changes its range in response to changed conditions. Szép et al. (Szép E, Sachdeva H, Barton NH. 2021 Polygenic local adaptation in metapopulations: a stochastic eco-evolutionary model. Evolution75, 1030–1045 (doi:10.1111/evo.14210)) used the infinite island model to find the stationary distribution of allele frequencies and deme sizes. We extend this to find how a metapopulation responds to changes in carrying capacity, selection strength, or migration rate when deme sizes are fixed. We further develop a ‘fixed-state’ approximation. Under this approximation, polymorphism is only possible for a narrow range of habitat proportions when selection is weak compared to drift, but for a much wider range otherwise. When rates of selection or migration relative to drift change in a single deme of the metapopulation, the population takes a time of order m−1 to reach the new equilibrium. However, even with many loci, there can be substantial fluctuations in net adaptation, because at each locus, alleles randomly get lost or fixed. Thus, in a finite metapopulation, variation may gradually be lost by chance, even if it would persist in an infinite metapopulation. When conditions change across the whole metapopulation, there can be rapid change, which is predicted well by the fixed-state approximation. This work helps towards an understanding of how metapopulations extend their range across diverse environments.\r\nThis article is part of the theme issue ‘Species’ ranges in the face of changing environments (Part II)’.","lang":"eng"}],"issue":"1848","type":"journal_article","oa_version":"Published Version","file":[{"date_created":"2022-08-02T06:14:32Z","date_updated":"2022-08-02T06:14:32Z","checksum":"3b0243738f01bf3c07e0d7e8dc64f71d","success":1,"relation":"main_file","file_id":"11719","file_size":1349672,"content_type":"application/pdf","creator":"dernst","file_name":"2022_PhilosophicalTransactionsRSB_Barton.pdf","access_level":"open_access"}],"title":"The response of a metapopulation to a changing environment","ddc":["570"],"status":"public","intvolume":" 377","_id":"10787","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","month":"04","publication_identifier":{"eissn":["1471-2970"],"issn":["0962-8436"]},"language":[{"iso":"eng"}],"doi":"10.1098/rstb.2021.0009","quality_controlled":"1","isi":1,"project":[{"name":"Causes and consequences of population fragmentation","grant_number":"P32896","_id":"c08d3278-5a5b-11eb-8a69-fdb09b55f4b8"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["35184588"],"isi":["000758140300001"]},"file_date_updated":"2022-08-02T06:14:32Z","date_created":"2022-02-21T16:08:10Z","date_updated":"2024-01-26T12:00:53Z","volume":377,"author":[{"full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Oluwafunmilola O","last_name":"Olusanya","id":"41AD96DC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1971-8314","full_name":"Olusanya, Oluwafunmilola O"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"14711"}]},"publication_status":"published","publisher":"The Royal Society","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"acknowledgement":"This research was partly funded by the Austrian Science Fund (FWF) [FWF P-32896B].","year":"2022","pmid":1},{"article_processing_charge":"No","has_accepted_license":"1","day":"24","article_type":"original","citation":{"ista":"Sachdeva H, Olusanya OO, Barton NH. 2022. Genetic load and extinction in peripheral populations: The roles of migration, drift and demographic stochasticity. Philosophical Transactions of the Royal Society B. 377(1846), 20210010.","apa":"Sachdeva, H., Olusanya, O. O., & Barton, N. H. (2022). Genetic load and extinction in peripheral populations: The roles of migration, drift and demographic stochasticity. Philosophical Transactions of the Royal Society B. The Royal Society. https://doi.org/10.1098/rstb.2021.0010","ieee":"H. Sachdeva, O. O. Olusanya, and N. H. Barton, “Genetic load and extinction in peripheral populations: The roles of migration, drift and demographic stochasticity,” Philosophical Transactions of the Royal Society B, vol. 377, no. 1846. The Royal Society, 2022.","ama":"Sachdeva H, Olusanya OO, Barton NH. Genetic load and extinction in peripheral populations: The roles of migration, drift and demographic stochasticity. Philosophical Transactions of the Royal Society B. 2022;377(1846). doi:10.1098/rstb.2021.0010","chicago":"Sachdeva, Himani, Oluwafunmilola O Olusanya, and Nicholas H Barton. “Genetic Load and Extinction in Peripheral Populations: The Roles of Migration, Drift and Demographic Stochasticity.” Philosophical Transactions of the Royal Society B. The Royal Society, 2022. https://doi.org/10.1098/rstb.2021.0010.","mla":"Sachdeva, Himani, et al. “Genetic Load and Extinction in Peripheral Populations: The Roles of Migration, Drift and Demographic Stochasticity.” Philosophical Transactions of the Royal Society B, vol. 377, no. 1846, 20210010, The Royal Society, 2022, doi:10.1098/rstb.2021.0010.","short":"H. Sachdeva, O.O. Olusanya, N.H. Barton, Philosophical Transactions of the Royal Society B 377 (2022)."},"publication":"Philosophical Transactions of the Royal Society B","date_published":"2022-01-24T00:00:00Z","type":"journal_article","issue":"1846","abstract":[{"lang":"eng","text":"We analyse how migration from a large mainland influences genetic load and population numbers on an island, in a scenario where fitness-affecting variants are unconditionally deleterious, and where numbers decline with increasing load. Our analysis shows that migration can have qualitatively different effects, depending on the total mutation target and fitness effects of deleterious variants. In particular, we find that populations exhibit a genetic Allee effect across a wide range of parameter combinations, when variants are partially recessive, cycling between low-load (large-population) and high-load (sink) states. Increased migration reduces load in the sink state (by increasing heterozygosity) but further inflates load in the large-population state (by hindering purging). We identify various critical parameter thresholds at which one or other stable state collapses, and discuss how these thresholds are influenced by the genetic versus demographic effects of migration. Our analysis is based on a ‘semi-deterministic’ analysis, which accounts for genetic drift but neglects demographic stochasticity. We also compare against simulations which account for both demographic stochasticity and drift. Our results clarify the importance of gene flow as a key determinant of extinction risk in peripheral populations, even in the absence of ecological gradients. This article is part of the theme issue ‘Species’ ranges in the face of changing environments (part I)’."}],"intvolume":" 377","title":"Genetic load and extinction in peripheral populations: The roles of migration, drift and demographic stochasticity","ddc":["576"],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10658","oa_version":"Published Version","file":[{"creator":"oolusany","content_type":"application/pdf","file_size":1845792,"file_name":"rstb.2021.0010.pdf","access_level":"open_access","date_updated":"2022-01-24T10:34:45Z","date_created":"2022-01-24T10:34:45Z","checksum":"04ca9e2f0e344d680b947f2457df8d0a","file_id":"10659","relation":"main_file"}],"publication_identifier":{"issn":["0962-8436"],"eissn":["1471-2970"]},"month":"01","project":[{"grant_number":"P32896","_id":"c08d3278-5a5b-11eb-8a69-fdb09b55f4b8","name":"Causes and consequences of population fragmentation"}],"isi":1,"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000745854300008"],"pmid":["35067097"]},"language":[{"iso":"eng"}],"doi":"10.1098/rstb.2021.0010","article_number":"20210010","file_date_updated":"2022-01-24T10:34:45Z","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"publisher":"The Royal Society","publication_status":"published","pmid":1,"acknowledgement":"This research was partly funded by the Austrian Science Fund (FWF) (grant no. P-32896B).","year":"2022","volume":377,"date_created":"2022-01-24T10:34:53Z","date_updated":"2024-01-26T12:00:53Z","related_material":{"record":[{"id":"14711","relation":"dissertation_contains","status":"public"}],"link":[{"relation":"earlier_version","url":"https://doi.org/10.1101/2021.08.05.455207"}]},"author":[{"full_name":"Sachdeva, Himani","first_name":"Himani","last_name":"Sachdeva"},{"full_name":"Olusanya, Oluwafunmilola O","first_name":"Oluwafunmilola O","last_name":"Olusanya","id":"41AD96DC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1971-8314"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H"}]},{"publication_identifier":{"eissn":["1943-2631"]},"month":"07","oa":1,"external_id":{"isi":["000803735800001"],"pmid":["35639938"]},"project":[{"name":"The maintenance of alternative adaptive peaks in snapdragons","grant_number":"P32166","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E"}],"quality_controlled":"1","isi":1,"doi":"10.1093/genetics/iyac083","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"article_number":"iyac083","file_date_updated":"2022-05-26T12:48:21Z","pmid":1,"year":"2022","acknowledgement":"Part of this work was funded by Marie Curie COFUND Doctoral Fellowship and Austrian Science Fund FWF (grant P32166).\r\nWe thank the many volunteers and friends who have contributed to data collection in the field site over the years, in particular those who have managed field seasons: Barbora Trubenova, Maria Clara Melo, Tom Ellis, Eva Cereghetti, Lenka Matejovicova, Beatriz Pablo Carmona. Frederic Ferrer and Eva Salmerón Mateu have been immensely helpful with logistics at our informal field station, El Serrat de Planoles. We thank Sean Stankowski for technical help in\r\nproducing figure 1. This research was also supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing (SciComp).","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"publisher":"Oxford University Press","publication_status":"published","related_material":{"record":[{"id":"14651","status":"public","relation":"dissertation_contains"},{"id":"11321","status":"public","relation":"research_data"},{"status":"public","relation":"research_data","id":"9192"}]},"author":[{"id":"455235B8-F248-11E8-B48F-1D18A9856A87","last_name":"Surendranadh","first_name":"Parvathy","full_name":"Surendranadh, Parvathy"},{"orcid":"0000-0003-1771-714X","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","last_name":"Arathoon","first_name":"Louise S","full_name":"Arathoon, Louise S"},{"orcid":"0000-0002-7354-8574","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","last_name":"Baskett","first_name":"Carina","full_name":"Baskett, Carina"},{"full_name":"Field, David","orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field","first_name":"David"},{"orcid":"0000-0001-6118-0541","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","last_name":"Pickup","first_name":"Melinda","full_name":"Pickup, Melinda"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H"}],"volume":221,"date_created":"2022-05-26T13:44:50Z","date_updated":"2024-02-21T12:38:33Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"01","citation":{"chicago":"Surendranadh, Parvathy, Louise S Arathoon, Carina Baskett, David Field, Melinda Pickup, and Nicholas H Barton. “Effects of Fine-Scale Population Structure on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus.” Genetics. Oxford University Press, 2022. https://doi.org/10.1093/genetics/iyac083.","mla":"Surendranadh, Parvathy, et al. “Effects of Fine-Scale Population Structure on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus.” Genetics, vol. 221, no. 3, iyac083, Oxford University Press, 2022, doi:10.1093/genetics/iyac083.","short":"P. Surendranadh, L.S. Arathoon, C. Baskett, D. Field, M. Pickup, N.H. Barton, Genetics 221 (2022).","ista":"Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. 2022. Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. Genetics. 221(3), iyac083.","apa":"Surendranadh, P., Arathoon, L. S., Baskett, C., Field, D., Pickup, M., & Barton, N. H. (2022). Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. Genetics. Oxford University Press. https://doi.org/10.1093/genetics/iyac083","ieee":"P. Surendranadh, L. S. Arathoon, C. Baskett, D. Field, M. Pickup, and N. H. Barton, “Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus,” Genetics, vol. 221, no. 3. Oxford University Press, 2022.","ama":"Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. Genetics. 2022;221(3). doi:10.1093/genetics/iyac083"},"publication":"Genetics","article_type":"original","date_published":"2022-07-01T00:00:00Z","type":"journal_article","issue":"3","abstract":[{"lang":"eng","text":"Many studies have quantified the distribution of heterozygosity and relatedness in natural populations, but few have examined the demographic processes driving these patterns. In this study, we take a novel approach by studying how population structure affects both pairwise identity and the distribution of heterozygosity in a natural population of the self-incompatible plant Antirrhinum majus. Excess variance in heterozygosity between individuals is due to identity disequilibrium, which reflects the variance in inbreeding between individuals; it is measured by the statistic g2. We calculated g2 together with FST and pairwise relatedness (Fij) using 91 SNPs in 22,353 individuals collected over 11 years. We find that pairwise Fij declines rapidly over short spatial scales, and the excess variance in heterozygosity between individuals reflects significant variation in inbreeding. Additionally, we detect an excess of individuals with around half the average heterozygosity, indicating either selfing or matings between close relatives. We use 2 types of simulation to ask whether variation in heterozygosity is consistent with fine-scale spatial population structure. First, by simulating offspring using parents drawn from a range of spatial scales, we show that the known pollen dispersal kernel explains g2. Second, we simulate a 1,000-generation pedigree using the known dispersal and spatial distribution and find that the resulting g2 is consistent with that observed from the field data. In contrast, a simulated population with uniform density underestimates g2, indicating that heterogeneous density promotes identity disequilibrium. Our study shows that heterogeneous density and leptokurtic dispersal can together explain the distribution of heterozygosity."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"11411","intvolume":" 221","title":"Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus","ddc":["576"],"status":"public","oa_version":"Submitted Version","file":[{"file_id":"11412","relation":"main_file","date_updated":"2022-05-26T12:48:15Z","date_created":"2022-05-26T12:48:15Z","success":1,"checksum":"cc2d56deb608bd53c5cc02f03a875107","file_name":"Manuscript.pdf","access_level":"open_access","creator":"larathoo","content_type":"application/pdf","file_size":885374},{"content_type":"application/pdf","file_size":1401704,"creator":"larathoo","access_level":"open_access","file_name":"SupplementalMaterial.pdf","checksum":"693742595b6c7ed809423be01460d083","success":1,"date_created":"2022-05-26T12:48:21Z","date_updated":"2022-05-26T12:48:21Z","relation":"main_file","file_id":"11413"}]},{"scopus_import":"1","day":"29","article_processing_charge":"No","has_accepted_license":"1","article_type":"original","publication":"Proceedings of the National Academy of Sciences","citation":{"ama":"Hledik M, Barton NH, Tkačik G. Accumulation and maintenance of information in evolution. Proceedings of the National Academy of Sciences. 2022;119(36). doi:10.1073/pnas.2123152119","ista":"Hledik M, Barton NH, Tkačik G. 2022. Accumulation and maintenance of information in evolution. Proceedings of the National Academy of Sciences. 119(36), e2123152119.","apa":"Hledik, M., Barton, N. H., & Tkačik, G. (2022). Accumulation and maintenance of information in evolution. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2123152119","ieee":"M. Hledik, N. H. Barton, and G. Tkačik, “Accumulation and maintenance of information in evolution,” Proceedings of the National Academy of Sciences, vol. 119, no. 36. Proceedings of the National Academy of Sciences, 2022.","mla":"Hledik, Michal, et al. “Accumulation and Maintenance of Information in Evolution.” Proceedings of the National Academy of Sciences, vol. 119, no. 36, e2123152119, Proceedings of the National Academy of Sciences, 2022, doi:10.1073/pnas.2123152119.","short":"M. Hledik, N.H. Barton, G. Tkačik, Proceedings of the National Academy of Sciences 119 (2022).","chicago":"Hledik, Michal, Nicholas H Barton, and Gašper Tkačik. “Accumulation and Maintenance of Information in Evolution.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2022. https://doi.org/10.1073/pnas.2123152119."},"date_published":"2022-08-29T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Selection accumulates information in the genome—it guides stochastically evolving populations toward states (genotype frequencies) that would be unlikely under neutrality. This can be quantified as the Kullback–Leibler (KL) divergence between the actual distribution of genotype frequencies and the corresponding neutral distribution. First, we show that this population-level information sets an upper bound on the information at the level of genotype and phenotype, limiting how precisely they can be specified by selection. Next, we study how the accumulation and maintenance of information is limited by the cost of selection, measured as the genetic load or the relative fitness variance, both of which we connect to the control-theoretic KL cost of control. The information accumulation rate is upper bounded by the population size times the cost of selection. This bound is very general, and applies across models (Wright–Fisher, Moran, diffusion) and to arbitrary forms of selection, mutation, and recombination. Finally, the cost of maintaining information depends on how it is encoded: Specifying a single allele out of two is expensive, but one bit encoded among many weakly specified loci (as in a polygenic trait) is cheap."}],"issue":"36","status":"public","title":"Accumulation and maintenance of information in evolution","ddc":["570"],"intvolume":" 119","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12081","file":[{"file_size":2165752,"content_type":"application/pdf","creator":"dernst","file_name":"2022_PNAS_Hledik.pdf","access_level":"open_access","date_updated":"2022-09-12T08:08:12Z","date_created":"2022-09-12T08:08:12Z","checksum":"6dec51f6567da9039982a571508a8e4d","success":1,"relation":"main_file","file_id":"12091"}],"oa_version":"Published Version","month":"08","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"isi":1,"quality_controlled":"1","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation"},{"name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?","_id":"2665AAFE-B435-11E9-9278-68D0E5697425","grant_number":"RGP0034/2018"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"pmid":["36037343"],"isi":["000889278400014"]},"language":[{"iso":"eng"}],"doi":"10.1073/pnas.2123152119","article_number":"e2123152119","file_date_updated":"2022-09-12T08:08:12Z","ec_funded":1,"publication_status":"published","publisher":"Proceedings of the National Academy of Sciences","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"acknowledgement":"We thank Ksenia Khudiakova, Wiktor Młynarski, Sean Stankowski, and two anonymous reviewers for discussions and comments on the manuscript. G.T. and M.H. acknowledge funding from the Human Frontier Science Program Grant RGP0032/2018. N.B. acknowledges funding from ERC Grant 250152 “Information and Evolution.”","year":"2022","pmid":1,"date_updated":"2024-03-06T14:22:51Z","date_created":"2022-09-11T22:01:55Z","volume":119,"author":[{"first_name":"Michal","last_name":"Hledik","id":"4171253A-F248-11E8-B48F-1D18A9856A87","full_name":"Hledik, Michal"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"},{"full_name":"Tkačik, Gašper","last_name":"Tkačik","first_name":"Gašper","orcid":"1","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"15020"}]}},{"has_accepted_license":"1","article_processing_charge":"No","day":"18","date_published":"2022-05-18T00:00:00Z","citation":{"apa":"Belohlavy, S. (2022). The genetic basis of complex traits studied via analysis of evolve and resequence experiments. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11388","ieee":"S. Belohlavy, “The genetic basis of complex traits studied via analysis of evolve and resequence experiments,” Institute of Science and Technology Austria, 2022.","ista":"Belohlavy S. 2022. The genetic basis of complex traits studied via analysis of evolve and resequence experiments. Institute of Science and Technology Austria.","ama":"Belohlavy S. The genetic basis of complex traits studied via analysis of evolve and resequence experiments. 2022. doi:10.15479/at:ista:11388","chicago":"Belohlavy, Stefanie. “The Genetic Basis of Complex Traits Studied via Analysis of Evolve and Resequence Experiments.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11388.","short":"S. Belohlavy, The Genetic Basis of Complex Traits Studied via Analysis of Evolve and Resequence Experiments, Institute of Science and Technology Austria, 2022.","mla":"Belohlavy, Stefanie. The Genetic Basis of Complex Traits Studied via Analysis of Evolve and Resequence Experiments. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11388."},"page":"98","abstract":[{"text":"In evolve and resequence experiments, a population is sequenced, subjected to selection and\r\nthen sequenced again, so that genetic changes before and after selection can be observed at\r\nthe genetic level. Here, I use these studies to better understand the genetic basis of complex\r\ntraits - traits which depend on more than a few genes.\r\nIn the first chapter, I discuss the first evolve and resequence experiment, in which a population\r\nof mice, the so-called \"Longshanks\" mice, were selected for tibia length while their body mass\r\nwas kept constant. The full pedigree is known. We observed a selection response on all\r\nchromosomes and used the infinitesimal model with linkage, a model which assumes an infinite\r\nnumber of genes with infinitesimally small effect sizes, as a null model. Results implied a very\r\npolygenic basis with a few loci of major effect standing out and changing in parallel. There\r\nwas large variability between the different chromosomes in this study, probably due to LD.\r\nIn chapter two, I go on to discuss the impact of LD, on the variability in an allele-frequency\r\nbased summary statistic, giving an equation based on the initial allele frequencies, average\r\npairwise LD, and the first four moments of the haplotype block copy number distribution. I\r\ndescribe this distribution by referring back to the founder generation. I then demonstrate\r\nhow to infer selection via a maximum likelihood scheme on the example of a single locus and\r\ndiscuss how to extend this to more realistic scenarios.\r\nIn chapter three, I discuss the second evolve and resequence experiment, in which a small\r\npopulation of Drosophila melanogaster was selected for increased pupal case size over 6\r\ngenerations. The experiment was highly replicated with 27 lines selected within family and a\r\nknown pedigree. We observed a phenotypic selection response of over one standard deviation.\r\nI describe the patterns in allele frequency data, including allele frequency changes and patterns\r\nof heterozygosity, and give ideas for future work.","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"file":[{"checksum":"4d75e6a619df7e8a9d6e840aee182380","date_updated":"2023-05-20T22:30:03Z","date_created":"2022-05-19T13:03:13Z","relation":"main_file","embargo":"2023-05-19","file_id":"11398","content_type":"application/pdf","file_size":8247240,"creator":"sbelohla","access_level":"open_access","file_name":"thesis_sb_final_pdfa.pdf"},{"access_level":"closed","embargo_to":"open_access","file_name":"thesis_sb_final.zip","file_size":7094,"content_type":"application/x-zip-compressed","creator":"sbelohla","relation":"source_file","file_id":"11399","checksum":"7a5d8b6dd0ca00784f860075b0a7d8f0","date_created":"2022-05-19T13:07:47Z","date_updated":"2023-05-20T22:30:03Z"}],"oa_version":"Published Version","_id":"11388","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","ddc":["576"],"status":"public","title":"The genetic basis of complex traits studied via analysis of evolve and resequence experiments","publication_identifier":{"isbn":["978-3-99078-018-3"]},"month":"05","doi":"10.15479/at:ista:11388","language":[{"iso":"eng"}],"supervisor":[{"full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"degree_awarded":"PhD","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"file_date_updated":"2023-05-20T22:30:03Z","related_material":{"record":[{"id":"6713","status":"public","relation":"part_of_dissertation"}]},"author":[{"full_name":"Belohlavy, Stefanie","orcid":"0000-0002-9849-498X","id":"43FE426A-F248-11E8-B48F-1D18A9856A87","last_name":"Belohlavy","first_name":"Stefanie"}],"date_updated":"2023-08-29T06:41:51Z","date_created":"2022-05-16T16:49:18Z","year":"2022","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"publication_status":"published"},{"date_published":"2021-12-01T00:00:00Z","publication":"PLoS Computational Biology","citation":{"chicago":"Bodova, Katarina, Eniko Szep, and Nicholas H Barton. “Dynamic Maximum Entropy Provides Accurate Approximation of Structured Population Dynamics.” PLoS Computational Biology. Public Library of Science, 2021. https://doi.org/10.1371/journal.pcbi.1009661.","mla":"Bodova, Katarina, et al. “Dynamic Maximum Entropy Provides Accurate Approximation of Structured Population Dynamics.” PLoS Computational Biology, vol. 17, no. 12, e1009661, Public Library of Science, 2021, doi:10.1371/journal.pcbi.1009661.","short":"K. Bodova, E. Szep, N.H. Barton, PLoS Computational Biology 17 (2021).","ista":"Bodova K, Szep E, Barton NH. 2021. Dynamic maximum entropy provides accurate approximation of structured population dynamics. PLoS Computational Biology. 17(12), e1009661.","ieee":"K. Bodova, E. Szep, and N. H. Barton, “Dynamic maximum entropy provides accurate approximation of structured population dynamics,” PLoS Computational Biology, vol. 17, no. 12. Public Library of Science, 2021.","apa":"Bodova, K., Szep, E., & Barton, N. H. (2021). Dynamic maximum entropy provides accurate approximation of structured population dynamics. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1009661","ama":"Bodova K, Szep E, Barton NH. Dynamic maximum entropy provides accurate approximation of structured population dynamics. PLoS Computational Biology. 2021;17(12). doi:10.1371/journal.pcbi.1009661"},"article_type":"original","day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"11383","date_created":"2022-05-16T08:53:11Z","date_updated":"2022-05-16T08:53:11Z","checksum":"dcd185d4f7e0acee25edf1d6537f447e","success":1,"file_name":"2021_PLOsComBio_Bodova.pdf","access_level":"open_access","file_size":2299486,"content_type":"application/pdf","creator":"dernst"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"10535","title":"Dynamic maximum entropy provides accurate approximation of structured population dynamics","ddc":["570"],"status":"public","intvolume":" 17","abstract":[{"lang":"eng","text":"Realistic models of biological processes typically involve interacting components on multiple scales, driven by changing environment and inherent stochasticity. Such models are often analytically and numerically intractable. We revisit a dynamic maximum entropy method that combines a static maximum entropy with a quasi-stationary approximation. This allows us to reduce stochastic non-equilibrium dynamics expressed by the Fokker-Planck equation to a simpler low-dimensional deterministic dynamics, without the need to track microscopic details. Although the method has been previously applied to a few (rather complicated) applications in population genetics, our main goal here is to explain and to better understand how the method works. We demonstrate the usefulness of the method for two widely studied stochastic problems, highlighting its accuracy in capturing important macroscopic quantities even in rapidly changing non-stationary conditions. For the Ornstein-Uhlenbeck process, the method recovers the exact dynamics whilst for a stochastic island model with migration from other habitats, the approximation retains high macroscopic accuracy under a wide range of scenarios in a dynamic environment."}],"issue":"12","type":"journal_article","doi":"10.1371/journal.pcbi.1009661","acknowledged_ssus":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2102.03669"],"pmid":["34851948"]},"quality_controlled":"1","month":"12","publication_identifier":{"eissn":["1553-7358"],"issn":["1553-734X"]},"author":[{"id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7214-0171","first_name":"Katarína","last_name":"Bod'ová","full_name":"Bod'ová, Katarína"},{"last_name":"Szep","first_name":"Eniko","id":"485BB5A4-F248-11E8-B48F-1D18A9856A87","full_name":"Szep, Eniko"},{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton"}],"date_updated":"2022-08-01T10:48:04Z","date_created":"2021-12-12T23:01:27Z","volume":17,"year":"2021","acknowledgement":"Computational resources for the study were provided by the Institute of Science and Technology, Austria.\r\nKB received funding from the Scientific Grant Agency of the Slovak Republic under the Grants Nos. 1/0755/19 and 1/0521/20.","pmid":1,"publication_status":"published","publisher":"Public Library of Science","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"file_date_updated":"2022-05-16T08:53:11Z","article_number":"e1009661"},{"date_published":"2021-01-01T00:00:00Z","publication":"Journal of Evolutionary Biology","citation":{"short":"A. Simon, C. Fraisse, T. El Ayari, C. Liautard‐Haag, P. Strelkov, J.J. Welch, N. Bierne, Journal of Evolutionary Biology 34 (2021) 208–223.","mla":"Simon, Alexis, et al. “How Do Species Barriers Decay? Concordance and Local Introgression in Mosaic Hybrid Zones of Mussels.” Journal of Evolutionary Biology, vol. 34, no. 1, Wiley, 2021, pp. 208–23, doi:10.1111/jeb.13709.","chicago":"Simon, Alexis, Christelle Fraisse, Tahani El Ayari, Cathy Liautard‐Haag, Petr Strelkov, John J Welch, and Nicolas Bierne. “How Do Species Barriers Decay? Concordance and Local Introgression in Mosaic Hybrid Zones of Mussels.” Journal of Evolutionary Biology. Wiley, 2021. https://doi.org/10.1111/jeb.13709.","ama":"Simon A, Fraisse C, El Ayari T, et al. How do species barriers decay? Concordance and local introgression in mosaic hybrid zones of mussels. Journal of Evolutionary Biology. 2021;34(1):208-223. doi:10.1111/jeb.13709","apa":"Simon, A., Fraisse, C., El Ayari, T., Liautard‐Haag, C., Strelkov, P., Welch, J. J., & Bierne, N. (2021). How do species barriers decay? Concordance and local introgression in mosaic hybrid zones of mussels. Journal of Evolutionary Biology. Wiley. https://doi.org/10.1111/jeb.13709","ieee":"A. Simon et al., “How do species barriers decay? Concordance and local introgression in mosaic hybrid zones of mussels,” Journal of Evolutionary Biology, vol. 34, no. 1. Wiley, pp. 208–223, 2021.","ista":"Simon A, Fraisse C, El Ayari T, Liautard‐Haag C, Strelkov P, Welch JJ, Bierne N. 2021. How do species barriers decay? Concordance and local introgression in mosaic hybrid zones of mussels. Journal of Evolutionary Biology. 34(1), 208–223."},"article_type":"original","page":"208-223","day":"01","article_processing_charge":"No","scopus_import":"1","oa_version":"Preprint","_id":"8708","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"How do species barriers decay? Concordance and local introgression in mosaic hybrid zones of mussels","intvolume":" 34","abstract":[{"lang":"eng","text":"The Mytilus complex of marine mussel species forms a mosaic of hybrid zones, found across temperate regions of the globe. This allows us to study ‘replicated’ instances of secondary contact between closely related species. Previous work on this complex has shown that local introgression is both widespread and highly heterogeneous, and has identified SNPs that are outliers of differentiation between lineages. Here, we developed an ancestry‐informative panel of such SNPs. We then compared their frequencies in newly sampled populations, including samples from within the hybrid zones, and parental populations at different distances from the contact. Results show that close to the hybrid zones, some outlier loci are near to fixation for the heterospecific allele, suggesting enhanced local introgression, or the local sweep of a shared ancestral allele. Conversely, genomic cline analyses, treating local parental populations as the reference, reveal a globally high concordance among loci, albeit with a few signals of asymmetric introgression. Enhanced local introgression at specific loci is consistent with the early transfer of adaptive variants after contact, possibly including asymmetric bi‐stable variants (Dobzhansky‐Muller incompatibilities), or haplotypes loaded with fewer deleterious mutations. Having escaped one barrier, however, these variants can be trapped or delayed at the next barrier, confining the introgression locally. These results shed light on the decay of species barriers during phases of contact."}],"issue":"1","type":"journal_article","doi":"10.1111/jeb.13709","language":[{"iso":"eng"}],"external_id":{"pmid":["33045123"],"isi":["000579599700001"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/818559"}],"oa":1,"quality_controlled":"1","isi":1,"month":"01","publication_identifier":{"eissn":["14209101"],"issn":["1010061X"]},"author":[{"first_name":"Alexis","last_name":"Simon","full_name":"Simon, Alexis"},{"full_name":"Fraisse, Christelle","last_name":"Fraisse","first_name":"Christelle","orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"},{"full_name":"El Ayari, Tahani","last_name":"El Ayari","first_name":"Tahani"},{"first_name":"Cathy","last_name":"Liautard‐Haag","full_name":"Liautard‐Haag, Cathy"},{"last_name":"Strelkov","first_name":"Petr","full_name":"Strelkov, Petr"},{"full_name":"Welch, John J","first_name":"John J","last_name":"Welch"},{"last_name":"Bierne","first_name":"Nicolas","full_name":"Bierne, Nicolas"}],"related_material":{"record":[{"status":"public","relation":"research_data","id":"13073"}]},"date_updated":"2023-08-04T11:04:11Z","date_created":"2020-10-25T23:01:20Z","volume":34,"acknowledgement":"Data used in this work were partly produced through the genotyping and sequencing facilities of ISEM and LabEx CeMEB, an ANR ‘Investissements d'avenir’ program (ANR‐10‐LABX‐04‐01) This project benefited from the Montpellier Bioinformatics Biodiversity platform supported by the LabEx CeMEB. We thank Norah Saarman, Grant Pogson, Célia Gosset and Pierre‐Alexandre Gagnaire for providing samples. This work was funded by a Languedoc‐Roussillon ‘Chercheur(se)s d'Avenir’ grant (Connect7 project). P. Strelkov was supported by the Russian Science Foundation project 19‐74‐20024. This is article 2020‐240 of Institut des Sciences de l'Evolution de Montpellier.","year":"2021","pmid":1,"publication_status":"published","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"publisher":"Wiley"},{"isi":1,"quality_controlled":"1","main_file_link":[{"url":"http://hdl.handle.net/10261/223937","open_access":"1"}],"external_id":{"isi":["000583190600001"],"pmid":["33078844"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1111/evo.14111","publication_identifier":{"eissn":["1558-5646"],"issn":["0014-3820"]},"month":"02","department":[{"_id":"NiBa"}],"publisher":"Wiley","publication_status":"published","pmid":1,"year":"2021","acknowledgement":"This work was financed by the Spanish Agencia Estatal de Investigación (CGL2017‐85718‐P), awarded to BCE, and co‐financed by FEDER. It was also supported by the Spanish Ministerio de Ciencia, Innovación y Universidades (EQC2018‐004418‐P), awarded to BCE. AS‐C was funded by the Spanish Ministerio de Ciencia, Innovación y Universidades through an FPU PhD fellowship (FPU014/02948). The authors thank Instituto Tecnológico y de Energías Renovables (ITER), S.A for providing access to the Teide High‐Performance Computing facility (Teide‐HPC). Fieldwork was supported by collecting permit AFF 107/17 (sigma number 2017‐00572) kindly provided by the Cabildo of Tenerife. The authors wish to thank the following for field work and sample sorting and identification: A. J. Pérez‐Delgado, H. López, and C. Andújar. We also thank V. García‐Olivares for assistance with laboratory and bioinformatic work.","volume":75,"date_updated":"2023-08-04T11:09:49Z","date_created":"2020-11-08T23:01:26Z","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1111/evo.14225"}]},"author":[{"full_name":"Salces-Castellano, Antonia","last_name":"Salces-Castellano","first_name":"Antonia"},{"full_name":"Stankowski, Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","last_name":"Stankowski","first_name":"Sean"},{"full_name":"Arribas, Paula","first_name":"Paula","last_name":"Arribas"},{"full_name":"Patino, Jairo","last_name":"Patino","first_name":"Jairo"},{"first_name":"Dirk N. ","last_name":"Karger","full_name":"Karger, Dirk N. "},{"first_name":"Roger","last_name":"Butlin","full_name":"Butlin, Roger"},{"last_name":"Emerson","first_name":"Brent C.","full_name":"Emerson, Brent C."}],"page":"231-244","article_type":"original","citation":{"chicago":"Salces-Castellano, Antonia, Sean Stankowski, Paula Arribas, Jairo Patino, Dirk N. Karger, Roger Butlin, and Brent C. Emerson. “Long-Term Cloud Forest Response to Climate Warming Revealed by Insect Speciation History.” Evolution. Wiley, 2021. https://doi.org/10.1111/evo.14111.","mla":"Salces-Castellano, Antonia, et al. “Long-Term Cloud Forest Response to Climate Warming Revealed by Insect Speciation History.” Evolution, vol. 75, no. 2, Wiley, 2021, pp. 231–44, doi:10.1111/evo.14111.","short":"A. Salces-Castellano, S. Stankowski, P. Arribas, J. Patino, D.N. Karger, R. Butlin, B.C. Emerson, Evolution 75 (2021) 231–244.","ista":"Salces-Castellano A, Stankowski S, Arribas P, Patino J, Karger DN, Butlin R, Emerson BC. 2021. Long-term cloud forest response to climate warming revealed by insect speciation history. Evolution. 75(2), 231–244.","ieee":"A. Salces-Castellano et al., “Long-term cloud forest response to climate warming revealed by insect speciation history,” Evolution, vol. 75, no. 2. Wiley, pp. 231–244, 2021.","apa":"Salces-Castellano, A., Stankowski, S., Arribas, P., Patino, J., Karger, D. N., Butlin, R., & Emerson, B. C. (2021). Long-term cloud forest response to climate warming revealed by insect speciation history. Evolution. Wiley. https://doi.org/10.1111/evo.14111","ama":"Salces-Castellano A, Stankowski S, Arribas P, et al. Long-term cloud forest response to climate warming revealed by insect speciation history. Evolution. 2021;75(2):231-244. doi:10.1111/evo.14111"},"publication":"Evolution","date_published":"2021-02-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"01","intvolume":" 75","title":"Long-term cloud forest response to climate warming revealed by insect speciation history","status":"public","_id":"8743","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Submitted Version","type":"journal_article","issue":"2","abstract":[{"lang":"eng","text":"Montane cloud forests are areas of high endemism, and are one of the more vulnerable terrestrial ecosystems to climate change. Thus, understanding how they both contribute to the generation of biodiversity, and will respond to ongoing climate change, are important and related challenges. The widely accepted model for montane cloud forest dynamics involves upslope forcing of their range limits with global climate warming. However, limited climate data provides some support for an alternative model, where range limits are forced downslope with climate warming. Testing between these two models is challenging, due to the inherent limitations of climate and pollen records. We overcome this with an alternative source of historical information, testing between competing model predictions using genomic data and demographic analyses for a species of beetle tightly associated to an oceanic island cloud forest. Results unequivocally support the alternative model: populations that were isolated at higher elevation peaks during the Last Glacial Maximum are now in contact and hybridizing at lower elevations. Our results suggest that genomic data are a rich source of information to further understand how montane cloud forest biodiversity originates, and how it is likely to be impacted by ongoing climate change."}]},{"issue":"2","abstract":[{"lang":"eng","text":"Domestication is a human‐induced selection process that imprints the genomes of domesticated populations over a short evolutionary time scale and that occurs in a given demographic context. Reconstructing historical gene flow, effective population size changes and their timing is therefore of fundamental interest to understand how plant demography and human selection jointly shape genomic divergence during domestication. Yet, the comparison under a single statistical framework of independent domestication histories across different crop species has been little evaluated so far. Thus, it is unclear whether domestication leads to convergent demographic changes that similarly affect crop genomes. To address this question, we used existing and new transcriptome data on three crop species of Solanaceae (eggplant, pepper and tomato), together with their close wild relatives. We fitted twelve demographic models of increasing complexity on the unfolded joint allele frequency spectrum for each wild/crop pair, and we found evidence for both shared and species‐specific demographic processes between species. A convergent history of domestication with gene flow was inferred for all three species, along with evidence of strong reduction in the effective population size during the cultivation stage of tomato and pepper. The absence of any reduction in size of the crop in eggplant stands out from the classical view of the domestication process; as does the existence of a “protracted period” of management before cultivation. Our results also suggest divergent management strategies of modern cultivars among species as their current demography substantially differs. Finally, the timing of domestication is species‐specific and supported by the few historical records available."}],"type":"journal_article","oa_version":"Published Version","intvolume":" 34","title":"Genomic inference of complex domestication histories in three Solanaceae species","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8928","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2021-02-01T00:00:00Z","page":"270-283","article_type":"original","citation":{"chicago":"Arnoux, Stéphanie, Christelle Fraisse, and Christopher Sauvage. “Genomic Inference of Complex Domestication Histories in Three Solanaceae Species.” Journal of Evolutionary Biology. Wiley, 2021. https://doi.org/10.1111/jeb.13723.","short":"S. Arnoux, C. Fraisse, C. Sauvage, Journal of Evolutionary Biology 34 (2021) 270–283.","mla":"Arnoux, Stéphanie, et al. “Genomic Inference of Complex Domestication Histories in Three Solanaceae Species.” Journal of Evolutionary Biology, vol. 34, no. 2, Wiley, 2021, pp. 270–83, doi:10.1111/jeb.13723.","apa":"Arnoux, S., Fraisse, C., & Sauvage, C. (2021). Genomic inference of complex domestication histories in three Solanaceae species. Journal of Evolutionary Biology. Wiley. https://doi.org/10.1111/jeb.13723","ieee":"S. Arnoux, C. Fraisse, and C. Sauvage, “Genomic inference of complex domestication histories in three Solanaceae species,” Journal of Evolutionary Biology, vol. 34, no. 2. Wiley, pp. 270–283, 2021.","ista":"Arnoux S, Fraisse C, Sauvage C. 2021. Genomic inference of complex domestication histories in three Solanaceae species. Journal of Evolutionary Biology. 34(2), 270–283.","ama":"Arnoux S, Fraisse C, Sauvage C. Genomic inference of complex domestication histories in three Solanaceae species. Journal of Evolutionary Biology. 2021;34(2):270-283. doi:10.1111/jeb.13723"},"publication":"Journal of Evolutionary Biology","volume":34,"date_created":"2020-12-06T23:01:16Z","date_updated":"2023-08-04T11:19:26Z","related_material":{"record":[{"id":"13065","status":"public","relation":"research_data"}]},"author":[{"full_name":"Arnoux, Stéphanie","last_name":"Arnoux","first_name":"Stéphanie"},{"full_name":"Fraisse, Christelle","orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse","first_name":"Christelle"},{"first_name":"Christopher","last_name":"Sauvage","full_name":"Sauvage, Christopher"}],"publisher":"Wiley","department":[{"_id":"NiBa"}],"publication_status":"published","pmid":1,"year":"2021","acknowledgement":"This work was supported by the EU Marie Curie Career Integration grant (FP7‐PEOPLE‐2011‐CIG grant agreement PCIG10‐GA‐2011‐304164) attributed to CS. SA was supported by a PhD fellowship from the French Région PACA and the Plant Breeding division of INRA, in partnership with Gautier Semences. CF was supported by an Austrian Science Foundation FWF grant (Project M 2463‐B29). Authors thank Mathilde Causse and Beatriz Vicoso for their team leading. Thanks to the Italian Eggplant Genome Consortium, which includes the DISAFA, Plant Genetics and Breeding (University of Torino), the Biotechnology Department (University of Verona), the CREA‐ORL in Montanaso Lombardo (LO) and the ENEA in Rome for providing access to the eggplant genome reference. Thanks to CRB‐lég ( https://www6.paca.inra.fr/gafl_eng/Vegetables-GRC ) for managing and providing the genetic resources, to Marie‐Christine Daunay and Alain Palloix (INRA UR1052) for assistance in choosing the biological material used, to Muriel Latreille and Sylvain Santoni from the UMR AGAP (INRA Montpellier, France) for their help with RNAseq library preparation, to Jean‐Paul Bouchet and Jacques Lagnel (INRA UR1052) for their Bioinformatics assistance.","publication_identifier":{"eissn":["14209101"],"issn":["1010061X"]},"month":"02","language":[{"iso":"eng"}],"doi":"10.1111/jeb.13723","project":[{"_id":"2662AADE-B435-11E9-9278-68D0E5697425","grant_number":"M02463","name":"Sex chromosomes and species barriers","call_identifier":"FWF"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000587769700001"],"pmid":["33107098"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/jeb.13723"}]},{"scopus_import":"1","day":"18","has_accepted_license":"1","article_processing_charge":"No","article_type":"original","page":"4-15","publication":"Journal of Evolutionary Biology","citation":{"short":"R. Faria, K. Johannesson, S. Stankowski, Journal of Evolutionary Biology 34 (2021) 4–15.","mla":"Faria, Rui, et al. “Speciation in Marine Environments: Diving under the Surface.” Journal of Evolutionary Biology, vol. 34, no. 1, Wiley, 2021, pp. 4–15, doi:10.1111/jeb.13756.","chicago":"Faria, Rui, Kerstin Johannesson, and Sean Stankowski. “Speciation in Marine Environments: Diving under the Surface.” Journal of Evolutionary Biology. Wiley, 2021. https://doi.org/10.1111/jeb.13756.","ama":"Faria R, Johannesson K, Stankowski S. Speciation in marine environments: Diving under the surface. Journal of Evolutionary Biology. 2021;34(1):4-15. doi:10.1111/jeb.13756","ieee":"R. Faria, K. Johannesson, and S. Stankowski, “Speciation in marine environments: Diving under the surface,” Journal of Evolutionary Biology, vol. 34, no. 1. Wiley, pp. 4–15, 2021.","apa":"Faria, R., Johannesson, K., & Stankowski, S. (2021). Speciation in marine environments: Diving under the surface. Journal of Evolutionary Biology. Wiley. https://doi.org/10.1111/jeb.13756","ista":"Faria R, Johannesson K, Stankowski S. 2021. Speciation in marine environments: Diving under the surface. Journal of Evolutionary Biology. 34(1), 4–15."},"date_published":"2021-01-18T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Marine environments are inhabited by a broad representation of the tree of life, yet our understanding of speciation in marine ecosystems is extremely limited compared with terrestrial and freshwater environments. Developing a more comprehensive picture of speciation in marine environments requires that we 'dive under the surface' by studying a wider range of taxa and ecosystems is necessary for a more comprehensive picture of speciation. Although studying marine evolutionary processes is often challenging, recent technological advances in different fields, from maritime engineering to genomics, are making it increasingly possible to study speciation of marine life forms across diverse ecosystems and taxa. Motivated by recent research in the field, including the 14 contributions in this issue, we highlight and discuss six axes of research that we think will deepen our understanding of speciation in the marine realm: (a) study a broader range of marine environments and organisms; (b) identify the reproductive barriers driving speciation between marine taxa; (c) understand the role of different genomic architectures underlying reproductive isolation; (d) infer the evolutionary history of divergence using model‐based approaches; (e) study patterns of hybridization and introgression between marine taxa; and (f) implement highly interdisciplinary, collaborative research programmes. In outlining these goals, we hope to inspire researchers to continue filling this critical knowledge gap surrounding the origins of marine biodiversity."}],"issue":"1","status":"public","ddc":["570"],"title":"Speciation in marine environments: Diving under the surface","intvolume":" 34","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9100","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"9108","date_updated":"2021-02-09T09:04:02Z","date_created":"2021-02-09T09:04:02Z","checksum":"5755856a5368d4b4cdd6fad5ab27f4d1","success":1,"file_name":"2021_JourEvolBiology_Faria.pdf","access_level":"open_access","file_size":561340,"content_type":"application/pdf","creator":"dernst"}],"month":"01","publication_identifier":{"issn":["1010061X"],"eissn":["14209101"]},"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000608367500001"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1111/jeb.13756","file_date_updated":"2021-02-09T09:04:02Z","publication_status":"published","publisher":"Wiley","department":[{"_id":"NiBa"}],"acknowledgement":"We would like to thank all the participants in the speciation symposium of the Marine Evolution Conference in Sweden for the interesting discussions and to all the contributors to this special\r\nissue. We thank Nicolas Bierne and Wolf Blanckenhorn (reviewer and editor, respectively) for valuable suggestions during the revision of the manuscript, and Roger K. Butlin and Anja M. Westram for very helpful comments on a previous draft. We would also like to thank Wolf Blanckenhorn and Nicola Cook, the Editor in Chief and the Managing Editor of the Journal of Evolutionary Biology, respectively, for the encouragement and support in putting together this special issue, and to all reviewers involved. RF was financed by the European Union's Horizon 2020 Research and Innovation Programme under the Marie Sklodowska-Curie Grant Agreement Number 706376 and is currently financed by the FEDER Funds through the Operational Competitiveness Factors Program COMPETE and by National Funds through the Foundation for Science and Technology (FCT) within the scope of the project ‘Hybrabbid' (PTDC/BIA-EVL/30628/2017-POCI-01-0145-FEDER-030628). KJ was funded by the Swedish\r\nResearch Council, VR. SS was supported by NERC and ERC funding awarded to Roger K. Butlin.","year":"2021","date_created":"2021-02-07T23:01:13Z","date_updated":"2023-08-07T13:42:08Z","volume":34,"author":[{"last_name":"Faria","first_name":"Rui","full_name":"Faria, Rui"},{"full_name":"Johannesson, Kerstin","first_name":"Kerstin","last_name":"Johannesson"},{"full_name":"Stankowski, Sean","last_name":"Stankowski","first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E"}]},{"article_number":"iyaa025","author":[{"first_name":"Christelle","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle"},{"full_name":"Sachdeva, Himani","id":"42377A0A-F248-11E8-B48F-1D18A9856A87","first_name":"Himani","last_name":"Sachdeva"}],"date_created":"2021-02-18T14:41:30Z","date_updated":"2023-08-07T13:47:01Z","volume":217,"year":"2021","acknowledgement":"The computations were performed with the IST Austria High-Performance Computing (HPC) Cluster and the Institut Français de Bioinformatique (IFB) Core Cluster. We are grateful to Nick Barton and Beatriz Vicoso for critical comments on the model and the manuscript. We also thank Brian Charlesworth, Stuart Baird, and an anonymous reviewer for insightful comments.\r\nC.F. was supported by an Austrian Science Foundation FWF grant (Project M 2463-B29).","publication_status":"published","publisher":"Genetics Society of America","department":[{"_id":"NiBa"}],"month":"02","publication_identifier":{"issn":["1943-2631"]},"doi":"10.1093/genetics/iyaa025","acknowledged_ssus":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"external_id":{"isi":["000637218100005"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/genetics/iyaa025"}],"quality_controlled":"1","isi":1,"project":[{"_id":"2662AADE-B435-11E9-9278-68D0E5697425","grant_number":"M02463","name":"Sex chromosomes and species barriers","call_identifier":"FWF"}],"abstract":[{"text":"Interspecific crossing experiments have shown that sex chromosomes play a major role in reproductive isolation between many pairs of species. However, their ability to act as reproductive barriers, which hamper interspecific genetic exchange, has rarely been evaluated quantitatively compared to Autosomes. This genome-wide limitation of gene flow is essential for understanding the complete separation of species, and thus speciation. Here, we develop a mainland-island model of secondary contact between hybridizing species of an XY (or ZW) sexual system. We obtain theoretical predictions for the frequency of introgressed alleles, and the strength of the barrier to neutral gene flow for the two types of chromosomes carrying multiple interspecific barrier loci. Theoretical predictions are obtained for scenarios where introgressed alleles are rare. We show that the same analytical expressions apply for sex chromosomes and autosomes, but with different sex-averaged effective parameters. The specific features of sex chromosomes (hemizygosity and absence of recombination in the heterogametic sex) lead to reduced levels of introgression on the X (or Z) compared to autosomes. This effect can be enhanced by certain types of sex-biased forces, but it remains overall small (except when alleles causing incompatibilities are recessive). We discuss these predictions in the light of empirical data comprising model-based tests of introgression and cline surveys in various biological systems.","lang":"eng"}],"issue":"2","type":"journal_article","oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9168","status":"public","title":"The rates of introgression and barriers to genetic exchange between hybridizing species: Sex chromosomes vs autosomes","intvolume":" 217","day":"01","article_processing_charge":"No","date_published":"2021-02-01T00:00:00Z","publication":"Genetics","citation":{"short":"C. Fraisse, H. Sachdeva, Genetics 217 (2021).","mla":"Fraisse, Christelle, and Himani Sachdeva. “The Rates of Introgression and Barriers to Genetic Exchange between Hybridizing Species: Sex Chromosomes vs Autosomes.” Genetics, vol. 217, no. 2, iyaa025, Genetics Society of America, 2021, doi:10.1093/genetics/iyaa025.","chicago":"Fraisse, Christelle, and Himani Sachdeva. “The Rates of Introgression and Barriers to Genetic Exchange between Hybridizing Species: Sex Chromosomes vs Autosomes.” Genetics. Genetics Society of America, 2021. https://doi.org/10.1093/genetics/iyaa025.","ama":"Fraisse C, Sachdeva H. The rates of introgression and barriers to genetic exchange between hybridizing species: Sex chromosomes vs autosomes. Genetics. 2021;217(2). doi:10.1093/genetics/iyaa025","ieee":"C. Fraisse and H. Sachdeva, “The rates of introgression and barriers to genetic exchange between hybridizing species: Sex chromosomes vs autosomes,” Genetics, vol. 217, no. 2. Genetics Society of America, 2021.","apa":"Fraisse, C., & Sachdeva, H. (2021). The rates of introgression and barriers to genetic exchange between hybridizing species: Sex chromosomes vs autosomes. Genetics. Genetics Society of America. https://doi.org/10.1093/genetics/iyaa025","ista":"Fraisse C, Sachdeva H. 2021. The rates of introgression and barriers to genetic exchange between hybridizing species: Sex chromosomes vs autosomes. Genetics. 217(2), iyaa025."},"article_type":"original"},{"doi":"10.1111/1755-0998.13323","language":[{"iso":"eng"}],"external_id":{"isi":["000614183100001"]},"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2020.06.15.151597v2"}],"oa":1,"quality_controlled":"1","isi":1,"month":"01","publication_identifier":{"issn":["1755098X"],"eissn":["17550998"]},"author":[{"first_name":"Christelle","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle"},{"full_name":"Popovic, Iva","last_name":"Popovic","first_name":"Iva"},{"full_name":"Mazoyer, Clément","last_name":"Mazoyer","first_name":"Clément"},{"full_name":"Spataro, Bruno","first_name":"Bruno","last_name":"Spataro"},{"last_name":"Delmotte","first_name":"Stéphane","full_name":"Delmotte, Stéphane"},{"last_name":"Romiguier","first_name":"Jonathan","full_name":"Romiguier, Jonathan"},{"last_name":"Loire","first_name":"Étienne","full_name":"Loire, Étienne"},{"last_name":"Simon","first_name":"Alexis","full_name":"Simon, Alexis"},{"full_name":"Galtier, Nicolas","first_name":"Nicolas","last_name":"Galtier"},{"last_name":"Duret","first_name":"Laurent","full_name":"Duret, Laurent"},{"full_name":"Bierne, Nicolas","last_name":"Bierne","first_name":"Nicolas"},{"first_name":"Xavier","last_name":"Vekemans","full_name":"Vekemans, Xavier"},{"full_name":"Roux, Camille","last_name":"Roux","first_name":"Camille"}],"date_updated":"2023-08-07T13:45:18Z","date_created":"2021-02-14T23:01:14Z","volume":21,"year":"2021","publication_status":"published","publisher":"Wiley","department":[{"_id":"NiBa"}],"date_published":"2021-01-15T00:00:00Z","publication":"Molecular Ecology Resources","citation":{"chicago":"Fraisse, Christelle, Iva Popovic, Clément Mazoyer, Bruno Spataro, Stéphane Delmotte, Jonathan Romiguier, Étienne Loire, et al. “DILS: Demographic Inferences with Linked Selection by Using ABC.” Molecular Ecology Resources. Wiley, 2021. https://doi.org/10.1111/1755-0998.13323.","mla":"Fraisse, Christelle, et al. “DILS: Demographic Inferences with Linked Selection by Using ABC.” Molecular Ecology Resources, vol. 21, Wiley, 2021, pp. 2629–44, doi:10.1111/1755-0998.13323.","short":"C. Fraisse, I. Popovic, C. Mazoyer, B. Spataro, S. Delmotte, J. Romiguier, É. Loire, A. Simon, N. Galtier, L. Duret, N. Bierne, X. Vekemans, C. Roux, Molecular Ecology Resources 21 (2021) 2629–2644.","ista":"Fraisse C, Popovic I, Mazoyer C, Spataro B, Delmotte S, Romiguier J, Loire É, Simon A, Galtier N, Duret L, Bierne N, Vekemans X, Roux C. 2021. DILS: Demographic inferences with linked selection by using ABC. Molecular Ecology Resources. 21, 2629–2644.","ieee":"C. Fraisse et al., “DILS: Demographic inferences with linked selection by using ABC,” Molecular Ecology Resources, vol. 21. Wiley, pp. 2629–2644, 2021.","apa":"Fraisse, C., Popovic, I., Mazoyer, C., Spataro, B., Delmotte, S., Romiguier, J., … Roux, C. (2021). DILS: Demographic inferences with linked selection by using ABC. Molecular Ecology Resources. Wiley. https://doi.org/10.1111/1755-0998.13323","ama":"Fraisse C, Popovic I, Mazoyer C, et al. DILS: Demographic inferences with linked selection by using ABC. Molecular Ecology Resources. 2021;21:2629-2644. doi:10.1111/1755-0998.13323"},"article_type":"original","page":"2629-2644","day":"15","article_processing_charge":"No","scopus_import":"1","oa_version":"Preprint","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9119","status":"public","title":"DILS: Demographic inferences with linked selection by using ABC","intvolume":" 21","abstract":[{"text":"We present DILS, a deployable statistical analysis platform for conducting demographic inferences with linked selection from population genomic data using an Approximate Bayesian Computation framework. DILS takes as input single‐population or two‐population data sets (multilocus fasta sequences) and performs three types of analyses in a hierarchical manner, identifying: (a) the best demographic model to study the importance of gene flow and population size change on the genetic patterns of polymorphism and divergence, (b) the best genomic model to determine whether the effective size Ne and migration rate N, m are heterogeneously distributed along the genome (implying linked selection) and (c) loci in genomic regions most associated with barriers to gene flow. Also available via a Web interface, an objective of DILS is to facilitate collaborative research in speciation genomics. Here, we show the performance and limitations of DILS by using simulations and finally apply the method to published data on a divergence continuum composed by 28 pairs of Mytilus mussel populations/species.","lang":"eng"}],"type":"journal_article"},{"_id":"9375","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"Haplotype tagging reveals parallel formation of hybrid races in two butterfly species","ddc":["570"],"intvolume":" 118","oa_version":"Published Version","file":[{"date_updated":"2022-03-08T08:18:16Z","date_created":"2022-03-08T08:18:16Z","checksum":"cb30c6166b2132ee60d616b31a1a7c29","success":1,"relation":"main_file","file_id":"10835","file_size":20592929,"content_type":"application/pdf","creator":"dernst","file_name":"2021_PNAS_Meier.pdf","access_level":"open_access"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Genetic variation segregates as linked sets of variants, or haplotypes. Haplotypes and linkage are central to genetics and underpin virtually all genetic and selection analysis. And yet, genomic data often lack haplotype information, due to constraints in sequencing technologies. Here we present “haplotagging”, a simple, low-cost linked-read sequencing technique that allows sequencing of hundreds of individuals while retaining linkage information. We apply haplotagging to construct megabase-size haplotypes for over 600 individual butterflies (Heliconius erato and H. melpomene), which form overlapping hybrid zones across an elevational gradient in Ecuador. Haplotagging identifies loci controlling distinctive high- and lowland wing color patterns. Divergent haplotypes are found at the same major loci in both species, while chromosome rearrangements show no parallelism. Remarkably, in both species the geographic clines for the major wing pattern loci are displaced by 18 km, leading to the rise of a novel hybrid morph in the centre of the hybrid zone. We propose that shared warning signalling (Müllerian mimicry) may couple the cline shifts seen in both species, and facilitate the parallel co-emergence of a novel hybrid morph in both co-mimetic species. Our results show the power of efficient haplotyping methods when combined with large-scale sequencing data from natural populations."}],"issue":"25","publication":"PNAS","citation":{"chicago":"Meier, Joana I., Patricio A. Salazar, Marek Kučka, Robert William Davies, Andreea Dréau, Ismael Aldás, Olivia Box Power, et al. “Haplotype Tagging Reveals Parallel Formation of Hybrid Races in Two Butterfly Species.” PNAS. Proceedings of the National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2015005118.","short":"J.I. Meier, P.A. Salazar, M. Kučka, R.W. Davies, A. Dréau, I. Aldás, O.B. Power, N.J. Nadeau, J.R. Bridle, C. Rolian, N.H. Barton, W.O. McMillan, C.D. Jiggins, Y.F. Chan, PNAS 118 (2021).","mla":"Meier, Joana I., et al. “Haplotype Tagging Reveals Parallel Formation of Hybrid Races in Two Butterfly Species.” PNAS, vol. 118, no. 25, e2015005118, Proceedings of the National Academy of Sciences, 2021, doi:10.1073/pnas.2015005118.","ieee":"J. I. Meier et al., “Haplotype tagging reveals parallel formation of hybrid races in two butterfly species,” PNAS, vol. 118, no. 25. Proceedings of the National Academy of Sciences, 2021.","apa":"Meier, J. I., Salazar, P. A., Kučka, M., Davies, R. W., Dréau, A., Aldás, I., … Chan, Y. F. (2021). Haplotype tagging reveals parallel formation of hybrid races in two butterfly species. PNAS. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2015005118","ista":"Meier JI, Salazar PA, Kučka M, Davies RW, Dréau A, Aldás I, Power OB, Nadeau NJ, Bridle JR, Rolian C, Barton NH, McMillan WO, Jiggins CD, Chan YF. 2021. Haplotype tagging reveals parallel formation of hybrid races in two butterfly species. PNAS. 118(25), e2015005118.","ama":"Meier JI, Salazar PA, Kučka M, et al. Haplotype tagging reveals parallel formation of hybrid races in two butterfly species. PNAS. 2021;118(25). doi:10.1073/pnas.2015005118"},"article_type":"original","date_published":"2021-06-21T00:00:00Z","scopus_import":"1","day":"21","article_processing_charge":"No","has_accepted_license":"1","acknowledgement":"We thank Felicity Jones for input into experimental design, helpful discussion and improving the manuscript. We thank the Rolian, Jiggins, Chan and Jones Labs members for support, insightful scientific discussion and improving the manuscript. We thank the Rolian lab members, the Animal Resource Centre staff at the University of Calgary, and Caroline Schmid and Ann-Katrin Geysel at the Friedrich Miescher Laboratory for animal husbandry. We thank Christa Lanz, Rebecca Schwab and Ilja Bezrukov for assistance with high-throughput sequencing and associated data processing; Andre Noll and the MPI Tübingen IT team for computational support. We thank Ben Haller and Richard Durbin for helpful discussions. We thank David M. Kingsley for thoughtful input that has greatly improved our manuscript. J.I.M. is supported by a Research Fellowship from St. John’s College, Cambridge. A.D. was supported by a European Research Council Consolidator Grant (No. 617279 “EvolRecombAdapt”, P/I Felicity Jones). C.R. is supported by Discovery Grant #4181932 from the Natural Sciences and Engineering Research Council of Canada and by the Faculty of Veterinary Medicine at the University of Calgary. C.D.J. is supported by a BBSRC grant BB/R007500 and a European Research Council Advanced Grant (No. 339873 “SpeciationGenetics”). M.K. and Y.F.C. are supported by the Max Planck Society and a European Research Council Starting Grant (No. 639096 “HybridMiX”).","year":"2021","pmid":1,"publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Proceedings of the National Academy of Sciences","author":[{"first_name":"Joana I.","last_name":"Meier","full_name":"Meier, Joana I."},{"last_name":"Salazar","first_name":"Patricio A.","full_name":"Salazar, Patricio A."},{"full_name":"Kučka, Marek","last_name":"Kučka","first_name":"Marek"},{"first_name":"Robert William","last_name":"Davies","full_name":"Davies, Robert William"},{"full_name":"Dréau, Andreea","last_name":"Dréau","first_name":"Andreea"},{"full_name":"Aldás, Ismael","first_name":"Ismael","last_name":"Aldás"},{"full_name":"Power, Olivia Box","last_name":"Power","first_name":"Olivia Box"},{"full_name":"Nadeau, Nicola J.","first_name":"Nicola J.","last_name":"Nadeau"},{"full_name":"Bridle, Jon R.","last_name":"Bridle","first_name":"Jon R."},{"last_name":"Rolian","first_name":"Campbell","full_name":"Rolian, Campbell"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H"},{"last_name":"McMillan","first_name":"W. Owen","full_name":"McMillan, W. Owen"},{"first_name":"Chris D.","last_name":"Jiggins","full_name":"Jiggins, Chris D."},{"first_name":"Yingguang Frank","last_name":"Chan","full_name":"Chan, Yingguang Frank"}],"date_created":"2021-05-07T17:10:21Z","date_updated":"2023-08-08T13:33:09Z","volume":118,"article_number":"e2015005118","file_date_updated":"2022-03-08T08:18:16Z","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"external_id":{"pmid":["34155138"],"isi":["000671755600001"]},"isi":1,"quality_controlled":"1","doi":"10.1073/pnas.2015005118","language":[{"iso":"eng"}],"month":"06","publication_identifier":{"eissn":["0027-8424"]}},{"publication_identifier":{"eissn":["2056-3744"]},"month":"05","language":[{"iso":"eng"}],"doi":"10.1002/evl3.227","project":[{"name":"Theoretical and empirical approaches to understanding Parallel Adaptation","call_identifier":"H2020","grant_number":"797747","_id":"265B41B8-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000647846200001"]},"oa":1,"ec_funded":1,"file_date_updated":"2021-10-15T08:26:02Z","volume":5,"date_created":"2021-05-16T22:01:47Z","date_updated":"2023-08-08T13:34:08Z","related_material":{"record":[{"status":"public","relation":"research_data","id":"12987"}]},"author":[{"full_name":"Koch, Eva L.","last_name":"Koch","first_name":"Eva L."},{"first_name":"Hernán E.","last_name":"Morales","full_name":"Morales, Hernán E."},{"full_name":"Larsson, Jenny","last_name":"Larsson","first_name":"Jenny"},{"last_name":"Westram","first_name":"Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","full_name":"Westram, Anja M"},{"full_name":"Faria, Rui","first_name":"Rui","last_name":"Faria"},{"full_name":"Lemmon, Alan R.","first_name":"Alan R.","last_name":"Lemmon"},{"last_name":"Lemmon","first_name":"E. Moriarty","full_name":"Lemmon, E. Moriarty"},{"first_name":"Kerstin","last_name":"Johannesson","full_name":"Johannesson, Kerstin"},{"first_name":"Roger K.","last_name":"Butlin","full_name":"Butlin, Roger K."}],"publisher":"Wiley","department":[{"_id":"NiBa"}],"publication_status":"published","year":"2021","acknowledgement":"We are very grateful to Irena Senčić for technical assistance and to Michelle Kortyna and Sean Holland at the Center for Anchored Phylogenomics for assistance with data collection. RKB was funded by the Natural Environment Research Council and by the European Research Council. KJ was funded by the Swedish Research Councils VR and Formas (Linnaeus Grant: 217‐2008‐1719). JL was funded by a studentship from the Leverhulme Centre for Advanced Biological Modelling. AMW was funded by the European Union's Horizon 2020 research and innovation program under Marie Skłodowska‐Curie Grant agreement no. 797747. RF was funded by the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska‐Curie Grant agreement No. 706376 and by FEDER Funds through the Operational Competitiveness Factors Program—COMPETE and by National Funds through FCT—Foundation for Science and Technology within the scope of the project “Hybrabbid” (PTDC/BIA‐EVL/30628/2017‐ POCI‐01‐0145‐FEDER‐030628). We are grateful to other members of the Littorina research group for helpful discussions. We thank Claire Mérot and an anonymous referee for insightful comments on an earlier version. ","article_processing_charge":"No","has_accepted_license":"1","day":"07","scopus_import":"1","date_published":"2021-05-07T00:00:00Z","page":"196-213","article_type":"original","citation":{"chicago":"Koch, Eva L., Hernán E. Morales, Jenny Larsson, Anja M Westram, Rui Faria, Alan R. Lemmon, E. Moriarty Lemmon, Kerstin Johannesson, and Roger K. Butlin. “Genetic Variation for Adaptive Traits Is Associated with Polymorphic Inversions in Littorina Saxatilis.” Evolution Letters. Wiley, 2021. https://doi.org/10.1002/evl3.227.","mla":"Koch, Eva L., et al. “Genetic Variation for Adaptive Traits Is Associated with Polymorphic Inversions in Littorina Saxatilis.” Evolution Letters, vol. 5, no. 3, Wiley, 2021, pp. 196–213, doi:10.1002/evl3.227.","short":"E.L. Koch, H.E. Morales, J. Larsson, A.M. Westram, R. Faria, A.R. Lemmon, E.M. Lemmon, K. Johannesson, R.K. Butlin, Evolution Letters 5 (2021) 196–213.","ista":"Koch EL, Morales HE, Larsson J, Westram AM, Faria R, Lemmon AR, Lemmon EM, Johannesson K, Butlin RK. 2021. Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis. Evolution Letters. 5(3), 196–213.","ieee":"E. L. Koch et al., “Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis,” Evolution Letters, vol. 5, no. 3. Wiley, pp. 196–213, 2021.","apa":"Koch, E. L., Morales, H. E., Larsson, J., Westram, A. M., Faria, R., Lemmon, A. R., … Butlin, R. K. (2021). Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis. Evolution Letters. Wiley. https://doi.org/10.1002/evl3.227","ama":"Koch EL, Morales HE, Larsson J, et al. Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis. Evolution Letters. 2021;5(3):196-213. doi:10.1002/evl3.227"},"publication":"Evolution Letters","issue":"3","abstract":[{"text":"Chromosomal inversions have long been recognized for their role in local adaptation. By suppressing recombination in heterozygous individuals, they can maintain coadapted gene complexes and protect them from homogenizing effects of gene flow. However, to fully understand their importance for local adaptation we need to know their influence on phenotypes under divergent selection. For this, the marine snail Littorina saxatilis provides an ideal study system. Divergent ecotypes adapted to wave action and crab predation occur in close proximity on intertidal shores with gene flow between them. Here, we used F2 individuals obtained from crosses between the ecotypes to test for associations between genomic regions and traits distinguishing the Crab‐/Wave‐adapted ecotypes including size, shape, shell thickness, and behavior. We show that most of these traits are influenced by two previously detected inversion regions that are divergent between ecotypes. We thus gain a better understanding of one important underlying mechanism responsible for the rapid and repeated formation of ecotypes: divergent selection acting on inversions. We also found that some inversions contributed to more than one trait suggesting that they may contain several loci involved in adaptation, consistent with the hypothesis that suppression of recombination within inversions facilitates differentiation in the presence of gene flow.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"creator":"cchlebak","content_type":"application/pdf","file_size":3021108,"file_name":"2021_EvolutionLetters_Koch.pdf","access_level":"open_access","date_created":"2021-10-15T08:26:02Z","date_updated":"2021-10-15T08:26:02Z","success":1,"checksum":"023b1608e311f0fda30593ba3d0a4e0b","file_id":"10142","relation":"main_file"}],"intvolume":" 5","title":"Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis","ddc":["570"],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9394"},{"pmid":1,"acknowledgement":"We thank Christopher Cooney, Martin Garlovsky, Anja M. Westram, Carina Baskett, Stefanie Belohlavy, Michal Hledik, Arka Pal, Nicholas H. Barton, Roger K. Butlin and members of the University of Sheffield Speciation Journal Club for feedback on draft survey questions and/or comments on a draft manuscript. Three anonymous reviewers gave thoughtful feedback that improved the manuscript. We thank Ahmad Nadeem, who was paid to build the Shiny app. We are especially grateful to everyone who took part in the survey. Ethical approval for the survey was obtained through the University of Sheffield Ethics Review Procedure (Application 029768). S.S. was supported by a NERC grant awarded to Roger K. Butlin.","year":"2021","publisher":"Cell Press","department":[{"_id":"NiBa"}],"publication_status":"published","author":[{"first_name":"Sean","last_name":"Stankowski","id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean"},{"full_name":"Ravinet, Mark","last_name":"Ravinet","first_name":"Mark"}],"volume":31,"date_updated":"2023-08-08T13:34:38Z","date_created":"2021-05-16T22:01:46Z","publication_identifier":{"issn":["09609822"],"eissn":["18790445"]},"month":"05","main_file_link":[{"url":"https://doi.org/10.1016/j.cub.2021.03.060","open_access":"1"}],"oa":1,"external_id":{"isi":["000654741200004"],"pmid":["33974865"]},"quality_controlled":"1","isi":1,"doi":"10.1016/j.cub.2021.03.060","language":[{"iso":"eng"}],"type":"journal_article","issue":"9","abstract":[{"text":"Humans conceptualize the diversity of life by classifying individuals into types we call ‘species’1. The species we recognize influence political and financial decisions and guide our understanding of how units of diversity evolve and interact. Although the idea of species may seem intuitive, a debate about the best way to define them has raged even before Darwin2. So much energy has been devoted to the so-called ‘species problem’ that no amount of discourse will ever likely solve it2,3. Dozens of species concepts are currently recognized3, but we lack a concrete understanding of how much researchers actually disagree and the factors that cause them to think differently1,2. To address this, we used a survey to quantify the species problem for the first time. The results indicate that the disagreement is extensive: two randomly chosen respondents will most likely disagree on the nature of species. The probability of disagreement is not predicted by researcher experience or broad study system, but tended to be lower among researchers with similar focus, training and who study the same organism. Should we see this diversity of perspectives as a problem? We argue that we should not.","lang":"eng"}],"_id":"9392","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 31","title":"Quantifying the use of species concepts","status":"public","oa_version":"Published Version","scopus_import":"1","article_processing_charge":"No","day":"10","citation":{"ama":"Stankowski S, Ravinet M. Quantifying the use of species concepts. Current Biology. 2021;31(9):R428-R429. doi:10.1016/j.cub.2021.03.060","apa":"Stankowski, S., & Ravinet, M. (2021). Quantifying the use of species concepts. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2021.03.060","ieee":"S. Stankowski and M. Ravinet, “Quantifying the use of species concepts,” Current Biology, vol. 31, no. 9. Cell Press, pp. R428–R429, 2021.","ista":"Stankowski S, Ravinet M. 2021. Quantifying the use of species concepts. Current Biology. 31(9), R428–R429.","short":"S. Stankowski, M. Ravinet, Current Biology 31 (2021) R428–R429.","mla":"Stankowski, Sean, and Mark Ravinet. “Quantifying the Use of Species Concepts.” Current Biology, vol. 31, no. 9, Cell Press, 2021, pp. R428–29, doi:10.1016/j.cub.2021.03.060.","chicago":"Stankowski, Sean, and Mark Ravinet. “Quantifying the Use of Species Concepts.” Current Biology. Cell Press, 2021. https://doi.org/10.1016/j.cub.2021.03.060."},"publication":"Current Biology","page":"R428-R429","article_type":"original","date_published":"2021-05-10T00:00:00Z"},{"day":"10","month":"04","has_accepted_license":"1","article_processing_charge":"No","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"citation":{"short":"E. Koch, H.E. Morales, J. Larsson, A.M. Westram, R. Faria, A.R. Lemmon, E.M. Lemmon, K. Johannesson, R.K. Butlin, (2021).","mla":"Koch, Eva, et al. Data from: Genetic Variation for Adaptive Traits Is Associated with Polymorphic Inversions in Littorina Saxatilis. Dryad, 2021, doi:10.5061/DRYAD.ZGMSBCCB4.","chicago":"Koch, Eva, Hernán E. Morales, Jenny Larsson, Anja M Westram, Rui Faria, Alan R. Lemmon, E. Moriarty Lemmon, Kerstin Johannesson, and Roger K. Butlin. “Data from: Genetic Variation for Adaptive Traits Is Associated with Polymorphic Inversions in Littorina Saxatilis.” Dryad, 2021. https://doi.org/10.5061/DRYAD.ZGMSBCCB4.","ama":"Koch E, Morales HE, Larsson J, et al. Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis. 2021. doi:10.5061/DRYAD.ZGMSBCCB4","ieee":"E. Koch et al., “Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis.” Dryad, 2021.","apa":"Koch, E., Morales, H. E., Larsson, J., Westram, A. M., Faria, R., Lemmon, A. R., … Butlin, R. K. (2021). Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis. Dryad. https://doi.org/10.5061/DRYAD.ZGMSBCCB4","ista":"Koch E, Morales HE, Larsson J, Westram AM, Faria R, Lemmon AR, Lemmon EM, Johannesson K, Butlin RK. 2021. Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis, Dryad, 10.5061/DRYAD.ZGMSBCCB4."},"main_file_link":[{"url":"https://doi.org/10.5061/dryad.zgmsbccb4","open_access":"1"}],"oa":1,"doi":"10.5061/DRYAD.ZGMSBCCB4","date_published":"2021-04-10T00:00:00Z","type":"research_data_reference","abstract":[{"text":"Chromosomal inversion polymorphisms, segments of chromosomes that are flipped in orientation and occur in reversed order in some individuals, have long been recognized to play an important role in local adaptation. They can reduce recombination in heterozygous individuals and thus help to maintain sets of locally adapted alleles. In a wide range of organisms, populations adapted to different habitats differ in frequency of inversion arrangements. However, getting a full understanding of the importance of inversions for adaptation requires confirmation of their influence on traits under divergent selection. Here, we studied a marine snail, Littorina saxatilis, that has evolved ecotypes adapted to wave exposure or crab predation. These two types occur in close proximity on different parts of the shore. Gene flow between them exists in contact zones. However, they exhibit strong phenotypic divergence in several traits under habitat-specific selection, including size, shape and behaviour. We used crosses between these ecotypes to identify genomic regions that explain variation in these traits by using QTL analysis and variance partitioning across linkage groups. We could show that previously detected inversion regions contribute to adaptive divergence. Some inversions influenced multiple traits suggesting that they contain sets of locally adaptive alleles. Our study also identified regions without known inversions that are important for phenotypic divergence. Thus, we provide a more complete overview of the importance of inversions in relation to the remaining genome.","lang":"eng"}],"status":"public","ddc":["570"],"title":"Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis","department":[{"_id":"NiBa"}],"publisher":"Dryad","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12987","year":"2021","date_created":"2023-05-16T12:34:09Z","date_updated":"2023-08-08T13:34:07Z","oa_version":"Published Version","author":[{"full_name":"Koch, Eva","last_name":"Koch","first_name":"Eva"},{"full_name":"Morales, Hernán E.","first_name":"Hernán E.","last_name":"Morales"},{"full_name":"Larsson, Jenny","first_name":"Jenny","last_name":"Larsson"},{"first_name":"Anja M","last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M"},{"full_name":"Faria, Rui","last_name":"Faria","first_name":"Rui"},{"full_name":"Lemmon, Alan R.","first_name":"Alan R.","last_name":"Lemmon"},{"full_name":"Lemmon, E. Moriarty","first_name":"E. Moriarty","last_name":"Lemmon"},{"full_name":"Johannesson, Kerstin","last_name":"Johannesson","first_name":"Kerstin"},{"full_name":"Butlin, Roger K.","first_name":"Roger K.","last_name":"Butlin"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"9394"}]}},{"abstract":[{"text":"Antibiotic concentrations vary dramatically in the body and the environment. Hence, understanding the dynamics of resistance evolution along antibiotic concentration gradients is critical for predicting and slowing the emergence and spread of resistance. While it has been shown that increasing the concentration of an antibiotic slows resistance evolution, how adaptation to one antibiotic concentration correlates with fitness at other points along the gradient has not received much attention. Here, we selected populations of Escherichia coli at several points along a concentration gradient for three different antibiotics, asking how rapidly resistance evolved and whether populations became specialized to the antibiotic concentration they were selected on. Populations selected at higher concentrations evolved resistance more slowly but exhibited equal or higher fitness across the whole gradient. Populations selected at lower concentrations evolved resistance rapidly, but overall fitness in the presence of antibiotics was lower. However, these populations readily adapted to higher concentrations upon subsequent selection. Our results indicate that resistance management strategies must account not only for the rates of resistance evolution but also for the fitness of evolved strains.","lang":"eng"}],"issue":"5","type":"journal_article","oa_version":"Published Version","file":[{"date_created":"2021-05-25T14:09:03Z","date_updated":"2021-05-25T14:09:03Z","checksum":"9c13c1f5af7609c97c741f11d293188a","success":1,"relation":"main_file","file_id":"9425","content_type":"application/pdf","file_size":726759,"creator":"kschuh","file_name":"2021_BiologyLetters_Lagator.pdf","access_level":"open_access"}],"_id":"9410","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Adaptation at different points along antibiotic concentration gradients","ddc":["570"],"status":"public","intvolume":" 17","day":"12","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2021-05-12T00:00:00Z","publication":"Biology letters","citation":{"chicago":"Lagator, Mato, Hildegard Uecker, and Paul Neve. “Adaptation at Different Points along Antibiotic Concentration Gradients.” Biology Letters. Royal Society of London, 2021. https://doi.org/10.1098/rsbl.2020.0913.","mla":"Lagator, Mato, et al. “Adaptation at Different Points along Antibiotic Concentration Gradients.” Biology Letters, vol. 17, no. 5, 20200913, Royal Society of London, 2021, doi:10.1098/rsbl.2020.0913.","short":"M. Lagator, H. Uecker, P. Neve, Biology Letters 17 (2021).","ista":"Lagator M, Uecker H, Neve P. 2021. Adaptation at different points along antibiotic concentration gradients. Biology letters. 17(5), 20200913.","apa":"Lagator, M., Uecker, H., & Neve, P. (2021). Adaptation at different points along antibiotic concentration gradients. Biology Letters. Royal Society of London. https://doi.org/10.1098/rsbl.2020.0913","ieee":"M. Lagator, H. Uecker, and P. Neve, “Adaptation at different points along antibiotic concentration gradients,” Biology letters, vol. 17, no. 5. Royal Society of London, 2021.","ama":"Lagator M, Uecker H, Neve P. Adaptation at different points along antibiotic concentration gradients. Biology letters. 2021;17(5). doi:10.1098/rsbl.2020.0913"},"file_date_updated":"2021-05-25T14:09:03Z","ec_funded":1,"article_number":"20200913","author":[{"id":"345D25EC-F248-11E8-B48F-1D18A9856A87","last_name":"Lagator","first_name":"Mato","full_name":"Lagator, Mato"},{"first_name":"Hildegard","last_name":"Uecker","id":"2DB8F68A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9435-2813","full_name":"Uecker, Hildegard"},{"last_name":"Neve","first_name":"Paul","full_name":"Neve, Paul"}],"date_created":"2021-05-23T22:01:43Z","date_updated":"2023-08-08T13:44:35Z","volume":17,"year":"2021","acknowledgement":"We would like to thank Martin Ackermann, Camilo Barbosa, Nick Barton, Jonathan Bollback, Sebastian Bonhoeffer, Nick Colegrave, Calin Guet, Alex Hall, Sally Otto, Tiago Paixao, Srdjan Sarikas, Hinrich Schulenburg, Marjon de Vos and Michael Whitlock for insightful support.","pmid":1,"publication_status":"published","publisher":"Royal Society of London","department":[{"_id":"NiBa"}],"month":"05","publication_identifier":{"eissn":["1744957X"]},"doi":"10.1098/rsbl.2020.0913","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000651501400001"],"pmid":[" 33975485"]},"quality_controlled":"1","isi":1,"project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation"}]},{"page":"2710-2723","publication":"Molecular Ecology","citation":{"ama":"Berdan EL, Blanckaert A, Slotte T, Suh A, Westram AM, Fragata I. Unboxing mutations: Connecting mutation types with evolutionary consequences. Molecular Ecology. 2021;30(12):2710-2723. doi:10.1111/mec.15936","ista":"Berdan EL, Blanckaert A, Slotte T, Suh A, Westram AM, Fragata I. 2021. Unboxing mutations: Connecting mutation types with evolutionary consequences. Molecular Ecology. 30(12), 2710–2723.","apa":"Berdan, E. L., Blanckaert, A., Slotte, T., Suh, A., Westram, A. M., & Fragata, I. (2021). Unboxing mutations: Connecting mutation types with evolutionary consequences. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.15936","ieee":"E. L. Berdan, A. Blanckaert, T. Slotte, A. Suh, A. M. Westram, and I. Fragata, “Unboxing mutations: Connecting mutation types with evolutionary consequences,” Molecular Ecology, vol. 30, no. 12. Wiley, pp. 2710–2723, 2021.","mla":"Berdan, Emma L., et al. “Unboxing Mutations: Connecting Mutation Types with Evolutionary Consequences.” Molecular Ecology, vol. 30, no. 12, Wiley, 2021, pp. 2710–23, doi:10.1111/mec.15936.","short":"E.L. Berdan, A. Blanckaert, T. Slotte, A. Suh, A.M. Westram, I. Fragata, Molecular Ecology 30 (2021) 2710–2723.","chicago":"Berdan, Emma L., Alexandre Blanckaert, Tanja Slotte, Alexander Suh, Anja M Westram, and Inês Fragata. “Unboxing Mutations: Connecting Mutation Types with Evolutionary Consequences.” Molecular Ecology. Wiley, 2021. https://doi.org/10.1111/mec.15936."},"date_published":"2021-06-01T00:00:00Z","scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"No","status":"public","title":"Unboxing mutations: Connecting mutation types with evolutionary consequences","ddc":["570"],"intvolume":" 30","_id":"9470","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"creator":"kschuh","file_size":1031978,"content_type":"application/pdf","access_level":"open_access","file_name":"2021_MolecularEcology_Berdan.pdf","success":1,"checksum":"e6f4731365bde2614b333040a08265d8","date_created":"2021-06-11T15:34:53Z","date_updated":"2021-06-11T15:34:53Z","file_id":"9545","relation":"main_file"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"A key step in understanding the genetic basis of different evolutionary outcomes (e.g., adaptation) is to determine the roles played by different mutation types (e.g., SNPs, translocations and inversions). To do this we must simultaneously consider different mutation types in an evolutionary framework. Here, we propose a research framework that directly utilizes the most important characteristics of mutations, their population genetic effects, to determine their relative evolutionary significance in a given scenario. We review known population genetic effects of different mutation types and show how these may be connected to different evolutionary outcomes. We provide examples of how to implement this framework and pinpoint areas where more data, theory and synthesis are needed. Linking experimental and theoretical approaches to examine different mutation types simultaneously is a critical step towards understanding their evolutionary significance.","lang":"eng"}],"issue":"12","quality_controlled":"1","isi":1,"project":[{"name":"Theoretical and empirical approaches to understanding Parallel Adaptation","call_identifier":"H2020","grant_number":"797747","_id":"265B41B8-B435-11E9-9278-68D0E5697425"}],"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"external_id":{"isi":["000652056400001"]},"language":[{"iso":"eng"}],"doi":"10.1111/mec.15936","month":"06","publication_identifier":{"eissn":["1365294X"],"issn":["09621083"]},"publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Wiley","acknowledgement":"We thank the editor, two helpful reviewers, Roger Butlin, Kerstin Johannesson, Valentina Peona, Rike Stelkens, Julie Blommaert, Nick Barton, and João Alpedrinha for helpful comments that improved the manuscript. The authors acknowledge funding from the Swedish Research Council Formas (2017-01597 to AS), the Swedish Research Council Vetenskapsrådet (2016-05139 to AS, 2019-04452 to TS) and from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 757451 to TS). ELB was funded by a Carl Tryggers grant awarded to Tanja Slotte. Anja M. Westram was funded by the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 797747. Inês Fragata was funded by a Junior Researcher contract from FCT (CEECIND/02616/2018).","year":"2021","date_updated":"2023-08-08T13:59:18Z","date_created":"2021-06-06T22:01:31Z","volume":30,"author":[{"first_name":"Emma L.","last_name":"Berdan","full_name":"Berdan, Emma L."},{"first_name":"Alexandre","last_name":"Blanckaert","full_name":"Blanckaert, Alexandre"},{"full_name":"Slotte, Tanja","last_name":"Slotte","first_name":"Tanja"},{"full_name":"Suh, Alexander","first_name":"Alexander","last_name":"Suh"},{"last_name":"Westram","first_name":"Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","full_name":"Westram, Anja M"},{"full_name":"Fragata, Inês","last_name":"Fragata","first_name":"Inês"}],"file_date_updated":"2021-06-11T15:34:53Z","ec_funded":1},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9816","status":"public","title":"Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program","ddc":["610"],"intvolume":" 16","file":[{"access_level":"open_access","file_name":"2021_PLoSONE_Hledík.pdf","file_size":773921,"content_type":"application/pdf","creator":"asandaue","relation":"main_file","file_id":"9835","checksum":"ae4df60eb62f4491278588548d0c1f93","success":1,"date_created":"2021-08-09T11:52:14Z","date_updated":"2021-08-09T11:52:14Z"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Aims: Mass antigen testing programs have been challenged because of an alleged insufficient specificity, leading to a large number of false positives. The objective of this study is to derive a lower bound of the specificity of the SD Biosensor Standard Q Ag-Test in large scale practical use.\r\nMethods: Based on county data from the nationwide tests for SARS-CoV-2 in Slovakia between 31.10.–1.11. 2020 we calculate a lower confidence bound for the specificity. As positive test results were not systematically verified by PCR tests, we base the lower bound on a worst case assumption, assuming all positives to be false positives.\r\nResults: 3,625,332 persons from 79 counties were tested. The lowest positivity rate was observed in the county of Rožňava where 100 out of 34307 (0.29%) tests were positive. This implies a test specificity of at least 99.6% (97.5% one-sided lower confidence bound, adjusted for multiplicity).\r\nConclusion: The obtained lower bound suggests a higher specificity compared to earlier studies in spite of the underlying worst case assumption and the application in a mass testing setting. The actual specificity is expected to exceed 99.6% if the prevalence in the respective regions was non-negligible at the time of testing. To our knowledge, this estimate constitutes the first bound obtained from large scale practical use of an antigen test.","lang":"eng"}],"issue":"7","publication":"PLoS ONE","citation":{"ista":"Hledik M, Polechova J, Beiglböck M, Herdina AN, Strassl R, Posch M. 2021. Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program. PLoS ONE. 16(7), e0255267.","apa":"Hledik, M., Polechova, J., Beiglböck, M., Herdina, A. N., Strassl, R., & Posch, M. (2021). Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program. PLoS ONE. Public Library of Science. https://doi.org/10.1371/journal.pone.0255267","ieee":"M. Hledik, J. Polechova, M. Beiglböck, A. N. Herdina, R. Strassl, and M. Posch, “Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program,” PLoS ONE, vol. 16, no. 7. Public Library of Science, 2021.","ama":"Hledik M, Polechova J, Beiglböck M, Herdina AN, Strassl R, Posch M. Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program. PLoS ONE. 2021;16(7). doi:10.1371/journal.pone.0255267","chicago":"Hledik, Michal, Jitka Polechova, Mathias Beiglböck, Anna Nele Herdina, Robert Strassl, and Martin Posch. “Analysis of the Specificity of a COVID-19 Antigen Test in the Slovak Mass Testing Program.” PLoS ONE. Public Library of Science, 2021. https://doi.org/10.1371/journal.pone.0255267.","mla":"Hledik, Michal, et al. “Analysis of the Specificity of a COVID-19 Antigen Test in the Slovak Mass Testing Program.” PLoS ONE, vol. 16, no. 7, e0255267, Public Library of Science, 2021, doi:10.1371/journal.pone.0255267.","short":"M. Hledik, J. Polechova, M. Beiglböck, A.N. Herdina, R. Strassl, M. Posch, PLoS ONE 16 (2021)."},"article_type":"original","date_published":"2021-07-29T00:00:00Z","scopus_import":"1","day":"29","has_accepted_license":"1","article_processing_charge":"Yes","acknowledgement":"We would like to thank Alfred Uhl, Richard Kollár and Katarína Bod’ová for very helpful comments. We also thank Matej Mišík for discussion and information regarding the Slovak testing data and Ag-Test used.","year":"2021","pmid":1,"publication_status":"published","publisher":"Public Library of Science","department":[{"_id":"NiBa"}],"author":[{"first_name":"Michal","last_name":"Hledik","id":"4171253A-F248-11E8-B48F-1D18A9856A87","full_name":"Hledik, Michal"},{"full_name":"Polechova, Jitka","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0951-3112","first_name":"Jitka","last_name":"Polechova"},{"first_name":"Mathias","last_name":"Beiglböck","full_name":"Beiglböck, Mathias"},{"first_name":"Anna Nele","last_name":"Herdina","full_name":"Herdina, Anna Nele"},{"full_name":"Strassl, Robert","first_name":"Robert","last_name":"Strassl"},{"last_name":"Posch","first_name":"Martin","full_name":"Posch, Martin"}],"date_created":"2021-08-08T22:01:26Z","date_updated":"2023-08-10T14:26:32Z","volume":16,"article_number":"e0255267","file_date_updated":"2021-08-09T11:52:14Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000685248200095"],"pmid":["34324553"]},"isi":1,"quality_controlled":"1","doi":"10.1371/journal.pone.0255267","language":[{"iso":"eng"}],"month":"07","publication_identifier":{"eissn":["1932-6203"]}},{"acknowledgement":"We thank the reviewers for their helpful comments, and also our colleagues, for illuminating discussions over the long gestation of this paper.","year":"2021","publisher":"Wiley","department":[{"_id":"NiBa"}],"publication_status":"published","related_material":{"record":[{"relation":"research_data","status":"public","id":"13062"}]},"author":[{"full_name":"Szep, Eniko","id":"485BB5A4-F248-11E8-B48F-1D18A9856A87","last_name":"Szep","first_name":"Eniko"},{"id":"42377A0A-F248-11E8-B48F-1D18A9856A87","last_name":"Sachdeva","first_name":"Himani","full_name":"Sachdeva, Himani"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"}],"volume":75,"date_created":"2021-03-20T08:22:10Z","date_updated":"2023-09-05T15:44:06Z","file_date_updated":"2021-08-11T13:39:19Z","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"isi":["000636966300001"]},"quality_controlled":"1","isi":1,"doi":"10.1111/evo.14210","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0014-3820"],"eissn":["1558-5646"]},"month":"05","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"9252","intvolume":" 75","status":"public","title":"Polygenic local adaptation in metapopulations: A stochastic eco‐evolutionary model","ddc":["570"],"oa_version":"Published Version","file":[{"creator":"kschuh","file_size":734102,"content_type":"application/pdf","access_level":"open_access","file_name":"2021_Evolution_Szep.pdf","success":1,"checksum":"b90fb5767d623602046fed03725e16ca","date_updated":"2021-08-11T13:39:19Z","date_created":"2021-08-11T13:39:19Z","file_id":"9886","relation":"main_file"}],"type":"journal_article","issue":"5","abstract":[{"text":"This paper analyses the conditions for local adaptation in a metapopulation with infinitely many islands under a model of hard selection, where population size depends on local fitness. Each island belongs to one of two distinct ecological niches or habitats. Fitness is influenced by an additive trait which is under habitat‐dependent directional selection. Our analysis is based on the diffusion approximation and accounts for both genetic drift and demographic stochasticity. By neglecting linkage disequilibria, it yields the joint distribution of allele frequencies and population size on each island. We find that under hard selection, the conditions for local adaptation in a rare habitat are more restrictive for more polygenic traits: even moderate migration load per locus at very many loci is sufficient for population sizes to decline. This further reduces the efficacy of selection at individual loci due to increased drift and because smaller populations are more prone to swamping due to migration, causing a positive feedback between increasing maladaptation and declining population sizes. Our analysis also highlights the importance of demographic stochasticity, which exacerbates the decline in numbers of maladapted populations, leading to population collapse in the rare habitat at significantly lower migration than predicted by deterministic arguments.","lang":"eng"}],"citation":{"chicago":"Szep, Eniko, Himani Sachdeva, and Nicholas H Barton. “Polygenic Local Adaptation in Metapopulations: A Stochastic Eco‐evolutionary Model.” Evolution. Wiley, 2021. https://doi.org/10.1111/evo.14210.","mla":"Szep, Eniko, et al. “Polygenic Local Adaptation in Metapopulations: A Stochastic Eco‐evolutionary Model.” Evolution, vol. 75, no. 5, Wiley, 2021, pp. 1030–45, doi:10.1111/evo.14210.","short":"E. Szep, H. Sachdeva, N.H. Barton, Evolution 75 (2021) 1030–1045.","ista":"Szep E, Sachdeva H, Barton NH. 2021. Polygenic local adaptation in metapopulations: A stochastic eco‐evolutionary model. Evolution. 75(5), 1030–1045.","ieee":"E. Szep, H. Sachdeva, and N. H. Barton, “Polygenic local adaptation in metapopulations: A stochastic eco‐evolutionary model,” Evolution, vol. 75, no. 5. Wiley, pp. 1030–1045, 2021.","apa":"Szep, E., Sachdeva, H., & Barton, N. H. (2021). Polygenic local adaptation in metapopulations: A stochastic eco‐evolutionary model. Evolution. Wiley. https://doi.org/10.1111/evo.14210","ama":"Szep E, Sachdeva H, Barton NH. Polygenic local adaptation in metapopulations: A stochastic eco‐evolutionary model. Evolution. 2021;75(5):1030-1045. doi:10.1111/evo.14210"},"publication":"Evolution","page":"1030-1045","article_type":"original","date_published":"2021-05-01T00:00:00Z","scopus_import":"1","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics","General Agricultural and Biological Sciences"],"article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"01"},{"abstract":[{"text":"If there are no constraints on the process of speciation, then the number of species might be expected to match the number of available niches and this number might be indefinitely large. One possible constraint is the opportunity for allopatric divergence. In 1981, Felsenstein used a simple and elegant model to ask if there might also be genetic constraints. He showed that progress towards speciation could be described by the build‐up of linkage disequilibrium among divergently selected loci and between these loci and those contributing to other forms of reproductive isolation. Therefore, speciation is opposed by recombination, because it tends to break down linkage disequilibria. Felsenstein then introduced a crucial distinction between “two‐allele” models, which are subject to this effect, and “one‐allele” models, which are free from the recombination constraint. These fundamentally important insights have been the foundation for both empirical and theoretical studies of speciation ever since.","lang":"eng"}],"issue":"5","type":"journal_article","oa_version":"Published Version","title":"Homage to Felsenstein 1981, or why are there so few/many species?","status":"public","intvolume":" 75","_id":"9374","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","day":"19","article_processing_charge":"No","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics","General Agricultural and Biological Sciences"],"date_published":"2021-04-19T00:00:00Z","article_type":"original","page":"978-988","publication":"Evolution","citation":{"chicago":"Butlin, Roger K., Maria R. Servedio, Carole M. Smadja, Claudia Bank, Nicholas H Barton, Samuel M. Flaxman, Tatiana Giraud, et al. “Homage to Felsenstein 1981, or Why Are There so Few/Many Species?” Evolution. Wiley, 2021. https://doi.org/10.1111/evo.14235.","short":"R.K. Butlin, M.R. Servedio, C.M. Smadja, C. Bank, N.H. Barton, S.M. Flaxman, T. Giraud, R. Hopkins, E.L. Larson, M.E. Maan, J. Meier, R. Merrill, M.A.F. Noor, D. Ortiz‐Barrientos, A. Qvarnström, Evolution 75 (2021) 978–988.","mla":"Butlin, Roger K., et al. “Homage to Felsenstein 1981, or Why Are There so Few/Many Species?” Evolution, vol. 75, no. 5, Wiley, 2021, pp. 978–88, doi:10.1111/evo.14235.","apa":"Butlin, R. K., Servedio, M. R., Smadja, C. M., Bank, C., Barton, N. H., Flaxman, S. M., … Qvarnström, A. (2021). Homage to Felsenstein 1981, or why are there so few/many species? Evolution. Wiley. https://doi.org/10.1111/evo.14235","ieee":"R. K. Butlin et al., “Homage to Felsenstein 1981, or why are there so few/many species?,” Evolution, vol. 75, no. 5. Wiley, pp. 978–988, 2021.","ista":"Butlin RK, Servedio MR, Smadja CM, Bank C, Barton NH, Flaxman SM, Giraud T, Hopkins R, Larson EL, Maan ME, Meier J, Merrill R, Noor MAF, Ortiz‐Barrientos D, Qvarnström A. 2021. Homage to Felsenstein 1981, or why are there so few/many species? Evolution. 75(5), 978–988.","ama":"Butlin RK, Servedio MR, Smadja CM, et al. Homage to Felsenstein 1981, or why are there so few/many species? Evolution. 2021;75(5):978-988. doi:10.1111/evo.14235"},"date_created":"2021-05-06T04:34:47Z","date_updated":"2023-09-05T15:44:33Z","volume":75,"author":[{"first_name":"Roger K.","last_name":"Butlin","full_name":"Butlin, Roger K."},{"first_name":"Maria R.","last_name":"Servedio","full_name":"Servedio, Maria R."},{"last_name":"Smadja","first_name":"Carole M.","full_name":"Smadja, Carole M."},{"full_name":"Bank, Claudia","last_name":"Bank","first_name":"Claudia"},{"full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Flaxman","first_name":"Samuel M.","full_name":"Flaxman, Samuel M."},{"last_name":"Giraud","first_name":"Tatiana","full_name":"Giraud, Tatiana"},{"first_name":"Robin","last_name":"Hopkins","full_name":"Hopkins, Robin"},{"full_name":"Larson, Erica L.","last_name":"Larson","first_name":"Erica L."},{"first_name":"Martine E.","last_name":"Maan","full_name":"Maan, Martine E."},{"last_name":"Meier","first_name":"Joana","full_name":"Meier, Joana"},{"last_name":"Merrill","first_name":"Richard","full_name":"Merrill, Richard"},{"full_name":"Noor, Mohamed A. F.","last_name":"Noor","first_name":"Mohamed A. F."},{"last_name":"Ortiz‐Barrientos","first_name":"Daniel","full_name":"Ortiz‐Barrientos, Daniel"},{"full_name":"Qvarnström, Anna","first_name":"Anna","last_name":"Qvarnström"}],"publication_status":"published","publisher":"Wiley","department":[{"_id":"NiBa"}],"year":"2021","acknowledgement":"RKB was funded by the Natural Environment Research Council (NE/P012272/1 & NE/P001610/1), the European Research Council (693030 BARRIERS), and the Swedish Research Council (VR) (2018‐03695). MRS was funded by the National Science Foundation (Grant No. DEB1939290).","month":"04","publication_identifier":{"issn":["0014-3820"],"eissn":["1558-5646"]},"language":[{"iso":"eng"}],"doi":"10.1111/evo.14235","quality_controlled":"1","isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"main_file_link":[{"url":"https://onlinelibrary.wiley.com/doi/10.1111/evo.14235","open_access":"1"}],"external_id":{"isi":["000647224000001"]}},{"title":"Supplementary code for: Polygenic local adaptation in metapopulations: A stochastic eco-evolutionary model","ddc":["570"],"status":"public","department":[{"_id":"NiBa"}],"publisher":"Dryad","_id":"13062","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2021","date_updated":"2023-09-05T15:44:05Z","date_created":"2023-05-23T16:17:02Z","oa_version":"Published Version","author":[{"full_name":"Szep, Eniko","first_name":"Eniko","last_name":"Szep","id":"485BB5A4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sachdeva, Himani","id":"42377A0A-F248-11E8-B48F-1D18A9856A87","last_name":"Sachdeva","first_name":"Himani"},{"last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"9252"}]},"type":"research_data_reference","abstract":[{"text":"This paper analyzes the conditions for local adaptation in a metapopulation with infinitely many islands under a model of hard selection, where population size depends on local fitness. Each island belongs to one of two distinct ecological niches or habitats. Fitness is influenced by an additive trait which is under habitat-dependent directional selection. Our analysis is based on the diffusion approximation and accounts for both genetic drift and demographic stochasticity. By neglecting linkage disequilibria, it yields the joint distribution of allele frequencies and population size on each island. We find that under hard selection, the conditions for local adaptation in a rare habitat are more restrictive for more polygenic traits: even moderate migration load per locus at very many loci is sufficient for population sizes to decline. This further reduces the efficacy of selection at individual loci due to increased drift and because smaller populations are more prone to swamping due to migration, causing a positive feedback between increasing maladaptation and declining population sizes. Our analysis also highlights the importance of demographic stochasticity, which exacerbates the decline in numbers of maladapted populations, leading to population collapse in the rare habitat at significantly lower migration than predicted by deterministic arguments.","lang":"eng"}],"oa":1,"tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.8gtht76p1"}],"citation":{"mla":"Szep, Eniko, et al. Supplementary Code for: Polygenic Local Adaptation in Metapopulations: A Stochastic Eco-Evolutionary Model. Dryad, 2021, doi:10.5061/DRYAD.8GTHT76P1.","short":"E. Szep, H. Sachdeva, N.H. Barton, (2021).","chicago":"Szep, Eniko, Himani Sachdeva, and Nicholas H Barton. “Supplementary Code for: Polygenic Local Adaptation in Metapopulations: A Stochastic Eco-Evolutionary Model.” Dryad, 2021. https://doi.org/10.5061/DRYAD.8GTHT76P1.","ama":"Szep E, Sachdeva H, Barton NH. Supplementary code for: Polygenic local adaptation in metapopulations: A stochastic eco-evolutionary model. 2021. doi:10.5061/DRYAD.8GTHT76P1","ista":"Szep E, Sachdeva H, Barton NH. 2021. Supplementary code for: Polygenic local adaptation in metapopulations: A stochastic eco-evolutionary model, Dryad, 10.5061/DRYAD.8GTHT76P1.","ieee":"E. Szep, H. Sachdeva, and N. H. Barton, “Supplementary code for: Polygenic local adaptation in metapopulations: A stochastic eco-evolutionary model.” Dryad, 2021.","apa":"Szep, E., Sachdeva, H., & Barton, N. H. (2021). Supplementary code for: Polygenic local adaptation in metapopulations: A stochastic eco-evolutionary model. Dryad. https://doi.org/10.5061/DRYAD.8GTHT76P1"},"date_published":"2021-03-02T00:00:00Z","doi":"10.5061/DRYAD.8GTHT76P1","day":"02","month":"03","article_processing_charge":"No"},{"volume":75,"date_updated":"2023-10-18T08:16:01Z","date_created":"2021-05-09T22:01:39Z","author":[{"id":"43161670-5719-11EA-8025-FABC3DDC885E","last_name":"Stankowski","first_name":"Sean","full_name":"Stankowski, Sean"},{"full_name":"Ravinet, Mark","first_name":"Mark","last_name":"Ravinet"}],"department":[{"_id":"NiBa"}],"publisher":"Oxford University Press","publication_status":"published","acknowledgement":"We thank M. Garlovsky, S. Martin, C. Cooney, C. Roux, J. Larson, and J. Mallet for critical feedback and for discussion. K. Lohse, M. de la Cámara, J. Cerca, M. A. Chase, C. Baskett, A. M. Westram, and N. H. Barton gave feedback on a draft of the manuscript. O. Seehausen, two anonymous reviewers, and the AE (Michael Kopp) provided comments that greatly improved the manuscript. V. Holzmann made many corrections to the proofs. G. Bisschop and K. Lohse kindly contributed the simulations and analyses presented in Box 3. We would also like to extend our thanks to everyone who took part in the speciation survey, which received ethical approval through the University of Sheffield Ethics Review Procedure (Application 029768). We are especially grateful to R. K. Butlin for stimulating discussion throughout the writing of the manuscript and for feedback on an earlier draft.","year":"2021","file_date_updated":"2022-03-25T12:02:04Z","language":[{"iso":"eng"}],"doi":"10.1111/evo.14215","isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"external_id":{"isi":["000647226400001"]},"oa":1,"publication_identifier":{"issn":["0014-3820"],"eissn":["1558-5646"]},"month":"03","oa_version":"Published Version","file":[{"creator":"kschuh","content_type":"application/pdf","file_size":719991,"file_name":"2021_Evolution_Stankowski.pdf","access_level":"open_access","date_created":"2022-03-25T12:02:04Z","date_updated":"2022-03-25T12:02:04Z","success":1,"checksum":"96f6ccf15d95a4e9f7c0b27eee570fa6","file_id":"10921","relation":"main_file"}],"intvolume":" 75","title":"Defining the speciation continuum","status":"public","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9383","issue":"6","abstract":[{"text":"A primary roadblock to our understanding of speciation is that it usually occurs over a timeframe that is too long to study from start to finish. The idea of a speciation continuum provides something of a solution to this problem; rather than observing the entire process, we can simply reconstruct it from the multitude of speciation events that surround us. But what do we really mean when we talk about the speciation continuum, and can it really help us understand speciation? We explored these questions using a literature review and online survey of speciation researchers. Although most researchers were familiar with the concept and thought it was useful, our survey revealed extensive disagreement about what the speciation continuum actually tells us. This is due partly to the lack of a clear definition. Here, we provide an explicit definition that is compatible with the Biological Species Concept. That is, the speciation continuum is a continuum of reproductive isolation. After outlining the logic of the definition in light of alternatives, we explain why attempts to reconstruct the speciation process from present‐day populations will ultimately fail. We then outline how we think the speciation continuum concept can continue to act as a foundation for understanding the continuum of reproductive isolation that surrounds us.","lang":"eng"}],"type":"journal_article","date_published":"2021-03-22T00:00:00Z","page":"1256-1273","article_type":"original","citation":{"mla":"Stankowski, Sean, and Mark Ravinet. “Defining the Speciation Continuum.” Evolution, vol. 75, no. 6, Oxford University Press, 2021, pp. 1256–73, doi:10.1111/evo.14215.","short":"S. Stankowski, M. Ravinet, Evolution 75 (2021) 1256–1273.","chicago":"Stankowski, Sean, and Mark Ravinet. “Defining the Speciation Continuum.” Evolution. Oxford University Press, 2021. https://doi.org/10.1111/evo.14215.","ama":"Stankowski S, Ravinet M. Defining the speciation continuum. Evolution. 2021;75(6):1256-1273. doi:10.1111/evo.14215","ista":"Stankowski S, Ravinet M. 2021. Defining the speciation continuum. Evolution. 75(6), 1256–1273.","ieee":"S. Stankowski and M. Ravinet, “Defining the speciation continuum,” Evolution, vol. 75, no. 6. Oxford University Press, pp. 1256–1273, 2021.","apa":"Stankowski, S., & Ravinet, M. (2021). Defining the speciation continuum. Evolution. Oxford University Press. https://doi.org/10.1111/evo.14215"},"publication":"Evolution","has_accepted_license":"1","article_processing_charge":"No","day":"22","scopus_import":"1"},{"series_title":"eLS","article_processing_charge":"No","publication_identifier":{"isbn":["9780470016176"],"eisbn":["9780470015902"]},"month":"05","day":"28","quality_controlled":"1","citation":{"ista":"Stankowski S, Shipilina D, Westram AM. 2021.Hybrid Zones. In: Encyclopedia of Life Sciences. vol. 2.","apa":"Stankowski, S., Shipilina, D., & Westram, A. M. (2021). Hybrid Zones. In Encyclopedia of Life Sciences (Vol. 2). Wiley. https://doi.org/10.1002/9780470015902.a0029355","ieee":"S. Stankowski, D. Shipilina, and A. M. Westram, “Hybrid Zones,” in Encyclopedia of Life Sciences, vol. 2, Wiley, 2021.","ama":"Stankowski S, Shipilina D, Westram AM. Hybrid Zones. In: Encyclopedia of Life Sciences. Vol 2. eLS. Wiley; 2021. doi:10.1002/9780470015902.a0029355","chicago":"Stankowski, Sean, Daria Shipilina, and Anja M Westram. “Hybrid Zones.” In Encyclopedia of Life Sciences, Vol. 2. ELS. Wiley, 2021. https://doi.org/10.1002/9780470015902.a0029355.","mla":"Stankowski, Sean, et al. “Hybrid Zones.” Encyclopedia of Life Sciences, vol. 2, Wiley, 2021, doi:10.1002/9780470015902.a0029355.","short":"S. Stankowski, D. Shipilina, A.M. Westram, in:, Encyclopedia of Life Sciences, Wiley, 2021."},"publication":"Encyclopedia of Life Sciences","language":[{"iso":"eng"}],"doi":"10.1002/9780470015902.a0029355","date_published":"2021-05-28T00:00:00Z","type":"book_chapter","abstract":[{"lang":"eng","text":"Hybrid zones are narrow geographic regions where different populations, races or interbreeding species meet and mate, producing mixed ‘hybrid’ offspring. They are relatively common and can be found in a diverse range of organisms and environments. The study of hybrid zones has played an important role in our understanding of the origin of species, with hybrid zones having been described as ‘natural laboratories’. This is because they allow us to study,in situ, the conditions and evolutionary forces that enable divergent taxa to remain distinct despite some ongoing gene exchange between them."}],"publisher":"Wiley","intvolume":" 2","department":[{"_id":"NiBa"}],"publication_status":"published","status":"public","title":"Hybrid Zones","year":"2021","_id":"14984","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","volume":2,"date_updated":"2024-02-19T09:54:18Z","date_created":"2024-02-14T12:05:50Z","author":[{"first_name":"Sean","last_name":"Stankowski","id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean"},{"full_name":"Shipilina, Daria","id":"428A94B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1145-9226","first_name":"Daria","last_name":"Shipilina"},{"full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","first_name":"Anja M"}]},{"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1098/rsif.2019.0721","publication_identifier":{"eissn":["1742-5662"],"issn":["1742-5689"]},"month":"02","publisher":"The Royal Society","department":[{"_id":"NiBa"}],"publication_status":"published","year":"2020","volume":17,"date_created":"2020-04-08T15:19:17Z","date_updated":"2021-01-12T08:14:41Z","author":[{"last_name":"Larsson","first_name":"J.","full_name":"Larsson, J."},{"full_name":"Westram, Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","first_name":"Anja M","last_name":"Westram"},{"full_name":"Bengmark, S.","last_name":"Bengmark","first_name":"S."},{"full_name":"Lundh, T.","last_name":"Lundh","first_name":"T."},{"full_name":"Butlin, R. K.","last_name":"Butlin","first_name":"R. K."}],"article_number":"20190721","file_date_updated":"2020-07-14T12:48:01Z","article_type":"original","citation":{"chicago":"Larsson, J., Anja M Westram, S. Bengmark, T. Lundh, and R. K. Butlin. “A Developmentally Descriptive Method for Quantifying Shape in Gastropod Shells.” Journal of The Royal Society Interface. The Royal Society, 2020. https://doi.org/10.1098/rsif.2019.0721.","short":"J. Larsson, A.M. Westram, S. Bengmark, T. Lundh, R.K. Butlin, Journal of The Royal Society Interface 17 (2020).","mla":"Larsson, J., et al. “A Developmentally Descriptive Method for Quantifying Shape in Gastropod Shells.” Journal of The Royal Society Interface, vol. 17, no. 163, 20190721, The Royal Society, 2020, doi:10.1098/rsif.2019.0721.","apa":"Larsson, J., Westram, A. M., Bengmark, S., Lundh, T., & Butlin, R. K. (2020). A developmentally descriptive method for quantifying shape in gastropod shells. Journal of The Royal Society Interface. The Royal Society. https://doi.org/10.1098/rsif.2019.0721","ieee":"J. Larsson, A. M. Westram, S. Bengmark, T. Lundh, and R. K. Butlin, “A developmentally descriptive method for quantifying shape in gastropod shells,” Journal of The Royal Society Interface, vol. 17, no. 163. The Royal Society, 2020.","ista":"Larsson J, Westram AM, Bengmark S, Lundh T, Butlin RK. 2020. A developmentally descriptive method for quantifying shape in gastropod shells. Journal of The Royal Society Interface. 17(163), 20190721.","ama":"Larsson J, Westram AM, Bengmark S, Lundh T, Butlin RK. A developmentally descriptive method for quantifying shape in gastropod shells. Journal of The Royal Society Interface. 2020;17(163). doi:10.1098/rsif.2019.0721"},"publication":"Journal of The Royal Society Interface","date_published":"2020-02-01T00:00:00Z","scopus_import":1,"article_processing_charge":"No","has_accepted_license":"1","day":"01","intvolume":" 17","title":"A developmentally descriptive method for quantifying shape in gastropod shells","ddc":["570"],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7651","file":[{"relation":"main_file","file_id":"7660","date_created":"2020-04-14T12:31:16Z","date_updated":"2020-07-14T12:48:01Z","checksum":"4eb102304402f5c56432516b84df86d6","file_name":"2020_JournRoyalSociety_Larsson.pdf","access_level":"open_access","content_type":"application/pdf","file_size":1556190,"creator":"dernst"}],"oa_version":"Published Version","type":"journal_article","issue":"163","abstract":[{"lang":"eng","text":"The growth of snail shells can be described by simple mathematical rules. Variation in a few parameters can explain much of the diversity of shell shapes seen in nature. However, empirical studies of gastropod shell shape variation typically use geometric morphometric approaches, which do not capture this growth pattern. We have developed a way to infer a set of developmentally descriptive shape parameters based on three-dimensional logarithmic helicospiral growth and using landmarks from two-dimensional shell images as input. We demonstrate the utility of this approach, and compare it to the geometric morphometric approach, using a large set of Littorina saxatilis shells in which locally adapted populations differ in shape. Our method can be modified easily to make it applicable to a wide range of shell forms, which would allow for investigations of the similarities and differences between and within many different species of gastropods."}]},{"day":"16","month":"05","publication_identifier":{"isbn":["9780470016176","9780470015902"]},"article_processing_charge":"No","quality_controlled":"1","publication":"eLS","citation":{"ama":"Westram AM, Faria R, Butlin R, Johannesson K. Inversions and Evolution. In: ELS. Wiley; 2020. doi:10.1002/9780470015902.a0029007","ista":"Westram AM, Faria R, Butlin R, Johannesson K. 2020.Inversions and Evolution. In: eLS. .","apa":"Westram, A. M., Faria, R., Butlin, R., & Johannesson, K. (2020). Inversions and Evolution. In eLS. Wiley. https://doi.org/10.1002/9780470015902.a0029007","ieee":"A. M. Westram, R. Faria, R. Butlin, and K. Johannesson, “Inversions and Evolution,” in eLS, Wiley, 2020.","mla":"Westram, Anja M., et al. “Inversions and Evolution.” ELS, Wiley, 2020, doi:10.1002/9780470015902.a0029007.","short":"A.M. Westram, R. Faria, R. Butlin, K. Johannesson, in:, ELS, Wiley, 2020.","chicago":"Westram, Anja M, Rui Faria, Roger Butlin, and Kerstin Johannesson. “Inversions and Evolution.” In ELS. Wiley, 2020. https://doi.org/10.1002/9780470015902.a0029007."},"language":[{"iso":"eng"}],"doi":"10.1002/9780470015902.a0029007","date_published":"2020-05-16T00:00:00Z","type":"book_chapter","abstract":[{"text":"Inversions are chromosomal rearrangements where the order of genes is reversed. Inversions originate by mutation and can be under positive, negative or balancing selection. Selective effects result from potential disruptive effects on meiosis, gene disruption at inversion breakpoints and, importantly, the effects of inversions as modifiers of recombination rate: Recombination is strongly reduced in individuals heterozygous for an inversion, allowing for alleles at different loci to be inherited as a ‘block’. This may lead to a selective advantage whenever it is favourable to keep certain combinations of alleles associated, for example under local adaptation with gene flow. Inversions can cover a considerable part of a chromosome and contain numerous loci under different selection pressures, so that the resulting overall effects may be complex. Empirical data from various systems show that inversions may have a prominent role in local adaptation, speciation, parallel evolution, the maintenance of polymorphism and sex chromosome evolution.","lang":"eng"}],"publication_status":"published","status":"public","title":"Inversions and Evolution","publisher":"Wiley","department":[{"_id":"NiBa"}],"_id":"9123","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2020","date_updated":"2021-02-15T13:18:16Z","date_created":"2021-02-15T12:39:04Z","oa_version":"None","author":[{"full_name":"Westram, Anja M","last_name":"Westram","first_name":"Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Faria, Rui","first_name":"Rui","last_name":"Faria"},{"full_name":"Butlin, Roger","last_name":"Butlin","first_name":"Roger"},{"last_name":"Johannesson","first_name":"Kerstin","full_name":"Johannesson, Kerstin"}]},{"month":"09","day":"22","article_processing_charge":"No","date_published":"2020-09-22T00:00:00Z","doi":"10.5061/DRYAD.R4XGXD29N","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"oa":1,"main_file_link":[{"url":"https://doi.org/10.5061/dryad.r4xgxd29n","open_access":"1"}],"citation":{"chicago":"Simon, Alexis, Christelle Fraisse, Tahani El Ayari, Cathy Liautard-Haag, Petr Strelkov, John Welch, and Nicolas Bierne. “How Do Species Barriers Decay? Concordance and Local Introgression in Mosaic Hybrid Zones of Mussels.” Dryad, 2020. https://doi.org/10.5061/DRYAD.R4XGXD29N.","short":"A. Simon, C. Fraisse, T. El Ayari, C. Liautard-Haag, P. Strelkov, J. Welch, N. Bierne, (2020).","mla":"Simon, Alexis, et al. How Do Species Barriers Decay? Concordance and Local Introgression in Mosaic Hybrid Zones of Mussels. Dryad, 2020, doi:10.5061/DRYAD.R4XGXD29N.","apa":"Simon, A., Fraisse, C., El Ayari, T., Liautard-Haag, C., Strelkov, P., Welch, J., & Bierne, N. (2020). How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels. Dryad. https://doi.org/10.5061/DRYAD.R4XGXD29N","ieee":"A. Simon et al., “How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels.” Dryad, 2020.","ista":"Simon A, Fraisse C, El Ayari T, Liautard-Haag C, Strelkov P, Welch J, Bierne N. 2020. How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels, Dryad, 10.5061/DRYAD.R4XGXD29N.","ama":"Simon A, Fraisse C, El Ayari T, et al. How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels. 2020. doi:10.5061/DRYAD.R4XGXD29N"},"abstract":[{"lang":"eng","text":"The Mytilus complex of marine mussel species forms a mosaic of hybrid zones, found across temperate regions of the globe. This allows us to study \"replicated\" instances of secondary contact between closely-related species. Previous work on this complex has shown that local introgression is both widespread and highly heterogeneous, and has identified SNPs that are outliers of differentiation between lineages. Here, we developed an ancestry-informative panel of such SNPs. We then compared their frequencies in newly-sampled populations, including samples from within the hybrid zones, and parental populations at different distances from the contact. Results show that close to the hybrid zones, some outlier loci are near to fixation for the heterospecific allele, suggesting enhanced local introgression, or the local sweep of a shared ancestral allele. Conversely, genomic cline analyses, treating local parental populations as the reference, reveal a globally high concordance among loci, albeit with a few signals of asymmetric introgression. Enhanced local introgression at specific loci is consistent with the early transfer of adaptive variants after contact, possibly including asymmetric bi-stable variants (Dobzhansky-Muller incompatibilities), or haplotypes loaded with fewer deleterious mutations. Having escaped one barrier, however, these variants can be trapped or delayed at the next barrier, confining the introgression locally. These results shed light on the decay of species barriers during phases of contact."}],"type":"research_data_reference","author":[{"full_name":"Simon, Alexis","last_name":"Simon","first_name":"Alexis"},{"full_name":"Fraisse, Christelle","orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse","first_name":"Christelle"},{"full_name":"El Ayari, Tahani","last_name":"El Ayari","first_name":"Tahani"},{"full_name":"Liautard-Haag, Cathy","last_name":"Liautard-Haag","first_name":"Cathy"},{"first_name":"Petr","last_name":"Strelkov","full_name":"Strelkov, Petr"},{"last_name":"Welch","first_name":"John","full_name":"Welch, John"},{"first_name":"Nicolas","last_name":"Bierne","full_name":"Bierne, Nicolas"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"8708"}]},"date_updated":"2023-08-04T11:04:11Z","date_created":"2023-05-23T16:48:27Z","oa_version":"Published Version","year":"2020","_id":"13073","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","ddc":["570"],"title":"How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels","publisher":"Dryad","department":[{"_id":"NiBa"}]},{"tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"oa":1,"citation":{"chicago":"Arnoux, Stephanie, Christelle Fraisse, and Christopher Sauvage. “VCF Files of Synonymous SNPs Related to: Genomic Inference of Complex Domestication Histories in Three Solanaceae Species.” Dryad, 2020. https://doi.org/10.5061/DRYAD.Q2BVQ83HD.","short":"S. Arnoux, C. Fraisse, C. Sauvage, (2020).","mla":"Arnoux, Stephanie, et al. VCF Files of Synonymous SNPs Related to: Genomic Inference of Complex Domestication Histories in Three Solanaceae Species. Dryad, 2020, doi:10.5061/DRYAD.Q2BVQ83HD.","apa":"Arnoux, S., Fraisse, C., & Sauvage, C. (2020). VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species. Dryad. https://doi.org/10.5061/DRYAD.Q2BVQ83HD","ieee":"S. Arnoux, C. Fraisse, and C. Sauvage, “VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species.” Dryad, 2020.","ista":"Arnoux S, Fraisse C, Sauvage C. 2020. VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species, Dryad, 10.5061/DRYAD.Q2BVQ83HD.","ama":"Arnoux S, Fraisse C, Sauvage C. VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species. 2020. doi:10.5061/DRYAD.Q2BVQ83HD"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.q2bvq83hd"}],"date_published":"2020-10-19T00:00:00Z","doi":"10.5061/DRYAD.Q2BVQ83HD","day":"19","month":"10","article_processing_charge":"No","ddc":["570"],"status":"public","title":"VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species","department":[{"_id":"NiBa"}],"publisher":"Dryad","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13065","year":"2020","date_created":"2023-05-23T16:30:20Z","date_updated":"2023-08-04T11:19:26Z","oa_version":"Published Version","author":[{"full_name":"Arnoux, Stephanie","first_name":"Stephanie","last_name":"Arnoux"},{"full_name":"Fraisse, Christelle","last_name":"Fraisse","first_name":"Christelle","orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sauvage","first_name":"Christopher","full_name":"Sauvage, Christopher"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"8928"}],"link":[{"url":"https://github.com/starnoux/arnoux_et_al_2019","relation":"software"}]},"type":"research_data_reference","abstract":[{"lang":"eng","text":"Domestication is a human-induced selection process that imprints the genomes of domesticated populations over a short evolutionary time scale, and that occurs in a given demographic context. Reconstructing historical gene flow, effective population size changes and their timing is therefore of fundamental interest to understand how plant demography and human selection jointly shape genomic divergence during domestication. Yet, the comparison under a single statistical framework of independent domestication histories across different crop species has been little evaluated so far. Thus, it is unclear whether domestication leads to convergent demographic changes that similarly affect crop genomes. To address this question, we used existing and new transcriptome data on three crop species of Solanaceae (eggplant, pepper and tomato), together with their close wild relatives. We fitted twelve demographic models of increasing complexity on the unfolded joint allele frequency spectrum for each wild/crop pair, and we found evidence for both shared and species-specific demographic processes between species. A convergent history of domestication with gene-flow was inferred for all three species, along with evidence of strong reduction in the effective population size during the cultivation stage of tomato and pepper. The absence of any reduction in size of the crop in eggplant stands out from the classical view of the domestication process; as does the existence of a “protracted period” of management before cultivation. Our results also suggest divergent management strategies of modern cultivars among species as their current demography substantially differs. Finally, the timing of domestication is species-specific and supported by the few historical records available."}]},{"type":"journal_article","abstract":[{"lang":"eng","text":"When divergent populations are connected by gene flow, the establishment of complete reproductive isolation usually requires the joint action of multiple barrier effects. One example where multiple barrier effects are coupled consists of a single trait that is under divergent natural selection and also mediates assortative mating. Such multiple‐effect traits can strongly reduce gene flow. However, there are few cases where patterns of assortative mating have been described quantitatively and their impact on gene flow has been determined. Two ecotypes of the coastal marine snail, Littorina saxatilis , occur in North Atlantic rocky‐shore habitats dominated by either crab predation or wave action. There is evidence for divergent natural selection acting on size, and size‐assortative mating has previously been documented. Here, we analyze the mating pattern in L. saxatilis with respect to size in intensively sampled transects across boundaries between the habitats. We show that the mating pattern is mostly conserved between ecotypes and that it generates both assortment and directional sexual selection for small male size. Using simulations, we show that the mating pattern can contribute to reproductive isolation between ecotypes but the barrier to gene flow is likely strengthened more by sexual selection than by assortment."}],"issue":"7","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7995","title":"Assortative mating, sexual selection, and their consequences for gene flow in Littorina","ddc":["570"],"status":"public","intvolume":" 74","oa_version":"Published Version","file":[{"file_name":"2020_Evolution_Perini.pdf","access_level":"open_access","file_size":1080810,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"8808","date_updated":"2020-11-25T10:49:48Z","date_created":"2020-11-25T10:49:48Z","checksum":"56235bf1e2a9e25f96196bb13b6b754d","success":1}],"scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"No","publication":"Evolution","citation":{"chicago":"Perini, Samuel, Marina Rafajlović, Anja M Westram, Kerstin Johannesson, and Roger K. Butlin. “Assortative Mating, Sexual Selection, and Their Consequences for Gene Flow in Littorina.” Evolution. Wiley, 2020. https://doi.org/10.1111/evo.14027.","short":"S. Perini, M. Rafajlović, A.M. Westram, K. Johannesson, R.K. Butlin, Evolution 74 (2020) 1482–1497.","mla":"Perini, Samuel, et al. “Assortative Mating, Sexual Selection, and Their Consequences for Gene Flow in Littorina.” Evolution, vol. 74, no. 7, Wiley, 2020, pp. 1482–97, doi:10.1111/evo.14027.","ieee":"S. Perini, M. Rafajlović, A. M. Westram, K. Johannesson, and R. K. Butlin, “Assortative mating, sexual selection, and their consequences for gene flow in Littorina,” Evolution, vol. 74, no. 7. Wiley, pp. 1482–1497, 2020.","apa":"Perini, S., Rafajlović, M., Westram, A. M., Johannesson, K., & Butlin, R. K. (2020). Assortative mating, sexual selection, and their consequences for gene flow in Littorina. Evolution. Wiley. https://doi.org/10.1111/evo.14027","ista":"Perini S, Rafajlović M, Westram AM, Johannesson K, Butlin RK. 2020. Assortative mating, sexual selection, and their consequences for gene flow in Littorina. Evolution. 74(7), 1482–1497.","ama":"Perini S, Rafajlović M, Westram AM, Johannesson K, Butlin RK. Assortative mating, sexual selection, and their consequences for gene flow in Littorina. Evolution. 2020;74(7):1482-1497. doi:10.1111/evo.14027"},"article_type":"original","page":"1482-1497","date_published":"2020-07-01T00:00:00Z","file_date_updated":"2020-11-25T10:49:48Z","ec_funded":1,"acknowledgement":"We are very grateful to I. Sencic, L. Brettell, A.‐L. Liabot, J. Galindo, M. Ravinet, and A. Butlin for their help with field sampling and mating experiments. This work was funded by the Natural Environment Research Council, European Research Council and Swedish Research Council VR and we are also very grateful for the support of the Linnaeus Centre for Marine Evolutionary Biology at the University of Gothenburg. The simulations were performed on resources at Chalmers Centre for Computational Science and Engineering (C3SE) provided by the Swedish National Infrastructure for Computing (SNIC). AMW was funded by the European Union's Horizon 2020 research and innovation program under Marie Skłodowska‐Curie grant agreement no. 797747.","year":"2020","publication_status":"published","publisher":"Wiley","department":[{"_id":"NiBa"}],"author":[{"first_name":"Samuel","last_name":"Perini","full_name":"Perini, Samuel"},{"last_name":"Rafajlović","first_name":"Marina","full_name":"Rafajlović, Marina"},{"full_name":"Westram, Anja M","first_name":"Anja M","last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969"},{"first_name":"Kerstin","last_name":"Johannesson","full_name":"Johannesson, Kerstin"},{"full_name":"Butlin, Roger K.","first_name":"Roger K.","last_name":"Butlin"}],"related_material":{"record":[{"relation":"research_data","status":"public","id":"8809"}]},"date_updated":"2023-08-22T07:13:38Z","date_created":"2020-06-22T09:14:21Z","volume":74,"month":"07","publication_identifier":{"issn":["00143820"],"eissn":["15585646"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000539780800001"]},"oa":1,"isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Theoretical and empirical approaches to understanding Parallel Adaptation","grant_number":"797747","_id":"265B41B8-B435-11E9-9278-68D0E5697425"}],"doi":"10.1111/evo.14027","language":[{"iso":"eng"}]},{"tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"oa":1,"main_file_link":[{"url":"https://doi.org/10.5061/dryad.qrfj6q5cn","open_access":"1"}],"citation":{"ista":"Perini S, Rafajlovic M, Westram AM, Johannesson K, Butlin R. 2020. Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina, Dryad, 10.5061/dryad.qrfj6q5cn.","apa":"Perini, S., Rafajlovic, M., Westram, A. M., Johannesson, K., & Butlin, R. (2020). Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina. Dryad. https://doi.org/10.5061/dryad.qrfj6q5cn","ieee":"S. Perini, M. Rafajlovic, A. M. Westram, K. Johannesson, and R. Butlin, “Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina.” Dryad, 2020.","ama":"Perini S, Rafajlovic M, Westram AM, Johannesson K, Butlin R. Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina. 2020. doi:10.5061/dryad.qrfj6q5cn","chicago":"Perini, Samuel, Marina Rafajlovic, Anja M Westram, Kerstin Johannesson, and Roger Butlin. “Data from: Assortative Mating, Sexual Selection and Their Consequences for Gene Flow in Littorina.” Dryad, 2020. https://doi.org/10.5061/dryad.qrfj6q5cn.","mla":"Perini, Samuel, et al. Data from: Assortative Mating, Sexual Selection and Their Consequences for Gene Flow in Littorina. Dryad, 2020, doi:10.5061/dryad.qrfj6q5cn.","short":"S. Perini, M. Rafajlovic, A.M. Westram, K. Johannesson, R. Butlin, (2020)."},"doi":"10.5061/dryad.qrfj6q5cn","date_published":"2020-07-01T00:00:00Z","month":"07","day":"01","has_accepted_license":"1","article_processing_charge":"No","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"8809","year":"2020","title":"Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina","status":"public","department":[{"_id":"NiBa"}],"publisher":"Dryad","author":[{"full_name":"Perini, Samuel","first_name":"Samuel","last_name":"Perini"},{"full_name":"Rafajlovic, Marina","last_name":"Rafajlovic","first_name":"Marina"},{"full_name":"Westram, Anja M","first_name":"Anja M","last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969"},{"first_name":"Kerstin","last_name":"Johannesson","full_name":"Johannesson, Kerstin"},{"full_name":"Butlin, Roger","last_name":"Butlin","first_name":"Roger"}],"related_material":{"record":[{"id":"7995","status":"public","relation":"used_in_publication"}]},"date_updated":"2023-08-22T07:13:37Z","date_created":"2020-11-25T11:07:25Z","oa_version":"Published Version","type":"research_data_reference","abstract":[{"text":"When divergent populations are connected by gene flow, the establishment of complete reproductive isolation usually requires the joint action of multiple barrier effects. One example where multiple barrier effects are coupled consists of a single trait that is under divergent natural selection and also mediates assortative mating. Such multiple-effect traits can strongly reduce gene flow. However, there are few cases where patterns of assortative mating have been described quantitatively and their impact on gene flow has been determined. Two ecotypes of the coastal marine snail, Littorina saxatilis, occur in North Atlantic rocky-shore habitats dominated by either crab predation or wave action. There is evidence for divergent natural selection acting on size, and size-assortative mating has previously been documented. Here, we analyze the mating pattern in L. saxatilis with respect to size in intensively-sampled transects across boundaries between the habitats. We show that the mating pattern is mostly conserved between ecotypes and that it generates both assortment and directional sexual selection for small male size. Using simulations, we show that the mating pattern can contribute to reproductive isolation between ecotypes but the barrier to gene flow is likely strengthened more by sexual selection than by assortment.","lang":"eng"}]},{"article_type":"letter_note","publication":"Philosophical Transactions of the Royal Society. Series B: Biological Sciences","citation":{"chicago":"Barton, Nicholas H. “On the Completion of Speciation.” Philosophical Transactions of the Royal Society. Series B: Biological Sciences. The Royal Society, 2020. https://doi.org/10.1098/rstb.2019.0530.","mla":"Barton, Nicholas H. “On the Completion of Speciation.” Philosophical Transactions of the Royal Society. Series B: Biological Sciences, vol. 375, no. 1806, 20190530, The Royal Society, 2020, doi:10.1098/rstb.2019.0530.","short":"N.H. Barton, Philosophical Transactions of the Royal Society. Series B: Biological Sciences 375 (2020).","ista":"Barton NH. 2020. On the completion of speciation. Philosophical Transactions of the Royal Society. Series B: Biological Sciences. 375(1806), 20190530.","apa":"Barton, N. H. (2020). On the completion of speciation. Philosophical Transactions of the Royal Society. Series B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rstb.2019.0530","ieee":"N. H. Barton, “On the completion of speciation,” Philosophical Transactions of the Royal Society. Series B: Biological Sciences, vol. 375, no. 1806. The Royal Society, 2020.","ama":"Barton NH. On the completion of speciation. Philosophical Transactions of the Royal Society Series B: Biological Sciences. 2020;375(1806). doi:10.1098/rstb.2019.0530"},"date_published":"2020-07-12T00:00:00Z","scopus_import":"1","day":"12","article_processing_charge":"No","status":"public","title":"On the completion of speciation","intvolume":" 375","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8112","oa_version":"None","type":"journal_article","issue":"1806","quality_controlled":"1","isi":1,"external_id":{"isi":["000552662100002"],"pmid":["32654647"]},"language":[{"iso":"eng"}],"doi":"10.1098/rstb.2019.0530","month":"07","publication_identifier":{"issn":["0962-8436"],"eissn":["1471-2970"]},"publication_status":"published","publisher":"The Royal Society","department":[{"_id":"NiBa"}],"year":"2020","pmid":1,"date_created":"2020-07-13T03:41:39Z","date_updated":"2023-08-22T07:53:52Z","volume":375,"author":[{"full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"article_number":"20190530"},{"citation":{"chicago":"Kulmuni, Jonna, Roger K. Butlin, Kay Lucek, Vincent Savolainen, and Anja M Westram. “Towards the Completion of Speciation: The Evolution of Reproductive Isolation beyond the First Barriers.” Philosophical Transactions of the Royal Society. Series B: Biological Sciences. The Royal Society, 2020. https://doi.org/10.1098/rstb.2019.0528.","short":"J. Kulmuni, R.K. Butlin, K. Lucek, V. Savolainen, A.M. Westram, Philosophical Transactions of the Royal Society. Series B: Biological Sciences 375 (2020).","mla":"Kulmuni, Jonna, et al. “Towards the Completion of Speciation: The Evolution of Reproductive Isolation beyond the First Barriers.” Philosophical Transactions of the Royal Society. Series B: Biological Sciences, vol. 375, no. 1806, 20190528, The Royal Society, 2020, doi:10.1098/rstb.2019.0528.","ieee":"J. Kulmuni, R. K. Butlin, K. Lucek, V. Savolainen, and A. M. Westram, “Towards the completion of speciation: The evolution of reproductive isolation beyond the first barriers,” Philosophical Transactions of the Royal Society. Series B: Biological sciences, vol. 375, no. 1806. The Royal Society, 2020.","apa":"Kulmuni, J., Butlin, R. K., Lucek, K., Savolainen, V., & Westram, A. M. (2020). Towards the completion of speciation: The evolution of reproductive isolation beyond the first barriers. Philosophical Transactions of the Royal Society. Series B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rstb.2019.0528","ista":"Kulmuni J, Butlin RK, Lucek K, Savolainen V, Westram AM. 2020. Towards the completion of speciation: The evolution of reproductive isolation beyond the first barriers. Philosophical Transactions of the Royal Society. Series B: Biological sciences. 375(1806), 20190528.","ama":"Kulmuni J, Butlin RK, Lucek K, Savolainen V, Westram AM. Towards the completion of speciation: The evolution of reproductive isolation beyond the first barriers. Philosophical Transactions of the Royal Society Series B: Biological sciences. 2020;375(1806). doi:10.1098/rstb.2019.0528"},"publication":"Philosophical Transactions of the Royal Society. Series B: Biological sciences","article_type":"original","date_published":"2020-07-12T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"12","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8168","intvolume":" 375","title":"Towards the completion of speciation: The evolution of reproductive isolation beyond the first barriers","status":"public","oa_version":"Published Version","type":"journal_article","issue":"1806","abstract":[{"text":"Speciation, that is, the evolution of reproductive barriers eventually leading to complete isolation, is a crucial process generating biodiversity. Recent work has contributed much to our understanding of how reproductive barriers begin to evolve, and how they are maintained in the face of gene flow. However, little is known about the transition from partial to strong reproductive isolation (RI) and the completion of speciation. We argue that the evolution of strong RI is likely to involve different processes, or new interactions among processes, compared with the evolution of the first reproductive barriers. Transition to strong RI may be brought about by changing external conditions, for example, following secondary contact. However, the increasing levels of RI themselves create opportunities for new barriers to evolve and, and interaction or coupling among barriers. These changing processes may depend on genomic architecture and leave detectable signals in the genome. We outline outstanding questions and suggest more theoretical and empirical work, considering both patterns and processes associated with strong RI, is needed to understand how speciation is completed.","lang":"eng"}],"external_id":{"isi":["000552662100001"],"pmid":["32654637"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1098/rstb.2019.0528"}],"oa":1,"project":[{"_id":"265B41B8-B435-11E9-9278-68D0E5697425","grant_number":"797747","call_identifier":"H2020","name":"Theoretical and empirical approaches to understanding Parallel Adaptation"}],"isi":1,"quality_controlled":"1","doi":"10.1098/rstb.2019.0528","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0962-8436"],"eissn":["1471-2970"]},"month":"07","pmid":1,"year":"2020","department":[{"_id":"NiBa"}],"publisher":"The Royal Society","publication_status":"published","author":[{"last_name":"Kulmuni","first_name":"Jonna","full_name":"Kulmuni, Jonna"},{"full_name":"Butlin, Roger K.","last_name":"Butlin","first_name":"Roger K."},{"first_name":"Kay","last_name":"Lucek","full_name":"Lucek, Kay"},{"full_name":"Savolainen, Vincent","first_name":"Vincent","last_name":"Savolainen"},{"first_name":"Anja M","last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M"}],"volume":375,"date_created":"2020-07-26T22:01:01Z","date_updated":"2023-08-22T08:21:31Z","article_number":"20190528","ec_funded":1},{"month":"07","publication_identifier":{"eissn":["1471-2970"]},"isi":1,"quality_controlled":"1","oa":1,"external_id":{"isi":["000552662100014"],"pmid":["32654639"]},"main_file_link":[{"url":"https://doi.org/10.1098/rstb.2019.0545","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1098/rstb.2019.0545","article_number":"20190545","publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"The Royal Society","acknowledgement":"Funding was provided by the Natural Environment Research Council (NERC) and the European Research Council. We thank Rui Faria, Nicola Nadeau, Martin Garlovsky and Hernan Morales for advice and/or useful discussion during the project. Richard Turney, Graciela Sotelo, Jenny Larson, Stéphane Loisel and Meghan Wharton participated in the collection and processing of samples. Mark Dunning helped with the development of bioinformatic pipelines. The analysis of genomic data was conducted on the University of Sheffield High-performance computer, ShARC. Jeffrey Feder and an anonymous reviewer provided comments that improved the manuscript.","year":"2020","pmid":1,"date_updated":"2023-08-22T08:22:13Z","date_created":"2020-07-26T22:01:01Z","volume":375,"author":[{"first_name":"Sean","last_name":"Stankowski","id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean"},{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","first_name":"Anja M","last_name":"Westram","full_name":"Westram, Anja M"},{"full_name":"Zagrodzka, Zuzanna B.","last_name":"Zagrodzka","first_name":"Zuzanna B."},{"full_name":"Eyres, Isobel","last_name":"Eyres","first_name":"Isobel"},{"last_name":"Broquet","first_name":"Thomas","full_name":"Broquet, Thomas"},{"full_name":"Johannesson, Kerstin","first_name":"Kerstin","last_name":"Johannesson"},{"full_name":"Butlin, Roger K.","last_name":"Butlin","first_name":"Roger K."}],"scopus_import":"1","day":"12","article_processing_charge":"No","article_type":"original","publication":"Philosophical Transactions of the Royal Society. Series B: Biological Sciences","citation":{"chicago":"Stankowski, Sean, Anja M Westram, Zuzanna B. Zagrodzka, Isobel Eyres, Thomas Broquet, Kerstin Johannesson, and Roger K. Butlin. “The Evolution of Strong Reproductive Isolation between Sympatric Intertidal Snails.” Philosophical Transactions of the Royal Society. Series B: Biological Sciences. The Royal Society, 2020. https://doi.org/10.1098/rstb.2019.0545.","mla":"Stankowski, Sean, et al. “The Evolution of Strong Reproductive Isolation between Sympatric Intertidal Snails.” Philosophical Transactions of the Royal Society. Series B: Biological Sciences, vol. 375, no. 1806, 20190545, The Royal Society, 2020, doi:10.1098/rstb.2019.0545.","short":"S. Stankowski, A.M. Westram, Z.B. Zagrodzka, I. Eyres, T. Broquet, K. Johannesson, R.K. Butlin, Philosophical Transactions of the Royal Society. Series B: Biological Sciences 375 (2020).","ista":"Stankowski S, Westram AM, Zagrodzka ZB, Eyres I, Broquet T, Johannesson K, Butlin RK. 2020. The evolution of strong reproductive isolation between sympatric intertidal snails. Philosophical Transactions of the Royal Society. Series B: Biological Sciences. 375(1806), 20190545.","apa":"Stankowski, S., Westram, A. M., Zagrodzka, Z. B., Eyres, I., Broquet, T., Johannesson, K., & Butlin, R. K. (2020). The evolution of strong reproductive isolation between sympatric intertidal snails. Philosophical Transactions of the Royal Society. Series B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rstb.2019.0545","ieee":"S. Stankowski et al., “The evolution of strong reproductive isolation between sympatric intertidal snails,” Philosophical Transactions of the Royal Society. Series B: Biological Sciences, vol. 375, no. 1806. The Royal Society, 2020.","ama":"Stankowski S, Westram AM, Zagrodzka ZB, et al. The evolution of strong reproductive isolation between sympatric intertidal snails. Philosophical Transactions of the Royal Society Series B: Biological Sciences. 2020;375(1806). doi:10.1098/rstb.2019.0545"},"date_published":"2020-07-12T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"The evolution of strong reproductive isolation (RI) is fundamental to the origins and maintenance of biological diversity, especially in situations where geographical distributions of taxa broadly overlap. But what is the history behind strong barriers currently acting in sympatry? Using whole-genome sequencing and single nucleotide polymorphism genotyping, we inferred (i) the evolutionary relationships, (ii) the strength of RI, and (iii) the demographic history of divergence between two broadly sympatric taxa of intertidal snail. Despite being cryptic, based on external morphology, Littorina arcana and Littorina saxatilis differ in their mode of female reproduction (egg-laying versus brooding), which may generate a strong post-zygotic barrier. We show that egg-laying and brooding snails are closely related, but genetically distinct. Genotyping of 3092 snails from three locations failed to recover any recent hybrid or backcrossed individuals, confirming that RI is strong. There was, however, evidence for a very low level of asymmetrical introgression, suggesting that isolation remains incomplete. The presence of strong, asymmetrical RI was further supported by demographic analysis of these populations. Although the taxa are currently broadly sympatric, demographic modelling suggests that they initially diverged during a short period of geographical separation involving very low gene flow. Our study suggests that some geographical separation may kick-start the evolution of strong RI, facilitating subsequent coexistence of taxa in sympatry. The strength of RI needed to achieve sympatry and the subsequent effect of sympatry on RI remain open questions."}],"issue":"1806","title":"The evolution of strong reproductive isolation between sympatric intertidal snails","status":"public","intvolume":" 375","_id":"8167","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version"},{"isi":1,"quality_controlled":"1","external_id":{"pmid":["32654641"],"isi":["000552662100013"]},"language":[{"iso":"eng"}],"doi":"10.1098/rstb.2019.0544","month":"07","publication_identifier":{"eissn":["14712970"]},"publication_status":"published","publisher":"The Royal Society","department":[{"_id":"NiBa"}],"acknowledgement":"This work was supported by a fellowship from the China Scholarship Council (CSC) to H.S., Swiss National Science Foundation (SNF) grant no. 31003A_149306 to C.L., doctoral programme grant W1225-B20 to a faculty team including C.L., and the University of Vienna. We thank members of J.L.’s lab for collecting samples, Michael Barfuss and Elfi Grasserbauer for help in the laboratory, the Next Generation Sequencing Platform of the University of Berne for sequencing, the Vienna Scientific Cluster (VSC) for access to computational resources, and Claus Vogel and members of the PopGen Vienna graduate school for helpful discussions.","year":"2020","pmid":1,"date_created":"2020-07-26T22:01:02Z","date_updated":"2023-08-22T08:23:24Z","volume":375,"author":[{"first_name":"Huiying","last_name":"Shang","full_name":"Shang, Huiying"},{"first_name":"Jaqueline","last_name":"Hess","full_name":"Hess, Jaqueline"},{"full_name":"Pickup, Melinda","last_name":"Pickup","first_name":"Melinda","orcid":"0000-0001-6118-0541","id":"2C78037E-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field","first_name":"David","full_name":"Field, David"},{"full_name":"Ingvarsson, Pär K.","last_name":"Ingvarsson","first_name":"Pär K."},{"full_name":"Liu, Jianquan","last_name":"Liu","first_name":"Jianquan"},{"first_name":"Christian","last_name":"Lexer","full_name":"Lexer, Christian"}],"article_number":"20190544","article_type":"original","publication":"Philosophical Transactions of the Royal Society. Series B: Biological Sciences","citation":{"ista":"Shang H, Hess J, Pickup M, Field D, Ingvarsson PK, Liu J, Lexer C. 2020. Evolution of strong reproductive isolation in plants: Broad-scale patterns and lessons from a perennial model group. Philosophical Transactions of the Royal Society. Series B: Biological Sciences. 375(1806), 20190544.","ieee":"H. Shang et al., “Evolution of strong reproductive isolation in plants: Broad-scale patterns and lessons from a perennial model group,” Philosophical Transactions of the Royal Society. Series B: Biological Sciences, vol. 375, no. 1806. The Royal Society, 2020.","apa":"Shang, H., Hess, J., Pickup, M., Field, D., Ingvarsson, P. K., Liu, J., & Lexer, C. (2020). Evolution of strong reproductive isolation in plants: Broad-scale patterns and lessons from a perennial model group. Philosophical Transactions of the Royal Society. Series B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rstb.2019.0544","ama":"Shang H, Hess J, Pickup M, et al. Evolution of strong reproductive isolation in plants: Broad-scale patterns and lessons from a perennial model group. Philosophical Transactions of the Royal Society Series B: Biological Sciences. 2020;375(1806). doi:10.1098/rstb.2019.0544","chicago":"Shang, Huiying, Jaqueline Hess, Melinda Pickup, David Field, Pär K. Ingvarsson, Jianquan Liu, and Christian Lexer. “Evolution of Strong Reproductive Isolation in Plants: Broad-Scale Patterns and Lessons from a Perennial Model Group.” Philosophical Transactions of the Royal Society. Series B: Biological Sciences. The Royal Society, 2020. https://doi.org/10.1098/rstb.2019.0544.","mla":"Shang, Huiying, et al. “Evolution of Strong Reproductive Isolation in Plants: Broad-Scale Patterns and Lessons from a Perennial Model Group.” Philosophical Transactions of the Royal Society. Series B: Biological Sciences, vol. 375, no. 1806, 20190544, The Royal Society, 2020, doi:10.1098/rstb.2019.0544.","short":"H. Shang, J. Hess, M. Pickup, D. Field, P.K. Ingvarsson, J. Liu, C. Lexer, Philosophical Transactions of the Royal Society. Series B: Biological Sciences 375 (2020)."},"date_published":"2020-07-12T00:00:00Z","scopus_import":"1","day":"12","article_processing_charge":"No","title":"Evolution of strong reproductive isolation in plants: Broad-scale patterns and lessons from a perennial model group","status":"public","intvolume":" 375","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8169","oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Many recent studies have addressed the mechanisms operating during the early stages of speciation, but surprisingly few studies have tested theoretical predictions on the evolution of strong reproductive isolation (RI). To help address this gap, we first undertook a quantitative review of the hybrid zone literature for flowering plants in relation to reproductive barriers. Then, using Populus as an exemplary model group, we analysed genome-wide variation for phylogenetic tree topologies in both early- and late-stage speciation taxa to determine how these patterns may be related to the genomic architecture of RI. Our plant literature survey revealed variation in barrier complexity and an association between barrier number and introgressive gene flow. Focusing on Populus, our genome-wide analysis of tree topologies in speciating poplar taxa points to unusually complex genomic architectures of RI, consistent with earlier genome-wide association studies. These architectures appear to facilitate the ‘escape’ of introgressed genome segments from polygenic barriers even with strong RI, thus affecting their relationships with recombination rates. Placed within the context of the broader literature, our data illustrate how phylogenomic approaches hold great promise for addressing the evolution and temporary breakdown of RI during late stages of speciation.","lang":"eng"}],"issue":"1806"},{"main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.7957469.v1","open_access":"1"}],"citation":{"chicago":"Fraisse, Christelle, and John J. Welch. “Simulation Code for Fig S1 from the Distribution of Epistasis on Simple Fitness Landscapes.” Royal Society of London, 2020. https://doi.org/10.6084/m9.figshare.7957469.v1.","mla":"Fraisse, Christelle, and John J. Welch. Simulation Code for Fig S1 from the Distribution of Epistasis on Simple Fitness Landscapes. Royal Society of London, 2020, doi:10.6084/m9.figshare.7957469.v1.","short":"C. Fraisse, J.J. Welch, (2020).","ista":"Fraisse C, Welch JJ. 2020. Simulation code for Fig S1 from the distribution of epistasis on simple fitness landscapes, Royal Society of London, 10.6084/m9.figshare.7957469.v1.","apa":"Fraisse, C., & Welch, J. J. (2020). Simulation code for Fig S1 from the distribution of epistasis on simple fitness landscapes. Royal Society of London. https://doi.org/10.6084/m9.figshare.7957469.v1","ieee":"C. Fraisse and J. J. Welch, “Simulation code for Fig S1 from the distribution of epistasis on simple fitness landscapes.” Royal Society of London, 2020.","ama":"Fraisse C, Welch JJ. Simulation code for Fig S1 from the distribution of epistasis on simple fitness landscapes. 2020. doi:10.6084/m9.figshare.7957469.v1"},"oa":1,"date_published":"2020-10-15T00:00:00Z","doi":"10.6084/m9.figshare.7957469.v1","day":"15","month":"10","article_processing_charge":"No","title":"Simulation code for Fig S1 from the distribution of epistasis on simple fitness landscapes","status":"public","publisher":"Royal Society of London","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9799","year":"2020","date_created":"2021-08-06T11:26:57Z","date_updated":"2023-08-25T10:34:41Z","oa_version":"Published Version","author":[{"full_name":"Fraisse, Christelle","last_name":"Fraisse","first_name":"Christelle","orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Welch, John J.","last_name":"Welch","first_name":"John J."}],"related_material":{"record":[{"id":"6467","status":"public","relation":"used_in_publication"}]},"type":"research_data_reference","abstract":[{"text":"Fitness interactions between mutations can influence a population’s evolution in many different ways. While epistatic effects are difficult to measure precisely, important information is captured by the mean and variance of log fitnesses for individuals carrying different numbers of mutations. We derive predictions for these quantities from a class of simple fitness landscapes, based on models of optimizing selection on quantitative traits. We also explore extensions to the models, including modular pleiotropy, variable effect sizes, mutational bias and maladaptation of the wild type. We illustrate our approach by reanalysing a large dataset of mutant effects in a yeast snoRNA. Though characterized by some large epistatic effects, these data give a good overall fit to the non-epistatic null model, suggesting that epistasis might have limited influence on the evolutionary dynamics in this system. We also show how the amount of epistasis depends on both the underlying fitness landscape and the distribution of mutations, and so is expected to vary in consistent ways between new mutations, standing variation and fixed mutations.","lang":"eng"}]},{"abstract":[{"text":"Fitness interactions between mutations can influence a population’s evolution in many different ways. While epistatic effects are difficult to measure precisely, important information is captured by the mean and variance of log fitnesses for individuals carrying different numbers of mutations. We derive predictions for these quantities from a class of simple fitness landscapes, based on models of optimizing selection on quantitative traits. We also explore extensions to the models, including modular pleiotropy, variable effect sizes, mutational bias and maladaptation of the wild type. We illustrate our approach by reanalysing a large dataset of mutant effects in a yeast snoRNA. Though characterized by some large epistatic effects, these data give a good overall fit to the non-epistatic null model, suggesting that epistasis might have limited influence on the evolutionary dynamics in this system. We also show how the amount of epistasis depends on both the underlying fitness landscape and the distribution of mutations, and so is expected to vary in consistent ways between new mutations, standing variation and fixed mutations.","lang":"eng"}],"type":"research_data_reference","date_created":"2021-08-06T11:18:15Z","date_updated":"2023-08-25T10:34:41Z","oa_version":"Published Version","author":[{"full_name":"Fraisse, Christelle","first_name":"Christelle","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075"},{"full_name":"Welch, John J.","last_name":"Welch","first_name":"John J."}],"related_material":{"record":[{"id":"6467","status":"public","relation":"used_in_publication"}]},"status":"public","title":"Simulation code for Fig S2 from the distribution of epistasis on simple fitness landscapes","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"publisher":"Royal Society of London","_id":"9798","year":"2020","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","month":"10","day":"15","article_processing_charge":"No","date_published":"2020-10-15T00:00:00Z","doi":"10.6084/m9.figshare.7957472.v1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.7957472.v1"}],"citation":{"ama":"Fraisse C, Welch JJ. Simulation code for Fig S2 from the distribution of epistasis on simple fitness landscapes. 2020. doi:10.6084/m9.figshare.7957472.v1","ista":"Fraisse C, Welch JJ. 2020. Simulation code for Fig S2 from the distribution of epistasis on simple fitness landscapes, Royal Society of London, 10.6084/m9.figshare.7957472.v1.","ieee":"C. Fraisse and J. J. Welch, “Simulation code for Fig S2 from the distribution of epistasis on simple fitness landscapes.” Royal Society of London, 2020.","apa":"Fraisse, C., & Welch, J. J. (2020). Simulation code for Fig S2 from the distribution of epistasis on simple fitness landscapes. Royal Society of London. https://doi.org/10.6084/m9.figshare.7957472.v1","mla":"Fraisse, Christelle, and John J. Welch. Simulation Code for Fig S2 from the Distribution of Epistasis on Simple Fitness Landscapes. Royal Society of London, 2020, doi:10.6084/m9.figshare.7957472.v1.","short":"C. Fraisse, J.J. Welch, (2020).","chicago":"Fraisse, Christelle, and John J. Welch. “Simulation Code for Fig S2 from the Distribution of Epistasis on Simple Fitness Landscapes.” Royal Society of London, 2020. https://doi.org/10.6084/m9.figshare.7957472.v1."},"oa":1},{"author":[{"full_name":"Baskett, Carina","orcid":"0000-0002-7354-8574","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","last_name":"Baskett","first_name":"Carina"},{"first_name":"Lucy","last_name":"Schroeder","full_name":"Schroeder, Lucy"},{"last_name":"Weber","first_name":"Marjorie G.","full_name":"Weber, Marjorie G."},{"last_name":"Schemske","first_name":"Douglas W.","full_name":"Schemske, Douglas W."}],"date_created":"2020-01-07T12:47:07Z","date_updated":"2023-09-05T15:43:19Z","volume":90,"year":"2020","publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Wiley","file_date_updated":"2020-07-14T12:47:54Z","ec_funded":1,"article_number":"e01397","doi":"10.1002/ecm.1397","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"external_id":{"isi":["000508511600001"]},"quality_controlled":"1","isi":1,"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"month":"02","publication_identifier":{"issn":["0012-9615"],"eissn":["1557-7015"]},"file":[{"checksum":"ab8130c6e68101f5a091d05324c36f08","date_updated":"2020-07-14T12:47:54Z","date_created":"2020-02-10T08:18:14Z","relation":"main_file","file_id":"7469","file_size":537941,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2020_EcologMono_Baskett.pdf"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7236","status":"public","ddc":["570"],"title":"Multiple metrics of latitudinal patterns in insect pollination and herbivory for a tropical‐temperate congener pair","intvolume":" 90","abstract":[{"text":"The biotic interactions hypothesis posits that biotic interactions are more important drivers of adaptation closer to the equator, evidenced by “stronger” contemporary interactions (e.g. greater interaction rates) and/or patterns of trait evolution consistent with a history of stronger interactions. Support for the hypothesis is mixed, but few studies span tropical and temperate regions while experimentally controlling for evolutionary history. Here, we integrate field observations and common garden experiments to quantify the relative importance of pollination and herbivory in a pair of tropical‐temperate congeneric perennial herbs. Phytolacca rivinoides and P. americana are pioneer species native to the Neotropics and the eastern USA, respectively. We compared plant‐pollinator and plant‐herbivore interactions between three tropical populations of P. rivinoides from Costa Rica and three temperate populations of P. americana from its northern range edge in Michigan and Ohio. For some metrics of interaction importance, we also included three subtropical populations of P. americana from its southern range edge in Florida. This approach confounds species and region but allows us, uniquely, to measure complementary proxies of interaction importance across a tropical‐temperate range in one system. To test the prediction that lower‐latitude plants are more reliant on insect pollinators, we quantified floral display and reward, insect visitation rates, and self‐pollination ability (autogamy). To test the prediction that lower‐latitude plants experience more herbivore pressure, we quantified herbivory rates, herbivore abundance, and leaf palatability. We found evidence supporting the biotic interactions hypothesis for most comparisons between P. rivinoides and north‐temperate P. americana (floral display, insect visitation, autogamy, herbivory, herbivore abundance, and young‐leaf palatability). Results for subtropical P. americana populations, however, were typically not intermediate between P. rivinoides and north‐temperate P. americana, as would be predicted by a linear latitudinal gradient in interaction importance. Subtropical young‐leaf palatability was intermediate, but subtropical mature leaves were the least palatable, and pollination‐related traits did not differ between temperate and subtropical regions. These nonlinear patterns of interaction importance suggest future work to relate interaction importance to climatic or biotic thresholds. In sum, we found that the biotic interactions hypothesis was more consistently supported at the larger spatial scale of our study.","lang":"eng"}],"issue":"1","type":"journal_article","date_published":"2020-02-01T00:00:00Z","publication":"Ecological Monographs","citation":{"chicago":"Baskett, Carina, Lucy Schroeder, Marjorie G. Weber, and Douglas W. Schemske. “Multiple Metrics of Latitudinal Patterns in Insect Pollination and Herbivory for a Tropical‐temperate Congener Pair.” Ecological Monographs. Wiley, 2020. https://doi.org/10.1002/ecm.1397.","short":"C. Baskett, L. Schroeder, M.G. Weber, D.W. Schemske, Ecological Monographs 90 (2020).","mla":"Baskett, Carina, et al. “Multiple Metrics of Latitudinal Patterns in Insect Pollination and Herbivory for a Tropical‐temperate Congener Pair.” Ecological Monographs, vol. 90, no. 1, e01397, Wiley, 2020, doi:10.1002/ecm.1397.","ieee":"C. Baskett, L. Schroeder, M. G. Weber, and D. W. Schemske, “Multiple metrics of latitudinal patterns in insect pollination and herbivory for a tropical‐temperate congener pair,” Ecological Monographs, vol. 90, no. 1. Wiley, 2020.","apa":"Baskett, C., Schroeder, L., Weber, M. G., & Schemske, D. W. (2020). Multiple metrics of latitudinal patterns in insect pollination and herbivory for a tropical‐temperate congener pair. Ecological Monographs. Wiley. https://doi.org/10.1002/ecm.1397","ista":"Baskett C, Schroeder L, Weber MG, Schemske DW. 2020. Multiple metrics of latitudinal patterns in insect pollination and herbivory for a tropical‐temperate congener pair. Ecological Monographs. 90(1), e01397.","ama":"Baskett C, Schroeder L, Weber MG, Schemske DW. Multiple metrics of latitudinal patterns in insect pollination and herbivory for a tropical‐temperate congener pair. Ecological Monographs. 2020;90(1). doi:10.1002/ecm.1397"},"article_type":"original","day":"01","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","scopus_import":"1"},{"article_type":"original","page":"342-351","publication":"Journal of Evolutionary Biology","citation":{"ama":"Johannesson K, Zagrodzka Z, Faria R, Westram AM, Butlin RK. Is embryo abortion a post-zygotic barrier to gene flow between Littorina ecotypes? Journal of Evolutionary Biology. 2020;33(3):342-351. doi:10.1111/jeb.13570","apa":"Johannesson, K., Zagrodzka, Z., Faria, R., Westram, A. M., & Butlin, R. K. (2020). Is embryo abortion a post-zygotic barrier to gene flow between Littorina ecotypes? Journal of Evolutionary Biology. Wiley. https://doi.org/10.1111/jeb.13570","ieee":"K. Johannesson, Z. Zagrodzka, R. Faria, A. M. Westram, and R. K. Butlin, “Is embryo abortion a post-zygotic barrier to gene flow between Littorina ecotypes?,” Journal of Evolutionary Biology, vol. 33, no. 3. Wiley, pp. 342–351, 2020.","ista":"Johannesson K, Zagrodzka Z, Faria R, Westram AM, Butlin RK. 2020. Is embryo abortion a post-zygotic barrier to gene flow between Littorina ecotypes? Journal of Evolutionary Biology. 33(3), 342–351.","short":"K. Johannesson, Z. Zagrodzka, R. Faria, A.M. Westram, R.K. Butlin, Journal of Evolutionary Biology 33 (2020) 342–351.","mla":"Johannesson, Kerstin, et al. “Is Embryo Abortion a Post-Zygotic Barrier to Gene Flow between Littorina Ecotypes?” Journal of Evolutionary Biology, vol. 33, no. 3, Wiley, 2020, pp. 342–51, doi:10.1111/jeb.13570.","chicago":"Johannesson, Kerstin, Zuzanna Zagrodzka, Rui Faria, Anja M Westram, and Roger K. Butlin. “Is Embryo Abortion a Post-Zygotic Barrier to Gene Flow between Littorina Ecotypes?” Journal of Evolutionary Biology. Wiley, 2020. https://doi.org/10.1111/jeb.13570."},"date_published":"2020-03-01T00:00:00Z","scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"No","status":"public","title":"Is embryo abortion a post-zygotic barrier to gene flow between Littorina ecotypes?","ddc":["570"],"intvolume":" 33","_id":"7205","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"content_type":"application/pdf","file_size":885611,"creator":"dernst","file_name":"2020_EvolBiology_Johannesson.pdf","access_level":"open_access","date_updated":"2020-09-22T09:42:18Z","date_created":"2020-09-22T09:42:18Z","checksum":"7534ff0839709c0c5265c12d29432f03","success":1,"relation":"main_file","file_id":"8553"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Genetic incompatibilities contribute to reproductive isolation between many diverging populations, but it is still unclear to what extent they play a role if divergence happens with gene flow. In contact zones between the \"Crab\" and \"Wave\" ecotypes of the snail Littorina saxatilis, divergent selection forms strong barriers to gene flow, while the role of post‐zygotic barriers due to selection against hybrids remains unclear. High embryo abortion rates in this species could indicate the presence of such barriers. Post‐zygotic barriers might include genetic incompatibilities (e.g. Dobzhansky–Muller incompatibilities) but also maladaptation, both expected to be most pronounced in contact zones. In addition, embryo abortion might reflect physiological stress on females and embryos independent of any genetic stress. We examined all embryos of >500 females sampled outside and inside contact zones of three populations in Sweden. Females' clutch size ranged from 0 to 1,011 embryos (mean 130 ± 123), and abortion rates varied between 0% and 100% (mean 12%). We described female genotypes by using a hybrid index based on hundreds of SNPs differentiated between ecotypes with which we characterized female genotypes. We also calculated female SNP heterozygosity and inversion karyotype. Clutch size did not vary with female hybrid index, and abortion rates were only weakly related to hybrid index in two sites but not at all in a third site. No additional variation in abortion rate was explained by female SNP heterozygosity, but increased female inversion heterozygosity added slightly to increased abortion. Our results show only weak and probably biologically insignificant post‐zygotic barriers contributing to ecotype divergence, and the high and variable abortion rates were marginally, if at all, explained by hybrid index of females."}],"issue":"3","quality_controlled":"1","isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["31724256"],"isi":["000500954800001"]},"language":[{"iso":"eng"}],"doi":"10.1111/jeb.13570","month":"03","publication_identifier":{"issn":["1010061X"],"eissn":["14209101"]},"publication_status":"published","publisher":"Wiley","department":[{"_id":"NiBa"}],"year":"2020","pmid":1,"date_created":"2019-12-22T23:00:43Z","date_updated":"2023-09-06T14:48:57Z","volume":33,"author":[{"first_name":"Kerstin","last_name":"Johannesson","full_name":"Johannesson, Kerstin"},{"last_name":"Zagrodzka","first_name":"Zuzanna","full_name":"Zagrodzka, Zuzanna"},{"full_name":"Faria, Rui","first_name":"Rui","last_name":"Faria"},{"full_name":"Westram, Anja M","first_name":"Anja M","last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969"},{"full_name":"Butlin, Roger K.","last_name":"Butlin","first_name":"Roger K."}],"related_material":{"record":[{"relation":"research_data","status":"public","id":"13067"}]},"file_date_updated":"2020-09-22T09:42:18Z"},{"ddc":["570"],"title":"Local adaptation in metapopulations","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"8574","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"8575","checksum":"20e71f015fbbd78fea708893ad634ed0","success":1,"date_created":"2020-09-28T07:25:35Z","date_updated":"2020-09-28T07:25:35Z","access_level":"open_access","file_name":"thesis_EnikoSzep_final.pdf","file_size":6354833,"content_type":"application/pdf","creator":"dernst"},{"relation":"source_file","file_id":"8576","checksum":"a8de2c14a1bb4e53c857787efbb289e1","date_updated":"2020-09-28T07:25:37Z","date_created":"2020-09-28T07:25:37Z","access_level":"closed","file_name":"thesisFiles_EnikoSzep.zip","file_size":23020401,"content_type":"application/x-zip-compressed","creator":"dernst"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"This thesis concerns itself with the interactions of evolutionary and ecological forces and the consequences on genetic diversity and the ultimate survival of populations. It is important to understand what signals processes \r\nleave on the genome and what we can infer from such data, which is usually abundant but noisy. Furthermore, understanding how and when populations adapt or go extinct is important for practical purposes, such as the genetic management of populations, as well as for theoretical questions, since local adaptation can be the first step toward speciation. \r\nIn Chapter 2, we introduce the method of maximum entropy to approximate the demographic changes of a population in a simple setting, namely the logistic growth model with immigration. We show that this method is not only a powerful \r\ntool in physics but can be gainfully applied in an ecological framework. We investigate how well it approximates the real \r\nbehavior of the system, and find that is does so, even in unexpected situations. Finally, we illustrate how it can model changing environments.\r\nIn Chapter 3, we analyze the co-evolution of allele frequencies and population sizes in an infinite island model.\r\nWe give conditions under which polygenic adaptation to a rare habitat is possible. The model we use is based on the diffusion approximation, considers eco-evolutionary feedback mechanisms (hard selection), and treats both \r\ndrift and environmental fluctuations explicitly. We also look at limiting scenarios, for which we derive analytical expressions. \r\nIn Chapter 4, we present a coalescent based simulation tool to obtain patterns of diversity in a spatially explicit subdivided population, in which the demographic history of each subpopulation can be specified. We compare \r\nthe results to existing predictions, and explore the relative importance of time and space under a variety of spatial arrangements and demographic histories, such as expansion and extinction. \r\nIn the last chapter, we give a brief outlook to further research. ","lang":"eng"}],"page":"158","citation":{"chicago":"Szep, Eniko. “Local Adaptation in Metapopulations.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8574.","short":"E. Szep, Local Adaptation in Metapopulations, Institute of Science and Technology Austria, 2020.","mla":"Szep, Eniko. Local Adaptation in Metapopulations. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8574.","ieee":"E. Szep, “Local adaptation in metapopulations,” Institute of Science and Technology Austria, 2020.","apa":"Szep, E. (2020). Local adaptation in metapopulations. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8574","ista":"Szep E. 2020. Local adaptation in metapopulations. Institute of Science and Technology Austria.","ama":"Szep E. Local adaptation in metapopulations. 2020. doi:10.15479/AT:ISTA:8574"},"date_published":"2020-09-20T00:00:00Z","has_accepted_license":"1","article_processing_charge":"No","day":"20","publisher":"Institute of Science and Technology Austria","department":[{"_id":"NiBa"}],"publication_status":"published","year":"2020","date_created":"2020-09-28T07:33:38Z","date_updated":"2023-09-07T13:11:39Z","author":[{"full_name":"Szep, Eniko","id":"485BB5A4-F248-11E8-B48F-1D18A9856A87","last_name":"Szep","first_name":"Eniko"}],"file_date_updated":"2020-09-28T07:25:37Z","oa":1,"language":[{"iso":"eng"}],"supervisor":[{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"}],"degree_awarded":"PhD","doi":"10.15479/AT:ISTA:8574","publication_identifier":{"eissn":["2663-337X"]},"month":"09"},{"day":"22","month":"06","article_processing_charge":"No","doi":"10.5061/dryad.5vv37","date_published":"2019-06-22T00:00:00Z","citation":{"chicago":"Polechova, Jitka. “Data from: Is the Sky the Limit? On the Expansion Threshold of a Species’ Range.” Dryad, 2019. https://doi.org/10.5061/dryad.5vv37.","short":"J. Polechova, (2019).","mla":"Polechova, Jitka. Data from: Is the Sky the Limit? On the Expansion Threshold of a Species’ Range. Dryad, 2019, doi:10.5061/dryad.5vv37.","apa":"Polechova, J. (2019). Data from: Is the sky the limit? On the expansion threshold of a species’ range. Dryad. https://doi.org/10.5061/dryad.5vv37","ieee":"J. Polechova, “Data from: Is the sky the limit? On the expansion threshold of a species’ range.” Dryad, 2019.","ista":"Polechova J. 2019. Data from: Is the sky the limit? On the expansion threshold of a species’ range, Dryad, 10.5061/dryad.5vv37.","ama":"Polechova J. Data from: Is the sky the limit? On the expansion threshold of a species’ range. 2019. doi:10.5061/dryad.5vv37"},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.5vv37"}],"abstract":[{"lang":"eng","text":"More than 100 years after Grigg’s influential analysis of species’ borders, the causes of limits to species’ ranges still represent a puzzle that has never been understood with clarity. The topic has become especially important recently as many scientists have become interested in the potential for species’ ranges to shift in response to climate change—and yet nearly all of those studies fail to recognise or incorporate evolutionary genetics in a way that relates to theoretical developments. I show that range margins can be understood based on just two measurable parameters: (i) the fitness cost of dispersal—a measure of environmental heterogeneity—and (ii) the strength of genetic drift, which reduces genetic diversity. Together, these two parameters define an ‘expansion threshold’: adaptation fails when genetic drift reduces genetic diversity below that required for adaptation to a heterogeneous environment. When the key parameters drop below this expansion threshold locally, a sharp range margin forms. When they drop below this threshold throughout the species’ range, adaptation collapses everywhere, resulting in either extinction or formation of a fragmented metapopulation. Because the effects of dispersal differ fundamentally with dimension, the second parameter—the strength of genetic drift—is qualitatively different compared to a linear habitat. In two-dimensional habitats, genetic drift becomes effectively independent of selection. It decreases with ‘neighbourhood size’—the number of individuals accessible by dispersal within one generation. Moreover, in contrast to earlier predictions, which neglected evolution of genetic variance and/or stochasticity in two dimensions, dispersal into small marginal populations aids adaptation. This is because the reduction of both genetic and demographic stochasticity has a stronger effect than the cost of dispersal through increased maladaptation. The expansion threshold thus provides a novel, theoretically justified, and testable prediction for formation of the range margin and collapse of the species’ range."}],"type":"research_data_reference","date_created":"2021-08-09T13:07:28Z","date_updated":"2023-02-23T11:14:30Z","oa_version":"Published Version","author":[{"full_name":"Polechova, Jitka","orcid":"0000-0003-0951-3112","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","last_name":"Polechova","first_name":"Jitka"}],"related_material":{"record":[{"id":"315","status":"public","relation":"used_in_publication"}]},"title":"Data from: Is the sky the limit? On the expansion threshold of a species' range","status":"public","department":[{"_id":"NiBa"}],"publisher":"Dryad","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9839","year":"2019"},{"date_published":"2019-03-01T00:00:00Z","publication":"Trends in Ecology and Evolution","citation":{"ieee":"R. Faria, K. Johannesson, R. K. Butlin, and A. M. Westram, “Evolving inversions,” Trends in Ecology and Evolution, vol. 34, no. 3. Elsevier, pp. 239–248, 2019.","apa":"Faria, R., Johannesson, K., Butlin, R. K., & Westram, A. M. (2019). Evolving inversions. Trends in Ecology and Evolution. Elsevier. https://doi.org/10.1016/j.tree.2018.12.005","ista":"Faria R, Johannesson K, Butlin RK, Westram AM. 2019. Evolving inversions. Trends in Ecology and Evolution. 34(3), 239–248.","ama":"Faria R, Johannesson K, Butlin RK, Westram AM. Evolving inversions. Trends in Ecology and Evolution. 2019;34(3):239-248. doi:10.1016/j.tree.2018.12.005","chicago":"Faria, Rui, Kerstin Johannesson, Roger K. Butlin, and Anja M Westram. “Evolving Inversions.” Trends in Ecology and Evolution. Elsevier, 2019. https://doi.org/10.1016/j.tree.2018.12.005.","short":"R. Faria, K. Johannesson, R.K. Butlin, A.M. Westram, Trends in Ecology and Evolution 34 (2019) 239–248.","mla":"Faria, Rui, et al. “Evolving Inversions.” Trends in Ecology and Evolution, vol. 34, no. 3, Elsevier, 2019, pp. 239–48, doi:10.1016/j.tree.2018.12.005."},"article_type":"original","page":"239-248","day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","oa_version":"Published Version","file":[{"file_name":"2019_Trends_Evolution_Faria.pdf","access_level":"open_access","creator":"cziletti","file_size":1946795,"content_type":"application/pdf","file_id":"7245","relation":"main_file","date_updated":"2020-07-14T12:47:13Z","date_created":"2020-01-09T10:55:58Z","checksum":"ef24572d6ebcc1452c067e05410cc4a2"}],"_id":"5911","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["570"],"title":"Evolving inversions","status":"public","intvolume":" 34","abstract":[{"text":"Empirical data suggest that inversions in many species contain genes important for intraspecific divergence and speciation, yet mechanisms of evolution remain unclear. While genes inside an inversion are tightly linked, inversions are not static but evolve separately from the rest of the genome by new mutations, recombination within arrangements, and gene flux between arrangements. Inversion polymorphisms are maintained by different processes, for example, divergent or balancing selection, or a mix of multiple processes. Moreover, the relative roles of selection, drift, mutation, and recombination will change over the lifetime of an inversion and within its area of distribution. We believe inversions are central to the evolution of many species, but we need many more data and new models to understand the complex mechanisms involved.","lang":"eng"}],"issue":"3","type":"journal_article","doi":"10.1016/j.tree.2018.12.005","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"isi":["000459899000013"]},"oa":1,"isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"month":"03","publication_identifier":{"issn":["01695347"]},"author":[{"full_name":"Faria, Rui","last_name":"Faria","first_name":"Rui"},{"full_name":"Johannesson, Kerstin","first_name":"Kerstin","last_name":"Johannesson"},{"first_name":"Roger K.","last_name":"Butlin","full_name":"Butlin, Roger K."},{"full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","first_name":"Anja M"}],"date_created":"2019-02-03T22:59:15Z","date_updated":"2023-08-24T14:29:48Z","volume":34,"year":"2019","publication_status":"published","publisher":"Elsevier","department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:47:13Z","ec_funded":1},{"article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2019-01-01T00:00:00Z","page":"80-92","citation":{"ista":"Andalo C, Burrus M, Paute S, Lauzeral C, Field D. 2019. Prevalence of legitimate pollinators and nectar robbers and the consequences for fruit set in an Antirrhinum majus hybrid zone. Botany Letters. 166(1), 80–92.","apa":"Andalo, C., Burrus, M., Paute, S., Lauzeral, C., & Field, D. (2019). Prevalence of legitimate pollinators and nectar robbers and the consequences for fruit set in an Antirrhinum majus hybrid zone. Botany Letters. Taylor and Francis. https://doi.org/10.1080/23818107.2018.1545142","ieee":"C. Andalo, M. Burrus, S. Paute, C. Lauzeral, and D. Field, “Prevalence of legitimate pollinators and nectar robbers and the consequences for fruit set in an Antirrhinum majus hybrid zone,” Botany Letters, vol. 166, no. 1. Taylor and Francis, pp. 80–92, 2019.","ama":"Andalo C, Burrus M, Paute S, Lauzeral C, Field D. Prevalence of legitimate pollinators and nectar robbers and the consequences for fruit set in an Antirrhinum majus hybrid zone. Botany Letters. 2019;166(1):80-92. doi:10.1080/23818107.2018.1545142","chicago":"Andalo, Christophe, Monique Burrus, Sandrine Paute, Christine Lauzeral, and David Field. “Prevalence of Legitimate Pollinators and Nectar Robbers and the Consequences for Fruit Set in an Antirrhinum Majus Hybrid Zone.” Botany Letters. Taylor and Francis, 2019. https://doi.org/10.1080/23818107.2018.1545142.","mla":"Andalo, Christophe, et al. “Prevalence of Legitimate Pollinators and Nectar Robbers and the Consequences for Fruit Set in an Antirrhinum Majus Hybrid Zone.” Botany Letters, vol. 166, no. 1, Taylor and Francis, 2019, pp. 80–92, doi:10.1080/23818107.2018.1545142.","short":"C. Andalo, M. Burrus, S. Paute, C. Lauzeral, D. Field, Botany Letters 166 (2019) 80–92."},"publication":"Botany Letters","issue":"1","abstract":[{"text":"Pollinators display a remarkable diversity of foraging strategies with flowering plants, from primarily mutualistic interactions to cheating through nectar robbery. Despite numerous studies on the effect of nectar robbing on components of plant fitness, its contribution to reproductive isolation is unclear. We experimentally tested the impact of different pollinator strategies in a natural hybrid zone between two subspecies of Antirrhinum majus with alternate flower colour guides. On either side of a steep cline in flower colour between Antirrhinum majus pseudomajus (magenta) and A. m. striatum (yellow), we quantified the behaviour of all floral visitors at different time points during the flowering season. Using long-run camera surveys, we quantify the impact of nectar robbing on the number of flowers visited per inflorescence and the flower probing time. We further experimentally tested the effect of nectar robbing on female reproductive success by manipulating the intensity of robbing. While robbing increased over time the number of legitimate visitors tended to decrease concomitantly. We found that the number of flowers pollinated on a focal inflorescence decreased with the number of prior robbing events. However, in the manipulative experiment, fruit set and fruit volume did not vary significantly between low robbing and control treatments. Our findings challenge the idea that robbers have a negative impact on plant fitness through female function. This study also adds to our understanding of the components of pollinator-mediated reproductive isolation and the maintenance of Antirrhinum hybrid zones.","lang":"eng"}],"type":"journal_article","oa_version":"None","intvolume":" 166","title":"Prevalence of legitimate pollinators and nectar robbers and the consequences for fruit set in an Antirrhinum majus hybrid zone","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"5680","publication_identifier":{"issn":["23818107"],"eissn":["23818115"]},"month":"01","language":[{"iso":"eng"}],"doi":"10.1080/23818107.2018.1545142","isi":1,"quality_controlled":"1","external_id":{"isi":["000463802800009"]},"volume":166,"date_created":"2018-12-16T22:59:20Z","date_updated":"2023-08-24T14:34:12Z","author":[{"full_name":"Andalo, Christophe","last_name":"Andalo","first_name":"Christophe"},{"full_name":"Burrus, Monique","last_name":"Burrus","first_name":"Monique"},{"full_name":"Paute, Sandrine","last_name":"Paute","first_name":"Sandrine"},{"last_name":"Lauzeral","first_name":"Christine","full_name":"Lauzeral, Christine"},{"orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field","first_name":"David","full_name":"Field, David"}],"publisher":"Taylor and Francis","department":[{"_id":"NiBa"}],"publication_status":"published","year":"2019"},{"month":"02","language":[{"iso":"eng"}],"doi":"10.1371/journal.pbio.2005902","quality_controlled":"1","isi":1,"tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"oa":1,"external_id":{"isi":["000460317100001"]},"file_date_updated":"2020-07-14T12:47:17Z","article_number":"e2005902","date_created":"2019-02-17T22:59:21Z","date_updated":"2023-08-24T14:46:23Z","volume":17,"author":[{"full_name":"Merrill, Richard M.","last_name":"Merrill","first_name":"Richard M."},{"first_name":"Pasi","last_name":"Rastas","full_name":"Rastas, Pasi"},{"first_name":"Simon H.","last_name":"Martin","full_name":"Martin, Simon H."},{"full_name":"Melo Hurtado, Maria C","id":"386D7308-F248-11E8-B48F-1D18A9856A87","first_name":"Maria C","last_name":"Melo Hurtado"},{"last_name":"Barker","first_name":"Sarah","full_name":"Barker, Sarah"},{"first_name":"John","last_name":"Davey","full_name":"Davey, John"},{"first_name":"W. Owen","last_name":"Mcmillan","full_name":"Mcmillan, W. Owen"},{"first_name":"Chris D.","last_name":"Jiggins","full_name":"Jiggins, Chris D."}],"related_material":{"record":[{"id":"9801","relation":"research_data","status":"public"}]},"publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Public Library of Science","year":"2019","day":"07","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2019-02-07T00:00:00Z","publication":"PLoS Biology","citation":{"chicago":"Merrill, Richard M., Pasi Rastas, Simon H. Martin, Maria C Melo Hurtado, Sarah Barker, John Davey, W. Owen Mcmillan, and Chris D. Jiggins. “Genetic Dissection of Assortative Mating Behavior.” PLoS Biology. Public Library of Science, 2019. https://doi.org/10.1371/journal.pbio.2005902.","mla":"Merrill, Richard M., et al. “Genetic Dissection of Assortative Mating Behavior.” PLoS Biology, vol. 17, no. 2, e2005902, Public Library of Science, 2019, doi:10.1371/journal.pbio.2005902.","short":"R.M. Merrill, P. Rastas, S.H. Martin, M.C. Melo Hurtado, S. Barker, J. Davey, W.O. Mcmillan, C.D. Jiggins, PLoS Biology 17 (2019).","ista":"Merrill RM, Rastas P, Martin SH, Melo Hurtado MC, Barker S, Davey J, Mcmillan WO, Jiggins CD. 2019. Genetic dissection of assortative mating behavior. PLoS Biology. 17(2), e2005902.","apa":"Merrill, R. M., Rastas, P., Martin, S. H., Melo Hurtado, M. C., Barker, S., Davey, J., … Jiggins, C. D. (2019). Genetic dissection of assortative mating behavior. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2005902","ieee":"R. M. Merrill et al., “Genetic dissection of assortative mating behavior,” PLoS Biology, vol. 17, no. 2. Public Library of Science, 2019.","ama":"Merrill RM, Rastas P, Martin SH, et al. Genetic dissection of assortative mating behavior. PLoS Biology. 2019;17(2). doi:10.1371/journal.pbio.2005902"},"abstract":[{"lang":"eng","text":"The evolution of new species is made easier when traits under divergent ecological selection are also mating cues. Such ecological mating cues are now considered more common than previously thought, but we still know little about the genetic changes underlying their evolution or more generally about the genetic basis for assortative mating behaviors. Both tight physical linkage and the existence of large-effect preference loci will strengthen genetic associations between behavioral and ecological barriers, promoting the evolution of assortative mating. The warning patterns of Heliconius melpomene and H. cydno are under disruptive selection due to increased predation of nonmimetic hybrids and are used during mate recognition. We carried out a genome-wide quantitative trait locus (QTL) analysis of preference behaviors between these species and showed that divergent male preference has a simple genetic basis. We identify three QTLs that together explain a large proportion (approximately 60%) of the difference in preference behavior observed between the parental species. One of these QTLs is just 1.2 (0-4.8) centiMorgans (cM) from the major color pattern gene optix, and, individually, all three have a large effect on the preference phenotype. Genomic divergence between H. cydno and H. melpomene is high but broadly heterogenous, and admixture is reduced at the preference-optix color pattern locus but not the other preference QTLs. The simple genetic architecture we reveal will facilitate the evolution and maintenance of new species despite ongoing gene flow by coupling behavioral and ecological aspects of reproductive isolation."}],"issue":"2","type":"journal_article","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2019_PLOS_Merrill.pdf","file_size":2005949,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"6036","checksum":"5f34001617ee729314ca520c049b1112","date_created":"2019-02-18T14:57:24Z","date_updated":"2020-07-14T12:47:17Z"}],"title":"Genetic dissection of assortative mating behavior","status":"public","ddc":["570"],"intvolume":" 17","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6022"},{"month":"02","day":"07","article_processing_charge":"No","doi":"10.1371/journal.pbio.2005902.s006","date_published":"2019-02-07T00:00:00Z","citation":{"ista":"Merrill RM, Rastas P, Martin SH, Melo Hurtado MC, Barker S, Davey J, Mcmillan WO, Jiggins CD. 2019. Raw behavioral data, Public Library of Science, 10.1371/journal.pbio.2005902.s006.","ieee":"R. M. Merrill et al., “Raw behavioral data.” Public Library of Science, 2019.","apa":"Merrill, R. M., Rastas, P., Martin, S. H., Melo Hurtado, M. C., Barker, S., Davey, J., … Jiggins, C. D. (2019). Raw behavioral data. Public Library of Science. https://doi.org/10.1371/journal.pbio.2005902.s006","ama":"Merrill RM, Rastas P, Martin SH, et al. Raw behavioral data. 2019. doi:10.1371/journal.pbio.2005902.s006","chicago":"Merrill, Richard M., Pasi Rastas, Simon H. Martin, Maria C Melo Hurtado, Sarah Barker, John Davey, W. Owen Mcmillan, and Chris D. Jiggins. “Raw Behavioral Data.” Public Library of Science, 2019. https://doi.org/10.1371/journal.pbio.2005902.s006.","mla":"Merrill, Richard M., et al. Raw Behavioral Data. Public Library of Science, 2019, doi:10.1371/journal.pbio.2005902.s006.","short":"R.M. Merrill, P. Rastas, S.H. Martin, M.C. Melo Hurtado, S. Barker, J. Davey, W.O. Mcmillan, C.D. Jiggins, (2019)."},"type":"research_data_reference","author":[{"full_name":"Merrill, Richard M.","last_name":"Merrill","first_name":"Richard M."},{"first_name":"Pasi","last_name":"Rastas","full_name":"Rastas, Pasi"},{"last_name":"Martin","first_name":"Simon H.","full_name":"Martin, Simon H."},{"full_name":"Melo Hurtado, Maria C","last_name":"Melo Hurtado","first_name":"Maria C","id":"386D7308-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Barker, Sarah","last_name":"Barker","first_name":"Sarah"},{"first_name":"John","last_name":"Davey","full_name":"Davey, John"},{"full_name":"Mcmillan, W. Owen","first_name":"W. Owen","last_name":"Mcmillan"},{"first_name":"Chris D.","last_name":"Jiggins","full_name":"Jiggins, Chris D."}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"6022"}]},"date_created":"2021-08-06T11:34:56Z","date_updated":"2023-08-24T14:46:23Z","oa_version":"Published Version","_id":"9801","year":"2019","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","title":"Raw behavioral data","status":"public","department":[{"_id":"NiBa"}],"publisher":"Public Library of Science"},{"doi":"10.1111/mec.14972","language":[{"iso":"eng"}],"external_id":{"isi":["000465219200013"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","isi":1,"publication_identifier":{"issn":["0962-1083"],"eissn":["1365-294X"]},"month":"03","related_material":{"record":[{"status":"public","relation":"research_data","id":"9837"}]},"author":[{"last_name":"Faria","first_name":"Rui","full_name":"Faria, Rui"},{"full_name":"Chaube, Pragya","first_name":"Pragya","last_name":"Chaube"},{"last_name":"Morales","first_name":"Hernán E.","full_name":"Morales, Hernán E."},{"full_name":"Larsson, Tomas","last_name":"Larsson","first_name":"Tomas"},{"last_name":"Lemmon","first_name":"Alan R.","full_name":"Lemmon, Alan R."},{"full_name":"Lemmon, Emily M.","first_name":"Emily M.","last_name":"Lemmon"},{"first_name":"Marina","last_name":"Rafajlović","full_name":"Rafajlović, Marina"},{"last_name":"Panova","first_name":"Marina","full_name":"Panova, Marina"},{"first_name":"Mark","last_name":"Ravinet","full_name":"Ravinet, Mark"},{"full_name":"Johannesson, Kerstin","last_name":"Johannesson","first_name":"Kerstin"},{"full_name":"Westram, Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","first_name":"Anja M","last_name":"Westram"},{"last_name":"Butlin","first_name":"Roger K.","full_name":"Butlin, Roger K."}],"volume":28,"date_created":"2019-03-10T22:59:21Z","date_updated":"2023-08-24T14:50:27Z","year":"2019","department":[{"_id":"NiBa"}],"publisher":"Wiley","publication_status":"published","file_date_updated":"2020-07-14T12:47:19Z","date_published":"2019-03-01T00:00:00Z","citation":{"mla":"Faria, Rui, et al. “Multiple Chromosomal Rearrangements in a Hybrid Zone between Littorina Saxatilis Ecotypes.” Molecular Ecology, vol. 28, no. 6, Wiley, 2019, pp. 1375–93, doi:10.1111/mec.14972.","short":"R. Faria, P. Chaube, H.E. Morales, T. Larsson, A.R. Lemmon, E.M. Lemmon, M. Rafajlović, M. Panova, M. Ravinet, K. Johannesson, A.M. Westram, R.K. Butlin, Molecular Ecology 28 (2019) 1375–1393.","chicago":"Faria, Rui, Pragya Chaube, Hernán E. Morales, Tomas Larsson, Alan R. Lemmon, Emily M. Lemmon, Marina Rafajlović, et al. “Multiple Chromosomal Rearrangements in a Hybrid Zone between Littorina Saxatilis Ecotypes.” Molecular Ecology. Wiley, 2019. https://doi.org/10.1111/mec.14972.","ama":"Faria R, Chaube P, Morales HE, et al. Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. Molecular Ecology. 2019;28(6):1375-1393. doi:10.1111/mec.14972","ista":"Faria R, Chaube P, Morales HE, Larsson T, Lemmon AR, Lemmon EM, Rafajlović M, Panova M, Ravinet M, Johannesson K, Westram AM, Butlin RK. 2019. Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. Molecular Ecology. 28(6), 1375–1393.","ieee":"R. Faria et al., “Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes,” Molecular Ecology, vol. 28, no. 6. Wiley, pp. 1375–1393, 2019.","apa":"Faria, R., Chaube, P., Morales, H. E., Larsson, T., Lemmon, A. R., Lemmon, E. M., … Butlin, R. K. (2019). Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.14972"},"publication":"Molecular Ecology","page":"1375-1393","article_processing_charge":"No","has_accepted_license":"1","day":"01","scopus_import":"1","file":[{"relation":"main_file","file_id":"6097","date_created":"2019-03-11T16:12:54Z","date_updated":"2020-07-14T12:47:19Z","checksum":"f915885756057ec0ca5912a41f46a887","file_name":"2019_MolecularEcology_Faria.pdf","access_level":"open_access","content_type":"application/pdf","file_size":1510715,"creator":"dernst"}],"oa_version":"Published Version","_id":"6095","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 28","title":"Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes","ddc":["570"],"status":"public","issue":"6","abstract":[{"text":"Both classical and recent studies suggest that chromosomal inversion polymorphisms are important in adaptation and speciation. However, biases in discovery and reporting of inversions make it difficult to assess their prevalence and biological importance. Here, we use an approach based on linkage disequilibrium among markers genotyped for samples collected across a transect between contrasting habitats to detect chromosomal rearrangements de novo. We report 17 polymorphic rearrangements in a single locality for the coastal marine snail, Littorina saxatilis. Patterns of diversity in the field and of recombination in controlled crosses provide strong evidence that at least the majority of these rearrangements are inversions. Most show clinal changes in frequency between habitats, suggestive of divergent selection, but only one appears to be fixed for different arrangements in the two habitats. Consistent with widespread evidence for balancing selection on inversion polymorphisms, we argue that a combination of heterosis and divergent selection can explain the observed patterns and should be considered in other systems spanning environmental gradients.","lang":"eng"}],"type":"journal_article"},{"publication_status":"published","publisher":"eLife Sciences Publications","department":[{"_id":"NiBa"}],"year":"2019","date_updated":"2023-08-25T08:59:38Z","date_created":"2019-04-07T21:59:15Z","volume":8,"author":[{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"},{"first_name":"Joachim","last_name":"Hermisson","full_name":"Hermisson, Joachim"},{"first_name":"Magnus","last_name":"Nordborg","full_name":"Nordborg, Magnus"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/body-height-bmi-disease-risk-co/","description":"News on IST Homepage","relation":"press_release"}]},"article_number":"e45380","file_date_updated":"2020-07-14T12:47:24Z","isi":1,"quality_controlled":"1","external_id":{"isi":["000461988300001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.7554/eLife.45380","month":"03","publication_identifier":{"eissn":["2050084X"]},"title":"Why structure matters","ddc":["570"],"status":"public","intvolume":" 8","_id":"6230","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"content_type":"application/pdf","file_size":298466,"creator":"dernst","file_name":"2019_eLife_Barton.pdf","access_level":"open_access","date_created":"2019-04-11T11:43:38Z","date_updated":"2020-07-14T12:47:24Z","checksum":"130d7544b57df4a6787e1263c2d7ea43","relation":"main_file","file_id":"6293"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Great care is needed when interpreting claims about the genetic basis of human variation based on data from genome-wide association studies.","lang":"eng"}],"publication":"eLife","citation":{"apa":"Barton, N. H., Hermisson, J., & Nordborg, M. (2019). Why structure matters. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.45380","ieee":"N. H. Barton, J. Hermisson, and M. Nordborg, “Why structure matters,” eLife, vol. 8. eLife Sciences Publications, 2019.","ista":"Barton NH, Hermisson J, Nordborg M. 2019. Why structure matters. eLife. 8, e45380.","ama":"Barton NH, Hermisson J, Nordborg M. Why structure matters. eLife. 2019;8. doi:10.7554/eLife.45380","chicago":"Barton, Nicholas H, Joachim Hermisson, and Magnus Nordborg. “Why Structure Matters.” ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/eLife.45380.","short":"N.H. Barton, J. Hermisson, M. Nordborg, ELife 8 (2019).","mla":"Barton, Nicholas H., et al. “Why Structure Matters.” ELife, vol. 8, e45380, eLife Sciences Publications, 2019, doi:10.7554/eLife.45380."},"date_published":"2019-03-21T00:00:00Z","scopus_import":"1","day":"21","article_processing_charge":"No","has_accepted_license":"1"},{"month":"04","publication_identifier":{"eissn":["1365294X"]},"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000474808300001"]},"isi":1,"quality_controlled":"1","doi":"10.1111/mec.15048","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:47:31Z","year":"2019","publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Wiley","author":[{"full_name":"Field, David","first_name":"David","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478"},{"full_name":"Fraisse, Christelle","last_name":"Fraisse","first_name":"Christelle","orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2019-05-19T21:59:15Z","date_updated":"2023-08-25T10:37:30Z","volume":28,"scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"No","publication":"Molecular ecology","citation":{"mla":"Field, David, and Christelle Fraisse. “Breaking down Barriers in Morning Glories.” Molecular Ecology, vol. 28, no. 7, Wiley, 2019, pp. 1579–81, doi:10.1111/mec.15048.","short":"D. Field, C. Fraisse, Molecular Ecology 28 (2019) 1579–1581.","chicago":"Field, David, and Christelle Fraisse. “Breaking down Barriers in Morning Glories.” Molecular Ecology. Wiley, 2019. https://doi.org/10.1111/mec.15048.","ama":"Field D, Fraisse C. Breaking down barriers in morning glories. Molecular ecology. 2019;28(7):1579-1581. doi:10.1111/mec.15048","ista":"Field D, Fraisse C. 2019. Breaking down barriers in morning glories. Molecular ecology. 28(7), 1579–1581.","ieee":"D. Field and C. Fraisse, “Breaking down barriers in morning glories,” Molecular ecology, vol. 28, no. 7. Wiley, pp. 1579–1581, 2019.","apa":"Field, D., & Fraisse, C. (2019). Breaking down barriers in morning glories. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.15048"},"page":"1579-1581","date_published":"2019-04-01T00:00:00Z","type":"journal_article","abstract":[{"text":"One of the most striking and consistent results in speciation genomics is the heterogeneous divergence observed across the genomes of closely related species. This pattern was initially attributed to different levels of gene exchange—with divergence preserved at loci generating a barrier to gene flow but homogenized at unlinked neutral loci. Although there is evidence to support this model, it is now recognized that interpreting patterns of divergence across genomes is not so straightforward. One \r\nproblem is that heterogenous divergence between populations can also be generated by other processes (e.g. recurrent selective sweeps or background selection) without any involvement of differential gene flow. Thus, integrated studies that identify which loci are likely subject to divergent selection are required to shed light on the interplay between selection and gene flow during the early phases of speciation. In this issue of Molecular Ecology, Rifkin et al. (2019) confront this challenge using a pair of sister morning glory species. They wisely design their sampling to take the geographic context of individuals into account, including geographically isolated (allopatric) and co‐occurring (sympatric) populations. This enabled them to show that individuals are phenotypically less differentiated in sympatry. They also found that the loci that resist introgression are enriched for those most differentiated in allopatry and loci that exhibit signals of divergent selection. One great strength of the \r\nstudy is the combination of methods from population genetics and molecular evolution, including the development of a model to simultaneously infer admixture proportions and selfing rates.","lang":"eng"}],"issue":"7","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6466","title":"Breaking down barriers in morning glories","status":"public","ddc":["580","576"],"intvolume":" 28","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2019_MolecularEcology_Field.pdf","creator":"dernst","content_type":"application/pdf","file_size":367711,"file_id":"6472","relation":"main_file","checksum":"521e3aff3e9263ddf2ffbfe0b6157715","date_created":"2019-05-20T11:49:06Z","date_updated":"2020-07-14T12:47:31Z"}]},{"ec_funded":1,"article_number":"0881","volume":15,"date_updated":"2023-08-25T10:34:41Z","date_created":"2019-05-19T21:59:15Z","related_material":{"record":[{"id":"9798","relation":"research_data","status":"public"},{"status":"public","relation":"research_data","id":"9799"}],"link":[{"relation":"supplementary_material","url":"https://dx.doi.org/10.6084/m9.figshare.c.4461008"}]},"author":[{"last_name":"Fraisse","first_name":"Christelle","orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","full_name":"Fraisse, Christelle"},{"full_name":"Welch, John J.","last_name":"Welch","first_name":"John J."}],"publisher":"Royal Society of London","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"publication_status":"published","pmid":1,"year":"2019","publication_identifier":{"eissn":["1744957X"],"issn":["17449561"]},"month":"04","language":[{"iso":"eng"}],"doi":"10.1098/rsbl.2018.0881","project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"external_id":{"pmid":["31014191"],"isi":["000465405300010"]},"oa":1,"main_file_link":[{"url":"https://doi.org/10.1098/rsbl.2018.0881","open_access":"1"}],"issue":"4","abstract":[{"text":"Fitness interactions between mutations can influence a population’s evolution in many different ways. While epistatic effects are difficult to measure precisely, important information is captured by the mean and variance of log fitnesses for individuals carrying different numbers of mutations. We derive predictions for these quantities from a class of simple fitness landscapes, based on models of optimizing selection on quantitative traits. We also explore extensions to the models, including modular pleiotropy, variable effect sizes, mutational bias and maladaptation of the wild type. We illustrate our approach by reanalysing a large dataset of mutant effects in a yeast snoRNA (small nucleolar RNA). Though characterized by some large epistatic effects, these data give a good overall fit to the non-epistatic null model, suggesting that epistasis might have limited influence on the evolutionary dynamics in this system. We also show how the amount of epistasis depends on both the underlying fitness landscape and the distribution of mutations, and so is expected to vary in consistent ways between new mutations, standing variation and fixed mutations.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","intvolume":" 15","title":"The distribution of epistasis on simple fitness landscapes","status":"public","_id":"6467","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","day":"03","scopus_import":"1","date_published":"2019-04-03T00:00:00Z","article_type":"original","citation":{"mla":"Fraisse, Christelle, and John J. Welch. “The Distribution of Epistasis on Simple Fitness Landscapes.” Biology Letters, vol. 15, no. 4, 0881, Royal Society of London, 2019, doi:10.1098/rsbl.2018.0881.","short":"C. Fraisse, J.J. Welch, Biology Letters 15 (2019).","chicago":"Fraisse, Christelle, and John J. Welch. “The Distribution of Epistasis on Simple Fitness Landscapes.” Biology Letters. Royal Society of London, 2019. https://doi.org/10.1098/rsbl.2018.0881.","ama":"Fraisse C, Welch JJ. The distribution of epistasis on simple fitness landscapes. Biology Letters. 2019;15(4). doi:10.1098/rsbl.2018.0881","ista":"Fraisse C, Welch JJ. 2019. The distribution of epistasis on simple fitness landscapes. Biology Letters. 15(4), 0881.","ieee":"C. Fraisse and J. J. Welch, “The distribution of epistasis on simple fitness landscapes,” Biology Letters, vol. 15, no. 4. Royal Society of London, 2019.","apa":"Fraisse, C., & Welch, J. J. (2019). The distribution of epistasis on simple fitness landscapes. Biology Letters. Royal Society of London. https://doi.org/10.1098/rsbl.2018.0881"},"publication":"Biology Letters"},{"file_date_updated":"2020-07-14T12:47:34Z","ec_funded":1,"publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Wiley","year":"2019","acknowledgement":"The authors would like to thank to Tiago Paixao and Nick Barton for useful comments and advice.","date_updated":"2023-08-29T06:31:14Z","date_created":"2019-07-14T21:59:20Z","volume":73,"author":[{"full_name":"Trubenova, Barbora","first_name":"Barbora","last_name":"Trubenova","id":"42302D54-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6873-2967"},{"first_name":"Martin ","last_name":"Krejca","full_name":"Krejca, Martin "},{"full_name":"Lehre, Per Kristian","last_name":"Lehre","first_name":"Per Kristian"},{"last_name":"Kötzing","first_name":"Timo","full_name":"Kötzing, Timo"}],"month":"07","isi":1,"quality_controlled":"1","project":[{"grant_number":"704172","_id":"25AEDD42-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Rate of Adaptation in Changing Environment"},{"grant_number":"618091","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation"}],"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"isi":["000474031600001"]},"language":[{"iso":"eng"}],"doi":"10.1111/evo.13784","type":"journal_article","abstract":[{"text":"The environment changes constantly at various time scales and, in order to survive, species need to keep adapting. Whether these species succeed in avoiding extinction is a major evolutionary question. Using a multilocus evolutionary model of a mutation‐limited population adapting under strong selection, we investigate the effects of the frequency of environmental fluctuations on adaptation. Our results rely on an “adaptive‐walk” approximation and use mathematical methods from evolutionary computation theory to investigate the interplay between fluctuation frequency, the similarity of environments, and the number of loci contributing to adaptation. First, we assume a linear additive fitness function, but later generalize our results to include several types of epistasis. We show that frequent environmental changes prevent populations from reaching a fitness peak, but they may also prevent the large fitness loss that occurs after a single environmental change. Thus, the population can survive, although not thrive, in a wide range of conditions. Furthermore, we show that in a frequently changing environment, the similarity of threats that a population faces affects the level of adaptation that it is able to achieve. We check and supplement our analytical results with simulations.","lang":"eng"}],"issue":"7","status":"public","ddc":["576"],"title":"Surfing on the seascape: Adaptation in a changing environment","intvolume":" 73","_id":"6637","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":815416,"creator":"apreinsp","access_level":"open_access","file_name":"2019_Evolution_TrubenovaBarbora.pdf","checksum":"9831ca65def2d62498c7b08338b6d237","date_updated":"2020-07-14T12:47:34Z","date_created":"2019-07-16T06:08:31Z","relation":"main_file","file_id":"6643"}],"scopus_import":"1","day":"01","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","article_type":"original","page":"1356-1374","publication":"Evolution","citation":{"mla":"Trubenova, Barbora, et al. “Surfing on the Seascape: Adaptation in a Changing Environment.” Evolution, vol. 73, no. 7, Wiley, 2019, pp. 1356–74, doi:10.1111/evo.13784.","short":"B. Trubenova, M. Krejca, P.K. Lehre, T. Kötzing, Evolution 73 (2019) 1356–1374.","chicago":"Trubenova, Barbora, Martin Krejca, Per Kristian Lehre, and Timo Kötzing. “Surfing on the Seascape: Adaptation in a Changing Environment.” Evolution. Wiley, 2019. https://doi.org/10.1111/evo.13784.","ama":"Trubenova B, Krejca M, Lehre PK, Kötzing T. Surfing on the seascape: Adaptation in a changing environment. Evolution. 2019;73(7):1356-1374. doi:10.1111/evo.13784","ista":"Trubenova B, Krejca M, Lehre PK, Kötzing T. 2019. Surfing on the seascape: Adaptation in a changing environment. Evolution. 73(7), 1356–1374.","ieee":"B. Trubenova, M. Krejca, P. K. Lehre, and T. Kötzing, “Surfing on the seascape: Adaptation in a changing environment,” Evolution, vol. 73, no. 7. Wiley, pp. 1356–1374, 2019.","apa":"Trubenova, B., Krejca, M., Lehre, P. K., & Kötzing, T. (2019). Surfing on the seascape: Adaptation in a changing environment. Evolution. Wiley. https://doi.org/10.1111/evo.13784"},"date_published":"2019-07-01T00:00:00Z"},{"publication_identifier":{"eissn":["1558-5646"],"issn":["0014-3820"]},"month":"09","isi":1,"quality_controlled":"1","external_id":{"isi":["000481300600001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1111/evo.13812","file_date_updated":"2020-07-14T12:47:37Z","department":[{"_id":"NiBa"}],"publisher":"Wiley","publication_status":"published","year":"2019","volume":73,"date_created":"2019-07-25T09:08:28Z","date_updated":"2023-08-29T06:43:58Z","related_material":{"record":[{"status":"public","relation":"research_data","id":"9802"}]},"author":[{"full_name":"Sachdeva, Himani","id":"42377A0A-F248-11E8-B48F-1D18A9856A87","first_name":"Himani","last_name":"Sachdeva"}],"scopus_import":"1","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"01","page":"1729-1745","citation":{"short":"H. Sachdeva, Evolution 73 (2019) 1729–1745.","mla":"Sachdeva, Himani. “Effect of Partial Selfing and Polygenic Selection on Establishment in a New Habitat.” Evolution, vol. 73, no. 9, Wiley, 2019, pp. 1729–45, doi:10.1111/evo.13812.","chicago":"Sachdeva, Himani. “Effect of Partial Selfing and Polygenic Selection on Establishment in a New Habitat.” Evolution. Wiley, 2019. https://doi.org/10.1111/evo.13812.","ama":"Sachdeva H. Effect of partial selfing and polygenic selection on establishment in a new habitat. Evolution. 2019;73(9):1729-1745. doi:10.1111/evo.13812","apa":"Sachdeva, H. (2019). Effect of partial selfing and polygenic selection on establishment in a new habitat. Evolution. Wiley. https://doi.org/10.1111/evo.13812","ieee":"H. Sachdeva, “Effect of partial selfing and polygenic selection on establishment in a new habitat,” Evolution, vol. 73, no. 9. Wiley, pp. 1729–1745, 2019.","ista":"Sachdeva H. 2019. Effect of partial selfing and polygenic selection on establishment in a new habitat. Evolution. 73(9), 1729–1745."},"publication":"Evolution","date_published":"2019-09-01T00:00:00Z","type":"journal_article","issue":"9","abstract":[{"text":"This paper analyzes how partial selfing in a large source population influences its ability to colonize a new habitat via the introduction of a few founder individuals. Founders experience inbreeding depression due to partially recessive deleterious alleles as well as maladaptation to the new environment due to selection on a large number of additive loci. I first introduce a simplified version of the Inbreeding History Model (Kelly, 2007) in order to characterize mutation‐selection balance in a large, partially selfing source population under selection involving multiple non‐identical loci. I then use individual‐based simulations to study the eco‐evolutionary dynamics of founders establishing in the new habitat under a model of hard selection. The study explores how selfing rate shapes establishment probabilities of founders via effects on both inbreeding depression and adaptability to the new environment, and also distinguishes the effects of selfing on the initial fitness of founders from its effects on the long‐term adaptive response of the populations they found. A high rate of (but not complete) selfing is found to aid establishment over a wide range of parameters, even in the absence of mate limitation. The sensitivity of the results to assumptions about the nature of polygenic selection are discussed.","lang":"eng"}],"intvolume":" 73","title":"Effect of partial selfing and polygenic selection on establishment in a new habitat","ddc":["576"],"status":"public","_id":"6680","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"file_id":"6881","relation":"main_file","checksum":"772ce7035965153959b946a1033de1ca","date_updated":"2020-07-14T12:47:37Z","date_created":"2019-09-17T10:56:27Z","access_level":"open_access","file_name":"2019_Evolution_Sachdeva.pdf","creator":"kschuh","content_type":"application/pdf","file_size":937573}],"oa_version":"Published Version"},{"type":"research_data_reference","abstract":[{"lang":"eng","text":"Evolutionary studies are often limited by missing data that are critical to understanding the history of selection. Selection experiments, which reproduce rapid evolution under controlled conditions, are excellent tools to study how genomes evolve under selection. Here we present a genomic dissection of the Longshanks selection experiment, in which mice were selectively bred over 20 generations for longer tibiae relative to body mass, resulting in 13% longer tibiae in two replicates. We synthesized evolutionary theory, genome sequences and molecular genetics to understand the selection response and found that it involved both polygenic adaptation and discrete loci of major effect, with the strongest loci tending to be selected in parallel between replicates. We show that selection may favor de-repression of bone growth through inactivating two limb enhancers of an inhibitor, Nkx3-2. Our integrative genomic analyses thus show that it is possible to connect individual base-pair changes to the overall selection response."}],"title":"Data from: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice","status":"public","publisher":"Dryad","department":[{"_id":"NiBa"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9804","year":"2019","date_updated":"2023-08-29T06:41:51Z","date_created":"2021-08-06T11:52:54Z","oa_version":"Published Version","author":[{"full_name":"Castro, João Pl","last_name":"Castro","first_name":"João Pl"},{"first_name":"Michelle N.","last_name":"Yancoskie","full_name":"Yancoskie, Michelle N."},{"last_name":"Marchini","first_name":"Marta","full_name":"Marchini, Marta"},{"full_name":"Belohlavy, Stefanie","orcid":"0000-0002-9849-498X","id":"43FE426A-F248-11E8-B48F-1D18A9856A87","last_name":"Belohlavy","first_name":"Stefanie"},{"full_name":"Hiramatsu, Layla","first_name":"Layla","last_name":"Hiramatsu"},{"full_name":"Kučka, Marek","first_name":"Marek","last_name":"Kučka"},{"last_name":"Beluch","first_name":"William H.","full_name":"Beluch, William H."},{"first_name":"Ronald","last_name":"Naumann","full_name":"Naumann, Ronald"},{"full_name":"Skuplik, Isabella","first_name":"Isabella","last_name":"Skuplik"},{"first_name":"John","last_name":"Cobb","full_name":"Cobb, John"},{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"last_name":"Rolian","first_name":"Campbell","full_name":"Rolian, Campbell"},{"first_name":"Yingguang Frank","last_name":"Chan","full_name":"Chan, Yingguang Frank"}],"related_material":{"record":[{"id":"6713","relation":"used_in_publication","status":"public"}]},"day":"06","month":"06","article_processing_charge":"No","citation":{"ista":"Castro JP, Yancoskie MN, Marchini M, Belohlavy S, Hiramatsu L, Kučka M, Beluch WH, Naumann R, Skuplik I, Cobb J, Barton NH, Rolian C, Chan YF. 2019. Data from: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice, Dryad, 10.5061/dryad.0q2h6tk.","ieee":"J. P. Castro et al., “Data from: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice.” Dryad, 2019.","apa":"Castro, J. P., Yancoskie, M. N., Marchini, M., Belohlavy, S., Hiramatsu, L., Kučka, M., … Chan, Y. F. (2019). Data from: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice. Dryad. https://doi.org/10.5061/dryad.0q2h6tk","ama":"Castro JP, Yancoskie MN, Marchini M, et al. Data from: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice. 2019. doi:10.5061/dryad.0q2h6tk","chicago":"Castro, João Pl, Michelle N. Yancoskie, Marta Marchini, Stefanie Belohlavy, Layla Hiramatsu, Marek Kučka, William H. Beluch, et al. “Data from: An Integrative Genomic Analysis of the Longshanks Selection Experiment for Longer Limbs in Mice.” Dryad, 2019. https://doi.org/10.5061/dryad.0q2h6tk.","mla":"Castro, João Pl, et al. Data from: An Integrative Genomic Analysis of the Longshanks Selection Experiment for Longer Limbs in Mice. Dryad, 2019, doi:10.5061/dryad.0q2h6tk.","short":"J.P. Castro, M.N. Yancoskie, M. Marchini, S. Belohlavy, L. Hiramatsu, M. Kučka, W.H. Beluch, R. Naumann, I. Skuplik, J. Cobb, N.H. Barton, C. Rolian, Y.F. Chan, (2019)."},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.0q2h6tk"}],"date_published":"2019-06-06T00:00:00Z","doi":"10.5061/dryad.0q2h6tk"},{"article_processing_charge":"No","day":"16","month":"07","citation":{"chicago":"Sachdeva, Himani. “Data from: Effect of Partial Selfing and Polygenic Selection on Establishment in a New Habitat.” Dryad, 2019. https://doi.org/10.5061/dryad.8tp0900.","mla":"Sachdeva, Himani. Data from: Effect of Partial Selfing and Polygenic Selection on Establishment in a New Habitat. Dryad, 2019, doi:10.5061/dryad.8tp0900.","short":"H. Sachdeva, (2019).","ista":"Sachdeva H. 2019. Data from: Effect of partial selfing and polygenic selection on establishment in a new habitat, Dryad, 10.5061/dryad.8tp0900.","apa":"Sachdeva, H. (2019). Data from: Effect of partial selfing and polygenic selection on establishment in a new habitat. Dryad. https://doi.org/10.5061/dryad.8tp0900","ieee":"H. Sachdeva, “Data from: Effect of partial selfing and polygenic selection on establishment in a new habitat.” Dryad, 2019.","ama":"Sachdeva H. Data from: Effect of partial selfing and polygenic selection on establishment in a new habitat. 2019. doi:10.5061/dryad.8tp0900"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.8tp0900"}],"oa":1,"doi":"10.5061/dryad.8tp0900","date_published":"2019-07-16T00:00:00Z","type":"research_data_reference","abstract":[{"lang":"eng","text":"This paper analyzes how partial selfing in a large source population influences its ability to colonize a new habitat via the introduction of a few founder individuals. Founders experience inbreeding depression due to partially recessive deleterious alleles as well as maladaptation to the new environment due to selection on a large number of additive loci. I first introduce a simplified version of the Inbreeding History Model (Kelly, 2007) in order to characterize mutation-selection balance in a large, partially selfing source population under selection involving multiple non-identical loci. I then use individual-based simulations to study the eco-evolutionary dynamics of founders establishing in the new habitat under a model of hard selection. The study explores how selfing rate shapes establishment probabilities of founders via effects on both inbreeding depression and adaptability to the new environment, and also distinguishes the effects of selfing on the initial fitness of founders from its effects on the long-term adaptive response of the populations they found. A high rate of (but not complete) selfing is found to aid establishment over a wide range of parameters, even in the absence of mate limitation. The sensitivity of the results to assumptions about the nature of polygenic selection are discussed."}],"_id":"9802","year":"2019","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","department":[{"_id":"NiBa"}],"publisher":"Dryad","title":"Data from: Effect of partial selfing and polygenic selection on establishment in a new habitat","status":"public","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"6680"}]},"author":[{"full_name":"Sachdeva, Himani","id":"42377A0A-F248-11E8-B48F-1D18A9856A87","last_name":"Sachdeva","first_name":"Himani"}],"oa_version":"Published Version","date_updated":"2023-08-29T06:43:57Z","date_created":"2021-08-06T11:45:11Z"},{"ec_funded":1,"file_date_updated":"2020-07-14T12:47:40Z","publisher":"Wiley","department":[{"_id":"NiBa"}],"publication_status":"published","year":"2019","volume":9,"date_created":"2019-08-11T21:59:24Z","date_updated":"2023-08-29T07:03:10Z","author":[{"full_name":"Trubenova, Barbora","id":"42302D54-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6873-2967","first_name":"Barbora","last_name":"Trubenova"},{"full_name":"Hager, Reinmar","first_name":"Reinmar","last_name":"Hager"}],"publication_identifier":{"eissn":["20457758"]},"month":"09","project":[{"_id":"25AEDD42-B435-11E9-9278-68D0E5697425","grant_number":"704172","call_identifier":"H2020","name":"Rate of Adaptation in Changing Environment"}],"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000479973400001"]},"language":[{"iso":"eng"}],"doi":"10.1002/ece3.5484","type":"journal_article","issue":"17","abstract":[{"lang":"eng","text":"The green‐beard effect is one proposed mechanism predicted to underpin the evolu‐tion of altruistic behavior. It relies on the recognition and the selective help of altruists to each other in order to promote and sustain altruistic behavior. However, this mechanism has often been dismissed as unlikely or uncommon, as it is assumed that both the signaling trait and altruistic trait need to be encoded by the same gene or through tightly linked genes. Here, we use models of indirect genetic effects (IGEs) to find the minimum correlation between the signaling and altruistic trait required for the evolution of the latter. We show that this correlation threshold depends on the strength of the interaction (influence of the green beard on the expression of the altruistic trait), as well as the costs and benefits of the altruistic behavior. We further show that this correlation does not necessarily have to be high and support our analytical results by simulations."}],"intvolume":" 9","title":"Green beards in the light of indirect genetic effects","ddc":["576"],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6795","file":[{"relation":"main_file","file_id":"6799","checksum":"adcb70af4901977d95b8747eeee01bd7","date_updated":"2020-07-14T12:47:40Z","date_created":"2019-08-12T07:30:30Z","access_level":"open_access","file_name":"2019_EcologyEvolution_Trubenova.pdf","content_type":"application/pdf","file_size":2839636,"creator":"dernst"}],"oa_version":"Published Version","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"01","page":"9597-9608","article_type":"original","citation":{"mla":"Trubenova, Barbora, and Reinmar Hager. “Green Beards in the Light of Indirect Genetic Effects.” Ecology and Evolution, vol. 9, no. 17, Wiley, 2019, pp. 9597–608, doi:10.1002/ece3.5484.","short":"B. Trubenova, R. Hager, Ecology and Evolution 9 (2019) 9597–9608.","chicago":"Trubenova, Barbora, and Reinmar Hager. “Green Beards in the Light of Indirect Genetic Effects.” Ecology and Evolution. Wiley, 2019. https://doi.org/10.1002/ece3.5484.","ama":"Trubenova B, Hager R. Green beards in the light of indirect genetic effects. Ecology and Evolution. 2019;9(17):9597-9608. doi:10.1002/ece3.5484","ista":"Trubenova B, Hager R. 2019. Green beards in the light of indirect genetic effects. Ecology and Evolution. 9(17), 9597–9608.","apa":"Trubenova, B., & Hager, R. (2019). Green beards in the light of indirect genetic effects. Ecology and Evolution. Wiley. https://doi.org/10.1002/ece3.5484","ieee":"B. Trubenova and R. Hager, “Green beards in the light of indirect genetic effects,” Ecology and Evolution, vol. 9, no. 17. Wiley, pp. 9597–9608, 2019."},"publication":"Ecology and Evolution","date_published":"2019-09-01T00:00:00Z"},{"doi":"10.1111/nph.16050","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000481376500001"]},"project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"isi":1,"quality_controlled":"1","publication_identifier":{"eissn":["1469-8137"]},"month":"11","related_material":{"record":[{"id":"9803","status":"public","relation":"research_data"},{"id":"14058","status":"public","relation":"dissertation_contains"}]},"author":[{"first_name":"Gemma","last_name":"Puixeu Sala","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8330-1754","full_name":"Puixeu Sala, Gemma"},{"id":"2C78037E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6118-0541","first_name":"Melinda","last_name":"Pickup","full_name":"Pickup, Melinda"},{"orcid":"0000-0002-4014-8478","first_name":"David","last_name":"Field","full_name":"Field, David"},{"full_name":"Barrett, Spencer C.H.","first_name":"Spencer C.H.","last_name":"Barrett"}],"volume":224,"date_updated":"2023-08-29T07:17:07Z","date_created":"2019-08-25T22:00:51Z","year":"2019","publisher":"Wiley","department":[{"_id":"NiBa"},{"_id":"BeVi"}],"publication_status":"published","ec_funded":1,"file_date_updated":"2020-07-14T12:47:42Z","date_published":"2019-11-01T00:00:00Z","citation":{"short":"G. Puixeu Sala, M. Pickup, D. Field, S.C.H. Barrett, New Phytologist 224 (2019) 1108–1120.","mla":"Puixeu Sala, Gemma, et al. “Variation in Sexual Dimorphism in a Wind-Pollinated Plant: The Influence of Geographical Context and Life-Cycle Dynamics.” New Phytologist, vol. 224, no. 3, Wiley, 2019, pp. 1108–20, doi:10.1111/nph.16050.","chicago":"Puixeu Sala, Gemma, Melinda Pickup, David Field, and Spencer C.H. Barrett. “Variation in Sexual Dimorphism in a Wind-Pollinated Plant: The Influence of Geographical Context and Life-Cycle Dynamics.” New Phytologist. Wiley, 2019. https://doi.org/10.1111/nph.16050.","ama":"Puixeu Sala G, Pickup M, Field D, Barrett SCH. Variation in sexual dimorphism in a wind-pollinated plant: The influence of geographical context and life-cycle dynamics. New Phytologist. 2019;224(3):1108-1120. doi:10.1111/nph.16050","ieee":"G. Puixeu Sala, M. Pickup, D. Field, and S. C. H. Barrett, “Variation in sexual dimorphism in a wind-pollinated plant: The influence of geographical context and life-cycle dynamics,” New Phytologist, vol. 224, no. 3. Wiley, pp. 1108–1120, 2019.","apa":"Puixeu Sala, G., Pickup, M., Field, D., & Barrett, S. C. H. (2019). Variation in sexual dimorphism in a wind-pollinated plant: The influence of geographical context and life-cycle dynamics. New Phytologist. Wiley. https://doi.org/10.1111/nph.16050","ista":"Puixeu Sala G, Pickup M, Field D, Barrett SCH. 2019. Variation in sexual dimorphism in a wind-pollinated plant: The influence of geographical context and life-cycle dynamics. New Phytologist. 224(3), 1108–1120."},"publication":"New Phytologist","page":"1108-1120","article_type":"original","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"01","scopus_import":"1","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"6833","date_updated":"2020-07-14T12:47:42Z","date_created":"2019-08-27T12:44:54Z","checksum":"6370e7567d96b7b562e77d8b89653f80","file_name":"2019_NewPhytologist_Puixeu.pdf","access_level":"open_access","content_type":"application/pdf","file_size":2314016,"creator":"apreinsp"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6831","intvolume":" 224","ddc":["570"],"title":"Variation in sexual dimorphism in a wind-pollinated plant: The influence of geographical context and life-cycle dynamics","status":"public","issue":"3","abstract":[{"text":"* Understanding the mechanisms causing phenotypic differences between females and males has long fascinated evolutionary biologists. An extensive literature exists on animal sexual dimorphism but less information is known about sex differences in plants, particularly the extent of geographical variation in sexual dimorphism and its life‐cycle dynamics.\r\n* Here, we investigated patterns of genetically based sexual dimorphism in vegetative and reproductive traits of a wind‐pollinated dioecious plant, Rumex hastatulus, across three life‐cycle stages using open‐pollinated families from 30 populations spanning the geographic range and chromosomal variation (XY and XY1Y2) of the species.\r\n* The direction and degree of sexual dimorphism was highly variable among populations and life‐cycle stages. Sex‐specific differences in reproductive function explained a significant amount of temporal change in sexual dimorphism. For several traits, geographical variation in sexual dimorphism was associated with bioclimatic parameters, likely due to the differential responses of the sexes to climate. We found no systematic differences in sexual dimorphism between chromosome races.\r\n* Sex‐specific trait differences in dioecious plants largely result from a balance between sexual and natural selection on resource allocation. Our results indicate that abiotic factors associated with geographical context also play a role in modifying sexual dimorphism during the plant life‐cycle.","lang":"eng"}],"type":"journal_article"},{"citation":{"ama":"Puixeu Sala G, Pickup M, Field D, Barrett SCH. Data from: Variation in sexual dimorphism in a wind-pollinated plant: the influence of geographical context and life-cycle dynamics. 2019. doi:10.5061/dryad.n1701c9","apa":"Puixeu Sala, G., Pickup, M., Field, D., & Barrett, S. C. H. (2019). Data from: Variation in sexual dimorphism in a wind-pollinated plant: the influence of geographical context and life-cycle dynamics. Dryad. https://doi.org/10.5061/dryad.n1701c9","ieee":"G. Puixeu Sala, M. Pickup, D. Field, and S. C. H. Barrett, “Data from: Variation in sexual dimorphism in a wind-pollinated plant: the influence of geographical context and life-cycle dynamics.” Dryad, 2019.","ista":"Puixeu Sala G, Pickup M, Field D, Barrett SCH. 2019. Data from: Variation in sexual dimorphism in a wind-pollinated plant: the influence of geographical context and life-cycle dynamics, Dryad, 10.5061/dryad.n1701c9.","short":"G. Puixeu Sala, M. Pickup, D. Field, S.C.H. Barrett, (2019).","mla":"Puixeu Sala, Gemma, et al. Data from: Variation in Sexual Dimorphism in a Wind-Pollinated Plant: The Influence of Geographical Context and Life-Cycle Dynamics. Dryad, 2019, doi:10.5061/dryad.n1701c9.","chicago":"Puixeu Sala, Gemma, Melinda Pickup, David Field, and Spencer C.H. Barrett. “Data from: Variation in Sexual Dimorphism in a Wind-Pollinated Plant: The Influence of Geographical Context and Life-Cycle Dynamics.” Dryad, 2019. https://doi.org/10.5061/dryad.n1701c9."},"main_file_link":[{"url":"https://doi.org/10.5061/dryad.n1701c9","open_access":"1"}],"oa":1,"doi":"10.5061/dryad.n1701c9","date_published":"2019-07-22T00:00:00Z","article_processing_charge":"No","month":"07","day":"22","department":[{"_id":"NiBa"},{"_id":"BeVi"}],"publisher":"Dryad","status":"public","title":"Data from: Variation in sexual dimorphism in a wind-pollinated plant: the influence of geographical context and life-cycle dynamics","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9803","year":"2019","oa_version":"Published Version","date_created":"2021-08-06T11:48:42Z","date_updated":"2023-08-29T07:17:07Z","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"14058"},{"id":"6831","relation":"used_in_publication","status":"public"}]},"author":[{"id":"33AB266C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8330-1754","first_name":"Gemma","last_name":"Puixeu Sala","full_name":"Puixeu Sala, Gemma"},{"last_name":"Pickup","first_name":"Melinda","orcid":"0000-0001-6118-0541","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","full_name":"Pickup, Melinda"},{"full_name":"Field, David","first_name":"David","last_name":"Field"},{"full_name":"Barrett, Spencer C.H.","last_name":"Barrett","first_name":"Spencer C.H."}],"type":"research_data_reference","abstract":[{"lang":"eng","text":"Understanding the mechanisms causing phenotypic differences between females and males has long fascinated evolutionary biologists. An extensive literature exists on animal sexual dimorphism but less is known about sex differences in plants, particularly the extent of geographical variation in sexual dimorphism and its life-cycle dynamics. Here, we investigate patterns of genetically-based sexual dimorphism in vegetative and reproductive traits of a wind-pollinated dioecious plant, Rumex hastatulus, across three life-cycle stages using open-pollinated families from 30 populations spanning the geographic range and chromosomal variation (XY and XY1Y2) of the species. The direction and degree of sexual dimorphism was highly variable among populations and life-cycle stages. Sex-specific differences in reproductive function explained a significant amount of temporal change in sexual dimorphism. For several traits, geographical variation in sexual dimorphism was associated with bioclimatic parameters, likely due to the differential responses of the sexes to climate. We found no systematic differences in sexual dimorphism between chromosome races. Sex-specific trait differences in dioecious plants largely result from a balance between sexual and natural selection on resource allocation. Our results indicate that abiotic factors associated with geographical context also play a role in modifying sexual dimorphism during the plant life cycle."}]},{"publication_identifier":{"issn":["1527-8204"],"eissn":["1545-293X"]},"month":"07","doi":"10.1146/annurev-genom-083115-022316","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000485148400020"],"pmid":["31283361"]},"quality_controlled":"1","isi":1,"file_date_updated":"2020-07-14T12:47:42Z","author":[{"full_name":"Sella, Guy","first_name":"Guy","last_name":"Sella"},{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"}],"volume":20,"date_updated":"2023-08-29T07:49:38Z","date_created":"2019-09-07T14:28:29Z","pmid":1,"year":"2019","publisher":"Annual Reviews","department":[{"_id":"NiBa"}],"publication_status":"published","article_processing_charge":"No","has_accepted_license":"1","day":"05","scopus_import":"1","date_published":"2019-07-05T00:00:00Z","citation":{"chicago":"Sella, Guy, and Nicholas H Barton. “Thinking about the Evolution of Complex Traits in the Era of Genome-Wide Association Studies.” Annual Review of Genomics and Human Genetics. Annual Reviews, 2019. https://doi.org/10.1146/annurev-genom-083115-022316.","mla":"Sella, Guy, and Nicholas H. Barton. “Thinking about the Evolution of Complex Traits in the Era of Genome-Wide Association Studies.” Annual Review of Genomics and Human Genetics, vol. 20, Annual Reviews, 2019, pp. 461–93, doi:10.1146/annurev-genom-083115-022316.","short":"G. Sella, N.H. Barton, Annual Review of Genomics and Human Genetics 20 (2019) 461–493.","ista":"Sella G, Barton NH. 2019. Thinking about the evolution of complex traits in the era of genome-wide association studies. Annual Review of Genomics and Human Genetics. 20, 461–493.","apa":"Sella, G., & Barton, N. H. (2019). Thinking about the evolution of complex traits in the era of genome-wide association studies. Annual Review of Genomics and Human Genetics. Annual Reviews. https://doi.org/10.1146/annurev-genom-083115-022316","ieee":"G. Sella and N. H. Barton, “Thinking about the evolution of complex traits in the era of genome-wide association studies,” Annual Review of Genomics and Human Genetics, vol. 20. Annual Reviews, pp. 461–493, 2019.","ama":"Sella G, Barton NH. Thinking about the evolution of complex traits in the era of genome-wide association studies. Annual Review of Genomics and Human Genetics. 2019;20:461-493. doi:10.1146/annurev-genom-083115-022316"},"publication":"Annual Review of Genomics and Human Genetics","page":"461-493","abstract":[{"text":"Many traits of interest are highly heritable and genetically complex, meaning that much of the variation they exhibit arises from differences at numerous loci in the genome. Complex traits and their evolution have been studied for more than a century, but only in the last decade have genome-wide association studies (GWASs) in humans begun to reveal their genetic basis. Here, we bring these threads of research together to ask how findings from GWASs can further our understanding of the processes that give rise to heritable variation in complex traits and of the genetic basis of complex trait evolution in response to changing selection pressures (i.e., of polygenic adaptation). Conversely, we ask how evolutionary thinking helps us to interpret findings from GWASs and informs related efforts of practical importance.","lang":"eng"}],"type":"journal_article","file":[{"file_id":"6862","relation":"main_file","checksum":"23d3978cf4739a89ce2c3e779f9305ca","date_updated":"2020-07-14T12:47:42Z","date_created":"2019-09-09T07:22:12Z","access_level":"open_access","file_name":"2019_AnnualReview_Sella.pdf","creator":"dernst","content_type":"application/pdf","file_size":411491}],"oa_version":"Published Version","_id":"6855","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 20","ddc":["576"],"status":"public","title":"Thinking about the evolution of complex traits in the era of genome-wide association studies"},{"year":"2019","publication_status":"published","publisher":"Oxford University Press","department":[{"_id":"NiBa"}],"author":[{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"}],"date_created":"2019-09-07T14:43:02Z","date_updated":"2023-08-29T07:51:09Z","volume":6,"file_date_updated":"2020-10-02T09:16:44Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000467957400025"]},"oa":1,"isi":1,"quality_controlled":"1","doi":"10.1093/nsr/nwy113","language":[{"iso":"eng"}],"month":"03","publication_identifier":{"issn":["2095-5138"],"eissn":["2053-714X"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6858","status":"public","ddc":["570"],"title":"Is speciation driven by cycles of mixing and isolation?","intvolume":" 6","file":[{"date_created":"2020-10-02T09:16:44Z","date_updated":"2020-10-02T09:16:44Z","checksum":"571d60fa21a568607d1fd04e119da88c","success":1,"relation":"main_file","file_id":"8595","file_size":106463,"content_type":"application/pdf","creator":"dernst","file_name":"2019_NSR_Barton.pdf","access_level":"open_access"}],"oa_version":"Published Version","type":"journal_article","issue":"2","publication":"National Science Review","citation":{"short":"N.H. Barton, National Science Review 6 (2019) 291–292.","mla":"Barton, Nicholas H. “Is Speciation Driven by Cycles of Mixing and Isolation?” National Science Review, vol. 6, no. 2, Oxford University Press, 2019, pp. 291–92, doi:10.1093/nsr/nwy113.","chicago":"Barton, Nicholas H. “Is Speciation Driven by Cycles of Mixing and Isolation?” National Science Review. Oxford University Press, 2019. https://doi.org/10.1093/nsr/nwy113.","ama":"Barton NH. Is speciation driven by cycles of mixing and isolation? National Science Review. 2019;6(2):291-292. doi:10.1093/nsr/nwy113","ieee":"N. H. Barton, “Is speciation driven by cycles of mixing and isolation?,” National Science Review, vol. 6, no. 2. Oxford University Press, pp. 291–292, 2019.","apa":"Barton, N. H. (2019). Is speciation driven by cycles of mixing and isolation? National Science Review. Oxford University Press. https://doi.org/10.1093/nsr/nwy113","ista":"Barton NH. 2019. Is speciation driven by cycles of mixing and isolation? National Science Review. 6(2), 291–292."},"article_type":"review","page":"291-292","date_published":"2019-03-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","has_accepted_license":"1"},{"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000489502000001"]},"language":[{"iso":"eng"}],"doi":"10.1002/bies.201900151","month":"11","publication_identifier":{"eissn":["1521-1878"]},"publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Wiley","year":"2019","date_created":"2019-09-07T14:40:03Z","date_updated":"2023-08-30T06:56:26Z","volume":41,"author":[{"full_name":"Giese, B","last_name":"Giese","first_name":"B"},{"full_name":"Friess, J L","last_name":"Friess","first_name":"J L"},{"last_name":"Schetelig","first_name":"M F ","full_name":"Schetelig, M F "},{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"first_name":"Philip","last_name":"Messer","full_name":"Messer, Philip"},{"first_name":"Florence","last_name":"Debarre","full_name":"Debarre, Florence"},{"full_name":"Meimberg, H","first_name":"H","last_name":"Meimberg"},{"last_name":"Windbichler","first_name":"N","full_name":"Windbichler, N"},{"full_name":"Boete, C","first_name":"C","last_name":"Boete"}],"article_number":"1900151","file_date_updated":"2020-07-14T12:47:42Z","article_type":"original","publication":"BioEssays","citation":{"chicago":"Giese, B, J L Friess, M F Schetelig, Nicholas H Barton, Philip Messer, Florence Debarre, H Meimberg, N Windbichler, and C Boete. “Gene Drives: Dynamics and Regulatory Matters – A Report from the Workshop ‘Evaluation of Spatial and Temporal Control of Gene Drives’, 4 – 5 April 2019, Vienna.” BioEssays. Wiley, 2019. https://doi.org/10.1002/bies.201900151.","mla":"Giese, B., et al. “Gene Drives: Dynamics and Regulatory Matters – A Report from the Workshop ‘Evaluation of Spatial and Temporal Control of Gene Drives’, 4 – 5 April 2019, Vienna.” BioEssays, vol. 41, no. 11, 1900151, Wiley, 2019, doi:10.1002/bies.201900151.","short":"B. Giese, J.L. Friess, M.F. Schetelig, N.H. Barton, P. Messer, F. Debarre, H. Meimberg, N. Windbichler, C. Boete, BioEssays 41 (2019).","ista":"Giese B, Friess JL, Schetelig MF, Barton NH, Messer P, Debarre F, Meimberg H, Windbichler N, Boete C. 2019. Gene Drives: Dynamics and regulatory matters – A report from the workshop “Evaluation of spatial and temporal control of Gene Drives”, 4 – 5 April 2019, Vienna. BioEssays. 41(11), 1900151.","ieee":"B. Giese et al., “Gene Drives: Dynamics and regulatory matters – A report from the workshop ‘Evaluation of spatial and temporal control of Gene Drives’, 4 – 5 April 2019, Vienna,” BioEssays, vol. 41, no. 11. Wiley, 2019.","apa":"Giese, B., Friess, J. L., Schetelig, M. F., Barton, N. H., Messer, P., Debarre, F., … Boete, C. (2019). Gene Drives: Dynamics and regulatory matters – A report from the workshop “Evaluation of spatial and temporal control of Gene Drives”, 4 – 5 April 2019, Vienna. BioEssays. Wiley. https://doi.org/10.1002/bies.201900151","ama":"Giese B, Friess JL, Schetelig MF, et al. Gene Drives: Dynamics and regulatory matters – A report from the workshop “Evaluation of spatial and temporal control of Gene Drives”, 4 – 5 April 2019, Vienna. BioEssays. 2019;41(11). doi:10.1002/bies.201900151"},"date_published":"2019-11-01T00:00:00Z","scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"No","title":"Gene Drives: Dynamics and regulatory matters – A report from the workshop “Evaluation of spatial and temporal control of Gene Drives”, 4 – 5 April 2019, Vienna","ddc":["570"],"status":"public","intvolume":" 41","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6857","oa_version":"Published Version","file":[{"file_id":"6939","relation":"main_file","checksum":"8cc7551bff70b2658f8d5630f228ee12","date_created":"2019-10-11T06:59:26Z","date_updated":"2020-07-14T12:47:42Z","access_level":"open_access","file_name":"2019_BioEssays_Giese.pdf","creator":"dernst","content_type":"application/pdf","file_size":193248}],"type":"journal_article","abstract":[{"text":"Gene Drives are regarded as future tools with a high potential for population control. Due to their inherent ability to overcome the rules of Mendelian inheritance, gene drives (GD) may spread genes rapidly through populations of sexually reproducing organisms. A release of organisms carrying a GD would constitute a paradigm shift in the handling of genetically modified organisms because gene drive organisms (GDO) are designed to drive their transgenes into wild populations and thereby increase the number of GDOs. The rapid development in this field and its focus on wild populations demand a prospective risk assessment with a focus on exposure related aspects. Presently, it is unclear how adequate risk management could be guaranteed to limit the spread of GDs in time and space, in order to avoid potential adverse effects in socio‐ecological systems.\r\n\r\nThe recent workshop on the “Evaluation of Spatial and Temporal Control of Gene Drives” hosted by the Institute of Safety/Security and Risk Sciences (ISR) in Vienna aimed at gaining some insight into the potential population dynamic behavior of GDs and appropriate measures of control. Scientists from France, Germany, England, and the USA discussed both topics in this meeting on April 4–5, 2019. This article summarizes results of the workshop.","lang":"eng"}],"issue":"11"},{"day":"02","month":"12","article_processing_charge":"No","doi":"10.5061/DRYAD.TB2RBNZWK","date_published":"2019-12-02T00:00:00Z","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"citation":{"short":"K. Johannesson, Z. Zagrodzka, R. Faria, A.M. Westram, R. Butlin, (2019).","mla":"Johannesson, Kerstin, et al. Data from: Is Embryo Abortion a Postzygotic Barrier to Gene Flow between Littorina Ecotypes? Dryad, 2019, doi:10.5061/DRYAD.TB2RBNZWK.","chicago":"Johannesson, Kerstin, Zuzanna Zagrodzka, Rui Faria, Anja M Westram, and Roger Butlin. “Data from: Is Embryo Abortion a Postzygotic Barrier to Gene Flow between Littorina Ecotypes?” Dryad, 2019. https://doi.org/10.5061/DRYAD.TB2RBNZWK.","ama":"Johannesson K, Zagrodzka Z, Faria R, Westram AM, Butlin R. Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes? 2019. doi:10.5061/DRYAD.TB2RBNZWK","apa":"Johannesson, K., Zagrodzka, Z., Faria, R., Westram, A. M., & Butlin, R. (2019). Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes? Dryad. https://doi.org/10.5061/DRYAD.TB2RBNZWK","ieee":"K. Johannesson, Z. Zagrodzka, R. Faria, A. M. Westram, and R. Butlin, “Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes?” Dryad, 2019.","ista":"Johannesson K, Zagrodzka Z, Faria R, Westram AM, Butlin R. 2019. Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes?, Dryad, 10.5061/DRYAD.TB2RBNZWK."},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.tb2rbnzwk"}],"abstract":[{"lang":"eng","text":"Genetic incompatibilities contribute to reproductive isolation between many diverging populations, but it is still unclear to what extent they play a role if divergence happens with gene flow. In contact zones between the \"Crab\" and \"Wave\" ecotypes of the snail Littorina saxatilis divergent selection forms strong barriers to gene flow, while the role of postzygotic barriers due to selection against hybrids remains unclear. High embryo abortion rates in this species could indicate the presence of such barriers. Postzygotic barriers might include genetic incompatibilities (e.g. Dobzhansky-Muller incompatibilities) but also maladaptation, both expected to be most pronounced in contact zones. In addition, embryo abortion might reflect physiological stress on females and embryos independent of any genetic stress. We examined all embryos of >500 females sampled outside and inside contact zones of three populations in Sweden. Females' clutch size ranged from 0 to 1011 embryos (mean 130±123) and abortion rates varied between 0 and100% (mean 12%). We described female genotypes by using a hybrid index based on hundreds of SNPs differentiated between ecotypes with which we characterised female genotypes. We also calculated female SNP heterozygosity and inversion karyotype. Clutch size did not vary with female hybrid index and abortion rates were only weakly related to hybrid index in two sites but not at all in a third site. No additional variation in abortion rate was explained by female SNP heterozygosity, but increased female inversion heterozygosity added slightly to increased abortion. Our results show only weak and probably biologically insignificant postzygotic barriers contributing to ecotype divergence and the high and variable abortion rates were marginally, if at all, explained by hybrid index of females."}],"type":"research_data_reference","author":[{"full_name":"Johannesson, Kerstin","first_name":"Kerstin","last_name":"Johannesson"},{"last_name":"Zagrodzka","first_name":"Zuzanna","full_name":"Zagrodzka, Zuzanna"},{"first_name":"Rui","last_name":"Faria","full_name":"Faria, Rui"},{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","first_name":"Anja M","last_name":"Westram","full_name":"Westram, Anja M"},{"full_name":"Butlin, Roger","last_name":"Butlin","first_name":"Roger"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"7205"}]},"date_created":"2023-05-23T16:36:27Z","date_updated":"2023-09-06T14:48:57Z","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13067","year":"2019","ddc":["570"],"title":"Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes?","status":"public","publisher":"Dryad","department":[{"_id":"NiBa"}]},{"language":[{"iso":"eng"}],"doi":"10.1126/sciadv.aav9963","quality_controlled":"1","isi":1,"project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"},{"grant_number":"797747","_id":"265B41B8-B435-11E9-9278-68D0E5697425","name":"Theoretical and empirical approaches to understanding Parallel Adaptation","call_identifier":"H2020"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"external_id":{"pmid":["31840052"],"isi":["000505069600008"]},"month":"12","publication_identifier":{"issn":["2375-2548"]},"date_created":"2020-01-29T15:58:27Z","date_updated":"2023-09-06T15:35:56Z","volume":5,"author":[{"last_name":"Morales","first_name":"Hernán E.","full_name":"Morales, Hernán E."},{"last_name":"Faria","first_name":"Rui","full_name":"Faria, Rui"},{"full_name":"Johannesson, Kerstin","first_name":"Kerstin","last_name":"Johannesson"},{"full_name":"Larsson, Tomas","first_name":"Tomas","last_name":"Larsson"},{"first_name":"Marina","last_name":"Panova","full_name":"Panova, Marina"},{"full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","first_name":"Anja M"},{"last_name":"Butlin","first_name":"Roger K.","full_name":"Butlin, Roger K."}],"publication_status":"published","publisher":"AAAS","department":[{"_id":"NiBa"}],"year":"2019","pmid":1,"file_date_updated":"2020-07-14T12:47:57Z","ec_funded":1,"article_number":"eaav9963","date_published":"2019-12-04T00:00:00Z","article_type":"original","publication":"Science Advances","citation":{"mla":"Morales, Hernán E., et al. “Genomic Architecture of Parallel Ecological Divergence: Beyond a Single Environmental Contrast.” Science Advances, vol. 5, no. 12, eaav9963, AAAS, 2019, doi:10.1126/sciadv.aav9963.","short":"H.E. Morales, R. Faria, K. Johannesson, T. Larsson, M. Panova, A.M. Westram, R.K. Butlin, Science Advances 5 (2019).","chicago":"Morales, Hernán E., Rui Faria, Kerstin Johannesson, Tomas Larsson, Marina Panova, Anja M Westram, and Roger K. Butlin. “Genomic Architecture of Parallel Ecological Divergence: Beyond a Single Environmental Contrast.” Science Advances. AAAS, 2019. https://doi.org/10.1126/sciadv.aav9963.","ama":"Morales HE, Faria R, Johannesson K, et al. Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast. Science Advances. 2019;5(12). doi:10.1126/sciadv.aav9963","ista":"Morales HE, Faria R, Johannesson K, Larsson T, Panova M, Westram AM, Butlin RK. 2019. Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast. Science Advances. 5(12), eaav9963.","ieee":"H. E. Morales et al., “Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast,” Science Advances, vol. 5, no. 12. AAAS, 2019.","apa":"Morales, H. E., Faria, R., Johannesson, K., Larsson, T., Panova, M., Westram, A. M., & Butlin, R. K. (2019). Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast. Science Advances. AAAS. https://doi.org/10.1126/sciadv.aav9963"},"day":"04","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","file":[{"file_id":"7442","relation":"main_file","checksum":"af99a5dcdc66c6d6102051faf3be48d8","date_created":"2020-02-03T13:33:25Z","date_updated":"2020-07-14T12:47:57Z","access_level":"open_access","file_name":"2019_ScienceAdvances_Morales.pdf","creator":"dernst","content_type":"application/pdf","file_size":1869449}],"oa_version":"Published Version","ddc":["570"],"title":"Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast","status":"public","intvolume":" 5","_id":"7393","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"text":"The study of parallel ecological divergence provides important clues to the operation of natural selection. Parallel divergence often occurs in heterogeneous environments with different kinds of environmental gradients in different locations, but the genomic basis underlying this process is unknown. We investigated the genomics of rapid parallel adaptation in the marine snail Littorina saxatilis in response to two independent environmental axes (crab-predation versus wave-action and low-shore versus high-shore). Using pooled whole-genome resequencing, we show that sharing of genomic regions of high differentiation between environments is generally low but increases at smaller spatial scales. We identify different shared genomic regions of divergence for each environmental axis and show that most of these regions overlap with candidate chromosomal inversions. Several inversion regions are divergent and polymorphic across many localities. We argue that chromosomal inversions could store shared variation that fuels rapid parallel adaptation to heterogeneous environments, possibly as balanced polymorphism shared by adaptive gene flow.","lang":"eng"}],"issue":"12","type":"journal_article"},{"year":"2019","publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Wiley","editor":[{"full_name":"Balding, David","first_name":"David","last_name":"Balding"},{"first_name":"Ida","last_name":"Moltke","full_name":"Moltke, Ida"},{"first_name":"John","last_name":"Marioni","full_name":"Marioni, John"}],"author":[{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton"},{"last_name":"Etheridge","first_name":"Alison","full_name":"Etheridge, Alison"}],"edition":"4","date_created":"2020-08-21T04:25:39Z","date_updated":"2023-09-08T11:24:15Z","external_id":{"isi":["000261343000003"]},"quality_controlled":"1","isi":1,"doi":"10.1002/9781119487845.ch4","language":[{"iso":"eng"}],"month":"07","publication_identifier":{"isbn":["9781119429142"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"8281","ddc":["576"],"title":"Mathematical models in population genetics","status":"public","oa_version":"None","type":"book_chapter","abstract":[{"text":"We review the history of population genetics, starting with its origins a century ago from the synthesis between Mendel and Darwin's ideas, through to the recent development of sophisticated schemes of inference from sequence data, based on the coalescent. We explain the close relation between the coalescent and a diffusion process, which we illustrate by their application to understand spatial structure. We summarise the powerful methods available for analysis of multiple loci, when linkage equilibrium can be assumed, and then discuss approaches to the more challenging case, where associations between alleles require that we follow genotype, rather than allele, frequencies. Though we can hardly cover the whole of population genetics, we give an overview of the current state of the subject, and future challenges to it.","lang":"eng"}],"publication":"Handbook of statistical genomics","citation":{"chicago":"Barton, Nicholas H, and Alison Etheridge. “Mathematical Models in Population Genetics.” In Handbook of Statistical Genomics, edited by David Balding, Ida Moltke, and John Marioni, 4th ed., 115–44. Wiley, 2019. https://doi.org/10.1002/9781119487845.ch4.","mla":"Barton, Nicholas H., and Alison Etheridge. “Mathematical Models in Population Genetics.” Handbook of Statistical Genomics, edited by David Balding et al., 4th ed., Wiley, 2019, pp. 115–44, doi:10.1002/9781119487845.ch4.","short":"N.H. Barton, A. Etheridge, in:, D. Balding, I. Moltke, J. Marioni (Eds.), Handbook of Statistical Genomics, 4th ed., Wiley, 2019, pp. 115–144.","ista":"Barton NH, Etheridge A. 2019.Mathematical models in population genetics. In: Handbook of statistical genomics. , 115–144.","ieee":"N. H. Barton and A. Etheridge, “Mathematical models in population genetics,” in Handbook of statistical genomics, 4th ed., D. Balding, I. Moltke, and J. Marioni, Eds. Wiley, 2019, pp. 115–144.","apa":"Barton, N. H., & Etheridge, A. (2019). Mathematical models in population genetics. In D. Balding, I. Moltke, & J. Marioni (Eds.), Handbook of statistical genomics (4th ed., pp. 115–144). Wiley. https://doi.org/10.1002/9781119487845.ch4","ama":"Barton NH, Etheridge A. Mathematical models in population genetics. In: Balding D, Moltke I, Marioni J, eds. Handbook of Statistical Genomics. 4th ed. Wiley; 2019:115-144. doi:10.1002/9781119487845.ch4"},"page":"115-144","date_published":"2019-07-29T00:00:00Z","day":"29","article_processing_charge":"No"},{"date_published":"2019-01-09T00:00:00Z","doi":"10.5061/dryad.2kb6fh4","citation":{"ista":"Barton NH. 2019. Data from: The consequences of an introgression event, Dryad, 10.5061/dryad.2kb6fh4.","apa":"Barton, N. H. (2019). Data from: The consequences of an introgression event. Dryad. https://doi.org/10.5061/dryad.2kb6fh4","ieee":"N. H. Barton, “Data from: The consequences of an introgression event.” Dryad, 2019.","ama":"Barton NH. Data from: The consequences of an introgression event. 2019. doi:10.5061/dryad.2kb6fh4","chicago":"Barton, Nicholas H. “Data from: The Consequences of an Introgression Event.” Dryad, 2019. https://doi.org/10.5061/dryad.2kb6fh4.","mla":"Barton, Nicholas H. Data from: The Consequences of an Introgression Event. Dryad, 2019, doi:10.5061/dryad.2kb6fh4.","short":"N.H. Barton, (2019)."},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.2kb6fh4"}],"day":"09","month":"01","article_processing_charge":"No","author":[{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton"}],"related_material":{"record":[{"id":"40","status":"public","relation":"used_in_publication"}]},"date_updated":"2023-09-19T10:06:07Z","date_created":"2021-08-06T12:03:50Z","oa_version":"Published Version","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9805","year":"2019","title":"Data from: The consequences of an introgression event","status":"public","department":[{"_id":"NiBa"}],"publisher":"Dryad","abstract":[{"lang":"eng","text":"The spread of adaptive alleles is fundamental to evolution, and in theory, this process is well‐understood. However, only rarely can we follow this process—whether it originates from the spread of a new mutation, or by introgression from another population. In this issue of Molecular Ecology, Hanemaaijer et al. (2018) report on a 25‐year long study of the mosquitoes Anopheles gambiae (Figure 1) and Anopheles coluzzi in Mali, based on genotypes at 15 single‐nucleotide polymorphism (SNP). The species are usually reproductively isolated from each other, but in 2002 and 2006, bursts of hybridization were observed, when F1 hybrids became abundant. Alleles backcrossed from A. gambiae into A. coluzzi, but after the first event, these declined over the following years. In contrast, after 2006, an insecticide resistance allele that had established in A. gambiae spread into A. coluzzi, and rose to high frequency there, over 6 years (~75 generations). Whole genome sequences of 74 individuals showed that A. gambiae SNP from across the genome had become common in the A. coluzzi population, but that most of these were clustered in 34 genes around the resistance locus. A new set of SNP from 25 of these genes were assayed over time; over the 4 years since near‐fixation of the resistance allele; some remained common, whereas others declined. What do these patterns tell us about this introgression event?"}],"type":"research_data_reference"},{"date_published":"2019-03-11T00:00:00Z","citation":{"short":"R. Prizak, Coevolution of Transcription Factors and Their Binding Sites in Sequence Space, Institute of Science and Technology Austria, 2019.","mla":"Prizak, Roshan. Coevolution of Transcription Factors and Their Binding Sites in Sequence Space. Institute of Science and Technology Austria, 2019, doi:10.15479/at:ista:th6071.","chicago":"Prizak, Roshan. “Coevolution of Transcription Factors and Their Binding Sites in Sequence Space.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/at:ista:th6071.","ama":"Prizak R. Coevolution of transcription factors and their binding sites in sequence space. 2019. doi:10.15479/at:ista:th6071","ieee":"R. Prizak, “Coevolution of transcription factors and their binding sites in sequence space,” Institute of Science and Technology Austria, 2019.","apa":"Prizak, R. (2019). Coevolution of transcription factors and their binding sites in sequence space. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:th6071","ista":"Prizak R. 2019. Coevolution of transcription factors and their binding sites in sequence space. Institute of Science and Technology Austria."},"page":"189","day":"11","article_processing_charge":"No","has_accepted_license":"1","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"Thesis_final_PDFA_RoshanPrizak.pdf","file_size":20995465,"content_type":"application/pdf","creator":"rprizak","relation":"main_file","file_id":"6072","checksum":"e60a72de35d270b31f1a23d50f224ec0","date_updated":"2020-07-14T12:47:18Z","date_created":"2019-03-06T16:05:07Z"},{"checksum":"67c2630333d05ebafef5f018863a8465","date_updated":"2020-07-14T12:47:18Z","date_created":"2019-03-06T16:09:39Z","relation":"source_file","title":"Latex files","file_id":"6073","content_type":"application/zip","file_size":85705272,"creator":"rprizak","access_level":"closed","file_name":"thesis_v2_merge.zip"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"6071","ddc":["576"],"status":"public","title":"Coevolution of transcription factors and their binding sites in sequence space","abstract":[{"lang":"eng","text":"Transcription factors, by binding to specific sequences on the DNA, control the precise spatio-temporal expression of genes inside a cell. However, this specificity is limited, leading to frequent incorrect binding of transcription factors that might have deleterious consequences on the cell. By constructing a biophysical model of TF-DNA binding in the context of gene regulation, I will first explore how regulatory constraints can strongly shape the distribution of a population in sequence space. Then, by directly linking this to a picture of multiple types of transcription factors performing their functions simultaneously inside the cell, I will explore the extent of regulatory crosstalk -- incorrect binding interactions between transcription factors and binding sites that lead to erroneous regulatory states -- and understand the constraints this places on the design of regulatory systems. I will then develop a generic theoretical framework to investigate the coevolution of multiple transcription factors and multiple binding sites, in the context of a gene regulatory network that performs a certain function. As a particular tractable version of this problem, I will consider the evolution of two transcription factors when they transmit upstream signals to downstream target genes. Specifically, I will describe the evolutionary steady states and the evolutionary pathways involved, along with their timescales, of a system that initially undergoes a transcription factor duplication event. To connect this important theoretical model to the prominent biological event of transcription factor duplication giving rise to paralogous families, I will then describe a bioinformatics analysis of C2H2 Zn-finger transcription factors, a major family in humans, and focus on the patterns of evolution that paralogs have undergone in their various protein domains in the recent past. "}],"type":"dissertation","alternative_title":["ISTA Thesis"],"doi":"10.15479/at:ista:th6071","supervisor":[{"full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","first_name":"Gašper","last_name":"Tkačik"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"oa":1,"project":[{"call_identifier":"FWF","name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27","_id":"254E9036-B435-11E9-9278-68D0E5697425"}],"month":"03","publication_identifier":{"issn":["2663-337X"]},"author":[{"last_name":"Prizak","first_name":"Roshan","id":"4456104E-F248-11E8-B48F-1D18A9856A87","full_name":"Prizak, Roshan"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"1358"},{"status":"public","relation":"part_of_dissertation","id":"955"}]},"date_updated":"2023-09-22T10:00:48Z","date_created":"2019-03-06T16:16:10Z","year":"2019","publication_status":"published","department":[{"_id":"GaTk"},{"_id":"NiBa"}],"publisher":"Institute of Science and Technology Austria","file_date_updated":"2020-07-14T12:47:18Z"},{"type":"journal_article","issue":"3","abstract":[{"lang":"eng","text":"Plant mating systems play a key role in structuring genetic variation both within and between species. In hybrid zones, the outcomes and dynamics of hybridization are usually interpreted as the balance between gene flow and selection against hybrids. Yet, mating systems can introduce selective forces that alter these expectations; with diverse outcomes for the level and direction of gene flow depending on variation in outcrossing and whether the mating systems of the species pair are the same or divergent. We present a survey of hybridization in 133 species pairs from 41 plant families and examine how patterns of hybridization vary with mating system. We examine if hybrid zone mode, level of gene flow, asymmetries in gene flow and the frequency of reproductive isolating barriers vary in relation to mating system/s of the species pair. We combine these results with a simulation model and examples from the literature to address two general themes: (i) the two‐way interaction between introgression and the evolution of reproductive systems, and (ii) how mating system can facilitate or restrict interspecific gene flow. We conclude that examining mating system with hybridization provides unique opportunities to understand divergence and the processes underlying reproductive isolation."}],"intvolume":" 224","ddc":["570"],"status":"public","title":"Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow","_id":"6856","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_name":"2019_NewPhytologist_Pickup.pdf","access_level":"open_access","content_type":"application/pdf","file_size":1511958,"creator":"dernst","relation":"main_file","file_id":"7011","date_created":"2019-11-13T08:15:05Z","date_updated":"2020-07-14T12:47:42Z","checksum":"21e4c95599bbcaf7c483b89954658672"}],"oa_version":"Published Version","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"01","page":"1035-1047","article_type":"original","citation":{"ista":"Pickup M, Barton NH, Brandvain Y, Fraisse C, Yakimowski S, Dixit T, Lexer C, Cereghetti E, Field D. 2019. Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow. New Phytologist. 224(3), 1035–1047.","ieee":"M. Pickup et al., “Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow,” New Phytologist, vol. 224, no. 3. Wiley, pp. 1035–1047, 2019.","apa":"Pickup, M., Barton, N. H., Brandvain, Y., Fraisse, C., Yakimowski, S., Dixit, T., … Field, D. (2019). Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow. New Phytologist. Wiley. https://doi.org/10.1111/nph.16180","ama":"Pickup M, Barton NH, Brandvain Y, et al. Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow. New Phytologist. 2019;224(3):1035-1047. doi:10.1111/nph.16180","chicago":"Pickup, Melinda, Nicholas H Barton, Yaniv Brandvain, Christelle Fraisse, Sarah Yakimowski, Tanmay Dixit, Christian Lexer, Eva Cereghetti, and David Field. “Mating System Variation in Hybrid Zones: Facilitation, Barriers and Asymmetries to Gene Flow.” New Phytologist. Wiley, 2019. https://doi.org/10.1111/nph.16180.","mla":"Pickup, Melinda, et al. “Mating System Variation in Hybrid Zones: Facilitation, Barriers and Asymmetries to Gene Flow.” New Phytologist, vol. 224, no. 3, Wiley, 2019, pp. 1035–47, doi:10.1111/nph.16180.","short":"M. Pickup, N.H. Barton, Y. Brandvain, C. Fraisse, S. Yakimowski, T. Dixit, C. Lexer, E. Cereghetti, D. Field, New Phytologist 224 (2019) 1035–1047."},"publication":"New Phytologist","date_published":"2019-11-01T00:00:00Z","ec_funded":1,"file_date_updated":"2020-07-14T12:47:42Z","publisher":"Wiley","department":[{"_id":"NiBa"}],"publication_status":"published","pmid":1,"year":"2019","volume":224,"date_created":"2019-09-07T14:35:40Z","date_updated":"2023-10-18T08:47:08Z","author":[{"full_name":"Pickup, Melinda","first_name":"Melinda","last_name":"Pickup","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6118-0541"},{"last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"},{"full_name":"Brandvain, Yaniv","first_name":"Yaniv","last_name":"Brandvain"},{"last_name":"Fraisse","first_name":"Christelle","orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","full_name":"Fraisse, Christelle"},{"full_name":"Yakimowski, Sarah","last_name":"Yakimowski","first_name":"Sarah"},{"last_name":"Dixit","first_name":"Tanmay","full_name":"Dixit, Tanmay"},{"first_name":"Christian","last_name":"Lexer","full_name":"Lexer, Christian"},{"full_name":"Cereghetti, Eva","last_name":"Cereghetti","first_name":"Eva","id":"71AA91B4-05ED-11EA-8BEB-F5833E63BD63"},{"first_name":"David","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478","full_name":"Field, David"}],"publication_identifier":{"eissn":["1469-8137"],"issn":["0028-646X"]},"month":"11","project":[{"call_identifier":"FP7","name":"Mating system and the evolutionary dynamics of hybrid zones","grant_number":"329960","_id":"25B36484-B435-11E9-9278-68D0E5697425"},{"name":"Sex chromosomes and species barriers","call_identifier":"FWF","grant_number":"M02463","_id":"2662AADE-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["31505037"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1111/nph.16180"},{"_id":"6089","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"Pleiotropy modulates the efficacy of selection in drosophila melanogaster","intvolume":" 36","oa_version":"Submitted Version","type":"journal_article","abstract":[{"text":"Pleiotropy is the well-established idea that a single mutation affects multiple phenotypes. If a mutation has opposite effects on fitness when expressed in different contexts, then genetic conflict arises. Pleiotropic conflict is expected to reduce the efficacy of selection by limiting the fixation of beneficial mutations through adaptation, and the removal of deleterious mutations through purifying selection. Although this has been widely discussed, in particular in the context of a putative “gender load,” it has yet to be systematically quantified. In this work, we empirically estimate to which extent different pleiotropic regimes impede the efficacy of selection in Drosophila melanogaster. We use whole-genome polymorphism data from a single African population and divergence data from D. simulans to estimate the fraction of adaptive fixations (α), the rate of adaptation (ωA), and the direction of selection (DoS). After controlling for confounding covariates, we find that the different pleiotropic regimes have a relatively small, but significant, effect on selection efficacy. Specifically, our results suggest that pleiotropic sexual antagonism may restrict the efficacy of selection, but that this conflict can be resolved by limiting the expression of genes to the sex where they are beneficial. Intermediate levels of pleiotropy across tissues and life stages can also lead to maladaptation in D. melanogaster, due to inefficient purifying selection combined with low frequency of mutations that confer a selective advantage. Thus, our study highlights the need to consider the efficacy of selection in the context of antagonistic pleiotropy, and of genetic conflict in general.","lang":"eng"}],"issue":"3","publication":"Molecular biology and evolution","citation":{"ieee":"C. Fraisse, G. Puixeu Sala, and B. Vicoso, “Pleiotropy modulates the efficacy of selection in drosophila melanogaster,” Molecular biology and evolution, vol. 36, no. 3. Oxford University Press, pp. 500–515, 2019.","apa":"Fraisse, C., Puixeu Sala, G., & Vicoso, B. (2019). Pleiotropy modulates the efficacy of selection in drosophila melanogaster. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msy246","ista":"Fraisse C, Puixeu Sala G, Vicoso B. 2019. Pleiotropy modulates the efficacy of selection in drosophila melanogaster. Molecular biology and evolution. 36(3), 500–515.","ama":"Fraisse C, Puixeu Sala G, Vicoso B. Pleiotropy modulates the efficacy of selection in drosophila melanogaster. Molecular biology and evolution. 2019;36(3):500-515. doi:10.1093/molbev/msy246","chicago":"Fraisse, Christelle, Gemma Puixeu Sala, and Beatriz Vicoso. “Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.” Molecular Biology and Evolution. Oxford University Press, 2019. https://doi.org/10.1093/molbev/msy246.","short":"C. Fraisse, G. Puixeu Sala, B. Vicoso, Molecular Biology and Evolution 36 (2019) 500–515.","mla":"Fraisse, Christelle, et al. “Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.” Molecular Biology and Evolution, vol. 36, no. 3, Oxford University Press, 2019, pp. 500–15, doi:10.1093/molbev/msy246."},"page":"500-515","date_published":"2019-03-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","year":"2019","pmid":1,"publication_status":"published","publisher":"Oxford University Press","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"author":[{"full_name":"Fraisse, Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075","first_name":"Christelle","last_name":"Fraisse"},{"last_name":"Puixeu Sala","first_name":"Gemma","orcid":"0000-0001-8330-1754","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","full_name":"Puixeu Sala, Gemma"},{"full_name":"Vicoso, Beatriz","first_name":"Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306"}],"related_material":{"record":[{"relation":"popular_science","status":"public","id":"5757"}]},"date_updated":"2024-02-21T13:59:17Z","date_created":"2019-03-10T22:59:19Z","volume":36,"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30590559","open_access":"1"}],"oa":1,"external_id":{"pmid":["30590559"],"isi":["000462585100006"]},"quality_controlled":"1","isi":1,"project":[{"_id":"250ED89C-B435-11E9-9278-68D0E5697425","grant_number":"P28842-B22","call_identifier":"FWF","name":"Sex chromosome evolution under male- and female- heterogamety"}],"doi":"10.1093/molbev/msy246","language":[{"iso":"eng"}],"month":"03","publication_identifier":{"issn":["0737-4038"],"eissn":["1537-1719"]}},{"scopus_import":"1","article_processing_charge":"No","day":"26","citation":{"chicago":"Carballo-Pacheco, Martín, Jonathan Desponds, Tatyana Gavrilchenko, Andreas Mayer, Roshan Prizak, Gautam Reddy, Ilya Nemenman, and Thierry Mora. “Receptor Crosstalk Improves Concentration Sensing of Multiple Ligands.” Physical Review E. American Physical Society, 2019. https://doi.org/10.1103/PhysRevE.99.022423.","short":"M. Carballo-Pacheco, J. Desponds, T. Gavrilchenko, A. Mayer, R. Prizak, G. Reddy, I. Nemenman, T. Mora, Physical Review E 99 (2019).","mla":"Carballo-Pacheco, Martín, et al. “Receptor Crosstalk Improves Concentration Sensing of Multiple Ligands.” Physical Review E, vol. 99, no. 2, 022423, American Physical Society, 2019, doi:10.1103/PhysRevE.99.022423.","ieee":"M. Carballo-Pacheco et al., “Receptor crosstalk improves concentration sensing of multiple ligands,” Physical Review E, vol. 99, no. 2. American Physical Society, 2019.","apa":"Carballo-Pacheco, M., Desponds, J., Gavrilchenko, T., Mayer, A., Prizak, R., Reddy, G., … Mora, T. (2019). Receptor crosstalk improves concentration sensing of multiple ligands. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.99.022423","ista":"Carballo-Pacheco M, Desponds J, Gavrilchenko T, Mayer A, Prizak R, Reddy G, Nemenman I, Mora T. 2019. Receptor crosstalk improves concentration sensing of multiple ligands. Physical Review E. 99(2), 022423.","ama":"Carballo-Pacheco M, Desponds J, Gavrilchenko T, et al. Receptor crosstalk improves concentration sensing of multiple ligands. Physical Review E. 2019;99(2). doi:10.1103/PhysRevE.99.022423"},"publication":"Physical Review E","date_published":"2019-02-26T00:00:00Z","type":"journal_article","issue":"2","abstract":[{"lang":"eng","text":"Cells need to reliably sense external ligand concentrations to achieve various biological functions such as chemotaxis or signaling. The molecular recognition of ligands by surface receptors is degenerate in many systems, leading to crosstalk between ligand-receptor pairs. Crosstalk is often thought of as a deviation from optimal specific recognition, as the binding of noncognate ligands can interfere with the detection of the receptor's cognate ligand, possibly leading to a false triggering of a downstream signaling pathway. Here we quantify the optimal precision of sensing the concentrations of multiple ligands by a collection of promiscuous receptors. We demonstrate that crosstalk can improve precision in concentration sensing and discrimination tasks. To achieve superior precision, the additional information about ligand concentrations contained in short binding events of the noncognate ligand should be exploited. We present a proofreading scheme to realize an approximate estimation of multiple ligand concentrations that reaches a precision close to the derived optimal bounds. Our results help rationalize the observed ubiquity of receptor crosstalk in molecular sensing."}],"intvolume":" 99","status":"public","title":"Receptor crosstalk improves concentration sensing of multiple ligands","_id":"6090","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","month":"02","quality_controlled":"1","isi":1,"oa":1,"main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/448118v1.abstract","open_access":"1"}],"external_id":{"isi":["000459916500007"]},"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevE.99.022423","article_number":"022423","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"publisher":"American Physical Society","publication_status":"published","year":"2019","volume":99,"date_created":"2019-03-10T22:59:20Z","date_updated":"2024-02-28T13:12:06Z","author":[{"last_name":"Carballo-Pacheco","first_name":"Martín","full_name":"Carballo-Pacheco, Martín"},{"last_name":"Desponds","first_name":"Jonathan","full_name":"Desponds, Jonathan"},{"first_name":"Tatyana","last_name":"Gavrilchenko","full_name":"Gavrilchenko, Tatyana"},{"full_name":"Mayer, Andreas","last_name":"Mayer","first_name":"Andreas"},{"full_name":"Prizak, Roshan","last_name":"Prizak","first_name":"Roshan","id":"4456104E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Gautam","last_name":"Reddy","full_name":"Reddy, Gautam"},{"full_name":"Nemenman, Ilya","last_name":"Nemenman","first_name":"Ilya"},{"full_name":"Mora, Thierry","last_name":"Mora","first_name":"Thierry"}]},{"file_date_updated":"2020-07-14T12:47:38Z","article_number":"e42014","volume":8,"date_created":"2019-07-28T21:59:17Z","date_updated":"2024-03-28T23:30:23Z","related_material":{"record":[{"id":"9804","status":"public","relation":"research_data"},{"relation":"dissertation_contains","status":"public","id":"11388"}]},"author":[{"full_name":"Castro, João Pl","last_name":"Castro","first_name":"João Pl"},{"full_name":"Yancoskie, Michelle N.","last_name":"Yancoskie","first_name":"Michelle N."},{"last_name":"Marchini","first_name":"Marta","full_name":"Marchini, Marta"},{"last_name":"Belohlavy","first_name":"Stefanie","orcid":"0000-0002-9849-498X","id":"43FE426A-F248-11E8-B48F-1D18A9856A87","full_name":"Belohlavy, Stefanie"},{"last_name":"Hiramatsu","first_name":"Layla","full_name":"Hiramatsu, Layla"},{"first_name":"Marek","last_name":"Kučka","full_name":"Kučka, Marek"},{"full_name":"Beluch, William H.","last_name":"Beluch","first_name":"William H."},{"last_name":"Naumann","first_name":"Ronald","full_name":"Naumann, Ronald"},{"first_name":"Isabella","last_name":"Skuplik","full_name":"Skuplik, Isabella"},{"full_name":"Cobb, John","last_name":"Cobb","first_name":"John"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"},{"first_name":"Campbell","last_name":"Rolian","full_name":"Rolian, Campbell"},{"full_name":"Chan, Yingguang Frank","first_name":"Yingguang Frank","last_name":"Chan"}],"department":[{"_id":"NiBa"}],"publisher":"eLife Sciences Publications","publication_status":"published","pmid":1,"year":"2019","month":"06","language":[{"iso":"eng"}],"doi":"10.7554/eLife.42014","isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000473588700001"],"pmid":["31169497"]},"oa":1,"abstract":[{"lang":"eng","text":"Evolutionary studies are often limited by missing data that are critical to understanding the history of selection. Selection experiments, which reproduce rapid evolution under controlled conditions, are excellent tools to study how genomes evolve under selection. Here we present a genomic dissection of the Longshanks selection experiment, in which mice were selectively bred over 20 generations for longer tibiae relative to body mass, resulting in 13% longer tibiae in two replicates. We synthesized evolutionary theory, genome sequences and molecular genetics to understand the selection response and found that it involved both polygenic adaptation and discrete loci of major effect, with the strongest loci tending to be selected in parallel between replicates. We show that selection may favor de-repression of bone growth through inactivating two limb enhancers of an inhibitor, Nkx3-2. Our integrative genomic analyses thus show that it is possible to connect individual base-pair changes to the overall selection response."}],"type":"journal_article","oa_version":"Published Version","file":[{"file_id":"6721","relation":"main_file","date_updated":"2020-07-14T12:47:38Z","date_created":"2019-07-29T07:41:18Z","checksum":"fa0936fe58f0d9e3f8e75038570e5a17","file_name":"2019_eLife_Castro.pdf","access_level":"open_access","creator":"apreinsp","file_size":6748249,"content_type":"application/pdf"}],"intvolume":" 8","status":"public","ddc":["576"],"title":"An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice","_id":"6713","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","has_accepted_license":"1","article_processing_charge":"No","day":"06","scopus_import":"1","date_published":"2019-06-06T00:00:00Z","citation":{"apa":"Castro, J. P., Yancoskie, M. N., Marchini, M., Belohlavy, S., Hiramatsu, L., Kučka, M., … Chan, Y. F. (2019). An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.42014","ieee":"J. P. Castro et al., “An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice,” eLife, vol. 8. eLife Sciences Publications, 2019.","ista":"Castro JP, Yancoskie MN, Marchini M, Belohlavy S, Hiramatsu L, Kučka M, Beluch WH, Naumann R, Skuplik I, Cobb J, Barton NH, Rolian C, Chan YF. 2019. An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice. eLife. 8, e42014.","ama":"Castro JP, Yancoskie MN, Marchini M, et al. An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice. eLife. 2019;8. doi:10.7554/eLife.42014","chicago":"Castro, João Pl, Michelle N. Yancoskie, Marta Marchini, Stefanie Belohlavy, Layla Hiramatsu, Marek Kučka, William H. Beluch, et al. “An Integrative Genomic Analysis of the Longshanks Selection Experiment for Longer Limbs in Mice.” ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/eLife.42014.","short":"J.P. Castro, M.N. Yancoskie, M. Marchini, S. Belohlavy, L. Hiramatsu, M. Kučka, W.H. Beluch, R. Naumann, I. Skuplik, J. Cobb, N.H. Barton, C. Rolian, Y.F. Chan, ELife 8 (2019).","mla":"Castro, João Pl, et al. “An Integrative Genomic Analysis of the Longshanks Selection Experiment for Longer Limbs in Mice.” ELife, vol. 8, e42014, eLife Sciences Publications, 2019, doi:10.7554/eLife.42014."},"publication":"eLife"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"315","title":"Is the sky the limit? On the expansion threshold of a species’ range","ddc":["576"],"status":"public","intvolume":" 16","file":[{"file_name":"2017_PLOS_Polechova.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":6968201,"file_id":"5870","relation":"main_file","date_updated":"2020-07-14T12:46:01Z","date_created":"2019-01-22T08:30:03Z","checksum":"908c52751bba30c55ed36789e5e4c84d"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"More than 100 years after Grigg’s influential analysis of species’ borders, the causes of limits to species’ ranges still represent a puzzle that has never been understood with clarity. The topic has become especially important recently as many scientists have become interested in the potential for species’ ranges to shift in response to climate change—and yet nearly all of those studies fail to recognise or incorporate evolutionary genetics in a way that relates to theoretical developments. I show that range margins can be understood based on just two measurable parameters: (i) the fitness cost of dispersal—a measure of environmental heterogeneity—and (ii) the strength of genetic drift, which reduces genetic diversity. Together, these two parameters define an ‘expansion threshold’: adaptation fails when genetic drift reduces genetic diversity below that required for adaptation to a heterogeneous environment. When the key parameters drop below this expansion threshold locally, a sharp range margin forms. When they drop below this threshold throughout the species’ range, adaptation collapses everywhere, resulting in either extinction or formation of a fragmented metapopulation. Because the effects of dispersal differ fundamentally with dimension, the second parameter—the strength of genetic drift—is qualitatively different compared to a linear habitat. In two-dimensional habitats, genetic drift becomes effectively independent of selection. It decreases with ‘neighbourhood size’—the number of individuals accessible by dispersal within one generation. Moreover, in contrast to earlier predictions, which neglected evolution of genetic variance and/or stochasticity in two dimensions, dispersal into small marginal populations aids adaptation. This is because the reduction of both genetic and demographic stochasticity has a stronger effect than the cost of dispersal through increased maladaptation. The expansion threshold thus provides a novel, theoretically justified, and testable prediction for formation of the range margin and collapse of the species’ range."}],"issue":"6","publication":"PLoS Biology","citation":{"ista":"Polechova J. 2018. Is the sky the limit? On the expansion threshold of a species’ range. PLoS Biology. 16(6), e2005372.","apa":"Polechova, J. (2018). Is the sky the limit? On the expansion threshold of a species’ range. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2005372","ieee":"J. Polechova, “Is the sky the limit? On the expansion threshold of a species’ range,” PLoS Biology, vol. 16, no. 6. Public Library of Science, 2018.","ama":"Polechova J. Is the sky the limit? On the expansion threshold of a species’ range. PLoS Biology. 2018;16(6). doi:10.1371/journal.pbio.2005372","chicago":"Polechova, Jitka. “Is the Sky the Limit? On the Expansion Threshold of a Species’ Range.” PLoS Biology. Public Library of Science, 2018. https://doi.org/10.1371/journal.pbio.2005372.","mla":"Polechova, Jitka. “Is the Sky the Limit? On the Expansion Threshold of a Species’ Range.” PLoS Biology, vol. 16, no. 6, e2005372, Public Library of Science, 2018, doi:10.1371/journal.pbio.2005372.","short":"J. Polechova, PLoS Biology 16 (2018)."},"date_published":"2018-06-15T00:00:00Z","scopus_import":1,"day":"15","has_accepted_license":"1","year":"2018","publication_status":"published","publisher":"Public Library of Science","department":[{"_id":"NiBa"}],"author":[{"first_name":"Jitka","last_name":"Polechova","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0951-3112","full_name":"Polechova, Jitka"}],"related_material":{"record":[{"relation":"research_data","status":"public","id":"9839"}]},"date_updated":"2023-02-23T14:10:16Z","date_created":"2018-12-11T11:45:46Z","volume":16,"article_number":"e2005372","file_date_updated":"2020-07-14T12:46:01Z","publist_id":"7550","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","doi":"10.1371/journal.pbio.2005372","language":[{"iso":"eng"}],"month":"06","publication_identifier":{"issn":["15449173"]}},{"date_published":"2018-10-09T00:00:00Z","doi":"10.5061/dryad.72cg113","citation":{"chicago":"Faria, Rui, Pragya Chaube, Hernán E. Morales, Tomas Larsson, Alan R. Lemmon, Emily M. Lemmon, Marina Rafajlović, et al. “Data from: Multiple Chromosomal Rearrangements in a Hybrid Zone between Littorina Saxatilis Ecotypes.” Dryad, 2018. https://doi.org/10.5061/dryad.72cg113.","short":"R. Faria, P. Chaube, H.E. Morales, T. Larsson, A.R. Lemmon, E.M. Lemmon, M. Rafajlović, M. Panova, M. Ravinet, K. Johannesson, A.M. Westram, R.K. Butlin, (2018).","mla":"Faria, Rui, et al. Data from: Multiple Chromosomal Rearrangements in a Hybrid Zone between Littorina Saxatilis Ecotypes. Dryad, 2018, doi:10.5061/dryad.72cg113.","ieee":"R. Faria et al., “Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes.” Dryad, 2018.","apa":"Faria, R., Chaube, P., Morales, H. E., Larsson, T., Lemmon, A. R., Lemmon, E. M., … Butlin, R. K. (2018). Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. Dryad. https://doi.org/10.5061/dryad.72cg113","ista":"Faria R, Chaube P, Morales HE, Larsson T, Lemmon AR, Lemmon EM, Rafajlović M, Panova M, Ravinet M, Johannesson K, Westram AM, Butlin RK. 2018. Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes, Dryad, 10.5061/dryad.72cg113.","ama":"Faria R, Chaube P, Morales HE, et al. Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. 2018. doi:10.5061/dryad.72cg113"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.72cg113"}],"oa":1,"day":"09","month":"10","article_processing_charge":"No","date_updated":"2023-08-24T14:50:26Z","date_created":"2021-08-09T12:46:39Z","oa_version":"Published Version","author":[{"last_name":"Faria","first_name":"Rui","full_name":"Faria, Rui"},{"full_name":"Chaube, Pragya","first_name":"Pragya","last_name":"Chaube"},{"full_name":"Morales, Hernán E.","last_name":"Morales","first_name":"Hernán E."},{"full_name":"Larsson, Tomas","last_name":"Larsson","first_name":"Tomas"},{"full_name":"Lemmon, Alan R.","last_name":"Lemmon","first_name":"Alan R."},{"last_name":"Lemmon","first_name":"Emily M.","full_name":"Lemmon, Emily M."},{"last_name":"Rafajlović","first_name":"Marina","full_name":"Rafajlović, Marina"},{"full_name":"Panova, Marina","first_name":"Marina","last_name":"Panova"},{"full_name":"Ravinet, Mark","last_name":"Ravinet","first_name":"Mark"},{"last_name":"Johannesson","first_name":"Kerstin","full_name":"Johannesson, Kerstin"},{"first_name":"Anja M","last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M"},{"full_name":"Butlin, Roger K.","last_name":"Butlin","first_name":"Roger K."}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"6095"}]},"title":"Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes","status":"public","department":[{"_id":"NiBa"}],"publisher":"Dryad","_id":"9837","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2018","abstract":[{"text":"Both classical and recent studies suggest that chromosomal inversion polymorphisms are important in adaptation and speciation. However, biases in discovery and reporting of inversions make it difficult to assess their prevalence and biological importance. Here, we use an approach based on linkage disequilibrium among markers genotyped for samples collected across a transect between contrasting habitats to detect chromosomal rearrangements de novo. We report 17 polymorphic rearrangements in a single locality for the coastal marine snail, Littorina saxatilis. Patterns of diversity in the field and of recombination in controlled crosses provide strong evidence that at least the majority of these rearrangements are inversions. Most show clinal changes in frequency between habitats, suggestive of divergent selection, but only one appears to be fixed for different arrangements in the two habitats. Consistent with widespread evidence for balancing selection on inversion polymorphisms, we argue that a combination of heterosis and divergent selection can explain the observed patterns and should be considered in other systems spanning environmental gradients.","lang":"eng"}],"type":"research_data_reference"},{"scopus_import":"1","day":"09","article_processing_charge":"No","has_accepted_license":"1","publication":"eLife","citation":{"chicago":"Payne, Pavel, Lukas Geyrhofer, Nicholas H Barton, and Jonathan P Bollback. “CRISPR-Based Herd Immunity Can Limit Phage Epidemics in Bacterial Populations.” ELife. eLife Sciences Publications, 2018. https://doi.org/10.7554/eLife.32035.","short":"P. Payne, L. Geyrhofer, N.H. Barton, J.P. Bollback, ELife 7 (2018).","mla":"Payne, Pavel, et al. “CRISPR-Based Herd Immunity Can Limit Phage Epidemics in Bacterial Populations.” ELife, vol. 7, e32035, eLife Sciences Publications, 2018, doi:10.7554/eLife.32035.","ieee":"P. Payne, L. Geyrhofer, N. H. Barton, and J. P. Bollback, “CRISPR-based herd immunity can limit phage epidemics in bacterial populations,” eLife, vol. 7. eLife Sciences Publications, 2018.","apa":"Payne, P., Geyrhofer, L., Barton, N. H., & Bollback, J. P. (2018). CRISPR-based herd immunity can limit phage epidemics in bacterial populations. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.32035","ista":"Payne P, Geyrhofer L, Barton NH, Bollback JP. 2018. CRISPR-based herd immunity can limit phage epidemics in bacterial populations. eLife. 7, e32035.","ama":"Payne P, Geyrhofer L, Barton NH, Bollback JP. CRISPR-based herd immunity can limit phage epidemics in bacterial populations. eLife. 2018;7. doi:10.7554/eLife.32035"},"date_published":"2018-03-09T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Herd immunity, a process in which resistant individuals limit the spread of a pathogen among susceptible hosts has been extensively studied in eukaryotes. Even though bacteria have evolved multiple immune systems against their phage pathogens, herd immunity in bacteria remains unexplored. Here we experimentally demonstrate that herd immunity arises during phage epidemics in structured and unstructured Escherichia coli populations consisting of differing frequencies of susceptible and resistant cells harboring CRISPR immunity. In addition, we develop a mathematical model that quantifies how herd immunity is affected by spatial population structure, bacterial growth rate, and phage replication rate. Using our model we infer a general epidemiological rule describing the relative speed of an epidemic in partially resistant spatially structured populations. Our experimental and theoretical findings indicate that herd immunity may be important in bacterial communities, allowing for stable coexistence of bacteria and their phages and the maintenance of polymorphism in bacterial immunity."}],"title":"CRISPR-based herd immunity can limit phage epidemics in bacterial populations","status":"public","ddc":["576"],"intvolume":" 7","_id":"423","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"content_type":"application/pdf","file_size":3533881,"creator":"dernst","access_level":"open_access","file_name":"2018_eLife_Payne.pdf","checksum":"447cf6e680bdc3c01062a8737d876569","date_created":"2018-12-17T10:36:07Z","date_updated":"2020-07-14T12:46:25Z","relation":"main_file","file_id":"5689"}],"oa_version":"Published Version","month":"03","isi":1,"quality_controlled":"1","project":[{"grant_number":"648440","_id":"2578D616-B435-11E9-9278-68D0E5697425","name":"Selective Barriers to Horizontal Gene Transfer","call_identifier":"H2020"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000431035800001"]},"language":[{"iso":"eng"}],"doi":"10.7554/eLife.32035","article_number":"e32035","file_date_updated":"2020-07-14T12:46:25Z","ec_funded":1,"publist_id":"7400","publication_status":"published","publisher":"eLife Sciences Publications","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"acknowledgement":"We are grateful to Remy Chait for his help and assistance with establishing our experimental setups and to Tobias Bergmiller for valuable insights into some specific experimental details. We thank Luciano Marraffini for donating us the pCas9 plasmid used in this study. We also want to express our gratitude to Seth Barribeau, Andrea Betancourt, Călin Guet, Mato Lagator, Tiago Paixão and Maroš Pleška for valuable discussions on the manuscript. Finally, we would like to thank the \r\neditors and reviewers for their helpful comments and suggestions.","year":"2018","date_created":"2018-12-11T11:46:23Z","date_updated":"2023-09-11T12:49:17Z","volume":7,"author":[{"full_name":"Payne, Pavel","last_name":"Payne","first_name":"Pavel","orcid":"0000-0002-2711-9453","id":"35F78294-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Geyrhofer, Lukas","last_name":"Geyrhofer","first_name":"Lukas"},{"last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"},{"first_name":"Jonathan P","last_name":"Bollback","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4624-4612","full_name":"Bollback, Jonathan P"}],"related_material":{"record":[{"status":"public","relation":"research_data","id":"9840"}]}},{"abstract":[{"lang":"eng","text":"Herd immunity, a process in which resistant individuals limit the spread of a pathogen among susceptible hosts has been extensively studied in eukaryotes. Even though bacteria have evolved multiple immune systems against their phage pathogens, herd immunity in bacteria remains unexplored. Here we experimentally demonstrate that herd immunity arises during phage epidemics in structured and unstructured Escherichia coli populations consisting of differing frequencies of susceptible and resistant cells harboring CRISPR immunity. In addition, we develop a mathematical model that quantifies how herd immunity is affected by spatial population structure, bacterial growth rate, and phage replication rate. Using our model we infer a general epidemiological rule describing the relative speed of an epidemic in partially resistant spatially structured populations. Our experimental and theoretical findings indicate that herd immunity may be important in bacterial communities, allowing for stable coexistence of bacteria and their phages and the maintenance of polymorphism in bacterial immunity."}],"type":"research_data_reference","oa_version":"Published Version","date_created":"2021-08-09T13:10:02Z","date_updated":"2023-09-11T12:49:17Z","related_material":{"record":[{"id":"423","relation":"used_in_publication","status":"public"}]},"author":[{"first_name":"Pavel","last_name":"Payne","id":"35F78294-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2711-9453","full_name":"Payne, Pavel"},{"first_name":"Lukas","last_name":"Geyrhofer","full_name":"Geyrhofer, Lukas"},{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"full_name":"Bollback, Jonathan P","orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","last_name":"Bollback","first_name":"Jonathan P"}],"publisher":"Dryad","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"status":"public","title":"Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations","year":"2018","_id":"9840","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","month":"03","day":"12","date_published":"2018-03-12T00:00:00Z","doi":"10.5061/dryad.42n44","oa":1,"main_file_link":[{"url":"https://doi.org/10.5061/dryad.42n44","open_access":"1"}],"citation":{"ama":"Payne P, Geyrhofer L, Barton NH, Bollback JP. Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations. 2018. doi:10.5061/dryad.42n44","ieee":"P. Payne, L. Geyrhofer, N. H. Barton, and J. P. Bollback, “Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations.” Dryad, 2018.","apa":"Payne, P., Geyrhofer, L., Barton, N. H., & Bollback, J. P. (2018). Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations. Dryad. https://doi.org/10.5061/dryad.42n44","ista":"Payne P, Geyrhofer L, Barton NH, Bollback JP. 2018. Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations, Dryad, 10.5061/dryad.42n44.","short":"P. Payne, L. Geyrhofer, N.H. Barton, J.P. Bollback, (2018).","mla":"Payne, Pavel, et al. Data from: CRISPR-Based Herd Immunity Limits Phage Epidemics in Bacterial Populations. Dryad, 2018, doi:10.5061/dryad.42n44.","chicago":"Payne, Pavel, Lukas Geyrhofer, Nicholas H Barton, and Jonathan P Bollback. “Data from: CRISPR-Based Herd Immunity Limits Phage Epidemics in Bacterial Populations.” Dryad, 2018. https://doi.org/10.5061/dryad.42n44."}},{"ddc":["519","576"],"title":"Establishment in a new habitat by polygenic adaptation","status":"public","intvolume":" 122","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"564","oa_version":"Submitted Version","file":[{"creator":"nbarton","content_type":"application/pdf","file_size":2287682,"file_name":"bartonetheridge.pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:09Z","date_created":"2019-12-21T09:36:39Z","checksum":"0b96f6db47e3e91b5e7d103b847c239d","file_id":"7199","relation":"main_file"}],"type":"journal_article","abstract":[{"text":"Maladapted individuals can only colonise a new habitat if they can evolve a\r\npositive growth rate fast enough to avoid extinction, a process known as evolutionary\r\nrescue. We treat log fitness at low density in the new habitat as a\r\nsingle polygenic trait and thus use the infinitesimal model to follow the evolution\r\nof the growth rate; this assumes that the trait values of offspring of a\r\nsexual union are normally distributed around the mean of the parents’ trait\r\nvalues, with variance that depends only on the parents’ relatedness. The\r\nprobability that a single migrant can establish depends on just two parameters:\r\nthe mean and genetic variance of the trait in the source population.\r\nThe chance of success becomes small if migrants come from a population\r\nwith mean growth rate in the new habitat more than a few standard deviations\r\nbelow zero; this chance depends roughly equally on the probability\r\nthat the initial founder is unusually fit, and on the subsequent increase in\r\ngrowth rate of its offspring as a result of selection. The loss of genetic variation\r\nduring the founding event is substantial, but highly variable. With\r\ncontinued migration at rate M, establishment is inevitable; when migration\r\nis rare, the expected time to establishment decreases inversely with M.\r\nHowever, above a threshold migration rate, the population may be trapped\r\nin a ‘sink’ state, in which adaptation is held back by gene flow; above this\r\nthreshold, the expected time to establishment increases exponentially with M. This threshold behaviour is captured by a deterministic approximation,\r\nwhich assumes a Gaussian distribution of the trait in the founder population\r\nwith mean and variance evolving deterministically. By assuming a constant\r\ngenetic variance, we also develop a diffusion approximation for the joint distribution\r\nof population size and trait mean, which extends to include stabilising\r\nselection and density regulation. Divergence of the population from its\r\nancestors causes partial reproductive isolation, which we measure through\r\nthe reproductive value of migrants into the newly established population.","lang":"eng"}],"issue":"7","article_type":"original","page":"110-127","publication":"Theoretical Population Biology","citation":{"ista":"Barton NH, Etheridge A. 2018. Establishment in a new habitat by polygenic adaptation. Theoretical Population Biology. 122(7), 110–127.","apa":"Barton, N. H., & Etheridge, A. (2018). Establishment in a new habitat by polygenic adaptation. Theoretical Population Biology. Academic Press. https://doi.org/10.1016/j.tpb.2017.11.007","ieee":"N. H. Barton and A. Etheridge, “Establishment in a new habitat by polygenic adaptation,” Theoretical Population Biology, vol. 122, no. 7. Academic Press, pp. 110–127, 2018.","ama":"Barton NH, Etheridge A. Establishment in a new habitat by polygenic adaptation. Theoretical Population Biology. 2018;122(7):110-127. doi:10.1016/j.tpb.2017.11.007","chicago":"Barton, Nicholas H, and Alison Etheridge. “Establishment in a New Habitat by Polygenic Adaptation.” Theoretical Population Biology. Academic Press, 2018. https://doi.org/10.1016/j.tpb.2017.11.007.","mla":"Barton, Nicholas H., and Alison Etheridge. “Establishment in a New Habitat by Polygenic Adaptation.” Theoretical Population Biology, vol. 122, no. 7, Academic Press, 2018, pp. 110–27, doi:10.1016/j.tpb.2017.11.007.","short":"N.H. Barton, A. Etheridge, Theoretical Population Biology 122 (2018) 110–127."},"date_published":"2018-07-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","has_accepted_license":"1","publication_status":"published","publisher":"Academic Press","department":[{"_id":"NiBa"}],"year":"2018","date_created":"2018-12-11T11:47:12Z","date_updated":"2023-09-11T13:41:22Z","volume":122,"author":[{"full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Etheridge, Alison","last_name":"Etheridge","first_name":"Alison"}],"related_material":{"record":[{"id":"9842","status":"public","relation":"research_data"}]},"file_date_updated":"2020-07-14T12:47:09Z","publist_id":"7250","ec_funded":1,"isi":1,"quality_controlled":"1","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"}],"external_id":{"isi":["000440392900014"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.tpb.2017.11.007","month":"07"},{"publist_id":"7251","related_material":{"record":[{"id":"200","relation":"dissertation_contains","status":"public"}]},"author":[{"full_name":"Ringbauer, Harald","id":"417FCFF4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4884-9682","first_name":"Harald","last_name":"Ringbauer"},{"full_name":"Kolesnikov, Alexander","id":"2D157DB6-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander","last_name":"Kolesnikov"},{"last_name":"Field","first_name":"David","full_name":"Field, David"},{"full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"volume":208,"date_created":"2018-12-11T11:47:12Z","date_updated":"2023-09-11T13:42:38Z","year":"2018","publisher":"Genetics Society of America","department":[{"_id":"NiBa"},{"_id":"ChLa"}],"publication_status":"published","month":"03","doi":"10.1534/genetics.117.300638","language":[{"iso":"eng"}],"oa":1,"external_id":{"isi":["000426219600025"]},"main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/205484v1","open_access":"1"}],"isi":1,"quality_controlled":"1","issue":"3","abstract":[{"text":"In continuous populations with local migration, nearby pairs of individuals have on average more similar genotypes\r\nthan geographically well separated pairs. A barrier to gene flow distorts this classical pattern of isolation by distance. Genetic similarity is decreased for sample pairs on different sides of the barrier and increased for pairs on the same side near the barrier. Here, we introduce an inference scheme that utilizes this signal to detect and estimate the strength of a linear barrier to gene flow in two-dimensions. We use a diffusion approximation to model the effects of a barrier on the geographical spread of ancestry backwards in time. This approach allows us to calculate the chance of recent coalescence and probability of identity by descent. We introduce an inference scheme that fits these theoretical results to the geographical covariance structure of bialleleic genetic markers. It can estimate the strength of the barrier as well as several demographic parameters. We investigate the power of our inference scheme to detect barriers by applying it to a wide range of simulated data. We also showcase an example application to a Antirrhinum majus (snapdragon) flower color hybrid zone, where we do not detect any signal of a strong genome wide barrier to gene flow.","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","_id":"563","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 208","status":"public","title":"Estimating barriers to gene flow from distorted isolation-by-distance patterns","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2018-03-01T00:00:00Z","citation":{"ama":"Ringbauer H, Kolesnikov A, Field D, Barton NH. Estimating barriers to gene flow from distorted isolation-by-distance patterns. Genetics. 2018;208(3):1231-1245. doi:10.1534/genetics.117.300638","ista":"Ringbauer H, Kolesnikov A, Field D, Barton NH. 2018. Estimating barriers to gene flow from distorted isolation-by-distance patterns. Genetics. 208(3), 1231–1245.","apa":"Ringbauer, H., Kolesnikov, A., Field, D., & Barton, N. H. (2018). Estimating barriers to gene flow from distorted isolation-by-distance patterns. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.117.300638","ieee":"H. Ringbauer, A. Kolesnikov, D. Field, and N. H. Barton, “Estimating barriers to gene flow from distorted isolation-by-distance patterns,” Genetics, vol. 208, no. 3. Genetics Society of America, pp. 1231–1245, 2018.","mla":"Ringbauer, Harald, et al. “Estimating Barriers to Gene Flow from Distorted Isolation-by-Distance Patterns.” Genetics, vol. 208, no. 3, Genetics Society of America, 2018, pp. 1231–45, doi:10.1534/genetics.117.300638.","short":"H. Ringbauer, A. Kolesnikov, D. Field, N.H. Barton, Genetics 208 (2018) 1231–1245.","chicago":"Ringbauer, Harald, Alexander Kolesnikov, David Field, and Nicholas H Barton. “Estimating Barriers to Gene Flow from Distorted Isolation-by-Distance Patterns.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.117.300638."},"publication":"Genetics","page":"1231-1245"},{"date_published":"2018-07-01T00:00:00Z","article_type":"original","page":"861-883","publication":"Genetics","citation":{"chicago":"Bodova, Katarina, Tadeas Priklopil, David Field, Nicholas H Barton, and Melinda Pickup. “Evolutionary Pathways for the Generation of New Self-Incompatibility Haplotypes in a Non-Self Recognition System.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.118.300748.","short":"K. Bodova, T. Priklopil, D. Field, N.H. Barton, M. Pickup, Genetics 209 (2018) 861–883.","mla":"Bodova, Katarina, et al. “Evolutionary Pathways for the Generation of New Self-Incompatibility Haplotypes in a Non-Self Recognition System.” Genetics, vol. 209, no. 3, Genetics Society of America, 2018, pp. 861–83, doi:10.1534/genetics.118.300748.","apa":"Bodova, K., Priklopil, T., Field, D., Barton, N. H., & Pickup, M. (2018). Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.118.300748","ieee":"K. Bodova, T. Priklopil, D. Field, N. H. Barton, and M. Pickup, “Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system,” Genetics, vol. 209, no. 3. Genetics Society of America, pp. 861–883, 2018.","ista":"Bodova K, Priklopil T, Field D, Barton NH, Pickup M. 2018. Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system. Genetics. 209(3), 861–883.","ama":"Bodova K, Priklopil T, Field D, Barton NH, Pickup M. Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system. Genetics. 2018;209(3):861-883. doi:10.1534/genetics.118.300748"},"day":"01","article_processing_charge":"No","scopus_import":"1","oa_version":"Preprint","title":"Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system","status":"public","intvolume":" 209","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"316","abstract":[{"text":"Self-incompatibility (SI) is a genetically based recognition system that functions to prevent self-fertilization and mating among related plants. An enduring puzzle in SI is how the high diversity observed in nature arises and is maintained. Based on the underlying recognition mechanism, SI can be classified into two main groups: self- and non-self recognition. Most work has focused on diversification within self-recognition systems despite expected differences between the two groups in the evolutionary pathways and outcomes of diversification. Here, we use a deterministic population genetic model and stochastic simulations to investigate how novel S-haplotypes evolve in a gametophytic non-self recognition (SRNase/S Locus F-box (SLF)) SI system. For this model the pathways for diversification involve either the maintenance or breakdown of SI and can vary in the order of mutations of the female (SRNase) and male (SLF) components. We show analytically that diversification can occur with high inbreeding depression and self-pollination, but this varies with evolutionary pathway and level of completeness (which determines the number of potential mating partners in the population), and in general is more likely for lower haplotype number. The conditions for diversification are broader in stochastic simulations of finite population size. However, the number of haplotypes observed under high inbreeding and moderate to high self-pollination is less than that commonly observed in nature. Diversification was observed through pathways that maintain SI as well as through self-compatible intermediates. Yet the lifespan of diversified haplotypes was sensitive to their level of completeness. By examining diversification in a non-self recognition SI system, this model extends our understanding of the evolution and maintenance of haplotype diversity observed in a self recognition system common in flowering plants.","lang":"eng"}],"issue":"3","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1534/genetics.118.300748","quality_controlled":"1","isi":1,"project":[{"call_identifier":"FP7","name":"Mating system and the evolutionary dynamics of hybrid zones","grant_number":"329960","_id":"25B36484-B435-11E9-9278-68D0E5697425"},{"name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"external_id":{"isi":["000437171700017"]},"oa":1,"main_file_link":[{"url":"https://www.biorxiv.org/node/80098.abstract","open_access":"1"}],"month":"07","date_updated":"2023-09-11T13:57:43Z","date_created":"2018-12-11T11:45:47Z","volume":209,"author":[{"full_name":"Bodova, Katarina","last_name":"Bodova","first_name":"Katarina","orcid":"0000-0002-7214-0171","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87"},{"id":"3C869AA0-F248-11E8-B48F-1D18A9856A87","first_name":"Tadeas","last_name":"Priklopil","full_name":"Priklopil, Tadeas"},{"full_name":"Field, David","orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field","first_name":"David"},{"full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Melinda","last_name":"Pickup","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6118-0541","full_name":"Pickup, Melinda"}],"related_material":{"record":[{"id":"9813","status":"public","relation":"research_data"}],"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/recognizing-others-but-not-yourself-new-insights-into-the-evolution-of-plant-mating/"}]},"publication_status":"published","publisher":"Genetics Society of America","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"year":"2018","ec_funded":1},{"article_processing_charge":"No","day":"30","month":"04","citation":{"ama":"Bodova K, Priklopil T, Field D, Barton NH, Pickup M. Supplemental material for Bodova et al., 2018. 2018. doi:10.25386/genetics.6148304.v1","apa":"Bodova, K., Priklopil, T., Field, D., Barton, N. H., & Pickup, M. (2018). Supplemental material for Bodova et al., 2018. Genetics Society of America. https://doi.org/10.25386/genetics.6148304.v1","ieee":"K. Bodova, T. Priklopil, D. Field, N. H. Barton, and M. Pickup, “Supplemental material for Bodova et al., 2018.” Genetics Society of America, 2018.","ista":"Bodova K, Priklopil T, Field D, Barton NH, Pickup M. 2018. Supplemental material for Bodova et al., 2018, Genetics Society of America, 10.25386/genetics.6148304.v1.","short":"K. Bodova, T. Priklopil, D. Field, N.H. Barton, M. Pickup, (2018).","mla":"Bodova, Katarina, et al. Supplemental Material for Bodova et Al., 2018. Genetics Society of America, 2018, doi:10.25386/genetics.6148304.v1.","chicago":"Bodova, Katarina, Tadeas Priklopil, David Field, Nicholas H Barton, and Melinda Pickup. “Supplemental Material for Bodova et Al., 2018.” Genetics Society of America, 2018. https://doi.org/10.25386/genetics.6148304.v1."},"main_file_link":[{"url":"https://doi.org/10.25386/genetics.6148304.v1","open_access":"1"}],"oa":1,"doi":"10.25386/genetics.6148304.v1","date_published":"2018-04-30T00:00:00Z","type":"research_data_reference","abstract":[{"lang":"eng","text":"File S1 contains figures that clarify the following features: (i) effect of population size on the average number/frequency of SI classes, (ii) changes in the minimal completeness deficit in time for a single class, and (iii) diversification diagrams for all studied pathways, including the summary figure for k = 8. File S2 contains the code required for a stochastic simulation of the SLF system with an example. This file also includes the output in the form of figures and tables."}],"_id":"9813","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2018","publisher":"Genetics Society of America","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"status":"public","title":"Supplemental material for Bodova et al., 2018","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"316"}]},"author":[{"full_name":"Bod'ová, Katarína","last_name":"Bod'ová","first_name":"Katarína","orcid":"0000-0002-7214-0171","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Priklopil, Tadeas","id":"3C869AA0-F248-11E8-B48F-1D18A9856A87","last_name":"Priklopil","first_name":"Tadeas"},{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478","first_name":"David","last_name":"Field","full_name":"Field, David"},{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"},{"orcid":"0000-0001-6118-0541","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","last_name":"Pickup","first_name":"Melinda","full_name":"Pickup, Melinda"}],"oa_version":"Published Version","date_updated":"2023-09-11T13:57:42Z","date_created":"2021-08-06T13:04:32Z"},{"has_accepted_license":"1","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2018-05-01T00:00:00Z","page":"1604 - 1633","citation":{"chicago":"Oliveto, Pietro, Tiago Paixao, Jorge Pérez Heredia, Dirk Sudholt, and Barbora Trubenova. “How to Escape Local Optima in Black Box Optimisation When Non Elitism Outperforms Elitism.” Algorithmica. Springer, 2018. https://doi.org/10.1007/s00453-017-0369-2.","mla":"Oliveto, Pietro, et al. “How to Escape Local Optima in Black Box Optimisation When Non Elitism Outperforms Elitism.” Algorithmica, vol. 80, no. 5, Springer, 2018, pp. 1604–33, doi:10.1007/s00453-017-0369-2.","short":"P. Oliveto, T. Paixao, J. Pérez Heredia, D. Sudholt, B. Trubenova, Algorithmica 80 (2018) 1604–1633.","ista":"Oliveto P, Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. 2018. How to escape local optima in black box optimisation when non elitism outperforms elitism. Algorithmica. 80(5), 1604–1633.","apa":"Oliveto, P., Paixao, T., Pérez Heredia, J., Sudholt, D., & Trubenova, B. (2018). How to escape local optima in black box optimisation when non elitism outperforms elitism. Algorithmica. Springer. https://doi.org/10.1007/s00453-017-0369-2","ieee":"P. Oliveto, T. Paixao, J. Pérez Heredia, D. Sudholt, and B. Trubenova, “How to escape local optima in black box optimisation when non elitism outperforms elitism,” Algorithmica, vol. 80, no. 5. Springer, pp. 1604–1633, 2018.","ama":"Oliveto P, Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. How to escape local optima in black box optimisation when non elitism outperforms elitism. Algorithmica. 2018;80(5):1604-1633. doi:10.1007/s00453-017-0369-2"},"publication":"Algorithmica","issue":"5","abstract":[{"lang":"eng","text":"Escaping local optima is one of the major obstacles to function optimisation. Using the metaphor of a fitness landscape, local optima correspond to hills separated by fitness valleys that have to be overcome. We define a class of fitness valleys of tunable difficulty by considering their length, representing the Hamming path between the two optima and their depth, the drop in fitness. For this function class we present a runtime comparison between stochastic search algorithms using different search strategies. The (1+1) EA is a simple and well-studied evolutionary algorithm that has to jump across the valley to a point of higher fitness because it does not accept worsening moves (elitism). In contrast, the Metropolis algorithm and the Strong Selection Weak Mutation (SSWM) algorithm, a famous process in population genetics, are both able to cross the fitness valley by accepting worsening moves. We show that the runtime of the (1+1) EA depends critically on the length of the valley while the runtimes of the non-elitist algorithms depend crucially on the depth of the valley. Moreover, we show that both SSWM and Metropolis can also efficiently optimise a rugged function consisting of consecutive valleys."}],"type":"journal_article","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":691245,"creator":"system","file_name":"IST-2018-1014-v1+1_2018_Paixao_Escape.pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:54Z","date_created":"2018-12-12T10:08:14Z","checksum":"7d92f5d7be81e387edeec4f06442791c","relation":"main_file","file_id":"4674"}],"pubrep_id":"1014","intvolume":" 80","status":"public","title":"How to escape local optima in black box optimisation when non elitism outperforms elitism","ddc":["576"],"_id":"723","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","month":"05","language":[{"iso":"eng"}],"doi":"10.1007/s00453-017-0369-2","project":[{"call_identifier":"FP7","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","grant_number":"618091","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000428239300010"]},"ec_funded":1,"publist_id":"6957","file_date_updated":"2020-07-14T12:47:54Z","volume":80,"date_updated":"2023-09-11T14:11:35Z","date_created":"2018-12-11T11:48:09Z","author":[{"last_name":"Oliveto","first_name":"Pietro","full_name":"Oliveto, Pietro"},{"full_name":"Paixao, Tiago","orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","last_name":"Paixao","first_name":"Tiago"},{"full_name":"Pérez Heredia, Jorge","last_name":"Pérez Heredia","first_name":"Jorge"},{"first_name":"Dirk","last_name":"Sudholt","full_name":"Sudholt, Dirk"},{"first_name":"Barbora","last_name":"Trubenova","id":"42302D54-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6873-2967","full_name":"Trubenova, Barbora"}],"publisher":"Springer","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"publication_status":"published","year":"2018"},{"publist_id":"7617","date_created":"2018-12-11T11:45:36Z","date_updated":"2023-09-13T08:22:32Z","volume":209,"author":[{"id":"42377A0A-F248-11E8-B48F-1D18A9856A87","last_name":"Sachdeva","first_name":"Himani","full_name":"Sachdeva, Himani"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H"}],"publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Genetics Society of America","year":"2018","month":"08","language":[{"iso":"eng"}],"doi":"10.1534/genetics.118.301018","isi":1,"quality_controlled":"1","oa":1,"external_id":{"isi":["000440014100020"]},"main_file_link":[{"url":"https://www.biorxiv.org/content/early/2017/11/30/227082","open_access":"1"}],"abstract":[{"text":"Adaptive introgression is common in nature and can be driven by selection acting on multiple, linked genes. We explore the effects of polygenic selection on introgression under the infinitesimal model with linkage. This model assumes that the introgressing block has an effectively infinite number of genes, each with an infinitesimal effect on the trait under selection. The block is assumed to introgress under directional selection within a native population that is genetically homogeneous. We use individual-based simulations and a branching process approximation to compute various statistics of the introgressing block, and explore how these depend on parameters such as the map length and initial trait value associated with the introgressing block, the genetic variability along the block, and the strength of selection. Our results show that the introgression dynamics of a block under infinitesimal selection is qualitatively different from the dynamics of neutral introgression. We also find that in the long run, surviving descendant blocks are likely to have intermediate lengths, and clarify how the length is shaped by the interplay between linkage and infinitesimal selection. Our results suggest that it may be difficult to distinguish introgression of single loci from that of genomic blocks with multiple, tightly linked and weakly selected loci.","lang":"eng"}],"issue":"4","type":"journal_article","oa_version":"Submitted Version","status":"public","title":"Introgression of a block of genome under infinitesimal selection","intvolume":" 209","_id":"282","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2018-08-01T00:00:00Z","page":"1279 - 1303","publication":"Genetics","citation":{"chicago":"Sachdeva, Himani, and Nicholas H Barton. “Introgression of a Block of Genome under Infinitesimal Selection.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.118.301018.","mla":"Sachdeva, Himani, and Nicholas H. Barton. “Introgression of a Block of Genome under Infinitesimal Selection.” Genetics, vol. 209, no. 4, Genetics Society of America, 2018, pp. 1279–303, doi:10.1534/genetics.118.301018.","short":"H. Sachdeva, N.H. Barton, Genetics 209 (2018) 1279–1303.","ista":"Sachdeva H, Barton NH. 2018. Introgression of a block of genome under infinitesimal selection. Genetics. 209(4), 1279–1303.","apa":"Sachdeva, H., & Barton, N. H. (2018). Introgression of a block of genome under infinitesimal selection. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.118.301018","ieee":"H. Sachdeva and N. H. Barton, “Introgression of a block of genome under infinitesimal selection,” Genetics, vol. 209, no. 4. Genetics Society of America, pp. 1279–1303, 2018.","ama":"Sachdeva H, Barton NH. Introgression of a block of genome under infinitesimal selection. Genetics. 2018;209(4):1279-1303. doi:10.1534/genetics.118.301018"}},{"issue":"4","abstract":[{"lang":"eng","text":"We study how a block of genome with a large number of weakly selected loci introgresses under directional selection into a genetically homogeneous population. We derive exact expressions for the expected rate of growth of any fragment of the introduced block during the initial phase of introgression, and show that the growth rate of a single-locus variant is largely insensitive to its own additive effect, but depends instead on the combined effect of all loci within a characteristic linkage scale. The expected growth rate of a fragment is highly correlated with its long-term introgression probability in populations of moderate size, and can hence identify variants that are likely to introgress across replicate populations. We clarify how the introgression probability of an individual variant is determined by the interplay between hitchhiking with relatively large fragments during the early phase of introgression and selection on fine-scale variation within these, which at longer times results in differential introgression probabilities for beneficial and deleterious loci within successful fragments. By simulating individuals, we also investigate how introgression probabilities at individual loci depend on the variance of fitness effects, the net fitness of the introduced block, and the size of the recipient population, and how this shapes the net advance under selection. Our work suggests that even highly replicable substitutions may be associated with a range of selective effects, which makes it challenging to fine map the causal loci that underlie polygenic adaptation."}],"type":"journal_article","oa_version":"Preprint","intvolume":" 210","status":"public","title":"Replicability of introgression under linked, polygenic selection","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"39","article_processing_charge":"No","day":"04","scopus_import":"1","date_published":"2018-12-04T00:00:00Z","page":"1411-1427","article_type":"original","citation":{"ista":"Sachdeva H, Barton NH. 2018. Replicability of introgression under linked, polygenic selection. Genetics. 210(4), 1411–1427.","ieee":"H. Sachdeva and N. H. Barton, “Replicability of introgression under linked, polygenic selection,” Genetics, vol. 210, no. 4. Genetics Society of America, pp. 1411–1427, 2018.","apa":"Sachdeva, H., & Barton, N. H. (2018). Replicability of introgression under linked, polygenic selection. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.118.301429","ama":"Sachdeva H, Barton NH. Replicability of introgression under linked, polygenic selection. Genetics. 2018;210(4):1411-1427. doi:10.1534/genetics.118.301429","chicago":"Sachdeva, Himani, and Nicholas H Barton. “Replicability of Introgression under Linked, Polygenic Selection.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.118.301429.","mla":"Sachdeva, Himani, and Nicholas H. Barton. “Replicability of Introgression under Linked, Polygenic Selection.” Genetics, vol. 210, no. 4, Genetics Society of America, 2018, pp. 1411–27, doi:10.1534/genetics.118.301429.","short":"H. Sachdeva, N.H. Barton, Genetics 210 (2018) 1411–1427."},"publication":"Genetics","volume":210,"date_created":"2018-12-11T11:44:18Z","date_updated":"2023-09-18T08:10:29Z","author":[{"full_name":"Sachdeva, Himani","id":"42377A0A-F248-11E8-B48F-1D18A9856A87","first_name":"Himani","last_name":"Sachdeva"},{"full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"NiBa"}],"publisher":"Genetics Society of America","publication_status":"published","year":"2018","publication_identifier":{"issn":["00166731"]},"month":"12","language":[{"iso":"eng"}],"doi":"10.1534/genetics.118.301429","isi":1,"quality_controlled":"1","external_id":{"isi":["000452315900021"]},"oa":1,"main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/379578v1","open_access":"1"}]},{"language":[{"iso":"eng"}],"doi":"10.1073/pnas.1801832115","isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"external_id":{"pmid":["30297406"],"isi":["000448040500065"]},"month":"10","publication_identifier":{"issn":["00278424"]},"date_updated":"2023-09-18T08:36:49Z","date_created":"2018-12-11T11:44:18Z","volume":115,"author":[{"full_name":"Tavares, Hugo","last_name":"Tavares","first_name":"Hugo"},{"full_name":"Whitley, Annabel","last_name":"Whitley","first_name":"Annabel"},{"orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field","first_name":"David","full_name":"Field, David"},{"full_name":"Bradley, Desmond","last_name":"Bradley","first_name":"Desmond"},{"first_name":"Matthew","last_name":"Couchman","full_name":"Couchman, Matthew"},{"full_name":"Copsey, Lucy","first_name":"Lucy","last_name":"Copsey"},{"full_name":"Elleouet, Joane","last_name":"Elleouet","first_name":"Joane"},{"full_name":"Burrus, Monique","first_name":"Monique","last_name":"Burrus"},{"last_name":"Andalo","first_name":"Christophe","full_name":"Andalo, Christophe"},{"last_name":"Li","first_name":"Miaomiao","full_name":"Li, Miaomiao"},{"last_name":"Li","first_name":"Qun","full_name":"Li, Qun"},{"first_name":"Yongbiao","last_name":"Xue","full_name":"Xue, Yongbiao"},{"full_name":"Rebocho, Alexandra B","last_name":"Rebocho","first_name":"Alexandra B"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"},{"last_name":"Coen","first_name":"Enrico","full_name":"Coen, Enrico"}],"publication_status":"published","publisher":"National Academy of Sciences","department":[{"_id":"NiBa"}],"acknowledgement":" ERC Grant 201252 (to N.H.B.)","year":"2018","pmid":1,"file_date_updated":"2020-07-14T12:46:16Z","publist_id":"8017","date_published":"2018-10-23T00:00:00Z","page":"11006 - 11011","publication":"PNAS","citation":{"chicago":"Tavares, Hugo, Annabel Whitley, David Field, Desmond Bradley, Matthew Couchman, Lucy Copsey, Joane Elleouet, et al. “Selection and Gene Flow Shape Genomic Islands That Control Floral Guides.” PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1801832115.","short":"H. Tavares, A. Whitley, D. Field, D. Bradley, M. Couchman, L. Copsey, J. Elleouet, M. Burrus, C. Andalo, M. Li, Q. Li, Y. Xue, A.B. Rebocho, N.H. Barton, E. Coen, PNAS 115 (2018) 11006–11011.","mla":"Tavares, Hugo, et al. “Selection and Gene Flow Shape Genomic Islands That Control Floral Guides.” PNAS, vol. 115, no. 43, National Academy of Sciences, 2018, pp. 11006–11, doi:10.1073/pnas.1801832115.","ieee":"H. Tavares et al., “Selection and gene flow shape genomic islands that control floral guides,” PNAS, vol. 115, no. 43. National Academy of Sciences, pp. 11006–11011, 2018.","apa":"Tavares, H., Whitley, A., Field, D., Bradley, D., Couchman, M., Copsey, L., … Coen, E. (2018). Selection and gene flow shape genomic islands that control floral guides. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1801832115","ista":"Tavares H, Whitley A, Field D, Bradley D, Couchman M, Copsey L, Elleouet J, Burrus M, Andalo C, Li M, Li Q, Xue Y, Rebocho AB, Barton NH, Coen E. 2018. Selection and gene flow shape genomic islands that control floral guides. PNAS. 115(43), 11006–11011.","ama":"Tavares H, Whitley A, Field D, et al. Selection and gene flow shape genomic islands that control floral guides. PNAS. 2018;115(43):11006-11011. doi:10.1073/pnas.1801832115"},"day":"23","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","oa_version":"Published Version","file":[{"date_updated":"2020-07-14T12:46:16Z","date_created":"2018-12-17T08:44:03Z","checksum":"d2305d0cc81dbbe4c1c677d64ad6f6d1","file_id":"5683","relation":"main_file","creator":"dernst","file_size":1911302,"content_type":"application/pdf","file_name":"11006.full.pdf","access_level":"open_access"}],"ddc":["570"],"status":"public","title":"Selection and gene flow shape genomic islands that control floral guides","intvolume":" 115","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"38","abstract":[{"text":"Genomes of closely-related species or populations often display localized regions of enhanced relative sequence divergence, termed genomic islands. It has been proposed that these islands arise through selective sweeps and/or barriers to gene flow. Here, we genetically dissect a genomic island that controls flower color pattern differences between two subspecies of Antirrhinum majus, A.m.striatum and A.m.pseudomajus, and relate it to clinal variation across a natural hybrid zone. We show that selective sweeps likely raised relative divergence at two tightly-linked MYB-like transcription factors, leading to distinct flower patterns in the two subspecies. The two patterns provide alternate floral guides and create a strong barrier to gene flow where populations come into contact. This barrier affects the selected flower color genes and tightlylinked loci, but does not extend outside of this domain, allowing gene flow to lower relative divergence for the rest of the chromosome. Thus, both selective sweeps and barriers to gene flow play a role in shaping genomic islands: sweeps cause elevation in relative divergence, while heterogeneous gene flow flattens the surrounding \"sea,\" making the island of divergence stand out. By showing how selective sweeps establish alternative adaptive phenotypes that lead to barriers to gene flow, our study sheds light on possible mechanisms leading to reproductive isolation and speciation.","lang":"eng"}],"issue":"43","type":"journal_article"},{"publication_status":"published","publisher":"Wiley","department":[{"_id":"NiBa"}],"year":"2018","pmid":1,"date_updated":"2023-09-19T10:06:08Z","date_created":"2018-12-11T11:44:18Z","volume":27,"author":[{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton"}],"related_material":{"record":[{"relation":"research_data","status":"public","id":"9805"}]},"file_date_updated":"2020-07-14T12:46:22Z","publist_id":"8014","isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000454600500001"],"pmid":["30599087"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1111/mec.14950","month":"12","publication_identifier":{"issn":["1365294X"]},"title":"The consequences of an introgression event","ddc":["576"],"status":"public","intvolume":" 27","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"40","oa_version":"Published Version","file":[{"file_id":"6652","relation":"main_file","date_created":"2019-07-19T06:54:46Z","date_updated":"2020-07-14T12:46:22Z","access_level":"open_access","file_name":"2018_MolecularEcology_BartonNick.pdf","creator":"apreinsp","file_size":295452,"content_type":"application/pdf"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Hanemaaijer et al. (Molecular Ecology, 27, 2018) describe the genetic consequences of the introgression of an insecticide resistance allele into a mosquito population. Linked alleles initially increased, but many of these later declined. It is hard to determine whether this decline was due to counter‐selection, rather than simply to chance."}],"issue":"24","article_type":"letter_note","page":"4973-4975","publication":"Molecular Ecology","citation":{"ama":"Barton NH. The consequences of an introgression event. Molecular Ecology. 2018;27(24):4973-4975. doi:10.1111/mec.14950","ieee":"N. H. Barton, “The consequences of an introgression event,” Molecular Ecology, vol. 27, no. 24. Wiley, pp. 4973–4975, 2018.","apa":"Barton, N. H. (2018). The consequences of an introgression event. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.14950","ista":"Barton NH. 2018. The consequences of an introgression event. Molecular Ecology. 27(24), 4973–4975.","short":"N.H. Barton, Molecular Ecology 27 (2018) 4973–4975.","mla":"Barton, Nicholas H. “The Consequences of an Introgression Event.” Molecular Ecology, vol. 27, no. 24, Wiley, 2018, pp. 4973–75, doi:10.1111/mec.14950.","chicago":"Barton, Nicholas H. “The Consequences of an Introgression Event.” Molecular Ecology. Wiley, 2018. https://doi.org/10.1111/mec.14950."},"date_published":"2018-12-31T00:00:00Z","scopus_import":"1","day":"31","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)"},{"article_type":"original","page":"377 - 382","publication":"Genetics","citation":{"ama":"Charlesworth B, Barton NH. The spread of an inversion with migration and selection. Genetics. 2018;208(1):377-382. doi:10.1534/genetics.117.300426","ieee":"B. Charlesworth and N. H. Barton, “The spread of an inversion with migration and selection,” Genetics, vol. 208, no. 1. Genetics , pp. 377–382, 2018.","apa":"Charlesworth, B., & Barton, N. H. (2018). The spread of an inversion with migration and selection. Genetics. Genetics . https://doi.org/10.1534/genetics.117.300426","ista":"Charlesworth B, Barton NH. 2018. The spread of an inversion with migration and selection. Genetics. 208(1), 377–382.","short":"B. Charlesworth, N.H. Barton, Genetics 208 (2018) 377–382.","mla":"Charlesworth, Brian, and Nicholas H. Barton. “The Spread of an Inversion with Migration and Selection.” Genetics, vol. 208, no. 1, Genetics , 2018, pp. 377–82, doi:10.1534/genetics.117.300426.","chicago":"Charlesworth, Brian, and Nicholas H Barton. “The Spread of an Inversion with Migration and Selection.” Genetics. Genetics , 2018. https://doi.org/10.1534/genetics.117.300426."},"date_published":"2018-01-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","title":"The spread of an inversion with migration and selection","status":"public","intvolume":" 208","_id":"565","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","type":"journal_article","abstract":[{"text":"We re-examine the model of Kirkpatrick and Barton for the spread of an inversion into a local population. This model assumes that local selection maintains alleles at two or more loci, despite immigration of alternative alleles at these loci from another population. We show that an inversion is favored because it prevents the breakdown of linkage disequilibrium generated by migration; the selective advantage of an inversion is proportional to the amount of recombination between the loci involved, as in other cases where inversions are selected for. We derive expressions for the rate of spread of an inversion; when the loci covered by the inversion are tightly linked, these conditions deviate substantially from those proposed previously, and imply that an inversion can then have only a small advantage. ","lang":"eng"}],"issue":"1","isi":1,"quality_controlled":"1","oa":1,"external_id":{"isi":["000419356300025"],"pmid":["29158424"]},"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753870/"}],"language":[{"iso":"eng"}],"doi":"10.1534/genetics.117.300426","month":"01","publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Genetics ","year":"2018","pmid":1,"date_updated":"2023-09-19T10:12:31Z","date_created":"2018-12-11T11:47:12Z","volume":208,"author":[{"full_name":"Charlesworth, Brian","last_name":"Charlesworth","first_name":"Brian"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"}],"publist_id":"7249"}]