[{"day":"17","publication":"Evolutionary Journal of the Linnean Society","_id":"14833","date_created":"2024-01-18T07:54:10Z","date_published":"2023-08-17T00:00:00Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication_status":"published","publisher":"Oxford University Press","title":"Whole-genome phylogeography of the intertidal snail Littorina saxatilis","file_date_updated":"2024-01-23T08:10:00Z","type":"journal_article","status":"public","month":"08","quality_controlled":"1","has_accepted_license":"1","tmp":{"image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"intvolume":"         2","year":"2023","abstract":[{"text":"Understanding the factors that have shaped the current distributions and diversity of species is a central and longstanding aim of evolutionary biology. The recent inclusion of genomic data into phylogeographic studies has dramatically improved our understanding in organisms where evolutionary relationships have been challenging to infer. We used whole-genome sequences to study the phylogeography of the intertidal snail Littorina saxatilis, which has successfully colonized and diversified across a broad range of coastal environments in the Northern Hemisphere amid repeated cycles of glaciation. Building on past studies based on short DNA sequences, we used genome-wide data to provide a clearer picture of the relationships among samples spanning most of the species natural range. Our results confirm the trans-Atlantic colonization of North America from Europe, and have allowed us to identify rough locations of glacial refugia and to infer likely routes of colonization within Europe. We also investigated the signals in different datasets to account for the effects of genomic architecture and non-neutral evolution, which provides new insights about diversification of four ecotypes of L. saxatilis (the crab, wave, barnacle, and brackish ecotypes) at different spatial scales. Overall, we provide a much clearer picture of the biogeography of L. saxatilis, providing a foundation for more detailed phylogenomic and demographic studies.","lang":"eng"}],"acknowledgement":"Isobel Eyres, Richard Turney, Graciela Sotelo, Jenny Larson, and Stéphane Loisel helped with the collection and processing of samples. Petri Kemppainen kindly provided samples from Trondheim Fjord. Mark Dunning helped with the development of bioinformatic pipelines. The analysis of genomic data was conducted on the University of Sheffield high-performance computing cluster, ShARC. Funding was provided by the Natural Environment Research Council (NERC) and the European Research Council (ERC). J.G. was funded by a Juntas Industriales y Navales (JIN) project (Ministerio de Ciencia, Innovación y Universidades, code RTI2018-101274-J-I00).","ddc":["570"],"doi":"10.1093/evolinnean/kzad002","citation":{"ama":"Stankowski S, Zagrodzka ZB, Galindo J, et al. Whole-genome phylogeography of the intertidal snail Littorina saxatilis. <i>Evolutionary Journal of the Linnean Society</i>. 2023;2(1). doi:<a href=\"https://doi.org/10.1093/evolinnean/kzad002\">10.1093/evolinnean/kzad002</a>","ista":"Stankowski S, Zagrodzka ZB, Galindo J, Montaño-Rendón M, Faria R, Mikhailova N, Blakeslee AMH, Arnason E, Broquet T, Morales HE, Grahame JW, Westram AM, Johannesson K, Butlin RK. 2023. Whole-genome phylogeography of the intertidal snail Littorina saxatilis. Evolutionary Journal of the Linnean Society. 2(1), kzad002.","apa":"Stankowski, S., Zagrodzka, Z. B., Galindo, J., Montaño-Rendón, M., Faria, R., Mikhailova, N., … Butlin, R. K. (2023). Whole-genome phylogeography of the intertidal snail Littorina saxatilis. <i>Evolutionary Journal of the Linnean Society</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/evolinnean/kzad002\">https://doi.org/10.1093/evolinnean/kzad002</a>","ieee":"S. Stankowski <i>et al.</i>, “Whole-genome phylogeography of the intertidal snail Littorina saxatilis,” <i>Evolutionary Journal of the Linnean Society</i>, vol. 2, no. 1. Oxford University Press, 2023.","mla":"Stankowski, Sean, et al. “Whole-Genome Phylogeography of the Intertidal Snail Littorina Saxatilis.” <i>Evolutionary Journal of the Linnean Society</i>, vol. 2, no. 1, kzad002, Oxford University Press, 2023, doi:<a href=\"https://doi.org/10.1093/evolinnean/kzad002\">10.1093/evolinnean/kzad002</a>.","short":"S. Stankowski, Z.B. Zagrodzka, J. Galindo, M. Montaño-Rendón, R. Faria, N. Mikhailova, A.M.H. Blakeslee, E. Arnason, T. Broquet, H.E. Morales, J.W. Grahame, A.M. Westram, K. Johannesson, R.K. Butlin, Evolutionary Journal of the Linnean Society 2 (2023).","chicago":"Stankowski, Sean, Zuzanna B Zagrodzka, Juan Galindo, Mauricio Montaño-Rendón, Rui Faria, Natalia Mikhailova, April M H Blakeslee, et al. “Whole-Genome Phylogeography of the Intertidal Snail Littorina Saxatilis.” <i>Evolutionary Journal of the Linnean Society</i>. Oxford University Press, 2023. <a href=\"https://doi.org/10.1093/evolinnean/kzad002\">https://doi.org/10.1093/evolinnean/kzad002</a>."},"issue":"1","article_processing_charge":"Yes","article_type":"original","volume":2,"department":[{"_id":"NiBa"}],"file":[{"success":1,"relation":"main_file","creator":"dernst","file_size":3408944,"date_created":"2024-01-23T08:10:00Z","date_updated":"2024-01-23T08:10:00Z","checksum":"ba6f9102d3a9fe6631c4fa398c5e4313","access_level":"open_access","content_type":"application/pdf","file_id":"14875","file_name":"2023_EvolJourLinneanSociety_Stankowski.pdf"}],"article_number":"kzad002","publication_identifier":{"eissn":["2752-938X"]},"fulldoi":"https://doi.org/10.1093/evolinnean/kzad002","corr_author":"1","oa_version":"Published Version","language":[{"iso":"eng"}],"author":[{"full_name":"Stankowski, Sean","last_name":"Stankowski","id":"43161670-5719-11EA-8025-FABC3DDC885E","first_name":"Sean"},{"last_name":"Zagrodzka","first_name":"Zuzanna B","full_name":"Zagrodzka, Zuzanna B"},{"first_name":"Juan","last_name":"Galindo","full_name":"Galindo, Juan"},{"first_name":"Mauricio","last_name":"Montaño-Rendón","full_name":"Montaño-Rendón, Mauricio"},{"first_name":"Rui","last_name":"Faria","full_name":"Faria, Rui"},{"full_name":"Mikhailova, Natalia","first_name":"Natalia","last_name":"Mikhailova"},{"last_name":"Blakeslee","first_name":"April M H","full_name":"Blakeslee, April M H"},{"first_name":"Einar","last_name":"Arnason","full_name":"Arnason, Einar"},{"last_name":"Broquet","first_name":"Thomas","full_name":"Broquet, Thomas"},{"full_name":"Morales, Hernán E","last_name":"Morales","first_name":"Hernán E"},{"full_name":"Grahame, John W","first_name":"John W","last_name":"Grahame"},{"orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","first_name":"Anja M"},{"last_name":"Johannesson","first_name":"Kerstin","full_name":"Johannesson, Kerstin"},{"full_name":"Butlin, Roger K","last_name":"Butlin","first_name":"Roger K"}],"date_updated":"2024-10-09T21:07:54Z","oa":1},{"oa":1,"author":[{"full_name":"Reynes, Lauric","last_name":"Reynes","first_name":"Lauric"}],"date_updated":"2026-09-09T09:33:38Z","oa_version":"None","fulldoi":"https://doi.org/10.5061/dryad.tb2rbp064","month":"06","status":"public","title":"Genomic datasets of Laminaria digitata: Paired-end reads from dd-RADseq, reference genome assembly and filtered VCF","type":"research_data_reference","department":[{"_id":"NiBa"}],"publisher":"Repository","article_processing_charge":"No","date_created":"2026-09-09T09:33:28Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2023-06-20T00:00:00Z","main_file_link":[{"url":"https://doi.org/10.5061/dryad.tb2rbp064","open_access":"1"}],"OA_type":"green","_id":"22867","citation":{"mla":"Reynes, Lauric. <i>Genomic Datasets of Laminaria Digitata: Paired-End Reads from Dd-RADseq, Reference Genome Assembly and Filtered VCF</i>. Repository, 2023, doi:<a href=\"https://doi.org/10.5061/dryad.tb2rbp064\">10.5061/dryad.tb2rbp064</a>.","short":"L. Reynes, (2023).","chicago":"Reynes, Lauric. “Genomic Datasets of Laminaria Digitata: Paired-End Reads from Dd-RADseq, Reference Genome Assembly and Filtered VCF.” Repository, 2023. <a href=\"https://doi.org/10.5061/dryad.tb2rbp064\">https://doi.org/10.5061/dryad.tb2rbp064</a>.","ista":"Reynes L. 2023. Genomic datasets of Laminaria digitata: Paired-end reads from dd-RADseq, reference genome assembly and filtered VCF, Repository, <a href=\"https://doi.org/10.5061/dryad.tb2rbp064\">10.5061/dryad.tb2rbp064</a>.","ama":"Reynes L. Genomic datasets of Laminaria digitata: Paired-end reads from dd-RADseq, reference genome assembly and filtered VCF. 2023. doi:<a href=\"https://doi.org/10.5061/dryad.tb2rbp064\">10.5061/dryad.tb2rbp064</a>","apa":"Reynes, L. (2023). Genomic datasets of Laminaria digitata: Paired-end reads from dd-RADseq, reference genome assembly and filtered VCF. Repository. <a href=\"https://doi.org/10.5061/dryad.tb2rbp064\">https://doi.org/10.5061/dryad.tb2rbp064</a>","ieee":"L. Reynes, “Genomic datasets of Laminaria digitata: Paired-end reads from dd-RADseq, reference genome assembly and filtered VCF.” Repository, 2023."},"OA_place":"repository","day":"20","doi":"10.5061/dryad.tb2rbp064","related_material":{"record":[{"relation":"used_in_publication","id":"17237","status":"public"}]},"abstract":[{"lang":"eng","text":"The impact of ongoing climate change on populations will be contingent upon their contemporary adaptive evolution. In this study, we investigated the contemporary evolution of four populations of the cold-water kelp Laminaria digitata by analysing their spatial and temporal genomic variation using ddRAD-sequencing. These populations were sampled from the center to the southern margin of its north-eastern Atlantic distribution at two-time points, spanning at least two generations. Through genome scans for local adaptation at a single time point, we identified candidate loci that showed clinal variation correlated with changes in sea surface temperature (SST) along latitudinal gradients. This finding suggests that SST may drive the adaptive response of these kelp populations, although factors such as species' demographic history should also be considered. Additionally, we performed a simulation approach to distinguish the effect of selection from genetic drift in allele frequency changes over time. This enabled the detection of loci in the southernmost population that exhibited temporal differentiation beyond what would be expected from genetic drift alone: these are candidate loci which could have evolved under selection over time. In contrast, we did not detect any outlier locus based on temporal differentiation in the population from the North Sea, which also displayed low and decreasing levels of genetic diversity. The diverse evolutionary scenarios observed among populations can be attributed to variations in the prevalence of selection relative to genetic drift across different environments. Therefore, our study highlights the potential of temporal genomics to offer valuable insights into the contemporary evolution of marine foundation species facing climate change."}],"year":"2023"},{"OA_type":"green","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2023-12-22T00:00:00Z","main_file_link":[{"url":"https://doi.org/10.5281/zenodo.10423539","open_access":"1"}],"article_processing_charge":"No","date_created":"2026-09-09T09:54:36Z","publisher":"Repository","department":[{"_id":"NiBa"}],"year":"2023","related_material":{"record":[{"relation":"used_in_publication","id":"14850","status":"public"}]},"doi":"10.5281/zenodo.10423539","day":"22","ddc":["570"],"OA_place":"repository","citation":{"chicago":"Pal, Arka, Joshi Mihir, and Maria Thaker. “Raw Data for: Too Much Information? Males Convey Parasite Levels Using More Signal Modalities than Females Utilise.” Repository, 2023. <a href=\"https://doi.org/10.5281/zenodo.10423539\">https://doi.org/10.5281/zenodo.10423539</a>.","short":"A. Pal, J. Mihir, M. Thaker, (2023).","mla":"Pal, Arka, et al. <i>Raw Data for: Too Much Information? Males Convey Parasite Levels Using More Signal Modalities than Females Utilise.</i> Repository, 2023, doi:<a href=\"https://doi.org/10.5281/zenodo.10423539\">10.5281/zenodo.10423539</a>.","ieee":"A. Pal, J. Mihir, and M. Thaker, “Raw data for: Too much information? Males convey parasite levels using more signal modalities than females utilise.” Repository, 2023.","apa":"Pal, A., Mihir, J., &#38; Thaker, M. (2023). Raw data for: Too much information? Males convey parasite levels using more signal modalities than females utilise. Repository. <a href=\"https://doi.org/10.5281/zenodo.10423539\">https://doi.org/10.5281/zenodo.10423539</a>","ista":"Pal A, Mihir J, Thaker M. 2023. Raw data for: Too much information? Males convey parasite levels using more signal modalities than females utilise., Repository, <a href=\"https://doi.org/10.5281/zenodo.10423539\">10.5281/zenodo.10423539</a>.","ama":"Pal A, Mihir J, Thaker M. Raw data for: Too much information? Males convey parasite levels using more signal modalities than females utilise. 2023. doi:<a href=\"https://doi.org/10.5281/zenodo.10423539\">10.5281/zenodo.10423539</a>"},"_id":"22868","date_updated":"2026-09-09T09:54:41Z","author":[{"first_name":"Arka","last_name":"Pal","full_name":"Pal, Arka"},{"full_name":"Mihir, Joshi","last_name":"Mihir","first_name":"Joshi"},{"full_name":"Thaker, Maria","last_name":"Thaker","first_name":"Maria"}],"oa":1,"type":"research_data_reference","title":"Raw data for: Too much information? Males convey parasite levels using more signal modalities than females utilise.","status":"public","month":"12","fulldoi":"https://doi.org/10.5281/zenodo.10423539","oa_version":"None"},{"department":[{"_id":"NiBa"},{"_id":"GradSch"}],"publisher":"Repository","date_created":"2026-09-11T08:15:46Z","article_processing_charge":"No","main_file_link":[{"url":"https://doi.org/10.5281/zenodo.8318994","open_access":"1"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2023-09-05T00:00:00Z","OA_type":"green","_id":"22905","citation":{"ieee":"S. Stankowski <i>et al.</i>, “Data and code for: The genetic architecture of a recent transition to live-bearing in marine snails.” Repository, 2023.","apa":"Stankowski, S., Zagrodzka, Z. B., Garlovsky, M. D., Pal, A., Shipilina, D., Garcia Castillo, D., … Butlin, R. K. (2023). Data and code for: The genetic architecture of a recent transition to live-bearing in marine snails. Repository. <a href=\"https://doi.org/10.5281/zenodo.8318994\">https://doi.org/10.5281/zenodo.8318994</a>","ista":"Stankowski S, Zagrodzka ZB, Garlovsky MD, Pal A, Shipilina D, Garcia Castillo D, Lifchitz H, Le Moan A, Leder E, Reeve J, Johannesson K, Westram AM, Butlin RK. 2023. Data and code for: The genetic architecture of a recent transition to live-bearing in marine snails, Repository, <a href=\"https://doi.org/10.5281/zenodo.8318994\">10.5281/zenodo.8318994</a>.","ama":"Stankowski S, Zagrodzka ZB, Garlovsky MD, et al. Data and code for: The genetic architecture of a recent transition to live-bearing in marine snails. 2023. doi:<a href=\"https://doi.org/10.5281/zenodo.8318994\">10.5281/zenodo.8318994</a>","chicago":"Stankowski, Sean, Zuzanna B. Zagrodzka, Martin D. Garlovsky, Arka Pal, Daria Shipilina, Diego Garcia Castillo, Hila Lifchitz, et al. “Data and Code for: The Genetic Architecture of a Recent Transition to Live-Bearing in Marine Snails.” Repository, 2023. <a href=\"https://doi.org/10.5281/zenodo.8318994\">https://doi.org/10.5281/zenodo.8318994</a>.","short":"S. Stankowski, Z.B. Zagrodzka, M.D. Garlovsky, A. Pal, D. Shipilina, D. Garcia Castillo, H. Lifchitz, A. Le Moan, E. Leder, J. Reeve, K. Johannesson, A.M. Westram, R.K. Butlin, (2023).","mla":"Stankowski, Sean, et al. <i>Data and Code for: The Genetic Architecture of a Recent Transition to Live-Bearing in Marine Snails</i>. Repository, 2023, doi:<a href=\"https://doi.org/10.5281/zenodo.8318994\">10.5281/zenodo.8318994</a>."},"OA_place":"repository","doi":"10.5281/zenodo.8318994","day":"05","related_material":{"record":[{"relation":"used_in_publication","id":"14796","status":"public"}]},"abstract":[{"text":"This repository contains the code and VCF files needed to conduct the analyses in our MS. 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","lang":"eng"}],"year":"2023","oa":1,"date_updated":"2026-09-11T08:15:51Z","author":[{"first_name":"Sean","last_name":"Stankowski","full_name":"Stankowski, Sean"},{"full_name":"Zagrodzka, Zuzanna B.","first_name":"Zuzanna B.","last_name":"Zagrodzka"},{"full_name":"Garlovsky, Martin D.","first_name":"Martin D.","last_name":"Garlovsky"},{"first_name":"Arka","last_name":"Pal","full_name":"Pal, Arka"},{"first_name":"Daria","last_name":"Shipilina","full_name":"Shipilina, Daria"},{"full_name":"Garcia Castillo, Diego","first_name":"Diego","last_name":"Garcia Castillo"},{"last_name":"Lifchitz","first_name":"Hila","full_name":"Lifchitz, Hila"},{"first_name":"Alan","last_name":"Le Moan","full_name":"Le Moan, Alan"},{"first_name":"Erica","last_name":"Leder","full_name":"Leder, Erica"},{"full_name":"Reeve, James","first_name":"James","last_name":"Reeve"},{"last_name":"Johannesson","first_name":"Kerstin","full_name":"Johannesson, Kerstin"},{"first_name":"Anja M.","last_name":"Westram","full_name":"Westram, Anja M."},{"last_name":"Butlin","first_name":"Roger K.","full_name":"Butlin, Roger K."}],"fulldoi":"https://doi.org/10.5281/zenodo.8318994","oa_version":"None","month":"09","status":"public","title":"Data and code for: The genetic architecture of a recent transition to live-bearing in marine snails","type":"research_data_reference"},{"day":"05","page":"21","_id":"12800","OA_place":"publisher","date_published":"2023-04-05T00:00:00Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_created":"2023-04-04T18:57:11Z","degree_awarded":"MS","publisher":"Institute of Science and Technology Austria","publication_status":"published","supervisor":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"}],"status":"public","type":"dissertation","file_date_updated":"2023-06-02T22:30:04Z","title":"The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone","month":"04","has_accepted_license":"1","ddc":["576"],"doi":"10.15479/at:ista:12800","abstract":[{"lang":"eng","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. "}],"year":"2023","alternative_title":["ISTA Master's Thesis"],"citation":{"apa":"Julseth, M. (2023). <i>The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:12800\">https://doi.org/10.15479/at:ista:12800</a>","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.","ama":"Julseth M. The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:12800\">10.15479/at:ista:12800</a>","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.","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.","mla":"Julseth, Mara. <i>The Effect of Local Population Structure on Genetic Variation at Selected Loci in the A. Majus Hybrid Zone</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:12800\">10.15479/at:ista:12800</a>.","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. <a href=\"https://doi.org/10.15479/at:ista:12800\">https://doi.org/10.15479/at:ista:12800</a>."},"article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"publication_identifier":{"issn":["2791-4585"]},"file":[{"relation":"supplementary_material","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet","file_name":"Dispersaldata.xlsx","file_id":"12805","file_size":52795,"access_level":"closed","date_updated":"2023-06-02T22:30:04Z","checksum":"b76cf6d69f2093d8248f6a3f9d4654a4","date_created":"2023-04-06T06:09:40Z","creator":"mjulseth"},{"embargo":"2023-06-01","relation":"supplementary_material","date_updated":"2023-06-02T22:30:04Z","date_created":"2023-04-06T06:11:27Z","checksum":"5a13b6d204371572e249f03795bc0d04","creator":"mjulseth","access_level":"open_access","file_size":787239,"content_type":"application/vnd.wolfram.nb","file_id":"12806","file_name":"2023_MSc_ThesisMaraJulseth_Notebook.nb"},{"checksum":"c3ec842839ed1e66bf2618ae33047df8","creator":"mjulseth","date_updated":"2023-06-02T22:30:04Z","date_created":"2023-04-06T08:26:12Z","file_size":1061763,"access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"12812","file_name":"ThesisMaraJulseth_04_23.docx","relation":"source_file","embargo_to":"open_access"},{"content_type":"application/pdf","file_name":"ThesisMaraJulseth_04_23.pdf","file_id":"12813","checksum":"3132cc998fbe3ae2a3a83c2a69367f37","creator":"mjulseth","date_updated":"2023-06-02T22:30:04Z","date_created":"2023-04-06T08:26:37Z","file_size":1741364,"access_level":"open_access","relation":"main_file","embargo":"2023-06-01"}],"fulldoi":"https://doi.org/10.15479/at:ista:12800","corr_author":"1","oa_version":"Published Version","date_updated":"2026-04-07T14:01:51Z","author":[{"full_name":"Julseth, Mara","first_name":"Mara","id":"1cf464b2-dc7d-11ea-9b2f-f9b1aa9417d1","last_name":"Julseth"}],"language":[{"iso":"eng"}],"oa":1},{"ddc":["570"],"doi":"10.1111/mec.16793","scopus_import":"1","acknowledgement":"We thank the Barton group for useful discussion and feedback during the writing of this article. Comments from Roger Butlin, Molly Schumer's Group, the tskit development team, editors and three reviewers greatly improved the manuscript. Funding was provided by SCAS (Natural Sciences Programme, Knut and Alice Wallenberg Foundation), an FWF Wittgenstein grant (PT1001Z211), an FWF standalone grant (grant P 32166), and an ERC Advanced Grant. YFC was supported by the Max Planck Society and an ERC Proof of Concept Grant #101069216 (HAPLOTAGGING).","year":"2023","abstract":[{"text":"The term “haplotype block” is commonly used in the developing field of haplotype-based inference methods. We argue that the term should be defined based on the structure of the Ancestral Recombination Graph (ARG), which contains complete information on the ancestry of a sample. We use simulated examples to demonstrate key features of the relationship between haplotype blocks and ancestral structure, emphasizing the stochasticity of the processes that generate them. Even the simplest cases of neutrality or of a “hard” selective sweep produce a rich structure, often missed by commonly used statistics. We highlight a number of novel methods for inferring haplotype structure, based on the full ARG, or on a sequence of trees, and illustrate how they can be used to define haplotype blocks using an empirical data set. While the advent of new, computationally efficient methods makes it possible to apply these concepts broadly, they (and additional new methods) could benefit from adding features to explore haplotype blocks, as we define them. Understanding and applying the concept of the haplotype block will be essential to fully exploit long and linked-read sequencing technologies.","lang":"eng"}],"citation":{"chicago":"Shipilina, Daria, Arka Pal, Sean Stankowski, Yingguang Frank Chan, and Nicholas H Barton. “On the Origin and Structure of Haplotype Blocks.” <i>Molecular Ecology</i>. Wiley, 2023. <a href=\"https://doi.org/10.1111/mec.16793\">https://doi.org/10.1111/mec.16793</a>.","short":"D. Shipilina, A. Pal, S. Stankowski, Y.F. Chan, N.H. Barton, Molecular Ecology 32 (2023) 1441–1457.","mla":"Shipilina, Daria, et al. “On the Origin and Structure of Haplotype Blocks.” <i>Molecular Ecology</i>, vol. 32, no. 6, Wiley, 2023, pp. 1441–57, doi:<a href=\"https://doi.org/10.1111/mec.16793\">10.1111/mec.16793</a>.","ieee":"D. Shipilina, A. Pal, S. Stankowski, Y. F. Chan, and N. H. Barton, “On the origin and structure of haplotype blocks,” <i>Molecular Ecology</i>, vol. 32, no. 6. Wiley, pp. 1441–1457, 2023.","apa":"Shipilina, D., Pal, A., Stankowski, S., Chan, Y. F., &#38; Barton, N. H. (2023). On the origin and structure of haplotype blocks. <i>Molecular Ecology</i>. Wiley. <a href=\"https://doi.org/10.1111/mec.16793\">https://doi.org/10.1111/mec.16793</a>","ista":"Shipilina D, Pal A, Stankowski S, Chan YF, Barton NH. 2023. On the origin and structure of haplotype blocks. Molecular Ecology. 32(6), 1441–1457.","ama":"Shipilina D, Pal A, Stankowski S, Chan YF, Barton NH. On the origin and structure of haplotype blocks. <i>Molecular Ecology</i>. 2023;32(6):1441-1457. doi:<a href=\"https://doi.org/10.1111/mec.16793\">10.1111/mec.16793</a>"},"article_processing_charge":"Yes (via OA deal)","issue":"6","department":[{"_id":"NiBa"}],"volume":32,"project":[{"name":"Snapdragon Speciation","grant_number":"P32166","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"Formal methods for the design and analysis of complex systems","call_identifier":"FWF"},{"name":"Understanding the evolution of continuous genomes","_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","grant_number":"101055327"}],"article_type":"original","publication_identifier":{"eissn":["1365-294X"],"issn":["0962-1083"]},"isi":1,"file":[{"success":1,"relation":"main_file","file_size":7144607,"creator":"dernst","access_level":"open_access","date_updated":"2023-08-16T08:15:41Z","date_created":"2023-08-16T08:15:41Z","checksum":"b10e0f8fa3dc4d72aaf77a557200978a","file_name":"2023_MolecularEcology_Shipilina.pdf","file_id":"14062","content_type":"application/pdf"}],"corr_author":"1","fulldoi":"https://doi.org/10.1111/mec.16793","oa_version":"Published Version","author":[{"id":"428A94B0-F248-11E8-B48F-1D18A9856A87","last_name":"Shipilina","first_name":"Daria","orcid":"0000-0002-1145-9226","full_name":"Shipilina, Daria"},{"id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425","last_name":"Pal","first_name":"Arka","orcid":"0000-0002-4530-8469","full_name":"Pal, Arka"},{"id":"43161670-5719-11EA-8025-FABC3DDC885E","last_name":"Stankowski","first_name":"Sean","full_name":"Stankowski, Sean"},{"full_name":"Chan, Yingguang Frank","last_name":"Chan","first_name":"Yingguang Frank"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}],"date_updated":"2026-09-27T22:30:40Z","language":[{"iso":"eng"}],"oa":1,"pmid":1,"page":"1441-1457","day":"01","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"related_material":{"record":[{"id":"20694","status":"public","relation":"dissertation_contains"}]},"publication":"Molecular Ecology","_id":"12159","date_created":"2023-01-12T12:09:17Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2023-03-01T00:00:00Z","publication_status":"published","publisher":"Wiley","status":"public","title":"On the origin and structure of haplotype blocks","file_date_updated":"2023-08-16T08:15:41Z","type":"journal_article","quality_controlled":"1","month":"03","has_accepted_license":"1","external_id":{"isi":["000900762000001"],"pmid":["36433653"]},"intvolume":"        32","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"}},{"has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"}],"title":"Genetic basis of flower colour as a model for adaptive evolution","file_date_updated":"2022-04-07T08:11:51Z","type":"dissertation","status":"public","month":"04","date_created":"2022-04-07T08:19:54Z","degree_awarded":"PhD","date_published":"2022-04-06T00:00:00Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","supervisor":[{"last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"}],"publication_status":"published","publisher":"Institute of Science and Technology Austria","day":"06","page":"112","OA_place":"publisher","_id":"11128","language":[{"iso":"eng"}],"date_updated":"2026-04-07T14:12:19Z","author":[{"first_name":"Lenka","last_name":"Matejovicova","id":"2DFDEC72-F248-11E8-B48F-1D18A9856A87","full_name":"Matejovicova, Lenka"}],"oa":1,"file":[{"relation":"main_file","date_created":"2022-04-07T08:11:34Z","date_updated":"2022-04-07T08:11:34Z","checksum":"e9609bc4e8f8e20146fc1125fd4f1bf7","access_level":"open_access","file_size":11906472,"creator":"cchlebak","content_type":"application/pdf","file_name":"LenkaPhD_Official_PDFA.pdf","file_id":"11129"},{"file_name":"LenkaPhD Official_source.zip","file_id":"11130","content_type":"application/x-zip-compressed","date_created":"2022-04-07T08:11:51Z","creator":"cchlebak","checksum":"99d67040432fd07a225643a212ee8588","access_level":"closed","file_size":23036766,"date_updated":"2022-04-07T08:11:51Z","relation":"source_file"}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-016-9"]},"corr_author":"1","fulldoi":"https://doi.org/10.15479/at:ista:11128","oa_version":"Published Version","article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"year":"2022","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"}],"doi":"10.15479/at:ista:11128","ddc":["576","582"],"citation":{"mla":"Matejovicova, Lenka. <i>Genetic Basis of Flower Colour as a Model for Adaptive Evolution</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11128\">10.15479/at:ista:11128</a>.","short":"L. Matejovicova, Genetic Basis of Flower Colour as a Model for Adaptive Evolution, Institute of Science and Technology Austria, 2022.","chicago":"Matejovicova, Lenka. “Genetic Basis of Flower Colour as a Model for Adaptive Evolution.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:11128\">https://doi.org/10.15479/at:ista:11128</a>.","ista":"Matejovicova L. 2022. Genetic basis of flower colour as a model for adaptive evolution. Institute of Science and Technology Austria.","ama":"Matejovicova L. Genetic basis of flower colour as a model for adaptive evolution. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11128\">10.15479/at:ista:11128</a>","apa":"Matejovicova, L. (2022). <i>Genetic basis of flower colour as a model for adaptive evolution</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11128\">https://doi.org/10.15479/at:ista:11128</a>","ieee":"L. Matejovicova, “Genetic basis of flower colour as a model for adaptive evolution,” Institute of Science and Technology Austria, 2022."},"alternative_title":["ISTA Thesis"]},{"article_processing_charge":"No","date_created":"2022-04-22T09:42:24Z","date_published":"2022-04-28T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"publisher":"Institute of Science and Technology Austria","day":"28","doi":"10.15479/at:ista:11321","ddc":["570"],"related_material":{"record":[{"status":"public","id":"9192","relation":"earlier_version"},{"relation":"earlier_version","status":"public","id":"8254"},{"relation":"used_in_publication","status":"public","id":"11411"}]},"year":"2022","abstract":[{"lang":"eng","text":"Here are the research data underlying the publication \"Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus\" Further information are summed up in the README document. "}],"_id":"11321","citation":{"mla":"Surendranadh, Parvathy, et al. <i>Effects of Fine-Scale Population Structure on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11321\">10.15479/at:ista:11321</a>.","short":"P. Surendranadh, L.S. Arathoon, C. Baskett, D. Field, M. Pickup, N.H. Barton, (2022).","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.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:11321\">https://doi.org/10.15479/at:ista:11321</a>.","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. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11321\">10.15479/at:ista:11321</a>","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, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/at:ista:11321\">10.15479/at:ista:11321</a>.","apa":"Surendranadh, P., Arathoon, L. S., Baskett, C., Field, D., Pickup, M., &#38; Barton, N. H. (2022). Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11321\">https://doi.org/10.15479/at:ista:11321</a>","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.” Institute of Science and Technology Austria, 2022."},"date_updated":"2025-04-15T08:20:40Z","author":[{"full_name":"Surendranadh, Parvathy","orcid":"0000-0001-6395-386X","first_name":"Parvathy","id":"455235B8-F248-11E8-B48F-1D18A9856A87","last_name":"Surendranadh"},{"last_name":"Arathoon","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","first_name":"Louise S","full_name":"Arathoon, Louise S","orcid":"0000-0003-1771-714X"},{"orcid":"0000-0002-7354-8574","full_name":"Baskett, Carina","last_name":"Baskett","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","first_name":"Carina"},{"orcid":"0000-0002-4014-8478","full_name":"Field, David","first_name":"David","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Melinda","last_name":"Pickup","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","full_name":"Pickup, Melinda","orcid":"0000-0001-6118-0541"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"has_accepted_license":"1","oa":1,"contributor":[{"id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","last_name":"Arathoon","first_name":"Louise S","contributor_type":"project_member"},{"last_name":"Baskett","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","first_name":"Carina","contributor_type":"project_member","orcid":"0000-0002-7354-8574"},{"contributor_type":"project_member","orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field","first_name":"David"},{"id":"2C78037E-F248-11E8-B48F-1D18A9856A87","last_name":"Pickup","first_name":"Melinda","contributor_type":"project_member","orcid":"0000-0001-6118-0541"},{"last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","contributor_type":"project_member","orcid":"0000-0002-8548-5240"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"status":"public","title":"Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus","file":[{"success":1,"relation":"main_file","creator":"larathoo","checksum":"96c1b86cdf25481f2a52972fcc45ca7f","file_size":13260571,"date_created":"2022-04-22T09:39:03Z","date_updated":"2022-04-22T09:39:03Z","access_level":"open_access","file_name":"Data_Code.zip","file_id":"11326","content_type":"application/x-zip-compressed"}],"file_date_updated":"2022-04-22T09:39:03Z","type":"research_data","oa_version":"Published Version","fulldoi":"https://doi.org/10.15479/at:ista:11321","corr_author":"1","month":"04"},{"issue":"5","article_processing_charge":"No","volume":76,"article_type":"original","project":[{"name":"Theoretical and empirical approaches to understanding Parallel Adaptation","call_identifier":"H2020","_id":"265B41B8-B435-11E9-9278-68D0E5697425","grant_number":"797747"}],"department":[{"_id":"NiBa"},{"_id":"BeVi"}],"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","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."}],"scopus_import":"1","ddc":["570"],"doi":"10.1111/evo.14462","citation":{"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.” <i>Evolution</i>. Wiley, 2022. <a href=\"https://doi.org/10.1111/evo.14462\">https://doi.org/10.1111/evo.14462</a>.","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.","mla":"Freitas, Susana, et al. “Parthenogenesis in Darevskia Lizards: A Rare Outcome of Common Hybridization, Not a Common Outcome of Rare Hybridization.” <i>Evolution</i>, vol. 76, no. 5, Wiley, 2022, pp. 899–914, doi:<a href=\"https://doi.org/10.1111/evo.14462\">10.1111/evo.14462</a>.","ieee":"S. Freitas <i>et al.</i>, “Parthenogenesis in Darevskia lizards: A rare outcome of common hybridization, not a common outcome of rare hybridization,” <i>Evolution</i>, vol. 76, no. 5. Wiley, pp. 899–914, 2022.","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. <i>Evolution</i>. Wiley. <a href=\"https://doi.org/10.1111/evo.14462\">https://doi.org/10.1111/evo.14462</a>","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.","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. <i>Evolution</i>. 2022;76(5):899-914. doi:<a href=\"https://doi.org/10.1111/evo.14462\">10.1111/evo.14462</a>"},"language":[{"iso":"eng"}],"author":[{"last_name":"Freitas","first_name":"Susana","full_name":"Freitas, Susana"},{"first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M"},{"full_name":"Schwander, Tanja","last_name":"Schwander","first_name":"Tanja"},{"full_name":"Arakelyan, Marine","first_name":"Marine","last_name":"Arakelyan"},{"last_name":"Ilgaz","first_name":"Çetin","full_name":"Ilgaz, Çetin"},{"full_name":"Kumlutas, Yusuf","last_name":"Kumlutas","first_name":"Yusuf"},{"last_name":"Harris","first_name":"David James","full_name":"Harris, David James"},{"first_name":"Miguel A.","last_name":"Carretero","full_name":"Carretero, Miguel A."},{"first_name":"Roger K.","last_name":"Butlin","full_name":"Butlin, Roger K."}],"date_updated":"2025-04-14T07:48:21Z","pmid":1,"oa":1,"file":[{"success":1,"relation":"main_file","date_created":"2022-08-05T06:19:28Z","checksum":"c27c025ae9afcf6c804d46a909775ee5","creator":"dernst","access_level":"open_access","date_updated":"2022-08-05T06:19:28Z","file_size":2855214,"content_type":"application/pdf","file_name":"2022_Evolution_Freitas.pdf","file_id":"11729"}],"ec_funded":1,"publication_identifier":{"issn":["0014-3820"],"eissn":["1558-5646"]},"isi":1,"oa_version":"Published Version","fulldoi":"https://doi.org/10.1111/evo.14462","date_published":"2022-05-01T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_created":"2022-04-24T22:01:44Z","publisher":"Wiley","publication_status":"published","day":"01","page":"899-914","_id":"11334","publication":"Evolution","external_id":{"pmid":["35323995"],"isi":["000781632500001"]},"has_accepted_license":"1","tmp":{"image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"intvolume":"        76","file_date_updated":"2022-08-05T06:19:28Z","type":"journal_article","title":"Parthenogenesis in Darevskia lizards: A rare outcome of common hybridization, not a common outcome of rare hybridization","status":"public","quality_controlled":"1","month":"05"},{"external_id":{"pmid":["35639938"],"isi":["000803735800001"]},"has_accepted_license":"1","acknowledged_ssus":[{"_id":"ScienComp"}],"intvolume":"       221","type":"journal_article","file_date_updated":"2022-05-26T12:48:21Z","title":"Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus","status":"public","quality_controlled":"1","month":"07","date_published":"2022-07-01T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_created":"2022-05-26T13:44:50Z","publisher":"Oxford University Press","publication_status":"published","related_material":{"record":[{"relation":"research_data","id":"9192","status":"public"},{"status":"public","id":"11321","relation":"research_data"},{"relation":"dissertation_contains","status":"public","id":"14651"}]},"day":"01","_id":"11411","publication":"Genetics","language":[{"iso":"eng"}],"author":[{"first_name":"Parvathy","id":"455235B8-F248-11E8-B48F-1D18A9856A87","last_name":"Surendranadh","orcid":"0000-0001-6395-386X","full_name":"Surendranadh, Parvathy"},{"id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","last_name":"Arathoon","first_name":"Louise S","full_name":"Arathoon, Louise S","orcid":"0000-0003-1771-714X"},{"first_name":"Carina","last_name":"Baskett","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","full_name":"Baskett, Carina","orcid":"0000-0002-7354-8574"},{"full_name":"Field, David","orcid":"0000-0002-4014-8478","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David"},{"orcid":"0000-0001-6118-0541","full_name":"Pickup, Melinda","first_name":"Melinda","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","last_name":"Pickup"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"}],"date_updated":"2026-04-07T13:28:29Z","pmid":1,"oa":1,"file":[{"creator":"larathoo","date_updated":"2022-05-26T12:48:15Z","date_created":"2022-05-26T12:48:15Z","checksum":"cc2d56deb608bd53c5cc02f03a875107","access_level":"open_access","file_size":885374,"content_type":"application/pdf","file_name":"Manuscript.pdf","file_id":"11412","success":1,"relation":"main_file"},{"content_type":"application/pdf","file_name":"SupplementalMaterial.pdf","file_id":"11413","file_size":1401704,"checksum":"693742595b6c7ed809423be01460d083","date_updated":"2022-05-26T12:48:21Z","date_created":"2022-05-26T12:48:21Z","creator":"larathoo","access_level":"open_access","relation":"main_file","success":1}],"isi":1,"publication_identifier":{"eissn":["1943-2631"]},"article_number":"iyac083","fulldoi":"https://doi.org/10.1093/genetics/iyac083","oa_version":"Submitted Version","corr_author":"1","issue":"3","article_processing_charge":"No","article_type":"original","volume":221,"project":[{"grant_number":"P32166","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","name":"Snapdragon Speciation"}],"department":[{"_id":"GradSch"},{"_id":"NiBa"}],"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).","year":"2022","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."}],"scopus_import":"1","ddc":["576"],"doi":"10.1093/genetics/iyac083","citation":{"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,” <i>Genetics</i>, vol. 221, no. 3. Oxford University Press, 2022.","apa":"Surendranadh, P., Arathoon, L. S., Baskett, C., Field, D., Pickup, M., &#38; Barton, N. H. (2022). Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. <i>Genetics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/genetics/iyac083\">https://doi.org/10.1093/genetics/iyac083</a>","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. <i>Genetics</i>. 2022;221(3). doi:<a href=\"https://doi.org/10.1093/genetics/iyac083\">10.1093/genetics/iyac083</a>","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.","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.” <i>Genetics</i>. Oxford University Press, 2022. <a href=\"https://doi.org/10.1093/genetics/iyac083\">https://doi.org/10.1093/genetics/iyac083</a>.","short":"P. Surendranadh, L.S. Arathoon, C. Baskett, D. Field, M. Pickup, N.H. Barton, Genetics 221 (2022).","mla":"Surendranadh, Parvathy, et al. “Effects of Fine-Scale Population Structure on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus.” <i>Genetics</i>, vol. 221, no. 3, iyac083, Oxford University Press, 2022, doi:<a href=\"https://doi.org/10.1093/genetics/iyac083\">10.1093/genetics/iyac083</a>."}},{"status":"public","type":"journal_article","file_date_updated":"2022-06-20T07:51:32Z","title":"Relation between the number of peaks and the number of reciprocal sign epistatic interactions","month":"06","quality_controlled":"1","has_accepted_license":"1","external_id":{"pmid":["35713756"],"isi":["000812509800001"]},"intvolume":"        84","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"related_material":{"record":[{"relation":"dissertation_contains","id":"21918","status":"public"}],"link":[{"url":"https://doi.org/10.1007/s11538-022-01118-z","relation":"erratum"}]},"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"],"day":"17","_id":"11447","publication":"Bulletin of Mathematical Biology","date_published":"2022-06-17T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2022-06-17T16:16:15Z","publisher":"Springer Nature","publication_status":"published","publication_identifier":{"issn":["0092-8240"],"eissn":["1522-9602"]},"article_number":"74","isi":1,"ec_funded":1,"file":[{"success":1,"relation":"main_file","creator":"dernst","date_updated":"2022-06-20T07:51:32Z","file_size":463025,"date_created":"2022-06-20T07:51:32Z","checksum":"05a1fe7d10914a00c2bca9b447993a65","access_level":"open_access","content_type":"application/pdf","file_name":"2022_BulletinMathBiology_Saona.pdf","file_id":"11455"}],"fulldoi":"https://doi.org/10.1007/s11538-022-01029-z","corr_author":"1","oa_version":"Published Version","date_updated":"2026-06-12T12:43:34Z","author":[{"orcid":"0000-0001-5103-038X","full_name":"Saona Urmeneta, Raimundo J","id":"BD1DF4C4-D767-11E9-B658-BC13E6697425","last_name":"Saona Urmeneta","first_name":"Raimundo J"},{"full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor"},{"first_name":"Kseniia","last_name":"Khudiakova","id":"4E6DC800-AE37-11E9-AC72-31CAE5697425","orcid":"0000-0002-6246-1465","full_name":"Khudiakova, Kseniia"}],"language":[{"iso":"eng"}],"oa":1,"pmid":1,"doi":"10.1007/s11538-022-01029-z","ddc":["510","570"],"year":"2022","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"}],"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.","scopus_import":"1","citation":{"mla":"Saona Urmeneta, Raimundo J., et al. “Relation between the Number of Peaks and the Number of Reciprocal Sign Epistatic Interactions.” <i>Bulletin of Mathematical Biology</i>, vol. 84, no. 8, 74, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1007/s11538-022-01029-z\">10.1007/s11538-022-01029-z</a>.","short":"R.J. Saona Urmeneta, F. Kondrashov, K. Khudiakova, Bulletin of Mathematical Biology 84 (2022).","chicago":"Saona Urmeneta, Raimundo J, Fyodor Kondrashov, and Kseniia Khudiakova. “Relation between the Number of Peaks and the Number of Reciprocal Sign Epistatic Interactions.” <i>Bulletin of Mathematical Biology</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s11538-022-01029-z\">https://doi.org/10.1007/s11538-022-01029-z</a>.","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.","ama":"Saona Urmeneta RJ, Kondrashov F, Khudiakova K. Relation between the number of peaks and the number of reciprocal sign epistatic interactions. <i>Bulletin of Mathematical Biology</i>. 2022;84(8). doi:<a href=\"https://doi.org/10.1007/s11538-022-01029-z\">10.1007/s11538-022-01029-z</a>","apa":"Saona Urmeneta, R. J., Kondrashov, F., &#38; Khudiakova, K. (2022). Relation between the number of peaks and the number of reciprocal sign epistatic interactions. <i>Bulletin of Mathematical Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s11538-022-01029-z\">https://doi.org/10.1007/s11538-022-01029-z</a>","ieee":"R. J. Saona Urmeneta, F. Kondrashov, and K. Khudiakova, “Relation between the number of peaks and the number of reciprocal sign epistatic interactions,” <i>Bulletin of Mathematical Biology</i>, vol. 84, no. 8. Springer Nature, 2022."},"article_processing_charge":"Yes (via OA deal)","issue":"8","department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"JaMa"}],"article_type":"original","project":[{"name":"Characterizing the fitness landscape on population and global scales","call_identifier":"H2020","_id":"26580278-B435-11E9-9278-68D0E5697425","grant_number":"771209"},{"grant_number":"I05127","_id":"34e076d6-11ca-11ed-8bc3-aec76c41a181","name":"Evolutionary analysis of gene regulation"}],"volume":84},{"status":"public","title":"Inversions and parallel evolution","type":"journal_article","file_date_updated":"2023-02-02T08:20:29Z","month":"08","quality_controlled":"1","external_id":{"pmid":["35694747"],"isi":["000812317300005"]},"has_accepted_license":"1","intvolume":"       377","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"01","keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology"],"publication":"Philosophical Transactions of the Royal Society B: Biological Sciences","_id":"11546","date_created":"2022-07-08T11:41:56Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2022-08-01T00:00:00Z","publication_status":"published","publisher":"Royal Society of London","isi":1,"article_number":"20210203","publication_identifier":{"issn":["0962-8436"],"eissn":["1471-2970"]},"file":[{"date_created":"2023-02-02T08:20:29Z","access_level":"open_access","checksum":"49f69428f3dcf5ce3ff281f7d199e9df","date_updated":"2023-02-02T08:20:29Z","file_size":920304,"creator":"dernst","file_name":"2022_PhilosophicalTransactionsB_Westram.pdf","file_id":"12479","content_type":"application/pdf","success":1,"relation":"main_file"}],"corr_author":"1","fulldoi":"https://doi.org/10.1098/rstb.2021.0203","oa_version":"Published Version","author":[{"first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969"},{"last_name":"Faria","first_name":"Rui","full_name":"Faria, Rui"},{"full_name":"Johannesson, Kerstin","first_name":"Kerstin","last_name":"Johannesson"},{"first_name":"Roger","last_name":"Butlin","full_name":"Butlin, Roger"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton"}],"date_updated":"2025-06-12T06:10:18Z","language":[{"iso":"eng"}],"oa":1,"pmid":1,"ddc":["570"],"doi":"10.1098/rstb.2021.0203","scopus_import":"1","year":"2022","acknowledgement":"We thank the editor and two anonymous reviewers for their helpful and interesting comments on this manuscript.","abstract":[{"lang":"eng","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."}],"citation":{"chicago":"Westram, Anja M, Rui Faria, Kerstin Johannesson, Roger Butlin, and Nicholas H Barton. “Inversions and Parallel Evolution.” <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>. Royal Society of London, 2022. <a href=\"https://doi.org/10.1098/rstb.2021.0203\">https://doi.org/10.1098/rstb.2021.0203</a>.","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.” <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>, vol. 377, no. 1856, 20210203, Royal Society of London, 2022, doi:<a href=\"https://doi.org/10.1098/rstb.2021.0203\">10.1098/rstb.2021.0203</a>.","ieee":"A. M. Westram, R. Faria, K. Johannesson, R. Butlin, and N. H. Barton, “Inversions and parallel evolution,” <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>, vol. 377, no. 1856. Royal Society of London, 2022.","apa":"Westram, A. M., Faria, R., Johannesson, K., Butlin, R., &#38; Barton, N. H. (2022). Inversions and parallel evolution. <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>. Royal Society of London. <a href=\"https://doi.org/10.1098/rstb.2021.0203\">https://doi.org/10.1098/rstb.2021.0203</a>","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. <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>. 2022;377(1856). doi:<a href=\"https://doi.org/10.1098/rstb.2021.0203\">10.1098/rstb.2021.0203</a>"},"article_processing_charge":"Yes (via OA deal)","issue":"1856","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"project":[{"grant_number":"P32166","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","name":"Snapdragon Speciation"}],"article_type":"original","volume":377},{"scopus_import":"1","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.","abstract":[{"lang":"eng","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."}],"year":"2022","doi":"10.1111/1755-0998.13676","ddc":["570"],"citation":{"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,” <i>Molecular Ecology Resources</i>, vol. 22, no. 8. Wiley, pp. 2941–2955, 2022.","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.","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. <i>Molecular Ecology Resources</i>. 2022;22(8):2941-2955. doi:<a href=\"https://doi.org/10.1111/1755-0998.13676\">10.1111/1755-0998.13676</a>","apa":"Szep, E., Trubenova, B., &#38; Csilléry, K. (2022). Using gridCoal to assess whether standard population genetic theory holds in the presence of spatio-temporal heterogeneity in population size. <i>Molecular Ecology Resources</i>. Wiley. <a href=\"https://doi.org/10.1111/1755-0998.13676\">https://doi.org/10.1111/1755-0998.13676</a>","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.” <i>Molecular Ecology Resources</i>. Wiley, 2022. <a href=\"https://doi.org/10.1111/1755-0998.13676\">https://doi.org/10.1111/1755-0998.13676</a>.","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.” <i>Molecular Ecology Resources</i>, vol. 22, no. 8, Wiley, 2022, pp. 2941–55, doi:<a href=\"https://doi.org/10.1111/1755-0998.13676\">10.1111/1755-0998.13676</a>.","short":"E. Szep, B. Trubenova, K. Csilléry, Molecular Ecology Resources 22 (2022) 2941–2955."},"issue":"8","article_processing_charge":"Yes (via OA deal)","volume":22,"article_type":"original","project":[{"name":"Rate of Adaptation in Changing Environment","call_identifier":"H2020","_id":"25AEDD42-B435-11E9-9278-68D0E5697425","grant_number":"704172"}],"department":[{"_id":"NiBa"}],"ec_funded":1,"file":[{"relation":"main_file","success":1,"file_name":"2022_MolecularEcologyRes_Szep.pdf","file_id":"12477","content_type":"application/pdf","file_size":6431779,"date_updated":"2023-02-02T08:11:23Z","date_created":"2023-02-02T08:11:23Z","access_level":"open_access","checksum":"3102e203e77b884bffffdbe8e548da88","creator":"dernst"}],"isi":1,"publication_identifier":{"eissn":["1755-0998"],"issn":["1755-098X"]},"fulldoi":"https://doi.org/10.1111/1755-0998.13676","corr_author":"1","oa_version":"Published Version","language":[{"iso":"eng"}],"author":[{"first_name":"Eniko","id":"485BB5A4-F248-11E8-B48F-1D18A9856A87","last_name":"Szep","full_name":"Szep, Eniko"},{"full_name":"Trubenova, Barbora","orcid":"0000-0002-6873-2967","first_name":"Barbora","last_name":"Trubenova","id":"42302D54-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Csilléry","first_name":"Katalin","full_name":"Csilléry, Katalin"}],"date_updated":"2025-06-11T14:01:43Z","pmid":1,"oa":1,"day":"01","page":"2941-2955","publication":"Molecular Ecology Resources","_id":"11640","date_created":"2022-07-24T22:01:43Z","date_published":"2022-11-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","publisher":"Wiley","title":"Using gridCoal to assess whether standard population genetic theory holds in the presence of spatio-temporal heterogeneity in population size","type":"journal_article","file_date_updated":"2023-02-02T08:11:23Z","status":"public","quality_controlled":"1","month":"11","has_accepted_license":"1","external_id":{"isi":["000825873600001"],"pmid":["35765749"]},"tmp":{"image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"intvolume":"        22"},{"tmp":{"image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode"},"oa":1,"author":[{"first_name":"Michael","last_name":"Turelli","full_name":"Turelli, Michael"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"}],"date_updated":"2025-06-11T13:45:56Z","month":"01","license":"https://creativecommons.org/publicdomain/zero/1.0/","oa_version":"Published Version","fulldoi":"https://doi.org/10.25338/B81931","corr_author":"1","title":"Wolbachia frequency data from: Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics and disease control","type":"research_data_reference","status":"public","department":[{"_id":"NiBa"}],"publisher":"Dryad","date_created":"2022-07-29T06:45:41Z","article_processing_charge":"No","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","main_file_link":[{"url":"https://doi.org/10.25338/B81931","open_access":"1"}],"date_published":"2022-01-06T00:00:00Z","citation":{"short":"M. Turelli, N.H. Barton, (2022).","mla":"Turelli, Michael, and Nicholas H. Barton. <i>Wolbachia Frequency Data from: Why Did the Wolbachia Transinfection Cross the Road? Drift, Deterministic Dynamics and Disease Control</i>. Dryad, 2022, doi:<a href=\"https://doi.org/10.25338/B81931\">10.25338/B81931</a>.","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. <a href=\"https://doi.org/10.25338/B81931\">https://doi.org/10.25338/B81931</a>.","apa":"Turelli, M., &#38; Barton, N. H. (2022). Wolbachia frequency data from: Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics and disease control. Dryad. <a href=\"https://doi.org/10.25338/B81931\">https://doi.org/10.25338/B81931</a>","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, <a href=\"https://doi.org/10.25338/B81931\">10.25338/B81931</a>.","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:<a href=\"https://doi.org/10.25338/B81931\">10.25338/B81931</a>","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."},"_id":"11686","acknowledgement":"Bill and Melinda Gates Foundation, Award: OPP1180815","year":"2022","abstract":[{"lang":"eng","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."}],"doi":"10.25338/B81931","ddc":["570"],"day":"06","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"10604"}]},"keyword":["Biological sciences"]},{"publisher":"National Academy of Sciences","publication_status":"published","date_published":"2022-07-18T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2022-07-31T22:01:47Z","_id":"11702","publication":"Proceedings of the National Academy of Sciences of the United States of America","day":"18","intvolume":"       119","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"external_id":{"pmid":["35858408"]},"has_accepted_license":"1","quality_controlled":"1","month":"07","status":"public","file_date_updated":"2022-08-01T10:58:28Z","type":"journal_article","title":"The \"New Synthesis\"","department":[{"_id":"NiBa"}],"article_type":"original","volume":119,"article_processing_charge":"No","issue":"30","citation":{"ieee":"N. H. Barton, “The ‘New Synthesis,’” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 30. National Academy of Sciences, 2022.","apa":"Barton, N. H. (2022). The “New Synthesis.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2122147119\">https://doi.org/10.1073/pnas.2122147119</a>","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.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2022;119(30). doi:<a href=\"https://doi.org/10.1073/pnas.2122147119\">10.1073/pnas.2122147119</a>","chicago":"Barton, Nicholas H. “The ‘New Synthesis.’” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2022. <a href=\"https://doi.org/10.1073/pnas.2122147119\">https://doi.org/10.1073/pnas.2122147119</a>.","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.’” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 30, e2122147119, National Academy of Sciences, 2022, doi:<a href=\"https://doi.org/10.1073/pnas.2122147119\">10.1073/pnas.2122147119</a>."},"doi":"10.1073/pnas.2122147119","ddc":["570"],"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"}],"acknowledgement":"I thank Laura Hayward, Jitka Polechova, and Anja Westram for discussions and comments.","year":"2022","scopus_import":"1","oa":1,"pmid":1,"date_updated":"2025-05-14T11:01:10Z","author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"}],"language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1073/pnas.2122147119","corr_author":"1","oa_version":"Published Version","article_number":"e2122147119","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"file":[{"content_type":"application/pdf","file_id":"11716","file_name":"2022_PNAS_Barton.pdf","date_updated":"2022-08-01T10:58:28Z","creator":"dernst","checksum":"06c866196a8957f0c37b8a121771c885","access_level":"open_access","file_size":848511,"date_created":"2022-08-01T10:58:28Z","relation":"main_file","success":1}]},{"department":[{"_id":"NiBa"}],"volume":6,"article_type":"original","article_processing_charge":"Yes","issue":"5","citation":{"mla":"Hearn, Katherine E., et al. “Differing Associations between Sex Determination and Sex-Linked Inversions in Two Ecotypes of Littorina Saxatilis.” <i>Evolution Letters</i>, vol. 6, no. 5, Oxford University Press, 2022, pp. 358–74, doi:<a href=\"https://doi.org/10.1002/evl3.295\">10.1002/evl3.295</a>.","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.” <i>Evolution Letters</i>. Oxford University Press, 2022. <a href=\"https://doi.org/10.1002/evl3.295\">https://doi.org/10.1002/evl3.295</a>.","ama":"Hearn KE, Koch EL, Stankowski S, et al. Differing associations between sex determination and sex-linked inversions in two ecotypes of Littorina saxatilis. <i>Evolution Letters</i>. 2022;6(5):358-374. doi:<a href=\"https://doi.org/10.1002/evl3.295\">10.1002/evl3.295</a>","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.","apa":"Hearn, K. E., Koch, E. L., Stankowski, S., Butlin, R. K., Faria, R., Johannesson, K., &#38; Westram, A. M. (2022). Differing associations between sex determination and sex-linked inversions in two ecotypes of Littorina saxatilis. <i>Evolution Letters</i>. Oxford University Press. <a href=\"https://doi.org/10.1002/evl3.295\">https://doi.org/10.1002/evl3.295</a>","ieee":"K. E. Hearn <i>et al.</i>, “Differing associations between sex determination and sex-linked inversions in two ecotypes of Littorina saxatilis,” <i>Evolution Letters</i>, vol. 6, no. 5. Oxford University Press, pp. 358–374, 2022."},"doi":"10.1002/evl3.295","ddc":["570"],"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).","year":"2022","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."}],"scopus_import":"1","oa":1,"pmid":1,"author":[{"full_name":"Hearn, Katherine E.","first_name":"Katherine E.","last_name":"Hearn"},{"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"},{"first_name":"Roger K.","last_name":"Butlin","full_name":"Butlin, Roger K."},{"last_name":"Faria","first_name":"Rui","full_name":"Faria, Rui"},{"first_name":"Kerstin","last_name":"Johannesson","full_name":"Johannesson, Kerstin"},{"orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","first_name":"Anja M","last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2025-06-12T06:22:56Z","language":[{"iso":"eng"}],"oa_version":"Published Version","fulldoi":"https://doi.org/10.1002/evl3.295","publication_identifier":{"eissn":["2056-3744"]},"isi":1,"file":[{"relation":"main_file","success":1,"file_id":"12686","file_name":"2022_EvolutionLetters_Hearn.pdf","content_type":"application/pdf","creator":"dernst","file_size":2368965,"checksum":"2dcd06186a11b7d1be4cddc6b189f8fb","date_updated":"2023-02-27T07:17:42Z","date_created":"2023-02-27T07:17:42Z","access_level":"open_access"}],"publisher":"Oxford University Press","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2022-10-01T00:00:00Z","date_created":"2022-08-28T22:02:02Z","_id":"12001","publication":"Evolution Letters","page":"358-374","day":"01","intvolume":"         6","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"external_id":{"pmid":["36254259"],"isi":["000839621100001"]},"has_accepted_license":"1","month":"10","quality_controlled":"1","status":"public","type":"journal_article","file_date_updated":"2023-02-27T07:17:42Z","title":"Differing associations between sex determination and sex-linked inversions in two ecotypes of Littorina saxatilis"},{"date_created":"2022-09-11T22:01:55Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2022-08-29T00:00:00Z","publication_status":"published","publisher":"National Academy of Sciences","day":"29","related_material":{"record":[{"status":"public","id":"15020","relation":"dissertation_contains"}]},"publication":"Proceedings of the National Academy of Sciences of the United States of America","_id":"12081","has_accepted_license":"1","external_id":{"pmid":["36037343"],"isi":["000889278400014"]},"intvolume":"       119","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"status":"public","title":"Accumulation and maintenance of information in evolution","file_date_updated":"2022-09-12T08:08:12Z","type":"journal_article","quality_controlled":"1","month":"08","article_processing_charge":"No","issue":"36","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"article_type":"original","project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"},{"name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?","_id":"2665AAFE-B435-11E9-9278-68D0E5697425","grant_number":"RGP0034/2018"}],"volume":119,"doi":"10.1073/pnas.2123152119","ddc":["570"],"scopus_import":"1","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","abstract":[{"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.","lang":"eng"}],"citation":{"ieee":"M. Hledik, N. H. Barton, and G. Tkačik, “Accumulation and maintenance of information in evolution,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 36. National Academy of Sciences, 2022.","ama":"Hledik M, Barton NH, Tkačik G. Accumulation and maintenance of information in evolution. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2022;119(36). doi:<a href=\"https://doi.org/10.1073/pnas.2123152119\">10.1073/pnas.2123152119</a>","ista":"Hledik M, Barton NH, Tkačik G. 2022. Accumulation and maintenance of information in evolution. Proceedings of the National Academy of Sciences of the United States of America. 119(36), e2123152119.","apa":"Hledik, M., Barton, N. H., &#38; Tkačik, G. (2022). Accumulation and maintenance of information in evolution. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2123152119\">https://doi.org/10.1073/pnas.2123152119</a>","chicago":"Hledik, Michal, Nicholas H Barton, and Gašper Tkačik. “Accumulation and Maintenance of Information in Evolution.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2022. <a href=\"https://doi.org/10.1073/pnas.2123152119\">https://doi.org/10.1073/pnas.2123152119</a>.","mla":"Hledik, Michal, et al. “Accumulation and Maintenance of Information in Evolution.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 36, e2123152119, National Academy of Sciences, 2022, doi:<a href=\"https://doi.org/10.1073/pnas.2123152119\">10.1073/pnas.2123152119</a>.","short":"M. Hledik, N.H. Barton, G. Tkačik, Proceedings of the National Academy of Sciences of the United States of America 119 (2022)."},"author":[{"full_name":"Hledik, Michal","first_name":"Michal","id":"4171253A-F248-11E8-B48F-1D18A9856A87","last_name":"Hledik"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"},{"last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","full_name":"Tkačik, Gašper","orcid":"1"}],"date_updated":"2026-04-07T12:59:24Z","language":[{"iso":"eng"}],"oa":1,"pmid":1,"article_number":"e2123152119","isi":1,"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"file":[{"content_type":"application/pdf","file_id":"12091","file_name":"2022_PNAS_Hledik.pdf","access_level":"open_access","creator":"dernst","date_created":"2022-09-12T08:08:12Z","date_updated":"2022-09-12T08:08:12Z","checksum":"6dec51f6567da9039982a571508a8e4d","file_size":2165752,"relation":"main_file","success":1}],"ec_funded":1,"fulldoi":"https://doi.org/10.1073/pnas.2123152119","corr_author":"1","oa_version":"Published Version"},{"keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"day":"26","_id":"12157","publication":"eLife","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2022-09-26T00:00:00Z","date_created":"2023-01-12T12:09:00Z","publisher":"eLife Sciences Publications","publication_status":"published","status":"public","file_date_updated":"2023-01-24T12:21:32Z","type":"journal_article","title":"Polygenic adaptation after a sudden change in environment","quality_controlled":"1","month":"09","has_accepted_license":"1","external_id":{"isi":["000890735600001"]},"intvolume":"        11","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.7554/elife.66697","ddc":["570"],"abstract":[{"lang":"eng","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."}],"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","scopus_import":"1","citation":{"ieee":"L. Hayward and G. Sella, “Polygenic adaptation after a sudden change in environment,” <i>eLife</i>, vol. 11. eLife Sciences Publications, 2022.","ama":"Hayward L, Sella G. Polygenic adaptation after a sudden change in environment. <i>eLife</i>. 2022;11. doi:<a href=\"https://doi.org/10.7554/elife.66697\">10.7554/elife.66697</a>","ista":"Hayward L, Sella G. 2022. Polygenic adaptation after a sudden change in environment. eLife. 11, 66697.","apa":"Hayward, L., &#38; Sella, G. (2022). Polygenic adaptation after a sudden change in environment. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.66697\">https://doi.org/10.7554/elife.66697</a>","chicago":"Hayward, Laura, and Guy Sella. “Polygenic Adaptation after a Sudden Change in Environment.” <i>ELife</i>. eLife Sciences Publications, 2022. <a href=\"https://doi.org/10.7554/elife.66697\">https://doi.org/10.7554/elife.66697</a>.","mla":"Hayward, Laura, and Guy Sella. “Polygenic Adaptation after a Sudden Change in Environment.” <i>ELife</i>, vol. 11, 66697, eLife Sciences Publications, 2022, doi:<a href=\"https://doi.org/10.7554/elife.66697\">10.7554/elife.66697</a>.","short":"L. Hayward, G. Sella, ELife 11 (2022)."},"article_processing_charge":"No","department":[{"_id":"NiBa"}],"article_type":"original","volume":11,"isi":1,"article_number":"66697","publication_identifier":{"eissn":["2050-084X"]},"file":[{"file_name":"2022_eLife_Hayward.pdf","file_id":"12363","content_type":"application/pdf","creator":"dernst","date_created":"2023-01-24T12:21:32Z","access_level":"open_access","date_updated":"2023-01-24T12:21:32Z","file_size":18935612,"checksum":"28de155b231ac1c8d4501c98b2fb359a","relation":"main_file","success":1}],"corr_author":"1","fulldoi":"https://doi.org/10.7554/elife.66697","oa_version":"Published Version","author":[{"last_name":"Hayward","id":"fc885ee5-24bf-11eb-ad7b-bcc5104c0c1b","first_name":"Laura","full_name":"Hayward, Laura"},{"full_name":"Sella, Guy","first_name":"Guy","last_name":"Sella"}],"date_updated":"2024-10-09T21:03:38Z","language":[{"iso":"eng"}],"oa":1},{"volume":76,"article_type":"original","department":[{"_id":"NiBa"}],"issue":"11","article_processing_charge":"Yes (via OA deal)","citation":{"chicago":"Stankowski, Sean. “Digest: On the Origin of a Possible Hybrid Species.” <i>Evolution</i>. Wiley, 2022. <a href=\"https://doi.org/10.1111/evo.14632\">https://doi.org/10.1111/evo.14632</a>.","short":"S. Stankowski, Evolution 76 (2022) 2784–2785.","mla":"Stankowski, Sean. “Digest: On the Origin of a Possible Hybrid Species.” <i>Evolution</i>, vol. 76, no. 11, Wiley, 2022, pp. 2784–85, doi:<a href=\"https://doi.org/10.1111/evo.14632\">10.1111/evo.14632</a>.","ieee":"S. Stankowski, “Digest: On the origin of a possible hybrid species,” <i>Evolution</i>, vol. 76, no. 11. Wiley, pp. 2784–2785, 2022.","apa":"Stankowski, S. (2022). Digest: On the origin of a possible hybrid species. <i>Evolution</i>. Wiley. <a href=\"https://doi.org/10.1111/evo.14632\">https://doi.org/10.1111/evo.14632</a>","ama":"Stankowski S. Digest: On the origin of a possible hybrid species. <i>Evolution</i>. 2022;76(11):2784-2785. doi:<a href=\"https://doi.org/10.1111/evo.14632\">10.1111/evo.14632</a>","ista":"Stankowski S. 2022. Digest: On the origin of a possible hybrid species. Evolution. 76(11), 2784–2785."},"year":"2022","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"}],"scopus_import":"1","doi":"10.1111/evo.14632","ddc":["570"],"pmid":1,"oa":1,"language":[{"iso":"eng"}],"date_updated":"2025-06-11T13:40:40Z","author":[{"first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","last_name":"Stankowski","full_name":"Stankowski, Sean"}],"oa_version":"Published Version","fulldoi":"https://doi.org/10.1111/evo.14632","corr_author":"1","file":[{"content_type":"application/pdf","file_id":"12425","file_name":"2022_Evolution_Stankowski.pdf","access_level":"open_access","file_size":287282,"creator":"dernst","date_updated":"2023-01-27T11:28:38Z","date_created":"2023-01-27T11:28:38Z","checksum":"4c0f05083b414ac0323a1b9ee1abc275","relation":"main_file","success":1}],"publication_identifier":{"issn":["0014-3820"],"eissn":["1558-5646"]},"isi":1,"publisher":"Wiley","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2022-11-01T00:00:00Z","date_created":"2023-01-16T09:50:48Z","_id":"12234","publication":"Evolution","keyword":["General Agricultural and Biological Sciences","Genetics","Ecology","Evolution","Behavior and Systematics"],"page":"2784-2785","day":"01","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"intvolume":"        76","has_accepted_license":"1","external_id":{"isi":["000855751600001"],"pmid":["36112597"]},"month":"11","quality_controlled":"1","type":"journal_article","file_date_updated":"2023-01-27T11:28:38Z","title":"Digest: On the origin of a possible hybrid species","status":"public"},{"oa":1,"pmid":1,"author":[{"last_name":"Koch","first_name":"Eva L.","full_name":"Koch, Eva L."},{"last_name":"Ravinet","first_name":"Mark","full_name":"Ravinet, Mark"},{"last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M","full_name":"Westram, Anja M","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"}],"date_updated":"2023-08-04T09:42:11Z","language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1111/evo.14602","oa_version":"Published Version","isi":1,"publication_identifier":{"issn":["0014-3820"],"eissn":["1558-5646"]},"file":[{"content_type":"application/pdf","file_id":"12439","file_name":"2022_Evolution_Koch.pdf","date_updated":"2023-01-30T08:45:35Z","checksum":"defd8a4bea61cf00a3c88d4a30e2728c","date_created":"2023-01-30T08:45:35Z","file_size":2990581,"access_level":"open_access","creator":"dernst","relation":"main_file","success":1}],"department":[{"_id":"NiBa"}],"volume":76,"article_type":"original","article_processing_charge":"No","issue":"10","citation":{"mla":"Koch, Eva L., et al. “Genetic Architecture of Repeated Phenotypic Divergence in Littorina Saxatilis Evolution.” <i>Evolution</i>, vol. 76, no. 10, Wiley, 2022, pp. 2332–46, doi:<a href=\"https://doi.org/10.1111/evo.14602\">10.1111/evo.14602</a>.","short":"E.L. Koch, M. Ravinet, A.M. Westram, K. Johannesson, R.K. Butlin, Evolution 76 (2022) 2332–2346.","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.” <i>Evolution</i>. Wiley, 2022. <a href=\"https://doi.org/10.1111/evo.14602\">https://doi.org/10.1111/evo.14602</a>.","ama":"Koch EL, Ravinet M, Westram AM, Johannesson K, Butlin RK. Genetic architecture of repeated phenotypic divergence in Littorina saxatilis evolution. <i>Evolution</i>. 2022;76(10):2332-2346. doi:<a href=\"https://doi.org/10.1111/evo.14602\">10.1111/evo.14602</a>","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.","apa":"Koch, E. L., Ravinet, M., Westram, A. M., Johannesson, K., &#38; Butlin, R. K. (2022). Genetic architecture of repeated phenotypic divergence in Littorina saxatilis evolution. <i>Evolution</i>. Wiley. <a href=\"https://doi.org/10.1111/evo.14602\">https://doi.org/10.1111/evo.14602</a>","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,” <i>Evolution</i>, vol. 76, no. 10. Wiley, pp. 2332–2346, 2022."},"doi":"10.1111/evo.14602","ddc":["570"],"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.","abstract":[{"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.","lang":"eng"}],"year":"2022","scopus_import":"1","intvolume":"        76","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"external_id":{"isi":["000848449100001"],"pmid":["35994296"]},"has_accepted_license":"1","month":"10","quality_controlled":"1","status":"public","file_date_updated":"2023-01-30T08:45:35Z","type":"journal_article","title":"Genetic architecture of repeated phenotypic divergence in Littorina saxatilis evolution","publisher":"Wiley","publication_status":"published","date_published":"2022-10-01T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_created":"2023-01-16T09:54:15Z","_id":"12247","publication":"Evolution","keyword":["General Agricultural and Biological Sciences","Genetics","Ecology","Evolution","Behavior and Systematics"],"related_material":{"record":[{"relation":"research_data","id":"13066","status":"public"}]},"page":"2332-2346","day":"01"}]