[{"publisher":"Public Library of Science","department":[{"_id":"NiBa"}],"publication_status":"published","pmid":1,"year":"2021","acknowledgement":"We would like to thank Alfred Uhl, Richard Kollár and Katarína Bod’ová for very helpful comments. We also thank Matej Mišík for discussion and information regarding the Slovak testing data and Ag-Test used.","volume":16,"date_updated":"2023-08-10T14:26:32Z","date_created":"2021-08-08T22:01:26Z","author":[{"full_name":"Hledik, Michal","first_name":"Michal","last_name":"Hledik","id":"4171253A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Polechova","first_name":"Jitka","orcid":"0000-0003-0951-3112","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","full_name":"Polechova, Jitka"},{"full_name":"Beiglböck, Mathias","first_name":"Mathias","last_name":"Beiglböck"},{"full_name":"Herdina, Anna Nele","last_name":"Herdina","first_name":"Anna Nele"},{"last_name":"Strassl","first_name":"Robert","full_name":"Strassl, Robert"},{"first_name":"Martin","last_name":"Posch","full_name":"Posch, Martin"}],"article_number":"e0255267","license":"https://creativecommons.org/licenses/by/4.0/","file_date_updated":"2021-08-09T11:52:14Z","isi":1,"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000685248200095"],"pmid":["34324553"]},"language":[{"iso":"eng"}],"doi":"10.1371/journal.pone.0255267","publication_identifier":{"eissn":["1932-6203"]},"month":"07","intvolume":" 16","title":"Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program","ddc":["610"],"status":"public","_id":"9816","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","file":[{"creator":"asandaue","file_size":773921,"content_type":"application/pdf","file_name":"2021_PLoSONE_Hledík.pdf","access_level":"open_access","date_created":"2021-08-09T11:52:14Z","date_updated":"2021-08-09T11:52:14Z","success":1,"checksum":"ae4df60eb62f4491278588548d0c1f93","file_id":"9835","relation":"main_file"}],"type":"journal_article","issue":"7","abstract":[{"lang":"eng","text":"Aims: Mass antigen testing programs have been challenged because of an alleged insufficient specificity, leading to a large number of false positives. The objective of this study is to derive a lower bound of the specificity of the SD Biosensor Standard Q Ag-Test in large scale practical use.\r\nMethods: Based on county data from the nationwide tests for SARS-CoV-2 in Slovakia between 31.10.–1.11. 2020 we calculate a lower confidence bound for the specificity. As positive test results were not systematically verified by PCR tests, we base the lower bound on a worst case assumption, assuming all positives to be false positives.\r\nResults: 3,625,332 persons from 79 counties were tested. The lowest positivity rate was observed in the county of Rožňava where 100 out of 34307 (0.29%) tests were positive. This implies a test specificity of at least 99.6% (97.5% one-sided lower confidence bound, adjusted for multiplicity).\r\nConclusion: The obtained lower bound suggests a higher specificity compared to earlier studies in spite of the underlying worst case assumption and the application in a mass testing setting. The actual specificity is expected to exceed 99.6% if the prevalence in the respective regions was non-negligible at the time of testing. To our knowledge, this estimate constitutes the first bound obtained from large scale practical use of an antigen test."}],"article_type":"original","citation":{"chicago":"Hledik, Michal, Jitka Polechova, Mathias Beiglböck, Anna Nele Herdina, Robert Strassl, and Martin Posch. “Analysis of the Specificity of a COVID-19 Antigen Test in the Slovak Mass Testing Program.” PLoS ONE. Public Library of Science, 2021. https://doi.org/10.1371/journal.pone.0255267.","short":"M. Hledik, J. Polechova, M. Beiglböck, A.N. Herdina, R. Strassl, M. Posch, PLoS ONE 16 (2021).","mla":"Hledik, Michal, et al. “Analysis of the Specificity of a COVID-19 Antigen Test in the Slovak Mass Testing Program.” PLoS ONE, vol. 16, no. 7, e0255267, Public Library of Science, 2021, doi:10.1371/journal.pone.0255267.","apa":"Hledik, M., Polechova, J., Beiglböck, M., Herdina, A. N., Strassl, R., & Posch, M. (2021). Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program. PLoS ONE. Public Library of Science. https://doi.org/10.1371/journal.pone.0255267","ieee":"M. Hledik, J. Polechova, M. Beiglböck, A. N. Herdina, R. Strassl, and M. Posch, “Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program,” PLoS ONE, vol. 16, no. 7. Public Library of Science, 2021.","ista":"Hledik M, Polechova J, Beiglböck M, Herdina AN, Strassl R, Posch M. 2021. Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program. PLoS ONE. 16(7), e0255267.","ama":"Hledik M, Polechova J, Beiglböck M, Herdina AN, Strassl R, Posch M. Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program. PLoS ONE. 2021;16(7). doi:10.1371/journal.pone.0255267"},"publication":"PLoS ONE","date_published":"2021-07-29T00:00:00Z","scopus_import":"1","article_processing_charge":"Yes","has_accepted_license":"1","day":"29"},{"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","file_date_updated":"2021-08-11T13:39:19Z","publisher":"Wiley","department":[{"_id":"NiBa"}],"publication_status":"published","year":"2021","acknowledgement":"We thank the reviewers for their helpful comments, and also our colleagues, for illuminating discussions over the long gestation of this paper.","volume":75,"date_updated":"2023-09-05T15:44:06Z","date_created":"2021-03-20T08:22:10Z","related_material":{"record":[{"status":"public","relation":"research_data","id":"13062"}]},"author":[{"full_name":"Szep, Eniko","last_name":"Szep","first_name":"Eniko","id":"485BB5A4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sachdeva, Himani","last_name":"Sachdeva","first_name":"Himani","id":"42377A0A-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"}],"publication_identifier":{"issn":["0014-3820"],"eissn":["1558-5646"]},"month":"05","isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"external_id":{"isi":["000636966300001"]},"language":[{"iso":"eng"}],"doi":"10.1111/evo.14210","type":"journal_article","issue":"5","abstract":[{"lang":"eng","text":"This paper analyses the conditions for local adaptation in a metapopulation with infinitely many islands under a model of hard selection, where population size depends on local fitness. Each island belongs to one of two distinct ecological niches or habitats. Fitness is influenced by an additive trait which is under habitat‐dependent directional selection. Our analysis is based on the diffusion approximation and accounts for both genetic drift and demographic stochasticity. By neglecting linkage disequilibria, it yields the joint distribution of allele frequencies and population size on each island. We find that under hard selection, the conditions for local adaptation in a rare habitat are more restrictive for more polygenic traits: even moderate migration load per locus at very many loci is sufficient for population sizes to decline. This further reduces the efficacy of selection at individual loci due to increased drift and because smaller populations are more prone to swamping due to migration, causing a positive feedback between increasing maladaptation and declining population sizes. Our analysis also highlights the importance of demographic stochasticity, which exacerbates the decline in numbers of maladapted populations, leading to population collapse in the rare habitat at significantly lower migration than predicted by deterministic arguments."}],"intvolume":" 75","status":"public","title":"Polygenic local adaptation in metapopulations: A stochastic eco‐evolutionary model","ddc":["570"],"_id":"9252","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","file":[{"file_id":"9886","relation":"main_file","date_updated":"2021-08-11T13:39:19Z","date_created":"2021-08-11T13:39:19Z","success":1,"checksum":"b90fb5767d623602046fed03725e16ca","file_name":"2021_Evolution_Szep.pdf","access_level":"open_access","creator":"kschuh","content_type":"application/pdf","file_size":734102}],"keyword":["Genetics","Ecology","Evolution","Behavior and Systematics","General Agricultural and Biological Sciences"],"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"01","page":"1030-1045","article_type":"original","citation":{"ista":"Szep E, Sachdeva H, Barton NH. 2021. Polygenic local adaptation in metapopulations: A stochastic eco‐evolutionary model. Evolution. 75(5), 1030–1045.","apa":"Szep, E., Sachdeva, H., & Barton, N. H. (2021). Polygenic local adaptation in metapopulations: A stochastic eco‐evolutionary model. Evolution. Wiley. https://doi.org/10.1111/evo.14210","ieee":"E. Szep, H. Sachdeva, and N. H. Barton, “Polygenic local adaptation in metapopulations: A stochastic eco‐evolutionary model,” Evolution, vol. 75, no. 5. Wiley, pp. 1030–1045, 2021.","ama":"Szep E, Sachdeva H, Barton NH. Polygenic local adaptation in metapopulations: A stochastic eco‐evolutionary model. Evolution. 2021;75(5):1030-1045. doi:10.1111/evo.14210","chicago":"Szep, Eniko, Himani Sachdeva, and Nicholas H Barton. “Polygenic Local Adaptation in Metapopulations: A Stochastic Eco‐evolutionary Model.” Evolution. Wiley, 2021. https://doi.org/10.1111/evo.14210.","mla":"Szep, Eniko, et al. “Polygenic Local Adaptation in Metapopulations: A Stochastic Eco‐evolutionary Model.” Evolution, vol. 75, no. 5, Wiley, 2021, pp. 1030–45, doi:10.1111/evo.14210.","short":"E. Szep, H. Sachdeva, N.H. Barton, Evolution 75 (2021) 1030–1045."},"publication":"Evolution","date_published":"2021-05-01T00:00:00Z"},{"author":[{"full_name":"Butlin, Roger K.","first_name":"Roger K.","last_name":"Butlin"},{"first_name":"Maria R.","last_name":"Servedio","full_name":"Servedio, Maria R."},{"last_name":"Smadja","first_name":"Carole M.","full_name":"Smadja, Carole M."},{"first_name":"Claudia","last_name":"Bank","full_name":"Bank, Claudia"},{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"last_name":"Flaxman","first_name":"Samuel M.","full_name":"Flaxman, Samuel M."},{"full_name":"Giraud, Tatiana","first_name":"Tatiana","last_name":"Giraud"},{"last_name":"Hopkins","first_name":"Robin","full_name":"Hopkins, Robin"},{"first_name":"Erica L.","last_name":"Larson","full_name":"Larson, Erica L."},{"last_name":"Maan","first_name":"Martine E.","full_name":"Maan, Martine E."},{"full_name":"Meier, Joana","first_name":"Joana","last_name":"Meier"},{"first_name":"Richard","last_name":"Merrill","full_name":"Merrill, Richard"},{"full_name":"Noor, Mohamed A. F.","first_name":"Mohamed A. F.","last_name":"Noor"},{"first_name":"Daniel","last_name":"Ortiz‐Barrientos","full_name":"Ortiz‐Barrientos, Daniel"},{"full_name":"Qvarnström, Anna","first_name":"Anna","last_name":"Qvarnström"}],"date_updated":"2023-09-05T15:44:33Z","date_created":"2021-05-06T04:34:47Z","volume":75,"acknowledgement":"RKB was funded by the Natural Environment Research Council (NE/P012272/1 & NE/P001610/1), the European Research Council (693030 BARRIERS), and the Swedish Research Council (VR) (2018‐03695). MRS was funded by the National Science Foundation (Grant No. DEB1939290).","year":"2021","publication_status":"published","publisher":"Wiley","department":[{"_id":"NiBa"}],"doi":"10.1111/evo.14235","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"main_file_link":[{"open_access":"1","url":"https://onlinelibrary.wiley.com/doi/10.1111/evo.14235"}],"external_id":{"isi":["000647224000001"]},"quality_controlled":"1","isi":1,"month":"04","publication_identifier":{"eissn":["1558-5646"],"issn":["0014-3820"]},"oa_version":"Published Version","_id":"9374","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"Homage to Felsenstein 1981, or why are there so few/many species?","intvolume":" 75","abstract":[{"lang":"eng","text":"If there are no constraints on the process of speciation, then the number of species might be expected to match the number of available niches and this number might be indefinitely large. One possible constraint is the opportunity for allopatric divergence. In 1981, Felsenstein used a simple and elegant model to ask if there might also be genetic constraints. He showed that progress towards speciation could be described by the build‐up of linkage disequilibrium among divergently selected loci and between these loci and those contributing to other forms of reproductive isolation. Therefore, speciation is opposed by recombination, because it tends to break down linkage disequilibria. Felsenstein then introduced a crucial distinction between “two‐allele” models, which are subject to this effect, and “one‐allele” models, which are free from the recombination constraint. These fundamentally important insights have been the foundation for both empirical and theoretical studies of speciation ever since."}],"issue":"5","type":"journal_article","date_published":"2021-04-19T00:00:00Z","publication":"Evolution","citation":{"short":"R.K. Butlin, M.R. Servedio, C.M. Smadja, C. Bank, N.H. Barton, S.M. Flaxman, T. Giraud, R. Hopkins, E.L. Larson, M.E. Maan, J. Meier, R. Merrill, M.A.F. Noor, D. Ortiz‐Barrientos, A. Qvarnström, Evolution 75 (2021) 978–988.","mla":"Butlin, Roger K., et al. “Homage to Felsenstein 1981, or Why Are There so Few/Many Species?” Evolution, vol. 75, no. 5, Wiley, 2021, pp. 978–88, doi:10.1111/evo.14235.","chicago":"Butlin, Roger K., Maria R. Servedio, Carole M. Smadja, Claudia Bank, Nicholas H Barton, Samuel M. Flaxman, Tatiana Giraud, et al. “Homage to Felsenstein 1981, or Why Are There so Few/Many Species?” Evolution. Wiley, 2021. https://doi.org/10.1111/evo.14235.","ama":"Butlin RK, Servedio MR, Smadja CM, et al. Homage to Felsenstein 1981, or why are there so few/many species? Evolution. 2021;75(5):978-988. doi:10.1111/evo.14235","apa":"Butlin, R. K., Servedio, M. R., Smadja, C. M., Bank, C., Barton, N. H., Flaxman, S. M., … Qvarnström, A. (2021). Homage to Felsenstein 1981, or why are there so few/many species? Evolution. Wiley. https://doi.org/10.1111/evo.14235","ieee":"R. K. Butlin et al., “Homage to Felsenstein 1981, or why are there so few/many species?,” Evolution, vol. 75, no. 5. Wiley, pp. 978–988, 2021.","ista":"Butlin RK, Servedio MR, Smadja CM, Bank C, Barton NH, Flaxman SM, Giraud T, Hopkins R, Larson EL, Maan ME, Meier J, Merrill R, Noor MAF, Ortiz‐Barrientos D, Qvarnström A. 2021. Homage to Felsenstein 1981, or why are there so few/many species? Evolution. 75(5), 978–988."},"article_type":"original","page":"978-988","day":"19","article_processing_charge":"No","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics","General Agricultural and Biological Sciences"]},{"doi":"10.5061/DRYAD.8GTHT76P1","date_published":"2021-03-02T00:00:00Z","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"oa":1,"citation":{"short":"E. Szep, H. Sachdeva, N.H. Barton, (2021).","mla":"Szep, Eniko, et al. Supplementary Code for: Polygenic Local Adaptation in Metapopulations: A Stochastic Eco-Evolutionary Model. Dryad, 2021, doi:10.5061/DRYAD.8GTHT76P1.","chicago":"Szep, Eniko, Himani Sachdeva, and Nicholas H Barton. “Supplementary Code for: Polygenic Local Adaptation in Metapopulations: A Stochastic Eco-Evolutionary Model.” Dryad, 2021. https://doi.org/10.5061/DRYAD.8GTHT76P1.","ama":"Szep E, Sachdeva H, Barton NH. Supplementary code for: Polygenic local adaptation in metapopulations: A stochastic eco-evolutionary model. 2021. doi:10.5061/DRYAD.8GTHT76P1","apa":"Szep, E., Sachdeva, H., & Barton, N. H. (2021). Supplementary code for: Polygenic local adaptation in metapopulations: A stochastic eco-evolutionary model. Dryad. https://doi.org/10.5061/DRYAD.8GTHT76P1","ieee":"E. Szep, H. Sachdeva, and N. H. Barton, “Supplementary code for: Polygenic local adaptation in metapopulations: A stochastic eco-evolutionary model.” Dryad, 2021.","ista":"Szep E, Sachdeva H, Barton NH. 2021. Supplementary code for: Polygenic local adaptation in metapopulations: A stochastic eco-evolutionary model, Dryad, 10.5061/DRYAD.8GTHT76P1."},"main_file_link":[{"url":"https://doi.org/10.5061/dryad.8gtht76p1","open_access":"1"}],"day":"02","month":"03","article_processing_charge":"No","date_created":"2023-05-23T16:17:02Z","date_updated":"2023-09-05T15:44:05Z","oa_version":"Published Version","author":[{"full_name":"Szep, Eniko","id":"485BB5A4-F248-11E8-B48F-1D18A9856A87","last_name":"Szep","first_name":"Eniko"},{"first_name":"Himani","last_name":"Sachdeva","id":"42377A0A-F248-11E8-B48F-1D18A9856A87","full_name":"Sachdeva, Himani"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"}],"related_material":{"record":[{"id":"9252","relation":"used_in_publication","status":"public"}]},"status":"public","ddc":["570"],"title":"Supplementary code for: Polygenic local adaptation in metapopulations: A stochastic eco-evolutionary model","department":[{"_id":"NiBa"}],"publisher":"Dryad","_id":"13062","year":"2021","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","license":"https://creativecommons.org/publicdomain/zero/1.0/","abstract":[{"text":"This paper analyzes the conditions for local adaptation in a metapopulation with infinitely many islands under a model of hard selection, where population size depends on local fitness. Each island belongs to one of two distinct ecological niches or habitats. Fitness is influenced by an additive trait which is under habitat-dependent directional selection. Our analysis is based on the diffusion approximation and accounts for both genetic drift and demographic stochasticity. By neglecting linkage disequilibria, it yields the joint distribution of allele frequencies and population size on each island. We find that under hard selection, the conditions for local adaptation in a rare habitat are more restrictive for more polygenic traits: even moderate migration load per locus at very many loci is sufficient for population sizes to decline. This further reduces the efficacy of selection at individual loci due to increased drift and because smaller populations are more prone to swamping due to migration, causing a positive feedback between increasing maladaptation and declining population sizes. Our analysis also highlights the importance of demographic stochasticity, which exacerbates the decline in numbers of maladapted populations, leading to population collapse in the rare habitat at significantly lower migration than predicted by deterministic arguments.","lang":"eng"}],"type":"research_data_reference"},{"volume":75,"date_created":"2021-05-09T22:01:39Z","date_updated":"2023-10-18T08:16:01Z","author":[{"full_name":"Stankowski, Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","first_name":"Sean","last_name":"Stankowski"},{"last_name":"Ravinet","first_name":"Mark","full_name":"Ravinet, Mark"}],"department":[{"_id":"NiBa"}],"publisher":"Oxford University Press","publication_status":"published","acknowledgement":"We thank M. Garlovsky, S. Martin, C. Cooney, C. Roux, J. Larson, and J. Mallet for critical feedback and for discussion. K. Lohse, M. de la Cámara, J. Cerca, M. A. Chase, C. Baskett, A. M. Westram, and N. H. Barton gave feedback on a draft of the manuscript. O. Seehausen, two anonymous reviewers, and the AE (Michael Kopp) provided comments that greatly improved the manuscript. V. Holzmann made many corrections to the proofs. G. Bisschop and K. Lohse kindly contributed the simulations and analyses presented in Box 3. We would also like to extend our thanks to everyone who took part in the speciation survey, which received ethical approval through the University of Sheffield Ethics Review Procedure (Application 029768). We are especially grateful to R. K. Butlin for stimulating discussion throughout the writing of the manuscript and for feedback on an earlier draft.","year":"2021","license":"https://creativecommons.org/licenses/by-nc/4.0/","file_date_updated":"2022-03-25T12:02:04Z","language":[{"iso":"eng"}],"doi":"10.1111/evo.14215","quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"external_id":{"isi":["000647226400001"]},"oa":1,"publication_identifier":{"issn":["0014-3820"],"eissn":["1558-5646"]},"month":"03","oa_version":"Published Version","file":[{"success":1,"checksum":"96f6ccf15d95a4e9f7c0b27eee570fa6","date_created":"2022-03-25T12:02:04Z","date_updated":"2022-03-25T12:02:04Z","file_id":"10921","relation":"main_file","creator":"kschuh","file_size":719991,"content_type":"application/pdf","access_level":"open_access","file_name":"2021_Evolution_Stankowski.pdf"}],"intvolume":" 75","title":"Defining the speciation continuum","ddc":["570"],"status":"public","_id":"9383","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"6","abstract":[{"lang":"eng","text":"A primary roadblock to our understanding of speciation is that it usually occurs over a timeframe that is too long to study from start to finish. The idea of a speciation continuum provides something of a solution to this problem; rather than observing the entire process, we can simply reconstruct it from the multitude of speciation events that surround us. But what do we really mean when we talk about the speciation continuum, and can it really help us understand speciation? We explored these questions using a literature review and online survey of speciation researchers. Although most researchers were familiar with the concept and thought it was useful, our survey revealed extensive disagreement about what the speciation continuum actually tells us. This is due partly to the lack of a clear definition. Here, we provide an explicit definition that is compatible with the Biological Species Concept. That is, the speciation continuum is a continuum of reproductive isolation. After outlining the logic of the definition in light of alternatives, we explain why attempts to reconstruct the speciation process from present‐day populations will ultimately fail. We then outline how we think the speciation continuum concept can continue to act as a foundation for understanding the continuum of reproductive isolation that surrounds us."}],"type":"journal_article","date_published":"2021-03-22T00:00:00Z","page":"1256-1273","article_type":"original","citation":{"short":"S. Stankowski, M. Ravinet, Evolution 75 (2021) 1256–1273.","mla":"Stankowski, Sean, and Mark Ravinet. “Defining the Speciation Continuum.” Evolution, vol. 75, no. 6, Oxford University Press, 2021, pp. 1256–73, doi:10.1111/evo.14215.","chicago":"Stankowski, Sean, and Mark Ravinet. “Defining the Speciation Continuum.” Evolution. Oxford University Press, 2021. https://doi.org/10.1111/evo.14215.","ama":"Stankowski S, Ravinet M. Defining the speciation continuum. Evolution. 2021;75(6):1256-1273. doi:10.1111/evo.14215","ieee":"S. Stankowski and M. Ravinet, “Defining the speciation continuum,” Evolution, vol. 75, no. 6. Oxford University Press, pp. 1256–1273, 2021.","apa":"Stankowski, S., & Ravinet, M. (2021). Defining the speciation continuum. Evolution. Oxford University Press. https://doi.org/10.1111/evo.14215","ista":"Stankowski S, Ravinet M. 2021. Defining the speciation continuum. Evolution. 75(6), 1256–1273."},"publication":"Evolution","article_processing_charge":"No","has_accepted_license":"1","day":"22","scopus_import":"1"},{"doi":"10.1002/9780470015902.a0029355","date_published":"2021-05-28T00:00:00Z","language":[{"iso":"eng"}],"publication":"Encyclopedia of Life Sciences","citation":{"ama":"Stankowski S, Shipilina D, Westram AM. Hybrid Zones. In: Encyclopedia of Life Sciences. Vol 2. eLS. Wiley; 2021. doi:10.1002/9780470015902.a0029355","ista":"Stankowski S, Shipilina D, Westram AM. 2021.Hybrid Zones. In: Encyclopedia of Life Sciences. vol. 2.","apa":"Stankowski, S., Shipilina, D., & Westram, A. M. (2021). Hybrid Zones. In Encyclopedia of Life Sciences (Vol. 2). Wiley. https://doi.org/10.1002/9780470015902.a0029355","ieee":"S. Stankowski, D. Shipilina, and A. M. Westram, “Hybrid Zones,” in Encyclopedia of Life Sciences, vol. 2, Wiley, 2021.","mla":"Stankowski, Sean, et al. “Hybrid Zones.” Encyclopedia of Life Sciences, vol. 2, Wiley, 2021, doi:10.1002/9780470015902.a0029355.","short":"S. Stankowski, D. Shipilina, A.M. Westram, in:, Encyclopedia of Life Sciences, Wiley, 2021.","chicago":"Stankowski, Sean, Daria Shipilina, and Anja M Westram. “Hybrid Zones.” In Encyclopedia of Life Sciences, Vol. 2. ELS. Wiley, 2021. https://doi.org/10.1002/9780470015902.a0029355."},"quality_controlled":"1","day":"28","month":"05","publication_identifier":{"isbn":["9780470016176"],"eisbn":["9780470015902"]},"article_processing_charge":"No","series_title":"eLS","author":[{"full_name":"Stankowski, Sean","first_name":"Sean","last_name":"Stankowski","id":"43161670-5719-11EA-8025-FABC3DDC885E"},{"id":"428A94B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1145-9226","first_name":"Daria","last_name":"Shipilina","full_name":"Shipilina, Daria"},{"full_name":"Westram, Anja M","first_name":"Anja M","last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969"}],"date_created":"2024-02-14T12:05:50Z","date_updated":"2024-02-19T09:54:18Z","volume":2,"oa_version":"None","_id":"14984","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2021","status":"public","title":"Hybrid Zones","publication_status":"published","publisher":"Wiley","intvolume":" 2","department":[{"_id":"NiBa"}],"abstract":[{"lang":"eng","text":"Hybrid zones are narrow geographic regions where different populations, races or interbreeding species meet and mate, producing mixed ‘hybrid’ offspring. They are relatively common and can be found in a diverse range of organisms and environments. The study of hybrid zones has played an important role in our understanding of the origin of species, with hybrid zones having been described as ‘natural laboratories’. This is because they allow us to study,in situ, the conditions and evolutionary forces that enable divergent taxa to remain distinct despite some ongoing gene exchange between them."}],"type":"book_chapter"},{"month":"02","day":"26","has_accepted_license":"1","article_processing_charge":"No","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"citation":{"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. 2021. doi:10.15479/AT:ISTA:9192","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, 2021.","apa":"Surendranadh, P., Arathoon, L. S., Baskett, C., Field, D., Pickup, M., & Barton, N. H. (2021). 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. https://doi.org/10.15479/AT:ISTA:9192","ista":"Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. 2021. 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, 10.15479/AT:ISTA:9192.","short":"P. Surendranadh, L.S. Arathoon, C. Baskett, D. Field, M. Pickup, N.H. Barton, (2021).","mla":"Surendranadh, Parvathy, et al. 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, 2021, doi:10.15479/AT:ISTA:9192.","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, 2021. https://doi.org/10.15479/AT:ISTA:9192."},"doi":"10.15479/AT:ISTA:9192","date_published":"2021-02-26T00:00:00Z","type":"research_data","file_date_updated":"2021-02-24T17:45:13Z","abstract":[{"text":"Here are the research data underlying the publication \" Effects of fine-scale population structure on inbreeding in a long-term study of snapdragons (Antirrhinum majus).\" Further information are summed up in the README document.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9192","year":"2021","title":"Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus","status":"public","ddc":["576"],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"author":[{"id":"455235B8-F248-11E8-B48F-1D18A9856A87","first_name":"Parvathy","last_name":"Surendranadh","full_name":"Surendranadh, Parvathy"},{"id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1771-714X","first_name":"Louise S","last_name":"Arathoon","full_name":"Arathoon, Louise S"},{"full_name":"Baskett, Carina","first_name":"Carina","last_name":"Baskett","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7354-8574"},{"full_name":"Field, David","orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field","first_name":"David"},{"full_name":"Pickup, Melinda","first_name":"Melinda","last_name":"Pickup","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6118-0541"},{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"11411"},{"relation":"later_version","status":"public","id":"11321"},{"id":"8254","relation":"earlier_version","status":"public"}]},"contributor":[{"first_name":"Parvathy","contributor_type":"project_member","last_name":"Surendranadh","id":"455235B8-F248-11E8-B48F-1D18A9856A87"},{"contributor_type":"project_member","last_name":"Arathoon","first_name":"Louise S","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87"},{"id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member","last_name":"Baskett","first_name":"Carina"},{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478","first_name":"David","contributor_type":"project_member","last_name":"Field"},{"orcid":"0000-0001-6118-0541","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member","last_name":"Pickup","first_name":"Melinda"},{"contributor_type":"project_leader","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2021-02-24T17:49:21Z","date_updated":"2024-02-21T12:41:09Z","file":[{"file_id":"9193","relation":"main_file","success":1,"checksum":"f85537815809a8a4b7da9d01163f88c0","date_created":"2021-02-24T17:45:13Z","date_updated":"2021-02-24T17:45:13Z","access_level":"open_access","file_name":"Data_Code.zip","creator":"larathoo","content_type":"application/x-zip-compressed","file_size":5934452}],"oa_version":"Published Version"},{"article_number":"20190721","file_date_updated":"2020-07-14T12:48:01Z","year":"2020","publisher":"The Royal Society","department":[{"_id":"NiBa"}],"publication_status":"published","author":[{"last_name":"Larsson","first_name":"J.","full_name":"Larsson, J."},{"full_name":"Westram, Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","first_name":"Anja M","last_name":"Westram"},{"last_name":"Bengmark","first_name":"S.","full_name":"Bengmark, S."},{"last_name":"Lundh","first_name":"T.","full_name":"Lundh, T."},{"last_name":"Butlin","first_name":"R. K.","full_name":"Butlin, R. K."}],"volume":17,"date_created":"2020-04-08T15:19:17Z","date_updated":"2021-01-12T08:14:41Z","publication_identifier":{"eissn":["1742-5662"],"issn":["1742-5689"]},"month":"02","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","doi":"10.1098/rsif.2019.0721","language":[{"iso":"eng"}],"type":"journal_article","issue":"163","abstract":[{"text":"The growth of snail shells can be described by simple mathematical rules. Variation in a few parameters can explain much of the diversity of shell shapes seen in nature. However, empirical studies of gastropod shell shape variation typically use geometric morphometric approaches, which do not capture this growth pattern. We have developed a way to infer a set of developmentally descriptive shape parameters based on three-dimensional logarithmic helicospiral growth and using landmarks from two-dimensional shell images as input. We demonstrate the utility of this approach, and compare it to the geometric morphometric approach, using a large set of Littorina saxatilis shells in which locally adapted populations differ in shape. Our method can be modified easily to make it applicable to a wide range of shell forms, which would allow for investigations of the similarities and differences between and within many different species of gastropods.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"7651","intvolume":" 17","status":"public","ddc":["570"],"title":"A developmentally descriptive method for quantifying shape in gastropod shells","file":[{"file_size":1556190,"content_type":"application/pdf","creator":"dernst","file_name":"2020_JournRoyalSociety_Larsson.pdf","access_level":"open_access","date_created":"2020-04-14T12:31:16Z","date_updated":"2020-07-14T12:48:01Z","checksum":"4eb102304402f5c56432516b84df86d6","relation":"main_file","file_id":"7660"}],"oa_version":"Published Version","scopus_import":1,"article_processing_charge":"No","has_accepted_license":"1","day":"01","citation":{"ama":"Larsson J, Westram AM, Bengmark S, Lundh T, Butlin RK. A developmentally descriptive method for quantifying shape in gastropod shells. Journal of The Royal Society Interface. 2020;17(163). doi:10.1098/rsif.2019.0721","apa":"Larsson, J., Westram, A. M., Bengmark, S., Lundh, T., & Butlin, R. K. (2020). A developmentally descriptive method for quantifying shape in gastropod shells. Journal of The Royal Society Interface. The Royal Society. https://doi.org/10.1098/rsif.2019.0721","ieee":"J. Larsson, A. M. Westram, S. Bengmark, T. Lundh, and R. K. Butlin, “A developmentally descriptive method for quantifying shape in gastropod shells,” Journal of The Royal Society Interface, vol. 17, no. 163. The Royal Society, 2020.","ista":"Larsson J, Westram AM, Bengmark S, Lundh T, Butlin RK. 2020. A developmentally descriptive method for quantifying shape in gastropod shells. Journal of The Royal Society Interface. 17(163), 20190721.","short":"J. Larsson, A.M. Westram, S. Bengmark, T. Lundh, R.K. Butlin, Journal of The Royal Society Interface 17 (2020).","mla":"Larsson, J., et al. “A Developmentally Descriptive Method for Quantifying Shape in Gastropod Shells.” Journal of The Royal Society Interface, vol. 17, no. 163, 20190721, The Royal Society, 2020, doi:10.1098/rsif.2019.0721.","chicago":"Larsson, J., Anja M Westram, S. Bengmark, T. Lundh, and R. K. Butlin. “A Developmentally Descriptive Method for Quantifying Shape in Gastropod Shells.” Journal of The Royal Society Interface. The Royal Society, 2020. https://doi.org/10.1098/rsif.2019.0721."},"publication":"Journal of The Royal Society Interface","article_type":"original","date_published":"2020-02-01T00:00:00Z"},{"day":"16","month":"05","publication_identifier":{"isbn":["9780470016176","9780470015902"]},"article_processing_charge":"No","date_published":"2020-05-16T00:00:00Z","doi":"10.1002/9780470015902.a0029007","language":[{"iso":"eng"}],"publication":"eLS","citation":{"chicago":"Westram, Anja M, Rui Faria, Roger Butlin, and Kerstin Johannesson. “Inversions and Evolution.” In ELS. Wiley, 2020. https://doi.org/10.1002/9780470015902.a0029007.","short":"A.M. Westram, R. Faria, R. Butlin, K. Johannesson, in:, ELS, Wiley, 2020.","mla":"Westram, Anja M., et al. “Inversions and Evolution.” ELS, Wiley, 2020, doi:10.1002/9780470015902.a0029007.","apa":"Westram, A. M., Faria, R., Butlin, R., & Johannesson, K. (2020). Inversions and Evolution. In eLS. Wiley. https://doi.org/10.1002/9780470015902.a0029007","ieee":"A. M. Westram, R. Faria, R. Butlin, and K. Johannesson, “Inversions and Evolution,” in eLS, Wiley, 2020.","ista":"Westram AM, Faria R, Butlin R, Johannesson K. 2020.Inversions and Evolution. In: eLS. .","ama":"Westram AM, Faria R, Butlin R, Johannesson K. Inversions and Evolution. In: ELS. Wiley; 2020. doi:10.1002/9780470015902.a0029007"},"quality_controlled":"1","abstract":[{"text":"Inversions are chromosomal rearrangements where the order of genes is reversed. Inversions originate by mutation and can be under positive, negative or balancing selection. Selective effects result from potential disruptive effects on meiosis, gene disruption at inversion breakpoints and, importantly, the effects of inversions as modifiers of recombination rate: Recombination is strongly reduced in individuals heterozygous for an inversion, allowing for alleles at different loci to be inherited as a ‘block’. This may lead to a selective advantage whenever it is favourable to keep certain combinations of alleles associated, for example under local adaptation with gene flow. Inversions can cover a considerable part of a chromosome and contain numerous loci under different selection pressures, so that the resulting overall effects may be complex. Empirical data from various systems show that inversions may have a prominent role in local adaptation, speciation, parallel evolution, the maintenance of polymorphism and sex chromosome evolution.","lang":"eng"}],"type":"book_chapter","author":[{"last_name":"Westram","first_name":"Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","full_name":"Westram, Anja M"},{"full_name":"Faria, Rui","first_name":"Rui","last_name":"Faria"},{"full_name":"Butlin, Roger","first_name":"Roger","last_name":"Butlin"},{"full_name":"Johannesson, Kerstin","last_name":"Johannesson","first_name":"Kerstin"}],"date_updated":"2021-02-15T13:18:16Z","date_created":"2021-02-15T12:39:04Z","oa_version":"None","_id":"9123","year":"2020","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Inversions and Evolution","publication_status":"published","status":"public","department":[{"_id":"NiBa"}],"publisher":"Wiley"},{"article_processing_charge":"No","day":"22","month":"09","date_published":"2020-09-22T00:00:00Z","doi":"10.5061/DRYAD.R4XGXD29N","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.r4xgxd29n"}],"oa":1,"citation":{"chicago":"Simon, Alexis, Christelle Fraisse, Tahani El Ayari, Cathy Liautard-Haag, Petr Strelkov, John Welch, and Nicolas Bierne. “How Do Species Barriers Decay? Concordance and Local Introgression in Mosaic Hybrid Zones of Mussels.” Dryad, 2020. https://doi.org/10.5061/DRYAD.R4XGXD29N.","short":"A. Simon, C. Fraisse, T. El Ayari, C. Liautard-Haag, P. Strelkov, J. Welch, N. Bierne, (2020).","mla":"Simon, Alexis, et al. How Do Species Barriers Decay? Concordance and Local Introgression in Mosaic Hybrid Zones of Mussels. Dryad, 2020, doi:10.5061/DRYAD.R4XGXD29N.","apa":"Simon, A., Fraisse, C., El Ayari, T., Liautard-Haag, C., Strelkov, P., Welch, J., & Bierne, N. (2020). How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels. Dryad. https://doi.org/10.5061/DRYAD.R4XGXD29N","ieee":"A. Simon et al., “How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels.” Dryad, 2020.","ista":"Simon A, Fraisse C, El Ayari T, Liautard-Haag C, Strelkov P, Welch J, Bierne N. 2020. How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels, Dryad, 10.5061/DRYAD.R4XGXD29N.","ama":"Simon A, Fraisse C, El Ayari T, et al. How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels. 2020. doi:10.5061/DRYAD.R4XGXD29N"},"abstract":[{"text":"The Mytilus complex of marine mussel species forms a mosaic of hybrid zones, found across temperate regions of the globe. This allows us to study \"replicated\" instances of secondary contact between closely-related species. Previous work on this complex has shown that local introgression is both widespread and highly heterogeneous, and has identified SNPs that are outliers of differentiation between lineages. Here, we developed an ancestry-informative panel of such SNPs. We then compared their frequencies in newly-sampled populations, including samples from within the hybrid zones, and parental populations at different distances from the contact. Results show that close to the hybrid zones, some outlier loci are near to fixation for the heterospecific allele, suggesting enhanced local introgression, or the local sweep of a shared ancestral allele. Conversely, genomic cline analyses, treating local parental populations as the reference, reveal a globally high concordance among loci, albeit with a few signals of asymmetric introgression. Enhanced local introgression at specific loci is consistent with the early transfer of adaptive variants after contact, possibly including asymmetric bi-stable variants (Dobzhansky-Muller incompatibilities), or haplotypes loaded with fewer deleterious mutations. Having escaped one barrier, however, these variants can be trapped or delayed at the next barrier, confining the introgression locally. These results shed light on the decay of species barriers during phases of contact.","lang":"eng"}],"type":"research_data_reference","oa_version":"Published Version","date_created":"2023-05-23T16:48:27Z","date_updated":"2023-08-04T11:04:11Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"8708"}]},"author":[{"first_name":"Alexis","last_name":"Simon","full_name":"Simon, Alexis"},{"last_name":"Fraisse","first_name":"Christelle","orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","full_name":"Fraisse, Christelle"},{"full_name":"El Ayari, Tahani","first_name":"Tahani","last_name":"El Ayari"},{"full_name":"Liautard-Haag, Cathy","last_name":"Liautard-Haag","first_name":"Cathy"},{"last_name":"Strelkov","first_name":"Petr","full_name":"Strelkov, Petr"},{"full_name":"Welch, John","last_name":"Welch","first_name":"John"},{"first_name":"Nicolas","last_name":"Bierne","full_name":"Bierne, Nicolas"}],"publisher":"Dryad","department":[{"_id":"NiBa"}],"status":"public","ddc":["570"],"title":"How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels","_id":"13073","year":"2020","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"doi":"10.5061/DRYAD.Q2BVQ83HD","date_published":"2020-10-19T00:00:00Z","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"oa":1,"citation":{"mla":"Arnoux, Stephanie, et al. VCF Files of Synonymous SNPs Related to: Genomic Inference of Complex Domestication Histories in Three Solanaceae Species. Dryad, 2020, doi:10.5061/DRYAD.Q2BVQ83HD.","short":"S. Arnoux, C. Fraisse, C. Sauvage, (2020).","chicago":"Arnoux, Stephanie, Christelle Fraisse, and Christopher Sauvage. “VCF Files of Synonymous SNPs Related to: Genomic Inference of Complex Domestication Histories in Three Solanaceae Species.” Dryad, 2020. https://doi.org/10.5061/DRYAD.Q2BVQ83HD.","ama":"Arnoux S, Fraisse C, Sauvage C. VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species. 2020. doi:10.5061/DRYAD.Q2BVQ83HD","ista":"Arnoux S, Fraisse C, Sauvage C. 2020. VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species, Dryad, 10.5061/DRYAD.Q2BVQ83HD.","apa":"Arnoux, S., Fraisse, C., & Sauvage, C. (2020). VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species. Dryad. https://doi.org/10.5061/DRYAD.Q2BVQ83HD","ieee":"S. Arnoux, C. Fraisse, and C. Sauvage, “VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species.” Dryad, 2020."},"main_file_link":[{"url":"https://doi.org/10.5061/dryad.q2bvq83hd","open_access":"1"}],"day":"19","month":"10","article_processing_charge":"No","author":[{"full_name":"Arnoux, Stephanie","first_name":"Stephanie","last_name":"Arnoux"},{"first_name":"Christelle","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle"},{"last_name":"Sauvage","first_name":"Christopher","full_name":"Sauvage, Christopher"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"8928"}],"link":[{"relation":"software","url":"https://github.com/starnoux/arnoux_et_al_2019"}]},"date_updated":"2023-08-04T11:19:26Z","date_created":"2023-05-23T16:30:20Z","oa_version":"Published Version","year":"2020","_id":"13065","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"title":"VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species","status":"public","department":[{"_id":"NiBa"}],"publisher":"Dryad","abstract":[{"text":"Domestication is a human-induced selection process that imprints the genomes of domesticated populations over a short evolutionary time scale, and that occurs in a given demographic context. Reconstructing historical gene flow, effective population size changes and their timing is therefore of fundamental interest to understand how plant demography and human selection jointly shape genomic divergence during domestication. Yet, the comparison under a single statistical framework of independent domestication histories across different crop species has been little evaluated so far. Thus, it is unclear whether domestication leads to convergent demographic changes that similarly affect crop genomes. To address this question, we used existing and new transcriptome data on three crop species of Solanaceae (eggplant, pepper and tomato), together with their close wild relatives. We fitted twelve demographic models of increasing complexity on the unfolded joint allele frequency spectrum for each wild/crop pair, and we found evidence for both shared and species-specific demographic processes between species. A convergent history of domestication with gene-flow was inferred for all three species, along with evidence of strong reduction in the effective population size during the cultivation stage of tomato and pepper. The absence of any reduction in size of the crop in eggplant stands out from the classical view of the domestication process; as does the existence of a “protracted period” of management before cultivation. Our results also suggest divergent management strategies of modern cultivars among species as their current demography substantially differs. Finally, the timing of domestication is species-specific and supported by the few historical records available.","lang":"eng"}],"type":"research_data_reference"},{"ec_funded":1,"file_date_updated":"2020-11-25T10:49:48Z","volume":74,"date_updated":"2023-08-22T07:13:38Z","date_created":"2020-06-22T09:14:21Z","related_material":{"record":[{"relation":"research_data","status":"public","id":"8809"}]},"author":[{"full_name":"Perini, Samuel","last_name":"Perini","first_name":"Samuel"},{"full_name":"Rafajlović, Marina","last_name":"Rafajlović","first_name":"Marina"},{"first_name":"Anja M","last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M"},{"last_name":"Johannesson","first_name":"Kerstin","full_name":"Johannesson, Kerstin"},{"full_name":"Butlin, Roger K.","first_name":"Roger K.","last_name":"Butlin"}],"department":[{"_id":"NiBa"}],"publisher":"Wiley","publication_status":"published","acknowledgement":"We are very grateful to I. Sencic, L. Brettell, A.‐L. Liabot, J. Galindo, M. Ravinet, and A. Butlin for their help with field sampling and mating experiments. This work was funded by the Natural Environment Research Council, European Research Council and Swedish Research Council VR and we are also very grateful for the support of the Linnaeus Centre for Marine Evolutionary Biology at the University of Gothenburg. The simulations were performed on resources at Chalmers Centre for Computational Science and Engineering (C3SE) provided by the Swedish National Infrastructure for Computing (SNIC). AMW was funded by the European Union's Horizon 2020 research and innovation program under Marie Skłodowska‐Curie grant agreement no. 797747.","year":"2020","publication_identifier":{"eissn":["15585646"],"issn":["00143820"]},"month":"07","language":[{"iso":"eng"}],"doi":"10.1111/evo.14027","project":[{"name":"Theoretical and empirical approaches to understanding Parallel Adaptation","call_identifier":"H2020","grant_number":"797747","_id":"265B41B8-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000539780800001"]},"oa":1,"issue":"7","abstract":[{"lang":"eng","text":"When divergent populations are connected by gene flow, the establishment of complete reproductive isolation usually requires the joint action of multiple barrier effects. One example where multiple barrier effects are coupled consists of a single trait that is under divergent natural selection and also mediates assortative mating. Such multiple‐effect traits can strongly reduce gene flow. However, there are few cases where patterns of assortative mating have been described quantitatively and their impact on gene flow has been determined. Two ecotypes of the coastal marine snail, Littorina saxatilis , occur in North Atlantic rocky‐shore habitats dominated by either crab predation or wave action. There is evidence for divergent natural selection acting on size, and size‐assortative mating has previously been documented. Here, we analyze the mating pattern in L. saxatilis with respect to size in intensively sampled transects across boundaries between the habitats. We show that the mating pattern is mostly conserved between ecotypes and that it generates both assortment and directional sexual selection for small male size. Using simulations, we show that the mating pattern can contribute to reproductive isolation between ecotypes but the barrier to gene flow is likely strengthened more by sexual selection than by assortment."}],"type":"journal_article","oa_version":"Published Version","file":[{"file_name":"2020_Evolution_Perini.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":1080810,"file_id":"8808","relation":"main_file","date_created":"2020-11-25T10:49:48Z","date_updated":"2020-11-25T10:49:48Z","success":1,"checksum":"56235bf1e2a9e25f96196bb13b6b754d"}],"intvolume":" 74","title":"Assortative mating, sexual selection, and their consequences for gene flow in Littorina","status":"public","ddc":["570"],"_id":"7995","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","has_accepted_license":"1","day":"01","scopus_import":"1","date_published":"2020-07-01T00:00:00Z","page":"1482-1497","article_type":"original","citation":{"mla":"Perini, Samuel, et al. “Assortative Mating, Sexual Selection, and Their Consequences for Gene Flow in Littorina.” Evolution, vol. 74, no. 7, Wiley, 2020, pp. 1482–97, doi:10.1111/evo.14027.","short":"S. Perini, M. Rafajlović, A.M. Westram, K. Johannesson, R.K. Butlin, Evolution 74 (2020) 1482–1497.","chicago":"Perini, Samuel, Marina Rafajlović, Anja M Westram, Kerstin Johannesson, and Roger K. Butlin. “Assortative Mating, Sexual Selection, and Their Consequences for Gene Flow in Littorina.” Evolution. Wiley, 2020. https://doi.org/10.1111/evo.14027.","ama":"Perini S, Rafajlović M, Westram AM, Johannesson K, Butlin RK. Assortative mating, sexual selection, and their consequences for gene flow in Littorina. Evolution. 2020;74(7):1482-1497. doi:10.1111/evo.14027","ista":"Perini S, Rafajlović M, Westram AM, Johannesson K, Butlin RK. 2020. Assortative mating, sexual selection, and their consequences for gene flow in Littorina. Evolution. 74(7), 1482–1497.","ieee":"S. Perini, M. Rafajlović, A. M. Westram, K. Johannesson, and R. K. Butlin, “Assortative mating, sexual selection, and their consequences for gene flow in Littorina,” Evolution, vol. 74, no. 7. Wiley, pp. 1482–1497, 2020.","apa":"Perini, S., Rafajlović, M., Westram, A. M., Johannesson, K., & Butlin, R. K. (2020). Assortative mating, sexual selection, and their consequences for gene flow in Littorina. Evolution. Wiley. https://doi.org/10.1111/evo.14027"},"publication":"Evolution"},{"title":"Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina","status":"public","department":[{"_id":"NiBa"}],"publisher":"Dryad","_id":"8809","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2020","date_updated":"2023-08-22T07:13:37Z","date_created":"2020-11-25T11:07:25Z","oa_version":"Published Version","author":[{"first_name":"Samuel","last_name":"Perini","full_name":"Perini, Samuel"},{"full_name":"Rafajlovic, Marina","last_name":"Rafajlovic","first_name":"Marina"},{"last_name":"Westram","first_name":"Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","full_name":"Westram, Anja M"},{"first_name":"Kerstin","last_name":"Johannesson","full_name":"Johannesson, Kerstin"},{"full_name":"Butlin, Roger","last_name":"Butlin","first_name":"Roger"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"7995"}]},"type":"research_data_reference","abstract":[{"lang":"eng","text":"When divergent populations are connected by gene flow, the establishment of complete reproductive isolation usually requires the joint action of multiple barrier effects. One example where multiple barrier effects are coupled consists of a single trait that is under divergent natural selection and also mediates assortative mating. Such multiple-effect traits can strongly reduce gene flow. However, there are few cases where patterns of assortative mating have been described quantitatively and their impact on gene flow has been determined. Two ecotypes of the coastal marine snail, Littorina saxatilis, occur in North Atlantic rocky-shore habitats dominated by either crab predation or wave action. There is evidence for divergent natural selection acting on size, and size-assortative mating has previously been documented. Here, we analyze the mating pattern in L. saxatilis with respect to size in intensively-sampled transects across boundaries between the habitats. We show that the mating pattern is mostly conserved between ecotypes and that it generates both assortment and directional sexual selection for small male size. Using simulations, we show that the mating pattern can contribute to reproductive isolation between ecotypes but the barrier to gene flow is likely strengthened more by sexual selection than by assortment."}],"oa":1,"tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"citation":{"mla":"Perini, Samuel, et al. Data from: Assortative Mating, Sexual Selection and Their Consequences for Gene Flow in Littorina. Dryad, 2020, doi:10.5061/dryad.qrfj6q5cn.","short":"S. Perini, M. Rafajlovic, A.M. Westram, K. Johannesson, R. Butlin, (2020).","chicago":"Perini, Samuel, Marina Rafajlovic, Anja M Westram, Kerstin Johannesson, and Roger Butlin. “Data from: Assortative Mating, Sexual Selection and Their Consequences for Gene Flow in Littorina.” Dryad, 2020. https://doi.org/10.5061/dryad.qrfj6q5cn.","ama":"Perini S, Rafajlovic M, Westram AM, Johannesson K, Butlin R. Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina. 2020. doi:10.5061/dryad.qrfj6q5cn","ista":"Perini S, Rafajlovic M, Westram AM, Johannesson K, Butlin R. 2020. Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina, Dryad, 10.5061/dryad.qrfj6q5cn.","ieee":"S. Perini, M. Rafajlovic, A. M. Westram, K. Johannesson, and R. Butlin, “Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina.” Dryad, 2020.","apa":"Perini, S., Rafajlovic, M., Westram, A. M., Johannesson, K., & Butlin, R. (2020). Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina. Dryad. https://doi.org/10.5061/dryad.qrfj6q5cn"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.qrfj6q5cn"}],"date_published":"2020-07-01T00:00:00Z","doi":"10.5061/dryad.qrfj6q5cn","month":"07","day":"01","has_accepted_license":"1","article_processing_charge":"No"},{"publication_identifier":{"eissn":["1471-2970"],"issn":["0962-8436"]},"month":"07","quality_controlled":"1","isi":1,"external_id":{"isi":["000552662100002"],"pmid":["32654647"]},"language":[{"iso":"eng"}],"doi":"10.1098/rstb.2019.0530","article_number":"20190530","publisher":"The Royal Society","department":[{"_id":"NiBa"}],"publication_status":"published","pmid":1,"year":"2020","volume":375,"date_updated":"2023-08-22T07:53:52Z","date_created":"2020-07-13T03:41:39Z","author":[{"full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"scopus_import":"1","article_processing_charge":"No","day":"12","article_type":"letter_note","citation":{"apa":"Barton, N. H. (2020). On the completion of speciation. Philosophical Transactions of the Royal Society. Series B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rstb.2019.0530","ieee":"N. H. Barton, “On the completion of speciation,” Philosophical Transactions of the Royal Society. Series B: Biological Sciences, vol. 375, no. 1806. The Royal Society, 2020.","ista":"Barton NH. 2020. On the completion of speciation. Philosophical Transactions of the Royal Society. Series B: Biological Sciences. 375(1806), 20190530.","ama":"Barton NH. On the completion of speciation. Philosophical Transactions of the Royal Society Series B: Biological Sciences. 2020;375(1806). doi:10.1098/rstb.2019.0530","chicago":"Barton, Nicholas H. “On the Completion of Speciation.” Philosophical Transactions of the Royal Society. Series B: Biological Sciences. The Royal Society, 2020. https://doi.org/10.1098/rstb.2019.0530.","short":"N.H. Barton, Philosophical Transactions of the Royal Society. Series B: Biological Sciences 375 (2020).","mla":"Barton, Nicholas H. “On the Completion of Speciation.” Philosophical Transactions of the Royal Society. Series B: Biological Sciences, vol. 375, no. 1806, 20190530, The Royal Society, 2020, doi:10.1098/rstb.2019.0530."},"publication":"Philosophical Transactions of the Royal Society. Series B: Biological Sciences","date_published":"2020-07-12T00:00:00Z","type":"journal_article","issue":"1806","intvolume":" 375","status":"public","title":"On the completion of speciation","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8112","oa_version":"None"},{"oa_version":"Published Version","status":"public","title":"Towards the completion of speciation: The evolution of reproductive isolation beyond the first barriers","intvolume":" 375","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8168","abstract":[{"text":"Speciation, that is, the evolution of reproductive barriers eventually leading to complete isolation, is a crucial process generating biodiversity. Recent work has contributed much to our understanding of how reproductive barriers begin to evolve, and how they are maintained in the face of gene flow. However, little is known about the transition from partial to strong reproductive isolation (RI) and the completion of speciation. We argue that the evolution of strong RI is likely to involve different processes, or new interactions among processes, compared with the evolution of the first reproductive barriers. Transition to strong RI may be brought about by changing external conditions, for example, following secondary contact. However, the increasing levels of RI themselves create opportunities for new barriers to evolve and, and interaction or coupling among barriers. These changing processes may depend on genomic architecture and leave detectable signals in the genome. We outline outstanding questions and suggest more theoretical and empirical work, considering both patterns and processes associated with strong RI, is needed to understand how speciation is completed.","lang":"eng"}],"issue":"1806","type":"journal_article","date_published":"2020-07-12T00:00:00Z","article_type":"original","publication":"Philosophical Transactions of the Royal Society. Series B: Biological sciences","citation":{"ama":"Kulmuni J, Butlin RK, Lucek K, Savolainen V, Westram AM. Towards the completion of speciation: The evolution of reproductive isolation beyond the first barriers. Philosophical Transactions of the Royal Society Series B: Biological sciences. 2020;375(1806). doi:10.1098/rstb.2019.0528","ieee":"J. Kulmuni, R. K. Butlin, K. Lucek, V. Savolainen, and A. M. Westram, “Towards the completion of speciation: The evolution of reproductive isolation beyond the first barriers,” Philosophical Transactions of the Royal Society. Series B: Biological sciences, vol. 375, no. 1806. The Royal Society, 2020.","apa":"Kulmuni, J., Butlin, R. K., Lucek, K., Savolainen, V., & Westram, A. M. (2020). Towards the completion of speciation: The evolution of reproductive isolation beyond the first barriers. Philosophical Transactions of the Royal Society. Series B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rstb.2019.0528","ista":"Kulmuni J, Butlin RK, Lucek K, Savolainen V, Westram AM. 2020. Towards the completion of speciation: The evolution of reproductive isolation beyond the first barriers. Philosophical Transactions of the Royal Society. Series B: Biological sciences. 375(1806), 20190528.","short":"J. Kulmuni, R.K. Butlin, K. Lucek, V. Savolainen, A.M. Westram, Philosophical Transactions of the Royal Society. Series B: Biological Sciences 375 (2020).","mla":"Kulmuni, Jonna, et al. “Towards the Completion of Speciation: The Evolution of Reproductive Isolation beyond the First Barriers.” Philosophical Transactions of the Royal Society. Series B: Biological Sciences, vol. 375, no. 1806, 20190528, The Royal Society, 2020, doi:10.1098/rstb.2019.0528.","chicago":"Kulmuni, Jonna, Roger K. Butlin, Kay Lucek, Vincent Savolainen, and Anja M Westram. “Towards the Completion of Speciation: The Evolution of Reproductive Isolation beyond the First Barriers.” Philosophical Transactions of the Royal Society. Series B: Biological Sciences. The Royal Society, 2020. https://doi.org/10.1098/rstb.2019.0528."},"day":"12","article_processing_charge":"No","scopus_import":"1","date_created":"2020-07-26T22:01:01Z","date_updated":"2023-08-22T08:21:31Z","volume":375,"author":[{"full_name":"Kulmuni, Jonna","last_name":"Kulmuni","first_name":"Jonna"},{"full_name":"Butlin, Roger K.","first_name":"Roger K.","last_name":"Butlin"},{"full_name":"Lucek, Kay","first_name":"Kay","last_name":"Lucek"},{"first_name":"Vincent","last_name":"Savolainen","full_name":"Savolainen, Vincent"},{"first_name":"Anja M","last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M"}],"publication_status":"published","publisher":"The Royal Society","department":[{"_id":"NiBa"}],"year":"2020","pmid":1,"ec_funded":1,"article_number":"20190528","language":[{"iso":"eng"}],"doi":"10.1098/rstb.2019.0528","isi":1,"quality_controlled":"1","project":[{"name":"Theoretical and empirical approaches to understanding Parallel Adaptation","call_identifier":"H2020","grant_number":"797747","_id":"265B41B8-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["000552662100001"],"pmid":["32654637"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1098/rstb.2019.0528"}],"oa":1,"month":"07","publication_identifier":{"eissn":["1471-2970"],"issn":["0962-8436"]}},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1098/rstb.2019.0545"}],"oa":1,"external_id":{"isi":["000552662100014"],"pmid":["32654639"]},"quality_controlled":"1","isi":1,"doi":"10.1098/rstb.2019.0545","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1471-2970"]},"month":"07","pmid":1,"acknowledgement":"Funding was provided by the Natural Environment Research Council (NERC) and the European Research Council. We thank Rui Faria, Nicola Nadeau, Martin Garlovsky and Hernan Morales for advice and/or useful discussion during the project. Richard Turney, Graciela Sotelo, Jenny Larson, Stéphane Loisel and Meghan Wharton participated in the collection and processing of samples. Mark Dunning helped with the development of bioinformatic pipelines. The analysis of genomic data was conducted on the University of Sheffield High-performance computer, ShARC. Jeffrey Feder and an anonymous reviewer provided comments that improved the manuscript.","year":"2020","department":[{"_id":"NiBa"}],"publisher":"The Royal Society","publication_status":"published","author":[{"full_name":"Stankowski, Sean","first_name":"Sean","last_name":"Stankowski","id":"43161670-5719-11EA-8025-FABC3DDC885E"},{"full_name":"Westram, Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","first_name":"Anja M","last_name":"Westram"},{"full_name":"Zagrodzka, Zuzanna B.","first_name":"Zuzanna B.","last_name":"Zagrodzka"},{"last_name":"Eyres","first_name":"Isobel","full_name":"Eyres, Isobel"},{"full_name":"Broquet, Thomas","first_name":"Thomas","last_name":"Broquet"},{"last_name":"Johannesson","first_name":"Kerstin","full_name":"Johannesson, Kerstin"},{"first_name":"Roger K.","last_name":"Butlin","full_name":"Butlin, Roger K."}],"volume":375,"date_created":"2020-07-26T22:01:01Z","date_updated":"2023-08-22T08:22:13Z","article_number":"20190545","citation":{"chicago":"Stankowski, Sean, Anja M Westram, Zuzanna B. Zagrodzka, Isobel Eyres, Thomas Broquet, Kerstin Johannesson, and Roger K. Butlin. “The Evolution of Strong Reproductive Isolation between Sympatric Intertidal Snails.” Philosophical Transactions of the Royal Society. Series B: Biological Sciences. The Royal Society, 2020. https://doi.org/10.1098/rstb.2019.0545.","short":"S. Stankowski, A.M. Westram, Z.B. Zagrodzka, I. Eyres, T. Broquet, K. Johannesson, R.K. Butlin, Philosophical Transactions of the Royal Society. Series B: Biological Sciences 375 (2020).","mla":"Stankowski, Sean, et al. “The Evolution of Strong Reproductive Isolation between Sympatric Intertidal Snails.” Philosophical Transactions of the Royal Society. Series B: Biological Sciences, vol. 375, no. 1806, 20190545, The Royal Society, 2020, doi:10.1098/rstb.2019.0545.","apa":"Stankowski, S., Westram, A. M., Zagrodzka, Z. B., Eyres, I., Broquet, T., Johannesson, K., & Butlin, R. K. (2020). The evolution of strong reproductive isolation between sympatric intertidal snails. Philosophical Transactions of the Royal Society. Series B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rstb.2019.0545","ieee":"S. Stankowski et al., “The evolution of strong reproductive isolation between sympatric intertidal snails,” Philosophical Transactions of the Royal Society. Series B: Biological Sciences, vol. 375, no. 1806. The Royal Society, 2020.","ista":"Stankowski S, Westram AM, Zagrodzka ZB, Eyres I, Broquet T, Johannesson K, Butlin RK. 2020. The evolution of strong reproductive isolation between sympatric intertidal snails. Philosophical Transactions of the Royal Society. Series B: Biological Sciences. 375(1806), 20190545.","ama":"Stankowski S, Westram AM, Zagrodzka ZB, et al. The evolution of strong reproductive isolation between sympatric intertidal snails. Philosophical Transactions of the Royal Society Series B: Biological Sciences. 2020;375(1806). doi:10.1098/rstb.2019.0545"},"publication":"Philosophical Transactions of the Royal Society. Series B: Biological Sciences","article_type":"original","date_published":"2020-07-12T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"12","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8167","intvolume":" 375","status":"public","title":"The evolution of strong reproductive isolation between sympatric intertidal snails","oa_version":"Published Version","type":"journal_article","issue":"1806","abstract":[{"lang":"eng","text":"The evolution of strong reproductive isolation (RI) is fundamental to the origins and maintenance of biological diversity, especially in situations where geographical distributions of taxa broadly overlap. But what is the history behind strong barriers currently acting in sympatry? Using whole-genome sequencing and single nucleotide polymorphism genotyping, we inferred (i) the evolutionary relationships, (ii) the strength of RI, and (iii) the demographic history of divergence between two broadly sympatric taxa of intertidal snail. Despite being cryptic, based on external morphology, Littorina arcana and Littorina saxatilis differ in their mode of female reproduction (egg-laying versus brooding), which may generate a strong post-zygotic barrier. We show that egg-laying and brooding snails are closely related, but genetically distinct. Genotyping of 3092 snails from three locations failed to recover any recent hybrid or backcrossed individuals, confirming that RI is strong. There was, however, evidence for a very low level of asymmetrical introgression, suggesting that isolation remains incomplete. The presence of strong, asymmetrical RI was further supported by demographic analysis of these populations. Although the taxa are currently broadly sympatric, demographic modelling suggests that they initially diverged during a short period of geographical separation involving very low gene flow. Our study suggests that some geographical separation may kick-start the evolution of strong RI, facilitating subsequent coexistence of taxa in sympatry. The strength of RI needed to achieve sympatry and the subsequent effect of sympatry on RI remain open questions."}]},{"article_type":"original","publication":"Philosophical Transactions of the Royal Society. Series B: Biological Sciences","citation":{"short":"H. Shang, J. Hess, M. Pickup, D. Field, P.K. Ingvarsson, J. Liu, C. Lexer, Philosophical Transactions of the Royal Society. Series B: Biological Sciences 375 (2020).","mla":"Shang, Huiying, et al. “Evolution of Strong Reproductive Isolation in Plants: Broad-Scale Patterns and Lessons from a Perennial Model Group.” Philosophical Transactions of the Royal Society. Series B: Biological Sciences, vol. 375, no. 1806, 20190544, The Royal Society, 2020, doi:10.1098/rstb.2019.0544.","chicago":"Shang, Huiying, Jaqueline Hess, Melinda Pickup, David Field, Pär K. Ingvarsson, Jianquan Liu, and Christian Lexer. “Evolution of Strong Reproductive Isolation in Plants: Broad-Scale Patterns and Lessons from a Perennial Model Group.” Philosophical Transactions of the Royal Society. Series B: Biological Sciences. The Royal Society, 2020. https://doi.org/10.1098/rstb.2019.0544.","ama":"Shang H, Hess J, Pickup M, et al. Evolution of strong reproductive isolation in plants: Broad-scale patterns and lessons from a perennial model group. Philosophical Transactions of the Royal Society Series B: Biological Sciences. 2020;375(1806). doi:10.1098/rstb.2019.0544","apa":"Shang, H., Hess, J., Pickup, M., Field, D., Ingvarsson, P. K., Liu, J., & Lexer, C. (2020). Evolution of strong reproductive isolation in plants: Broad-scale patterns and lessons from a perennial model group. Philosophical Transactions of the Royal Society. Series B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rstb.2019.0544","ieee":"H. Shang et al., “Evolution of strong reproductive isolation in plants: Broad-scale patterns and lessons from a perennial model group,” Philosophical Transactions of the Royal Society. Series B: Biological Sciences, vol. 375, no. 1806. The Royal Society, 2020.","ista":"Shang H, Hess J, Pickup M, Field D, Ingvarsson PK, Liu J, Lexer C. 2020. Evolution of strong reproductive isolation in plants: Broad-scale patterns and lessons from a perennial model group. Philosophical Transactions of the Royal Society. Series B: Biological Sciences. 375(1806), 20190544."},"date_published":"2020-07-12T00:00:00Z","scopus_import":"1","day":"12","article_processing_charge":"No","title":"Evolution of strong reproductive isolation in plants: Broad-scale patterns and lessons from a perennial model group","status":"public","intvolume":" 375","_id":"8169","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Many recent studies have addressed the mechanisms operating during the early stages of speciation, but surprisingly few studies have tested theoretical predictions on the evolution of strong reproductive isolation (RI). To help address this gap, we first undertook a quantitative review of the hybrid zone literature for flowering plants in relation to reproductive barriers. Then, using Populus as an exemplary model group, we analysed genome-wide variation for phylogenetic tree topologies in both early- and late-stage speciation taxa to determine how these patterns may be related to the genomic architecture of RI. Our plant literature survey revealed variation in barrier complexity and an association between barrier number and introgressive gene flow. Focusing on Populus, our genome-wide analysis of tree topologies in speciating poplar taxa points to unusually complex genomic architectures of RI, consistent with earlier genome-wide association studies. These architectures appear to facilitate the ‘escape’ of introgressed genome segments from polygenic barriers even with strong RI, thus affecting their relationships with recombination rates. Placed within the context of the broader literature, our data illustrate how phylogenomic approaches hold great promise for addressing the evolution and temporary breakdown of RI during late stages of speciation."}],"issue":"1806","isi":1,"quality_controlled":"1","external_id":{"isi":["000552662100013"],"pmid":["32654641"]},"language":[{"iso":"eng"}],"doi":"10.1098/rstb.2019.0544","month":"07","publication_identifier":{"eissn":["14712970"]},"publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"The Royal Society","acknowledgement":"This work was supported by a fellowship from the China Scholarship Council (CSC) to H.S., Swiss National Science Foundation (SNF) grant no. 31003A_149306 to C.L., doctoral programme grant W1225-B20 to a faculty team including C.L., and the University of Vienna. We thank members of J.L.’s lab for collecting samples, Michael Barfuss and Elfi Grasserbauer for help in the laboratory, the Next Generation Sequencing Platform of the University of Berne for sequencing, the Vienna Scientific Cluster (VSC) for access to computational resources, and Claus Vogel and members of the PopGen Vienna graduate school for helpful discussions.","year":"2020","pmid":1,"date_updated":"2023-08-22T08:23:24Z","date_created":"2020-07-26T22:01:02Z","volume":375,"author":[{"full_name":"Shang, Huiying","last_name":"Shang","first_name":"Huiying"},{"first_name":"Jaqueline","last_name":"Hess","full_name":"Hess, Jaqueline"},{"orcid":"0000-0001-6118-0541","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","last_name":"Pickup","first_name":"Melinda","full_name":"Pickup, Melinda"},{"full_name":"Field, David","orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field","first_name":"David"},{"last_name":"Ingvarsson","first_name":"Pär K.","full_name":"Ingvarsson, Pär K."},{"full_name":"Liu, Jianquan","last_name":"Liu","first_name":"Jianquan"},{"last_name":"Lexer","first_name":"Christian","full_name":"Lexer, Christian"}],"article_number":"20190544"},{"date_published":"2020-10-15T00:00:00Z","doi":"10.6084/m9.figshare.7957469.v1","citation":{"ista":"Fraisse C, Welch JJ. 2020. Simulation code for Fig S1 from the distribution of epistasis on simple fitness landscapes, Royal Society of London, 10.6084/m9.figshare.7957469.v1.","apa":"Fraisse, C., & Welch, J. J. (2020). Simulation code for Fig S1 from the distribution of epistasis on simple fitness landscapes. Royal Society of London. https://doi.org/10.6084/m9.figshare.7957469.v1","ieee":"C. Fraisse and J. J. Welch, “Simulation code for Fig S1 from the distribution of epistasis on simple fitness landscapes.” Royal Society of London, 2020.","ama":"Fraisse C, Welch JJ. Simulation code for Fig S1 from the distribution of epistasis on simple fitness landscapes. 2020. doi:10.6084/m9.figshare.7957469.v1","chicago":"Fraisse, Christelle, and John J. Welch. “Simulation Code for Fig S1 from the Distribution of Epistasis on Simple Fitness Landscapes.” Royal Society of London, 2020. https://doi.org/10.6084/m9.figshare.7957469.v1.","mla":"Fraisse, Christelle, and John J. Welch. Simulation Code for Fig S1 from the Distribution of Epistasis on Simple Fitness Landscapes. Royal Society of London, 2020, doi:10.6084/m9.figshare.7957469.v1.","short":"C. Fraisse, J.J. Welch, (2020)."},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.7957469.v1"}],"day":"15","month":"10","article_processing_charge":"No","date_updated":"2023-08-25T10:34:41Z","date_created":"2021-08-06T11:26:57Z","oa_version":"Published Version","author":[{"orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse","first_name":"Christelle","full_name":"Fraisse, Christelle"},{"last_name":"Welch","first_name":"John J.","full_name":"Welch, John J."}],"related_material":{"record":[{"id":"6467","relation":"used_in_publication","status":"public"}]},"status":"public","title":"Simulation code for Fig S1 from the distribution of epistasis on simple fitness landscapes","publisher":"Royal Society of London","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9799","year":"2020","abstract":[{"lang":"eng","text":"Fitness interactions between mutations can influence a population’s evolution in many different ways. While epistatic effects are difficult to measure precisely, important information is captured by the mean and variance of log fitnesses for individuals carrying different numbers of mutations. We derive predictions for these quantities from a class of simple fitness landscapes, based on models of optimizing selection on quantitative traits. We also explore extensions to the models, including modular pleiotropy, variable effect sizes, mutational bias and maladaptation of the wild type. We illustrate our approach by reanalysing a large dataset of mutant effects in a yeast snoRNA. Though characterized by some large epistatic effects, these data give a good overall fit to the non-epistatic null model, suggesting that epistasis might have limited influence on the evolutionary dynamics in this system. We also show how the amount of epistasis depends on both the underlying fitness landscape and the distribution of mutations, and so is expected to vary in consistent ways between new mutations, standing variation and fixed mutations."}],"type":"research_data_reference"},{"article_processing_charge":"No","month":"10","day":"15","date_published":"2020-10-15T00:00:00Z","doi":"10.6084/m9.figshare.7957472.v1","citation":{"chicago":"Fraisse, Christelle, and John J. Welch. “Simulation Code for Fig S2 from the Distribution of Epistasis on Simple Fitness Landscapes.” Royal Society of London, 2020. https://doi.org/10.6084/m9.figshare.7957472.v1.","mla":"Fraisse, Christelle, and John J. Welch. Simulation Code for Fig S2 from the Distribution of Epistasis on Simple Fitness Landscapes. Royal Society of London, 2020, doi:10.6084/m9.figshare.7957472.v1.","short":"C. Fraisse, J.J. Welch, (2020).","ista":"Fraisse C, Welch JJ. 2020. Simulation code for Fig S2 from the distribution of epistasis on simple fitness landscapes, Royal Society of London, 10.6084/m9.figshare.7957472.v1.","apa":"Fraisse, C., & Welch, J. J. (2020). Simulation code for Fig S2 from the distribution of epistasis on simple fitness landscapes. Royal Society of London. https://doi.org/10.6084/m9.figshare.7957472.v1","ieee":"C. Fraisse and J. J. Welch, “Simulation code for Fig S2 from the distribution of epistasis on simple fitness landscapes.” Royal Society of London, 2020.","ama":"Fraisse C, Welch JJ. Simulation code for Fig S2 from the distribution of epistasis on simple fitness landscapes. 2020. doi:10.6084/m9.figshare.7957472.v1"},"main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.7957472.v1","open_access":"1"}],"oa":1,"abstract":[{"text":"Fitness interactions between mutations can influence a population’s evolution in many different ways. While epistatic effects are difficult to measure precisely, important information is captured by the mean and variance of log fitnesses for individuals carrying different numbers of mutations. We derive predictions for these quantities from a class of simple fitness landscapes, based on models of optimizing selection on quantitative traits. We also explore extensions to the models, including modular pleiotropy, variable effect sizes, mutational bias and maladaptation of the wild type. We illustrate our approach by reanalysing a large dataset of mutant effects in a yeast snoRNA. Though characterized by some large epistatic effects, these data give a good overall fit to the non-epistatic null model, suggesting that epistasis might have limited influence on the evolutionary dynamics in this system. We also show how the amount of epistasis depends on both the underlying fitness landscape and the distribution of mutations, and so is expected to vary in consistent ways between new mutations, standing variation and fixed mutations.","lang":"eng"}],"type":"research_data_reference","oa_version":"Published Version","date_created":"2021-08-06T11:18:15Z","date_updated":"2023-08-25T10:34:41Z","related_material":{"record":[{"id":"6467","status":"public","relation":"used_in_publication"}]},"author":[{"full_name":"Fraisse, Christelle","first_name":"Christelle","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075"},{"full_name":"Welch, John J.","first_name":"John J.","last_name":"Welch"}],"publisher":"Royal Society of London","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"status":"public","title":"Simulation code for Fig S2 from the distribution of epistasis on simple fitness landscapes","year":"2020","_id":"9798","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf"},{"language":[{"iso":"eng"}],"doi":"10.1002/ecm.1397","project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"external_id":{"isi":["000508511600001"]},"publication_identifier":{"issn":["0012-9615"],"eissn":["1557-7015"]},"month":"02","volume":90,"date_updated":"2023-09-05T15:43:19Z","date_created":"2020-01-07T12:47:07Z","author":[{"full_name":"Baskett, Carina","orcid":"0000-0002-7354-8574","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","last_name":"Baskett","first_name":"Carina"},{"last_name":"Schroeder","first_name":"Lucy","full_name":"Schroeder, Lucy"},{"full_name":"Weber, Marjorie G.","last_name":"Weber","first_name":"Marjorie G."},{"first_name":"Douglas W.","last_name":"Schemske","full_name":"Schemske, Douglas W."}],"publisher":"Wiley","department":[{"_id":"NiBa"}],"publication_status":"published","year":"2020","ec_funded":1,"file_date_updated":"2020-07-14T12:47:54Z","article_number":"e01397","date_published":"2020-02-01T00:00:00Z","article_type":"original","citation":{"ista":"Baskett C, Schroeder L, Weber MG, Schemske DW. 2020. Multiple metrics of latitudinal patterns in insect pollination and herbivory for a tropical‐temperate congener pair. Ecological Monographs. 90(1), e01397.","ieee":"C. Baskett, L. Schroeder, M. G. Weber, and D. W. Schemske, “Multiple metrics of latitudinal patterns in insect pollination and herbivory for a tropical‐temperate congener pair,” Ecological Monographs, vol. 90, no. 1. Wiley, 2020.","apa":"Baskett, C., Schroeder, L., Weber, M. G., & Schemske, D. W. (2020). Multiple metrics of latitudinal patterns in insect pollination and herbivory for a tropical‐temperate congener pair. Ecological Monographs. Wiley. https://doi.org/10.1002/ecm.1397","ama":"Baskett C, Schroeder L, Weber MG, Schemske DW. Multiple metrics of latitudinal patterns in insect pollination and herbivory for a tropical‐temperate congener pair. Ecological Monographs. 2020;90(1). doi:10.1002/ecm.1397","chicago":"Baskett, Carina, Lucy Schroeder, Marjorie G. Weber, and Douglas W. Schemske. “Multiple Metrics of Latitudinal Patterns in Insect Pollination and Herbivory for a Tropical‐temperate Congener Pair.” Ecological Monographs. Wiley, 2020. https://doi.org/10.1002/ecm.1397.","mla":"Baskett, Carina, et al. “Multiple Metrics of Latitudinal Patterns in Insect Pollination and Herbivory for a Tropical‐temperate Congener Pair.” Ecological Monographs, vol. 90, no. 1, e01397, Wiley, 2020, doi:10.1002/ecm.1397.","short":"C. Baskett, L. Schroeder, M.G. Weber, D.W. Schemske, Ecological Monographs 90 (2020)."},"publication":"Ecological Monographs","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"01","scopus_import":"1","oa_version":"Published Version","file":[{"date_created":"2020-02-10T08:18:14Z","date_updated":"2020-07-14T12:47:54Z","checksum":"ab8130c6e68101f5a091d05324c36f08","relation":"main_file","file_id":"7469","file_size":537941,"content_type":"application/pdf","creator":"dernst","file_name":"2020_EcologMono_Baskett.pdf","access_level":"open_access"}],"intvolume":" 90","ddc":["570"],"status":"public","title":"Multiple metrics of latitudinal patterns in insect pollination and herbivory for a tropical‐temperate congener pair","_id":"7236","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"1","abstract":[{"text":"The biotic interactions hypothesis posits that biotic interactions are more important drivers of adaptation closer to the equator, evidenced by “stronger” contemporary interactions (e.g. greater interaction rates) and/or patterns of trait evolution consistent with a history of stronger interactions. Support for the hypothesis is mixed, but few studies span tropical and temperate regions while experimentally controlling for evolutionary history. Here, we integrate field observations and common garden experiments to quantify the relative importance of pollination and herbivory in a pair of tropical‐temperate congeneric perennial herbs. Phytolacca rivinoides and P. americana are pioneer species native to the Neotropics and the eastern USA, respectively. We compared plant‐pollinator and plant‐herbivore interactions between three tropical populations of P. rivinoides from Costa Rica and three temperate populations of P. americana from its northern range edge in Michigan and Ohio. For some metrics of interaction importance, we also included three subtropical populations of P. americana from its southern range edge in Florida. This approach confounds species and region but allows us, uniquely, to measure complementary proxies of interaction importance across a tropical‐temperate range in one system. To test the prediction that lower‐latitude plants are more reliant on insect pollinators, we quantified floral display and reward, insect visitation rates, and self‐pollination ability (autogamy). To test the prediction that lower‐latitude plants experience more herbivore pressure, we quantified herbivory rates, herbivore abundance, and leaf palatability. We found evidence supporting the biotic interactions hypothesis for most comparisons between P. rivinoides and north‐temperate P. americana (floral display, insect visitation, autogamy, herbivory, herbivore abundance, and young‐leaf palatability). Results for subtropical P. americana populations, however, were typically not intermediate between P. rivinoides and north‐temperate P. americana, as would be predicted by a linear latitudinal gradient in interaction importance. Subtropical young‐leaf palatability was intermediate, but subtropical mature leaves were the least palatable, and pollination‐related traits did not differ between temperate and subtropical regions. These nonlinear patterns of interaction importance suggest future work to relate interaction importance to climatic or biotic thresholds. In sum, we found that the biotic interactions hypothesis was more consistently supported at the larger spatial scale of our study.","lang":"eng"}],"type":"journal_article"},{"file":[{"file_name":"2020_EvolBiology_Johannesson.pdf","access_level":"open_access","content_type":"application/pdf","file_size":885611,"creator":"dernst","relation":"main_file","file_id":"8553","date_created":"2020-09-22T09:42:18Z","date_updated":"2020-09-22T09:42:18Z","checksum":"7534ff0839709c0c5265c12d29432f03","success":1}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7205","ddc":["570"],"status":"public","title":"Is embryo abortion a post-zygotic barrier to gene flow between Littorina ecotypes?","intvolume":" 33","abstract":[{"text":"Genetic incompatibilities contribute to reproductive isolation between many diverging populations, but it is still unclear to what extent they play a role if divergence happens with gene flow. In contact zones between the \"Crab\" and \"Wave\" ecotypes of the snail Littorina saxatilis, divergent selection forms strong barriers to gene flow, while the role of post‐zygotic barriers due to selection against hybrids remains unclear. High embryo abortion rates in this species could indicate the presence of such barriers. Post‐zygotic barriers might include genetic incompatibilities (e.g. Dobzhansky–Muller incompatibilities) but also maladaptation, both expected to be most pronounced in contact zones. In addition, embryo abortion might reflect physiological stress on females and embryos independent of any genetic stress. We examined all embryos of >500 females sampled outside and inside contact zones of three populations in Sweden. Females' clutch size ranged from 0 to 1,011 embryos (mean 130 ± 123), and abortion rates varied between 0% and 100% (mean 12%). We described female genotypes by using a hybrid index based on hundreds of SNPs differentiated between ecotypes with which we characterized female genotypes. We also calculated female SNP heterozygosity and inversion karyotype. Clutch size did not vary with female hybrid index, and abortion rates were only weakly related to hybrid index in two sites but not at all in a third site. No additional variation in abortion rate was explained by female SNP heterozygosity, but increased female inversion heterozygosity added slightly to increased abortion. Our results show only weak and probably biologically insignificant post‐zygotic barriers contributing to ecotype divergence, and the high and variable abortion rates were marginally, if at all, explained by hybrid index of females.","lang":"eng"}],"issue":"3","type":"journal_article","date_published":"2020-03-01T00:00:00Z","publication":"Journal of Evolutionary Biology","citation":{"ista":"Johannesson K, Zagrodzka Z, Faria R, Westram AM, Butlin RK. 2020. Is embryo abortion a post-zygotic barrier to gene flow between Littorina ecotypes? Journal of Evolutionary Biology. 33(3), 342–351.","apa":"Johannesson, K., Zagrodzka, Z., Faria, R., Westram, A. M., & Butlin, R. K. (2020). Is embryo abortion a post-zygotic barrier to gene flow between Littorina ecotypes? Journal of Evolutionary Biology. Wiley. https://doi.org/10.1111/jeb.13570","ieee":"K. Johannesson, Z. Zagrodzka, R. Faria, A. M. Westram, and R. K. Butlin, “Is embryo abortion a post-zygotic barrier to gene flow between Littorina ecotypes?,” Journal of Evolutionary Biology, vol. 33, no. 3. Wiley, pp. 342–351, 2020.","ama":"Johannesson K, Zagrodzka Z, Faria R, Westram AM, Butlin RK. Is embryo abortion a post-zygotic barrier to gene flow between Littorina ecotypes? Journal of Evolutionary Biology. 2020;33(3):342-351. doi:10.1111/jeb.13570","chicago":"Johannesson, Kerstin, Zuzanna Zagrodzka, Rui Faria, Anja M Westram, and Roger K. Butlin. “Is Embryo Abortion a Post-Zygotic Barrier to Gene Flow between Littorina Ecotypes?” Journal of Evolutionary Biology. Wiley, 2020. https://doi.org/10.1111/jeb.13570.","mla":"Johannesson, Kerstin, et al. “Is Embryo Abortion a Post-Zygotic Barrier to Gene Flow between Littorina Ecotypes?” Journal of Evolutionary Biology, vol. 33, no. 3, Wiley, 2020, pp. 342–51, doi:10.1111/jeb.13570.","short":"K. Johannesson, Z. Zagrodzka, R. Faria, A.M. Westram, R.K. Butlin, Journal of Evolutionary Biology 33 (2020) 342–351."},"article_type":"original","page":"342-351","day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","author":[{"first_name":"Kerstin","last_name":"Johannesson","full_name":"Johannesson, Kerstin"},{"full_name":"Zagrodzka, Zuzanna","last_name":"Zagrodzka","first_name":"Zuzanna"},{"last_name":"Faria","first_name":"Rui","full_name":"Faria, Rui"},{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","first_name":"Anja M","last_name":"Westram","full_name":"Westram, Anja M"},{"full_name":"Butlin, Roger K.","first_name":"Roger K.","last_name":"Butlin"}],"related_material":{"record":[{"id":"13067","relation":"research_data","status":"public"}]},"date_created":"2019-12-22T23:00:43Z","date_updated":"2023-09-06T14:48:57Z","volume":33,"year":"2020","pmid":1,"publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Wiley","file_date_updated":"2020-09-22T09:42:18Z","doi":"10.1111/jeb.13570","language":[{"iso":"eng"}],"external_id":{"pmid":["31724256"],"isi":["000500954800001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"isi":1,"quality_controlled":"1","month":"03","publication_identifier":{"issn":["1010061X"],"eissn":["14209101"]}},{"file_date_updated":"2020-09-28T07:25:37Z","year":"2020","publisher":"Institute of Science and Technology Austria","department":[{"_id":"NiBa"}],"publication_status":"published","author":[{"full_name":"Szep, Eniko","id":"485BB5A4-F248-11E8-B48F-1D18A9856A87","first_name":"Eniko","last_name":"Szep"}],"date_created":"2020-09-28T07:33:38Z","date_updated":"2023-09-07T13:11:39Z","publication_identifier":{"eissn":["2663-337X"]},"month":"09","oa":1,"doi":"10.15479/AT:ISTA:8574","language":[{"iso":"eng"}],"supervisor":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H"}],"degree_awarded":"PhD","type":"dissertation","alternative_title":["ISTA Thesis"],"abstract":[{"lang":"eng","text":"This thesis concerns itself with the interactions of evolutionary and ecological forces and the consequences on genetic diversity and the ultimate survival of populations. It is important to understand what signals processes \r\nleave on the genome and what we can infer from such data, which is usually abundant but noisy. Furthermore, understanding how and when populations adapt or go extinct is important for practical purposes, such as the genetic management of populations, as well as for theoretical questions, since local adaptation can be the first step toward speciation. \r\nIn Chapter 2, we introduce the method of maximum entropy to approximate the demographic changes of a population in a simple setting, namely the logistic growth model with immigration. We show that this method is not only a powerful \r\ntool in physics but can be gainfully applied in an ecological framework. We investigate how well it approximates the real \r\nbehavior of the system, and find that is does so, even in unexpected situations. Finally, we illustrate how it can model changing environments.\r\nIn Chapter 3, we analyze the co-evolution of allele frequencies and population sizes in an infinite island model.\r\nWe give conditions under which polygenic adaptation to a rare habitat is possible. The model we use is based on the diffusion approximation, considers eco-evolutionary feedback mechanisms (hard selection), and treats both \r\ndrift and environmental fluctuations explicitly. We also look at limiting scenarios, for which we derive analytical expressions. \r\nIn Chapter 4, we present a coalescent based simulation tool to obtain patterns of diversity in a spatially explicit subdivided population, in which the demographic history of each subpopulation can be specified. We compare \r\nthe results to existing predictions, and explore the relative importance of time and space under a variety of spatial arrangements and demographic histories, such as expansion and extinction. \r\nIn the last chapter, we give a brief outlook to further research. "}],"_id":"8574","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"Local adaptation in metapopulations","ddc":["570"],"file":[{"file_name":"thesis_EnikoSzep_final.pdf","access_level":"open_access","creator":"dernst","file_size":6354833,"content_type":"application/pdf","file_id":"8575","relation":"main_file","date_created":"2020-09-28T07:25:35Z","date_updated":"2020-09-28T07:25:35Z","success":1,"checksum":"20e71f015fbbd78fea708893ad634ed0"},{"date_updated":"2020-09-28T07:25:37Z","date_created":"2020-09-28T07:25:37Z","checksum":"a8de2c14a1bb4e53c857787efbb289e1","file_id":"8576","relation":"source_file","creator":"dernst","content_type":"application/x-zip-compressed","file_size":23020401,"file_name":"thesisFiles_EnikoSzep.zip","access_level":"closed"}],"oa_version":"Published Version","has_accepted_license":"1","article_processing_charge":"No","day":"20","citation":{"chicago":"Szep, Eniko. “Local Adaptation in Metapopulations.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8574.","short":"E. Szep, Local Adaptation in Metapopulations, Institute of Science and Technology Austria, 2020.","mla":"Szep, Eniko. Local Adaptation in Metapopulations. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8574.","apa":"Szep, E. (2020). Local adaptation in metapopulations. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8574","ieee":"E. Szep, “Local adaptation in metapopulations,” Institute of Science and Technology Austria, 2020.","ista":"Szep E. 2020. Local adaptation in metapopulations. Institute of Science and Technology Austria.","ama":"Szep E. Local adaptation in metapopulations. 2020. doi:10.15479/AT:ISTA:8574"},"page":"158","date_published":"2020-09-20T00:00:00Z"},{"_id":"8254","year":"2020","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["576"],"title":"Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus)","status":"public","publisher":"Institute of Science and Technology Austria","department":[{"_id":"NiBa"}],"author":[{"first_name":"Louise S","last_name":"Arathoon","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1771-714X","full_name":"Arathoon, Louise S"}],"related_material":{"record":[{"id":"11321","relation":"later_version","status":"public"},{"relation":"later_version","status":"public","id":"9192"}]},"contributor":[{"contributor_type":"data_collector","last_name":"Arathoon","first_name":"Louise S","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Parvathy","last_name":"Surendranadh","contributor_type":"project_member","id":"455235B8-F248-11E8-B48F-1D18A9856A87"},{"contributor_type":"project_member","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"first_name":"David","last_name":"Field","contributor_type":"project_member","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478"},{"id":"2C78037E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6118-0541","first_name":"Melinda","last_name":"Pickup","contributor_type":"project_member"},{"id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","first_name":"Carina","contributor_type":"project_member","last_name":"Baskett"}],"date_created":"2020-08-12T12:49:23Z","date_updated":"2024-02-21T12:41:09Z","file":[{"file_id":"8280","relation":"main_file","success":1,"checksum":"4f1382ed4384751b6013398c11557bf6","date_updated":"2020-08-18T08:03:23Z","date_created":"2020-08-18T08:03:23Z","access_level":"open_access","file_name":"Data_Rcode_MathematicaNB.zip","creator":"dernst","content_type":"application/x-zip-compressed","file_size":5778420}],"oa_version":"Published Version","type":"research_data","abstract":[{"lang":"eng","text":"Here are the research data underlying the publication \"Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus)\". Further information are summed up in the README document.\r\nThe files for this record have been updated and are now found in the linked DOI https://doi.org/10.15479/AT:ISTA:9192."}],"file_date_updated":"2020-08-18T08:03:23Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"citation":{"short":"L.S. Arathoon, (2020).","mla":"Arathoon, Louise S. Estimating Inbreeding and Its Effects in a Long-Term Study of Snapdragons (Antirrhinum Majus). Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8254.","chicago":"Arathoon, Louise S. “Estimating Inbreeding and Its Effects in a Long-Term Study of Snapdragons (Antirrhinum Majus).” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8254.","ama":"Arathoon LS. Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus). 2020. doi:10.15479/AT:ISTA:8254","ieee":"L. S. Arathoon, “Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus).” Institute of Science and Technology Austria, 2020.","apa":"Arathoon, L. S. (2020). Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus). Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8254","ista":"Arathoon LS. 2020. Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus), Institute of Science and Technology Austria, 10.15479/AT:ISTA:8254."},"oa":1,"date_published":"2020-08-18T00:00:00Z","doi":"10.15479/AT:ISTA:8254","month":"08","day":"18","has_accepted_license":"1","article_processing_charge":"No"},{"publisher":"Dryad","department":[{"_id":"NiBa"}],"status":"public","title":"Data from: Is the sky the limit? On the expansion threshold of a species' range","_id":"9839","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2019","oa_version":"Published Version","date_created":"2021-08-09T13:07:28Z","date_updated":"2023-02-23T11:14:30Z","related_material":{"record":[{"id":"315","status":"public","relation":"used_in_publication"}]},"author":[{"last_name":"Polechova","first_name":"Jitka","orcid":"0000-0003-0951-3112","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","full_name":"Polechova, Jitka"}],"type":"research_data_reference","abstract":[{"text":"More than 100 years after Grigg’s influential analysis of species’ borders, the causes of limits to species’ ranges still represent a puzzle that has never been understood with clarity. The topic has become especially important recently as many scientists have become interested in the potential for species’ ranges to shift in response to climate change—and yet nearly all of those studies fail to recognise or incorporate evolutionary genetics in a way that relates to theoretical developments. I show that range margins can be understood based on just two measurable parameters: (i) the fitness cost of dispersal—a measure of environmental heterogeneity—and (ii) the strength of genetic drift, which reduces genetic diversity. Together, these two parameters define an ‘expansion threshold’: adaptation fails when genetic drift reduces genetic diversity below that required for adaptation to a heterogeneous environment. When the key parameters drop below this expansion threshold locally, a sharp range margin forms. When they drop below this threshold throughout the species’ range, adaptation collapses everywhere, resulting in either extinction or formation of a fragmented metapopulation. Because the effects of dispersal differ fundamentally with dimension, the second parameter—the strength of genetic drift—is qualitatively different compared to a linear habitat. In two-dimensional habitats, genetic drift becomes effectively independent of selection. It decreases with ‘neighbourhood size’—the number of individuals accessible by dispersal within one generation. Moreover, in contrast to earlier predictions, which neglected evolution of genetic variance and/or stochasticity in two dimensions, dispersal into small marginal populations aids adaptation. This is because the reduction of both genetic and demographic stochasticity has a stronger effect than the cost of dispersal through increased maladaptation. The expansion threshold thus provides a novel, theoretically justified, and testable prediction for formation of the range margin and collapse of the species’ range.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.5vv37"}],"oa":1,"citation":{"chicago":"Polechova, Jitka. “Data from: Is the Sky the Limit? On the Expansion Threshold of a Species’ Range.” Dryad, 2019. https://doi.org/10.5061/dryad.5vv37.","short":"J. Polechova, (2019).","mla":"Polechova, Jitka. Data from: Is the Sky the Limit? On the Expansion Threshold of a Species’ Range. Dryad, 2019, doi:10.5061/dryad.5vv37.","ieee":"J. Polechova, “Data from: Is the sky the limit? On the expansion threshold of a species’ range.” Dryad, 2019.","apa":"Polechova, J. (2019). Data from: Is the sky the limit? On the expansion threshold of a species’ range. Dryad. https://doi.org/10.5061/dryad.5vv37","ista":"Polechova J. 2019. Data from: Is the sky the limit? On the expansion threshold of a species’ range, Dryad, 10.5061/dryad.5vv37.","ama":"Polechova J. Data from: Is the sky the limit? On the expansion threshold of a species’ range. 2019. doi:10.5061/dryad.5vv37"},"doi":"10.5061/dryad.5vv37","date_published":"2019-06-22T00:00:00Z","article_processing_charge":"No","month":"06","day":"22"},{"issue":"3","abstract":[{"lang":"eng","text":"Empirical data suggest that inversions in many species contain genes important for intraspecific divergence and speciation, yet mechanisms of evolution remain unclear. While genes inside an inversion are tightly linked, inversions are not static but evolve separately from the rest of the genome by new mutations, recombination within arrangements, and gene flux between arrangements. Inversion polymorphisms are maintained by different processes, for example, divergent or balancing selection, or a mix of multiple processes. Moreover, the relative roles of selection, drift, mutation, and recombination will change over the lifetime of an inversion and within its area of distribution. We believe inversions are central to the evolution of many species, but we need many more data and new models to understand the complex mechanisms involved."}],"type":"journal_article","file":[{"access_level":"open_access","file_name":"2019_Trends_Evolution_Faria.pdf","creator":"cziletti","file_size":1946795,"content_type":"application/pdf","file_id":"7245","relation":"main_file","checksum":"ef24572d6ebcc1452c067e05410cc4a2","date_updated":"2020-07-14T12:47:13Z","date_created":"2020-01-09T10:55:58Z"}],"oa_version":"Published Version","intvolume":" 34","ddc":["570"],"status":"public","title":"Evolving inversions","_id":"5911","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","has_accepted_license":"1","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2019-03-01T00:00:00Z","page":"239-248","article_type":"original","citation":{"ama":"Faria R, Johannesson K, Butlin RK, Westram AM. Evolving inversions. Trends in Ecology and Evolution. 2019;34(3):239-248. doi:10.1016/j.tree.2018.12.005","apa":"Faria, R., Johannesson, K., Butlin, R. K., & Westram, A. M. (2019). Evolving inversions. Trends in Ecology and Evolution. Elsevier. https://doi.org/10.1016/j.tree.2018.12.005","ieee":"R. Faria, K. Johannesson, R. K. Butlin, and A. M. Westram, “Evolving inversions,” Trends in Ecology and Evolution, vol. 34, no. 3. Elsevier, pp. 239–248, 2019.","ista":"Faria R, Johannesson K, Butlin RK, Westram AM. 2019. Evolving inversions. Trends in Ecology and Evolution. 34(3), 239–248.","short":"R. Faria, K. Johannesson, R.K. Butlin, A.M. Westram, Trends in Ecology and Evolution 34 (2019) 239–248.","mla":"Faria, Rui, et al. “Evolving Inversions.” Trends in Ecology and Evolution, vol. 34, no. 3, Elsevier, 2019, pp. 239–48, doi:10.1016/j.tree.2018.12.005.","chicago":"Faria, Rui, Kerstin Johannesson, Roger K. Butlin, and Anja M Westram. “Evolving Inversions.” Trends in Ecology and Evolution. Elsevier, 2019. https://doi.org/10.1016/j.tree.2018.12.005."},"publication":"Trends in Ecology and Evolution","ec_funded":1,"file_date_updated":"2020-07-14T12:47:13Z","volume":34,"date_updated":"2023-08-24T14:29:48Z","date_created":"2019-02-03T22:59:15Z","author":[{"full_name":"Faria, Rui","last_name":"Faria","first_name":"Rui"},{"full_name":"Johannesson, Kerstin","last_name":"Johannesson","first_name":"Kerstin"},{"last_name":"Butlin","first_name":"Roger K.","full_name":"Butlin, Roger K."},{"last_name":"Westram","first_name":"Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","full_name":"Westram, Anja M"}],"department":[{"_id":"NiBa"}],"publisher":"Elsevier","publication_status":"published","year":"2019","publication_identifier":{"issn":["01695347"]},"month":"03","language":[{"iso":"eng"}],"doi":"10.1016/j.tree.2018.12.005","project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"isi":["000459899000013"]},"oa":1},{"year":"2019","publication_status":"published","publisher":"Taylor and Francis","department":[{"_id":"NiBa"}],"author":[{"full_name":"Andalo, Christophe","last_name":"Andalo","first_name":"Christophe"},{"last_name":"Burrus","first_name":"Monique","full_name":"Burrus, Monique"},{"full_name":"Paute, Sandrine","last_name":"Paute","first_name":"Sandrine"},{"first_name":"Christine","last_name":"Lauzeral","full_name":"Lauzeral, Christine"},{"full_name":"Field, David","first_name":"David","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478"}],"date_updated":"2023-08-24T14:34:12Z","date_created":"2018-12-16T22:59:20Z","volume":166,"external_id":{"isi":["000463802800009"]},"quality_controlled":"1","isi":1,"doi":"10.1080/23818107.2018.1545142","language":[{"iso":"eng"}],"month":"01","publication_identifier":{"eissn":["23818115"],"issn":["23818107"]},"_id":"5680","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"Prevalence of legitimate pollinators and nectar robbers and the consequences for fruit set in an Antirrhinum majus hybrid zone","intvolume":" 166","oa_version":"None","type":"journal_article","abstract":[{"text":"Pollinators display a remarkable diversity of foraging strategies with flowering plants, from primarily mutualistic interactions to cheating through nectar robbery. Despite numerous studies on the effect of nectar robbing on components of plant fitness, its contribution to reproductive isolation is unclear. We experimentally tested the impact of different pollinator strategies in a natural hybrid zone between two subspecies of Antirrhinum majus with alternate flower colour guides. On either side of a steep cline in flower colour between Antirrhinum majus pseudomajus (magenta) and A. m. striatum (yellow), we quantified the behaviour of all floral visitors at different time points during the flowering season. Using long-run camera surveys, we quantify the impact of nectar robbing on the number of flowers visited per inflorescence and the flower probing time. We further experimentally tested the effect of nectar robbing on female reproductive success by manipulating the intensity of robbing. While robbing increased over time the number of legitimate visitors tended to decrease concomitantly. We found that the number of flowers pollinated on a focal inflorescence decreased with the number of prior robbing events. However, in the manipulative experiment, fruit set and fruit volume did not vary significantly between low robbing and control treatments. Our findings challenge the idea that robbers have a negative impact on plant fitness through female function. This study also adds to our understanding of the components of pollinator-mediated reproductive isolation and the maintenance of Antirrhinum hybrid zones.","lang":"eng"}],"issue":"1","publication":"Botany Letters","citation":{"ama":"Andalo C, Burrus M, Paute S, Lauzeral C, Field D. Prevalence of legitimate pollinators and nectar robbers and the consequences for fruit set in an Antirrhinum majus hybrid zone. Botany Letters. 2019;166(1):80-92. doi:10.1080/23818107.2018.1545142","ista":"Andalo C, Burrus M, Paute S, Lauzeral C, Field D. 2019. Prevalence of legitimate pollinators and nectar robbers and the consequences for fruit set in an Antirrhinum majus hybrid zone. Botany Letters. 166(1), 80–92.","ieee":"C. Andalo, M. Burrus, S. Paute, C. Lauzeral, and D. Field, “Prevalence of legitimate pollinators and nectar robbers and the consequences for fruit set in an Antirrhinum majus hybrid zone,” Botany Letters, vol. 166, no. 1. Taylor and Francis, pp. 80–92, 2019.","apa":"Andalo, C., Burrus, M., Paute, S., Lauzeral, C., & Field, D. (2019). Prevalence of legitimate pollinators and nectar robbers and the consequences for fruit set in an Antirrhinum majus hybrid zone. Botany Letters. Taylor and Francis. https://doi.org/10.1080/23818107.2018.1545142","mla":"Andalo, Christophe, et al. “Prevalence of Legitimate Pollinators and Nectar Robbers and the Consequences for Fruit Set in an Antirrhinum Majus Hybrid Zone.” Botany Letters, vol. 166, no. 1, Taylor and Francis, 2019, pp. 80–92, doi:10.1080/23818107.2018.1545142.","short":"C. Andalo, M. Burrus, S. Paute, C. Lauzeral, D. Field, Botany Letters 166 (2019) 80–92.","chicago":"Andalo, Christophe, Monique Burrus, Sandrine Paute, Christine Lauzeral, and David Field. “Prevalence of Legitimate Pollinators and Nectar Robbers and the Consequences for Fruit Set in an Antirrhinum Majus Hybrid Zone.” Botany Letters. Taylor and Francis, 2019. https://doi.org/10.1080/23818107.2018.1545142."},"page":"80-92","date_published":"2019-01-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No"},{"issue":"2","abstract":[{"text":"The evolution of new species is made easier when traits under divergent ecological selection are also mating cues. Such ecological mating cues are now considered more common than previously thought, but we still know little about the genetic changes underlying their evolution or more generally about the genetic basis for assortative mating behaviors. Both tight physical linkage and the existence of large-effect preference loci will strengthen genetic associations between behavioral and ecological barriers, promoting the evolution of assortative mating. The warning patterns of Heliconius melpomene and H. cydno are under disruptive selection due to increased predation of nonmimetic hybrids and are used during mate recognition. We carried out a genome-wide quantitative trait locus (QTL) analysis of preference behaviors between these species and showed that divergent male preference has a simple genetic basis. We identify three QTLs that together explain a large proportion (approximately 60%) of the difference in preference behavior observed between the parental species. One of these QTLs is just 1.2 (0-4.8) centiMorgans (cM) from the major color pattern gene optix, and, individually, all three have a large effect on the preference phenotype. Genomic divergence between H. cydno and H. melpomene is high but broadly heterogenous, and admixture is reduced at the preference-optix color pattern locus but not the other preference QTLs. The simple genetic architecture we reveal will facilitate the evolution and maintenance of new species despite ongoing gene flow by coupling behavioral and ecological aspects of reproductive isolation.","lang":"eng"}],"type":"journal_article","file":[{"relation":"main_file","file_id":"6036","date_updated":"2020-07-14T12:47:17Z","date_created":"2019-02-18T14:57:24Z","checksum":"5f34001617ee729314ca520c049b1112","file_name":"2019_PLOS_Merrill.pdf","access_level":"open_access","content_type":"application/pdf","file_size":2005949,"creator":"dernst"}],"oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6022","intvolume":" 17","title":"Genetic dissection of assortative mating behavior","status":"public","ddc":["570"],"has_accepted_license":"1","article_processing_charge":"No","day":"07","scopus_import":"1","date_published":"2019-02-07T00:00:00Z","citation":{"chicago":"Merrill, Richard M., Pasi Rastas, Simon H. Martin, Maria C Melo Hurtado, Sarah Barker, John Davey, W. Owen Mcmillan, and Chris D. Jiggins. “Genetic Dissection of Assortative Mating Behavior.” PLoS Biology. Public Library of Science, 2019. https://doi.org/10.1371/journal.pbio.2005902.","mla":"Merrill, Richard M., et al. “Genetic Dissection of Assortative Mating Behavior.” PLoS Biology, vol. 17, no. 2, e2005902, Public Library of Science, 2019, doi:10.1371/journal.pbio.2005902.","short":"R.M. Merrill, P. Rastas, S.H. Martin, M.C. Melo Hurtado, S. Barker, J. Davey, W.O. Mcmillan, C.D. Jiggins, PLoS Biology 17 (2019).","ista":"Merrill RM, Rastas P, Martin SH, Melo Hurtado MC, Barker S, Davey J, Mcmillan WO, Jiggins CD. 2019. Genetic dissection of assortative mating behavior. PLoS Biology. 17(2), e2005902.","ieee":"R. M. Merrill et al., “Genetic dissection of assortative mating behavior,” PLoS Biology, vol. 17, no. 2. Public Library of Science, 2019.","apa":"Merrill, R. M., Rastas, P., Martin, S. H., Melo Hurtado, M. C., Barker, S., Davey, J., … Jiggins, C. D. (2019). Genetic dissection of assortative mating behavior. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2005902","ama":"Merrill RM, Rastas P, Martin SH, et al. Genetic dissection of assortative mating behavior. PLoS Biology. 2019;17(2). doi:10.1371/journal.pbio.2005902"},"publication":"PLoS Biology","file_date_updated":"2020-07-14T12:47:17Z","article_number":"e2005902","related_material":{"record":[{"id":"9801","status":"public","relation":"research_data"}]},"author":[{"first_name":"Richard M.","last_name":"Merrill","full_name":"Merrill, Richard M."},{"first_name":"Pasi","last_name":"Rastas","full_name":"Rastas, Pasi"},{"first_name":"Simon H.","last_name":"Martin","full_name":"Martin, Simon H."},{"full_name":"Melo Hurtado, Maria C","first_name":"Maria C","last_name":"Melo Hurtado","id":"386D7308-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Barker, Sarah","last_name":"Barker","first_name":"Sarah"},{"full_name":"Davey, John","last_name":"Davey","first_name":"John"},{"full_name":"Mcmillan, W. Owen","first_name":"W. Owen","last_name":"Mcmillan"},{"first_name":"Chris D.","last_name":"Jiggins","full_name":"Jiggins, Chris D."}],"volume":17,"date_created":"2019-02-17T22:59:21Z","date_updated":"2023-08-24T14:46:23Z","year":"2019","publisher":"Public Library of Science","department":[{"_id":"NiBa"}],"publication_status":"published","month":"02","doi":"10.1371/journal.pbio.2005902","language":[{"iso":"eng"}],"tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"oa":1,"external_id":{"isi":["000460317100001"]},"quality_controlled":"1","isi":1},{"type":"research_data_reference","date_created":"2021-08-06T11:34:56Z","date_updated":"2023-08-24T14:46:23Z","oa_version":"Published Version","author":[{"full_name":"Merrill, Richard M.","first_name":"Richard M.","last_name":"Merrill"},{"full_name":"Rastas, Pasi","first_name":"Pasi","last_name":"Rastas"},{"full_name":"Martin, Simon H.","last_name":"Martin","first_name":"Simon H."},{"first_name":"Maria C","last_name":"Melo Hurtado","id":"386D7308-F248-11E8-B48F-1D18A9856A87","full_name":"Melo Hurtado, Maria C"},{"full_name":"Barker, Sarah","last_name":"Barker","first_name":"Sarah"},{"last_name":"Davey","first_name":"John","full_name":"Davey, John"},{"first_name":"W. Owen","last_name":"Mcmillan","full_name":"Mcmillan, W. Owen"},{"last_name":"Jiggins","first_name":"Chris D.","full_name":"Jiggins, Chris D."}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"6022"}]},"title":"Raw behavioral data","status":"public","department":[{"_id":"NiBa"}],"publisher":"Public Library of Science","_id":"9801","year":"2019","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","month":"02","day":"07","article_processing_charge":"No","doi":"10.1371/journal.pbio.2005902.s006","date_published":"2019-02-07T00:00:00Z","citation":{"ista":"Merrill RM, Rastas P, Martin SH, Melo Hurtado MC, Barker S, Davey J, Mcmillan WO, Jiggins CD. 2019. Raw behavioral data, Public Library of Science, 10.1371/journal.pbio.2005902.s006.","apa":"Merrill, R. M., Rastas, P., Martin, S. H., Melo Hurtado, M. C., Barker, S., Davey, J., … Jiggins, C. D. (2019). Raw behavioral data. Public Library of Science. https://doi.org/10.1371/journal.pbio.2005902.s006","ieee":"R. M. Merrill et al., “Raw behavioral data.” Public Library of Science, 2019.","ama":"Merrill RM, Rastas P, Martin SH, et al. Raw behavioral data. 2019. doi:10.1371/journal.pbio.2005902.s006","chicago":"Merrill, Richard M., Pasi Rastas, Simon H. Martin, Maria C Melo Hurtado, Sarah Barker, John Davey, W. Owen Mcmillan, and Chris D. Jiggins. “Raw Behavioral Data.” Public Library of Science, 2019. https://doi.org/10.1371/journal.pbio.2005902.s006.","mla":"Merrill, Richard M., et al. Raw Behavioral Data. Public Library of Science, 2019, doi:10.1371/journal.pbio.2005902.s006.","short":"R.M. Merrill, P. Rastas, S.H. Martin, M.C. Melo Hurtado, S. Barker, J. Davey, W.O. Mcmillan, C.D. Jiggins, (2019)."}},{"issue":"6","abstract":[{"lang":"eng","text":"Both classical and recent studies suggest that chromosomal inversion polymorphisms are important in adaptation and speciation. However, biases in discovery and reporting of inversions make it difficult to assess their prevalence and biological importance. Here, we use an approach based on linkage disequilibrium among markers genotyped for samples collected across a transect between contrasting habitats to detect chromosomal rearrangements de novo. We report 17 polymorphic rearrangements in a single locality for the coastal marine snail, Littorina saxatilis. Patterns of diversity in the field and of recombination in controlled crosses provide strong evidence that at least the majority of these rearrangements are inversions. Most show clinal changes in frequency between habitats, suggestive of divergent selection, but only one appears to be fixed for different arrangements in the two habitats. Consistent with widespread evidence for balancing selection on inversion polymorphisms, we argue that a combination of heterosis and divergent selection can explain the observed patterns and should be considered in other systems spanning environmental gradients."}],"type":"journal_article","file":[{"checksum":"f915885756057ec0ca5912a41f46a887","date_updated":"2020-07-14T12:47:19Z","date_created":"2019-03-11T16:12:54Z","file_id":"6097","relation":"main_file","creator":"dernst","file_size":1510715,"content_type":"application/pdf","access_level":"open_access","file_name":"2019_MolecularEcology_Faria.pdf"}],"oa_version":"Published Version","intvolume":" 28","status":"public","title":"Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes","ddc":["570"],"_id":"6095","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","has_accepted_license":"1","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2019-03-01T00:00:00Z","page":"1375-1393","citation":{"ista":"Faria R, Chaube P, Morales HE, Larsson T, Lemmon AR, Lemmon EM, Rafajlović M, Panova M, Ravinet M, Johannesson K, Westram AM, Butlin RK. 2019. Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. Molecular Ecology. 28(6), 1375–1393.","apa":"Faria, R., Chaube, P., Morales, H. E., Larsson, T., Lemmon, A. R., Lemmon, E. M., … Butlin, R. K. (2019). Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.14972","ieee":"R. Faria et al., “Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes,” Molecular Ecology, vol. 28, no. 6. Wiley, pp. 1375–1393, 2019.","ama":"Faria R, Chaube P, Morales HE, et al. Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. Molecular Ecology. 2019;28(6):1375-1393. doi:10.1111/mec.14972","chicago":"Faria, Rui, Pragya Chaube, Hernán E. Morales, Tomas Larsson, Alan R. Lemmon, Emily M. Lemmon, Marina Rafajlović, et al. “Multiple Chromosomal Rearrangements in a Hybrid Zone between Littorina Saxatilis Ecotypes.” Molecular Ecology. Wiley, 2019. https://doi.org/10.1111/mec.14972.","mla":"Faria, Rui, et al. “Multiple Chromosomal Rearrangements in a Hybrid Zone between Littorina Saxatilis Ecotypes.” Molecular Ecology, vol. 28, no. 6, Wiley, 2019, pp. 1375–93, doi:10.1111/mec.14972.","short":"R. Faria, P. Chaube, H.E. Morales, T. Larsson, A.R. Lemmon, E.M. Lemmon, M. Rafajlović, M. Panova, M. Ravinet, K. Johannesson, A.M. Westram, R.K. Butlin, Molecular Ecology 28 (2019) 1375–1393."},"publication":"Molecular Ecology","file_date_updated":"2020-07-14T12:47:19Z","volume":28,"date_created":"2019-03-10T22:59:21Z","date_updated":"2023-08-24T14:50:27Z","related_material":{"record":[{"id":"9837","status":"public","relation":"research_data"}]},"author":[{"full_name":"Faria, Rui","first_name":"Rui","last_name":"Faria"},{"full_name":"Chaube, Pragya","last_name":"Chaube","first_name":"Pragya"},{"first_name":"Hernán E.","last_name":"Morales","full_name":"Morales, Hernán E."},{"last_name":"Larsson","first_name":"Tomas","full_name":"Larsson, Tomas"},{"full_name":"Lemmon, Alan R.","first_name":"Alan R.","last_name":"Lemmon"},{"full_name":"Lemmon, Emily M.","first_name":"Emily M.","last_name":"Lemmon"},{"first_name":"Marina","last_name":"Rafajlović","full_name":"Rafajlović, Marina"},{"full_name":"Panova, Marina","last_name":"Panova","first_name":"Marina"},{"full_name":"Ravinet, Mark","first_name":"Mark","last_name":"Ravinet"},{"first_name":"Kerstin","last_name":"Johannesson","full_name":"Johannesson, Kerstin"},{"orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","first_name":"Anja M","full_name":"Westram, Anja M"},{"first_name":"Roger K.","last_name":"Butlin","full_name":"Butlin, Roger K."}],"department":[{"_id":"NiBa"}],"publisher":"Wiley","publication_status":"published","year":"2019","publication_identifier":{"eissn":["1365-294X"],"issn":["0962-1083"]},"month":"03","language":[{"iso":"eng"}],"doi":"10.1111/mec.14972","quality_controlled":"1","isi":1,"external_id":{"isi":["000465219200013"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1},{"abstract":[{"lang":"eng","text":"Great care is needed when interpreting claims about the genetic basis of human variation based on data from genome-wide association studies."}],"type":"journal_article","file":[{"file_id":"6293","relation":"main_file","date_created":"2019-04-11T11:43:38Z","date_updated":"2020-07-14T12:47:24Z","checksum":"130d7544b57df4a6787e1263c2d7ea43","file_name":"2019_eLife_Barton.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":298466}],"oa_version":"Published Version","_id":"6230","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["570"],"title":"Why structure matters","status":"public","intvolume":" 8","day":"21","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2019-03-21T00:00:00Z","publication":"eLife","citation":{"ama":"Barton NH, Hermisson J, Nordborg M. Why structure matters. eLife. 2019;8. doi:10.7554/eLife.45380","ieee":"N. H. Barton, J. Hermisson, and M. Nordborg, “Why structure matters,” eLife, vol. 8. eLife Sciences Publications, 2019.","apa":"Barton, N. H., Hermisson, J., & Nordborg, M. (2019). Why structure matters. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.45380","ista":"Barton NH, Hermisson J, Nordborg M. 2019. Why structure matters. eLife. 8, e45380.","short":"N.H. Barton, J. Hermisson, M. Nordborg, ELife 8 (2019).","mla":"Barton, Nicholas H., et al. “Why Structure Matters.” ELife, vol. 8, e45380, eLife Sciences Publications, 2019, doi:10.7554/eLife.45380.","chicago":"Barton, Nicholas H, Joachim Hermisson, and Magnus Nordborg. “Why Structure Matters.” ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/eLife.45380."},"file_date_updated":"2020-07-14T12:47:24Z","article_number":"e45380","author":[{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"},{"last_name":"Hermisson","first_name":"Joachim","full_name":"Hermisson, Joachim"},{"first_name":"Magnus","last_name":"Nordborg","full_name":"Nordborg, Magnus"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/body-height-bmi-disease-risk-co/","relation":"press_release","description":"News on IST Homepage"}]},"date_created":"2019-04-07T21:59:15Z","date_updated":"2023-08-25T08:59:38Z","volume":8,"year":"2019","publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"eLife Sciences Publications","month":"03","publication_identifier":{"eissn":["2050084X"]},"doi":"10.7554/eLife.45380","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000461988300001"]},"isi":1,"quality_controlled":"1"},{"publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Wiley","year":"2019","date_updated":"2023-08-25T10:37:30Z","date_created":"2019-05-19T21:59:15Z","volume":28,"author":[{"full_name":"Field, David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478","first_name":"David","last_name":"Field"},{"last_name":"Fraisse","first_name":"Christelle","orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","full_name":"Fraisse, Christelle"}],"file_date_updated":"2020-07-14T12:47:31Z","quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000474808300001"]},"language":[{"iso":"eng"}],"doi":"10.1111/mec.15048","month":"04","publication_identifier":{"eissn":["1365294X"]},"status":"public","title":"Breaking down barriers in morning glories","ddc":["580","576"],"intvolume":" 28","_id":"6466","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"content_type":"application/pdf","file_size":367711,"creator":"dernst","file_name":"2019_MolecularEcology_Field.pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:31Z","date_created":"2019-05-20T11:49:06Z","checksum":"521e3aff3e9263ddf2ffbfe0b6157715","relation":"main_file","file_id":"6472"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"One of the most striking and consistent results in speciation genomics is the heterogeneous divergence observed across the genomes of closely related species. This pattern was initially attributed to different levels of gene exchange—with divergence preserved at loci generating a barrier to gene flow but homogenized at unlinked neutral loci. Although there is evidence to support this model, it is now recognized that interpreting patterns of divergence across genomes is not so straightforward. One \r\nproblem is that heterogenous divergence between populations can also be generated by other processes (e.g. recurrent selective sweeps or background selection) without any involvement of differential gene flow. Thus, integrated studies that identify which loci are likely subject to divergent selection are required to shed light on the interplay between selection and gene flow during the early phases of speciation. In this issue of Molecular Ecology, Rifkin et al. (2019) confront this challenge using a pair of sister morning glory species. They wisely design their sampling to take the geographic context of individuals into account, including geographically isolated (allopatric) and co‐occurring (sympatric) populations. This enabled them to show that individuals are phenotypically less differentiated in sympatry. They also found that the loci that resist introgression are enriched for those most differentiated in allopatry and loci that exhibit signals of divergent selection. One great strength of the \r\nstudy is the combination of methods from population genetics and molecular evolution, including the development of a model to simultaneously infer admixture proportions and selfing rates."}],"issue":"7","page":"1579-1581","publication":"Molecular ecology","citation":{"mla":"Field, David, and Christelle Fraisse. “Breaking down Barriers in Morning Glories.” Molecular Ecology, vol. 28, no. 7, Wiley, 2019, pp. 1579–81, doi:10.1111/mec.15048.","short":"D. Field, C. Fraisse, Molecular Ecology 28 (2019) 1579–1581.","chicago":"Field, David, and Christelle Fraisse. “Breaking down Barriers in Morning Glories.” Molecular Ecology. Wiley, 2019. https://doi.org/10.1111/mec.15048.","ama":"Field D, Fraisse C. Breaking down barriers in morning glories. Molecular ecology. 2019;28(7):1579-1581. doi:10.1111/mec.15048","ista":"Field D, Fraisse C. 2019. Breaking down barriers in morning glories. Molecular ecology. 28(7), 1579–1581.","ieee":"D. Field and C. Fraisse, “Breaking down barriers in morning glories,” Molecular ecology, vol. 28, no. 7. Wiley, pp. 1579–1581, 2019.","apa":"Field, D., & Fraisse, C. (2019). Breaking down barriers in morning glories. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.15048"},"date_published":"2019-04-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","has_accepted_license":"1"},{"quality_controlled":"1","isi":1,"project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1098/rsbl.2018.0881"}],"external_id":{"isi":["000465405300010"],"pmid":["31014191"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1098/rsbl.2018.0881","month":"04","publication_identifier":{"eissn":["1744957X"],"issn":["17449561"]},"publication_status":"published","publisher":"Royal Society of London","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"year":"2019","pmid":1,"date_updated":"2023-08-25T10:34:41Z","date_created":"2019-05-19T21:59:15Z","volume":15,"author":[{"full_name":"Fraisse, Christelle","orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse","first_name":"Christelle"},{"full_name":"Welch, John J.","last_name":"Welch","first_name":"John J."}],"related_material":{"record":[{"relation":"research_data","status":"public","id":"9798"},{"id":"9799","relation":"research_data","status":"public"}],"link":[{"relation":"supplementary_material","url":"https://dx.doi.org/10.6084/m9.figshare.c.4461008"}]},"article_number":"0881","ec_funded":1,"article_type":"original","publication":"Biology Letters","citation":{"chicago":"Fraisse, Christelle, and John J. Welch. “The Distribution of Epistasis on Simple Fitness Landscapes.” Biology Letters. Royal Society of London, 2019. https://doi.org/10.1098/rsbl.2018.0881.","short":"C. Fraisse, J.J. Welch, Biology Letters 15 (2019).","mla":"Fraisse, Christelle, and John J. Welch. “The Distribution of Epistasis on Simple Fitness Landscapes.” Biology Letters, vol. 15, no. 4, 0881, Royal Society of London, 2019, doi:10.1098/rsbl.2018.0881.","apa":"Fraisse, C., & Welch, J. J. (2019). The distribution of epistasis on simple fitness landscapes. Biology Letters. Royal Society of London. https://doi.org/10.1098/rsbl.2018.0881","ieee":"C. Fraisse and J. J. Welch, “The distribution of epistasis on simple fitness landscapes,” Biology Letters, vol. 15, no. 4. Royal Society of London, 2019.","ista":"Fraisse C, Welch JJ. 2019. The distribution of epistasis on simple fitness landscapes. Biology Letters. 15(4), 0881.","ama":"Fraisse C, Welch JJ. The distribution of epistasis on simple fitness landscapes. Biology Letters. 2019;15(4). doi:10.1098/rsbl.2018.0881"},"date_published":"2019-04-03T00:00:00Z","scopus_import":"1","day":"03","article_processing_charge":"No","status":"public","title":"The distribution of epistasis on simple fitness landscapes","intvolume":" 15","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6467","oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Fitness interactions between mutations can influence a population’s evolution in many different ways. While epistatic effects are difficult to measure precisely, important information is captured by the mean and variance of log fitnesses for individuals carrying different numbers of mutations. We derive predictions for these quantities from a class of simple fitness landscapes, based on models of optimizing selection on quantitative traits. We also explore extensions to the models, including modular pleiotropy, variable effect sizes, mutational bias and maladaptation of the wild type. We illustrate our approach by reanalysing a large dataset of mutant effects in a yeast snoRNA (small nucleolar RNA). Though characterized by some large epistatic effects, these data give a good overall fit to the non-epistatic null model, suggesting that epistasis might have limited influence on the evolutionary dynamics in this system. We also show how the amount of epistasis depends on both the underlying fitness landscape and the distribution of mutations, and so is expected to vary in consistent ways between new mutations, standing variation and fixed mutations.","lang":"eng"}],"issue":"4"},{"month":"07","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"external_id":{"isi":["000474031600001"]},"project":[{"_id":"25AEDD42-B435-11E9-9278-68D0E5697425","grant_number":"704172","call_identifier":"H2020","name":"Rate of Adaptation in Changing Environment"},{"name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","call_identifier":"FP7","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","grant_number":"618091"}],"isi":1,"quality_controlled":"1","doi":"10.1111/evo.13784","language":[{"iso":"eng"}],"ec_funded":1,"file_date_updated":"2020-07-14T12:47:34Z","year":"2019","acknowledgement":"The authors would like to thank to Tiago Paixao and Nick Barton for useful comments and advice.","department":[{"_id":"NiBa"}],"publisher":"Wiley","publication_status":"published","author":[{"full_name":"Trubenova, Barbora","orcid":"0000-0002-6873-2967","id":"42302D54-F248-11E8-B48F-1D18A9856A87","last_name":"Trubenova","first_name":"Barbora"},{"full_name":"Krejca, Martin ","first_name":"Martin ","last_name":"Krejca"},{"full_name":"Lehre, Per Kristian","first_name":"Per Kristian","last_name":"Lehre"},{"last_name":"Kötzing","first_name":"Timo","full_name":"Kötzing, Timo"}],"volume":73,"date_created":"2019-07-14T21:59:20Z","date_updated":"2023-08-29T06:31:14Z","scopus_import":"1","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"01","citation":{"ama":"Trubenova B, Krejca M, Lehre PK, Kötzing T. Surfing on the seascape: Adaptation in a changing environment. Evolution. 2019;73(7):1356-1374. doi:10.1111/evo.13784","ista":"Trubenova B, Krejca M, Lehre PK, Kötzing T. 2019. Surfing on the seascape: Adaptation in a changing environment. Evolution. 73(7), 1356–1374.","ieee":"B. Trubenova, M. Krejca, P. K. Lehre, and T. Kötzing, “Surfing on the seascape: Adaptation in a changing environment,” Evolution, vol. 73, no. 7. Wiley, pp. 1356–1374, 2019.","apa":"Trubenova, B., Krejca, M., Lehre, P. K., & Kötzing, T. (2019). Surfing on the seascape: Adaptation in a changing environment. Evolution. Wiley. https://doi.org/10.1111/evo.13784","mla":"Trubenova, Barbora, et al. “Surfing on the Seascape: Adaptation in a Changing Environment.” Evolution, vol. 73, no. 7, Wiley, 2019, pp. 1356–74, doi:10.1111/evo.13784.","short":"B. Trubenova, M. Krejca, P.K. Lehre, T. Kötzing, Evolution 73 (2019) 1356–1374.","chicago":"Trubenova, Barbora, Martin Krejca, Per Kristian Lehre, and Timo Kötzing. “Surfing on the Seascape: Adaptation in a Changing Environment.” Evolution. Wiley, 2019. https://doi.org/10.1111/evo.13784."},"publication":"Evolution","page":"1356-1374","article_type":"original","date_published":"2019-07-01T00:00:00Z","type":"journal_article","issue":"7","abstract":[{"text":"The environment changes constantly at various time scales and, in order to survive, species need to keep adapting. Whether these species succeed in avoiding extinction is a major evolutionary question. Using a multilocus evolutionary model of a mutation‐limited population adapting under strong selection, we investigate the effects of the frequency of environmental fluctuations on adaptation. Our results rely on an “adaptive‐walk” approximation and use mathematical methods from evolutionary computation theory to investigate the interplay between fluctuation frequency, the similarity of environments, and the number of loci contributing to adaptation. First, we assume a linear additive fitness function, but later generalize our results to include several types of epistasis. We show that frequent environmental changes prevent populations from reaching a fitness peak, but they may also prevent the large fitness loss that occurs after a single environmental change. Thus, the population can survive, although not thrive, in a wide range of conditions. Furthermore, we show that in a frequently changing environment, the similarity of threats that a population faces affects the level of adaptation that it is able to achieve. We check and supplement our analytical results with simulations.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6637","intvolume":" 73","status":"public","ddc":["576"],"title":"Surfing on the seascape: Adaptation in a changing environment","oa_version":"Published Version","file":[{"file_name":"2019_Evolution_TrubenovaBarbora.pdf","access_level":"open_access","file_size":815416,"content_type":"application/pdf","creator":"apreinsp","relation":"main_file","file_id":"6643","date_created":"2019-07-16T06:08:31Z","date_updated":"2020-07-14T12:47:34Z","checksum":"9831ca65def2d62498c7b08338b6d237"}]},{"file":[{"checksum":"772ce7035965153959b946a1033de1ca","date_created":"2019-09-17T10:56:27Z","date_updated":"2020-07-14T12:47:37Z","relation":"main_file","file_id":"6881","file_size":937573,"content_type":"application/pdf","creator":"kschuh","access_level":"open_access","file_name":"2019_Evolution_Sachdeva.pdf"}],"oa_version":"Published Version","_id":"6680","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 73","ddc":["576"],"title":"Effect of partial selfing and polygenic selection on establishment in a new habitat","status":"public","issue":"9","abstract":[{"text":"This paper analyzes how partial selfing in a large source population influences its ability to colonize a new habitat via the introduction of a few founder individuals. Founders experience inbreeding depression due to partially recessive deleterious alleles as well as maladaptation to the new environment due to selection on a large number of additive loci. I first introduce a simplified version of the Inbreeding History Model (Kelly, 2007) in order to characterize mutation‐selection balance in a large, partially selfing source population under selection involving multiple non‐identical loci. I then use individual‐based simulations to study the eco‐evolutionary dynamics of founders establishing in the new habitat under a model of hard selection. The study explores how selfing rate shapes establishment probabilities of founders via effects on both inbreeding depression and adaptability to the new environment, and also distinguishes the effects of selfing on the initial fitness of founders from its effects on the long‐term adaptive response of the populations they found. A high rate of (but not complete) selfing is found to aid establishment over a wide range of parameters, even in the absence of mate limitation. The sensitivity of the results to assumptions about the nature of polygenic selection are discussed.","lang":"eng"}],"type":"journal_article","date_published":"2019-09-01T00:00:00Z","citation":{"short":"H. Sachdeva, Evolution 73 (2019) 1729–1745.","mla":"Sachdeva, Himani. “Effect of Partial Selfing and Polygenic Selection on Establishment in a New Habitat.” Evolution, vol. 73, no. 9, Wiley, 2019, pp. 1729–45, doi:10.1111/evo.13812.","chicago":"Sachdeva, Himani. “Effect of Partial Selfing and Polygenic Selection on Establishment in a New Habitat.” Evolution. Wiley, 2019. https://doi.org/10.1111/evo.13812.","ama":"Sachdeva H. Effect of partial selfing and polygenic selection on establishment in a new habitat. Evolution. 2019;73(9):1729-1745. doi:10.1111/evo.13812","apa":"Sachdeva, H. (2019). Effect of partial selfing and polygenic selection on establishment in a new habitat. Evolution. Wiley. https://doi.org/10.1111/evo.13812","ieee":"H. Sachdeva, “Effect of partial selfing and polygenic selection on establishment in a new habitat,” Evolution, vol. 73, no. 9. Wiley, pp. 1729–1745, 2019.","ista":"Sachdeva H. 2019. Effect of partial selfing and polygenic selection on establishment in a new habitat. Evolution. 73(9), 1729–1745."},"publication":"Evolution","page":"1729-1745","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"01","scopus_import":"1","related_material":{"record":[{"id":"9802","relation":"research_data","status":"public"}]},"author":[{"full_name":"Sachdeva, Himani","id":"42377A0A-F248-11E8-B48F-1D18A9856A87","first_name":"Himani","last_name":"Sachdeva"}],"volume":73,"date_updated":"2023-08-29T06:43:58Z","date_created":"2019-07-25T09:08:28Z","year":"2019","department":[{"_id":"NiBa"}],"publisher":"Wiley","publication_status":"published","file_date_updated":"2020-07-14T12:47:37Z","doi":"10.1111/evo.13812","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000481300600001"]},"oa":1,"quality_controlled":"1","isi":1,"publication_identifier":{"issn":["0014-3820"],"eissn":["1558-5646"]},"month":"09"},{"day":"06","month":"06","article_processing_charge":"No","oa":1,"main_file_link":[{"url":"https://doi.org/10.5061/dryad.0q2h6tk","open_access":"1"}],"citation":{"short":"J.P. Castro, M.N. Yancoskie, M. Marchini, S. Belohlavy, L. Hiramatsu, M. Kučka, W.H. Beluch, R. Naumann, I. Skuplik, J. Cobb, N.H. Barton, C. Rolian, Y.F. Chan, (2019).","mla":"Castro, João Pl, et al. Data from: An Integrative Genomic Analysis of the Longshanks Selection Experiment for Longer Limbs in Mice. Dryad, 2019, doi:10.5061/dryad.0q2h6tk.","chicago":"Castro, João Pl, Michelle N. Yancoskie, Marta Marchini, Stefanie Belohlavy, Layla Hiramatsu, Marek Kučka, William H. Beluch, et al. “Data from: An Integrative Genomic Analysis of the Longshanks Selection Experiment for Longer Limbs in Mice.” Dryad, 2019. https://doi.org/10.5061/dryad.0q2h6tk.","ama":"Castro JP, Yancoskie MN, Marchini M, et al. Data from: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice. 2019. doi:10.5061/dryad.0q2h6tk","ieee":"J. P. Castro et al., “Data from: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice.” Dryad, 2019.","apa":"Castro, J. P., Yancoskie, M. N., Marchini, M., Belohlavy, S., Hiramatsu, L., Kučka, M., … Chan, Y. F. (2019). Data from: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice. Dryad. https://doi.org/10.5061/dryad.0q2h6tk","ista":"Castro JP, Yancoskie MN, Marchini M, Belohlavy S, Hiramatsu L, Kučka M, Beluch WH, Naumann R, Skuplik I, Cobb J, Barton NH, Rolian C, Chan YF. 2019. Data from: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice, Dryad, 10.5061/dryad.0q2h6tk."},"date_published":"2019-06-06T00:00:00Z","doi":"10.5061/dryad.0q2h6tk","type":"research_data_reference","abstract":[{"text":"Evolutionary studies are often limited by missing data that are critical to understanding the history of selection. Selection experiments, which reproduce rapid evolution under controlled conditions, are excellent tools to study how genomes evolve under selection. Here we present a genomic dissection of the Longshanks selection experiment, in which mice were selectively bred over 20 generations for longer tibiae relative to body mass, resulting in 13% longer tibiae in two replicates. We synthesized evolutionary theory, genome sequences and molecular genetics to understand the selection response and found that it involved both polygenic adaptation and discrete loci of major effect, with the strongest loci tending to be selected in parallel between replicates. We show that selection may favor de-repression of bone growth through inactivating two limb enhancers of an inhibitor, Nkx3-2. Our integrative genomic analyses thus show that it is possible to connect individual base-pair changes to the overall selection response.","lang":"eng"}],"title":"Data from: An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice","status":"public","publisher":"Dryad","department":[{"_id":"NiBa"}],"year":"2019","_id":"9804","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-08-29T06:41:51Z","date_created":"2021-08-06T11:52:54Z","oa_version":"Published Version","author":[{"first_name":"João Pl","last_name":"Castro","full_name":"Castro, João Pl"},{"full_name":"Yancoskie, Michelle N.","last_name":"Yancoskie","first_name":"Michelle N."},{"last_name":"Marchini","first_name":"Marta","full_name":"Marchini, Marta"},{"full_name":"Belohlavy, Stefanie","id":"43FE426A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9849-498X","first_name":"Stefanie","last_name":"Belohlavy"},{"first_name":"Layla","last_name":"Hiramatsu","full_name":"Hiramatsu, Layla"},{"first_name":"Marek","last_name":"Kučka","full_name":"Kučka, Marek"},{"full_name":"Beluch, William H.","last_name":"Beluch","first_name":"William H."},{"first_name":"Ronald","last_name":"Naumann","full_name":"Naumann, Ronald"},{"first_name":"Isabella","last_name":"Skuplik","full_name":"Skuplik, Isabella"},{"full_name":"Cobb, John","first_name":"John","last_name":"Cobb"},{"full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Rolian, Campbell","first_name":"Campbell","last_name":"Rolian"},{"last_name":"Chan","first_name":"Yingguang Frank","full_name":"Chan, Yingguang Frank"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"6713"}]}},{"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"6680"}]},"author":[{"full_name":"Sachdeva, Himani","last_name":"Sachdeva","first_name":"Himani","id":"42377A0A-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Published Version","date_created":"2021-08-06T11:45:11Z","date_updated":"2023-08-29T06:43:57Z","_id":"9802","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2019","publisher":"Dryad","department":[{"_id":"NiBa"}],"status":"public","title":"Data from: Effect of partial selfing and polygenic selection on establishment in a new habitat","abstract":[{"text":"This paper analyzes how partial selfing in a large source population influences its ability to colonize a new habitat via the introduction of a few founder individuals. Founders experience inbreeding depression due to partially recessive deleterious alleles as well as maladaptation to the new environment due to selection on a large number of additive loci. I first introduce a simplified version of the Inbreeding History Model (Kelly, 2007) in order to characterize mutation-selection balance in a large, partially selfing source population under selection involving multiple non-identical loci. I then use individual-based simulations to study the eco-evolutionary dynamics of founders establishing in the new habitat under a model of hard selection. The study explores how selfing rate shapes establishment probabilities of founders via effects on both inbreeding depression and adaptability to the new environment, and also distinguishes the effects of selfing on the initial fitness of founders from its effects on the long-term adaptive response of the populations they found. A high rate of (but not complete) selfing is found to aid establishment over a wide range of parameters, even in the absence of mate limitation. The sensitivity of the results to assumptions about the nature of polygenic selection are discussed.","lang":"eng"}],"type":"research_data_reference","date_published":"2019-07-16T00:00:00Z","doi":"10.5061/dryad.8tp0900","oa":1,"citation":{"ama":"Sachdeva H. Data from: Effect of partial selfing and polygenic selection on establishment in a new habitat. 2019. doi:10.5061/dryad.8tp0900","ieee":"H. Sachdeva, “Data from: Effect of partial selfing and polygenic selection on establishment in a new habitat.” Dryad, 2019.","apa":"Sachdeva, H. (2019). Data from: Effect of partial selfing and polygenic selection on establishment in a new habitat. Dryad. https://doi.org/10.5061/dryad.8tp0900","ista":"Sachdeva H. 2019. Data from: Effect of partial selfing and polygenic selection on establishment in a new habitat, Dryad, 10.5061/dryad.8tp0900.","short":"H. Sachdeva, (2019).","mla":"Sachdeva, Himani. Data from: Effect of Partial Selfing and Polygenic Selection on Establishment in a New Habitat. Dryad, 2019, doi:10.5061/dryad.8tp0900.","chicago":"Sachdeva, Himani. “Data from: Effect of Partial Selfing and Polygenic Selection on Establishment in a New Habitat.” Dryad, 2019. https://doi.org/10.5061/dryad.8tp0900."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.8tp0900"}],"article_processing_charge":"No","month":"07","day":"16"},{"publication":"Ecology and Evolution","citation":{"mla":"Trubenova, Barbora, and Reinmar Hager. “Green Beards in the Light of Indirect Genetic Effects.” Ecology and Evolution, vol. 9, no. 17, Wiley, 2019, pp. 9597–608, doi:10.1002/ece3.5484.","short":"B. Trubenova, R. Hager, Ecology and Evolution 9 (2019) 9597–9608.","chicago":"Trubenova, Barbora, and Reinmar Hager. “Green Beards in the Light of Indirect Genetic Effects.” Ecology and Evolution. Wiley, 2019. https://doi.org/10.1002/ece3.5484.","ama":"Trubenova B, Hager R. Green beards in the light of indirect genetic effects. Ecology and Evolution. 2019;9(17):9597-9608. doi:10.1002/ece3.5484","ista":"Trubenova B, Hager R. 2019. Green beards in the light of indirect genetic effects. Ecology and Evolution. 9(17), 9597–9608.","ieee":"B. Trubenova and R. Hager, “Green beards in the light of indirect genetic effects,” Ecology and Evolution, vol. 9, no. 17. Wiley, pp. 9597–9608, 2019.","apa":"Trubenova, B., & Hager, R. (2019). Green beards in the light of indirect genetic effects. Ecology and Evolution. Wiley. https://doi.org/10.1002/ece3.5484"},"article_type":"original","page":"9597-9608","date_published":"2019-09-01T00:00:00Z","scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6795","status":"public","ddc":["576"],"title":"Green beards in the light of indirect genetic effects","intvolume":" 9","oa_version":"Published Version","file":[{"creator":"dernst","content_type":"application/pdf","file_size":2839636,"file_name":"2019_EcologyEvolution_Trubenova.pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:40Z","date_created":"2019-08-12T07:30:30Z","checksum":"adcb70af4901977d95b8747eeee01bd7","file_id":"6799","relation":"main_file"}],"type":"journal_article","abstract":[{"text":"The green‐beard effect is one proposed mechanism predicted to underpin the evolu‐tion of altruistic behavior. It relies on the recognition and the selective help of altruists to each other in order to promote and sustain altruistic behavior. However, this mechanism has often been dismissed as unlikely or uncommon, as it is assumed that both the signaling trait and altruistic trait need to be encoded by the same gene or through tightly linked genes. Here, we use models of indirect genetic effects (IGEs) to find the minimum correlation between the signaling and altruistic trait required for the evolution of the latter. We show that this correlation threshold depends on the strength of the interaction (influence of the green beard on the expression of the altruistic trait), as well as the costs and benefits of the altruistic behavior. We further show that this correlation does not necessarily have to be high and support our analytical results by simulations.","lang":"eng"}],"issue":"17","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000479973400001"]},"isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Rate of Adaptation in Changing Environment","_id":"25AEDD42-B435-11E9-9278-68D0E5697425","grant_number":"704172"}],"doi":"10.1002/ece3.5484","language":[{"iso":"eng"}],"month":"09","publication_identifier":{"eissn":["20457758"]},"year":"2019","publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Wiley","author":[{"full_name":"Trubenova, Barbora","first_name":"Barbora","last_name":"Trubenova","id":"42302D54-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6873-2967"},{"full_name":"Hager, Reinmar","first_name":"Reinmar","last_name":"Hager"}],"date_updated":"2023-08-29T07:03:10Z","date_created":"2019-08-11T21:59:24Z","volume":9,"file_date_updated":"2020-07-14T12:47:40Z","ec_funded":1},{"abstract":[{"text":"* Understanding the mechanisms causing phenotypic differences between females and males has long fascinated evolutionary biologists. An extensive literature exists on animal sexual dimorphism but less information is known about sex differences in plants, particularly the extent of geographical variation in sexual dimorphism and its life‐cycle dynamics.\r\n* Here, we investigated patterns of genetically based sexual dimorphism in vegetative and reproductive traits of a wind‐pollinated dioecious plant, Rumex hastatulus, across three life‐cycle stages using open‐pollinated families from 30 populations spanning the geographic range and chromosomal variation (XY and XY1Y2) of the species.\r\n* The direction and degree of sexual dimorphism was highly variable among populations and life‐cycle stages. Sex‐specific differences in reproductive function explained a significant amount of temporal change in sexual dimorphism. For several traits, geographical variation in sexual dimorphism was associated with bioclimatic parameters, likely due to the differential responses of the sexes to climate. We found no systematic differences in sexual dimorphism between chromosome races.\r\n* Sex‐specific trait differences in dioecious plants largely result from a balance between sexual and natural selection on resource allocation. Our results indicate that abiotic factors associated with geographical context also play a role in modifying sexual dimorphism during the plant life‐cycle.","lang":"eng"}],"issue":"3","type":"journal_article","oa_version":"Published Version","file":[{"file_name":"2019_NewPhytologist_Puixeu.pdf","access_level":"open_access","creator":"apreinsp","file_size":2314016,"content_type":"application/pdf","file_id":"6833","relation":"main_file","date_updated":"2020-07-14T12:47:42Z","date_created":"2019-08-27T12:44:54Z","checksum":"6370e7567d96b7b562e77d8b89653f80"}],"_id":"6831","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["570"],"status":"public","title":"Variation in sexual dimorphism in a wind-pollinated plant: The influence of geographical context and life-cycle dynamics","intvolume":" 224","day":"01","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","scopus_import":"1","date_published":"2019-11-01T00:00:00Z","publication":"New Phytologist","citation":{"mla":"Puixeu Sala, Gemma, et al. “Variation in Sexual Dimorphism in a Wind-Pollinated Plant: The Influence of Geographical Context and Life-Cycle Dynamics.” New Phytologist, vol. 224, no. 3, Wiley, 2019, pp. 1108–20, doi:10.1111/nph.16050.","short":"G. Puixeu Sala, M. Pickup, D. Field, S.C.H. Barrett, New Phytologist 224 (2019) 1108–1120.","chicago":"Puixeu Sala, Gemma, Melinda Pickup, David Field, and Spencer C.H. Barrett. “Variation in Sexual Dimorphism in a Wind-Pollinated Plant: The Influence of Geographical Context and Life-Cycle Dynamics.” New Phytologist. Wiley, 2019. https://doi.org/10.1111/nph.16050.","ama":"Puixeu Sala G, Pickup M, Field D, Barrett SCH. Variation in sexual dimorphism in a wind-pollinated plant: The influence of geographical context and life-cycle dynamics. New Phytologist. 2019;224(3):1108-1120. doi:10.1111/nph.16050","ista":"Puixeu Sala G, Pickup M, Field D, Barrett SCH. 2019. Variation in sexual dimorphism in a wind-pollinated plant: The influence of geographical context and life-cycle dynamics. New Phytologist. 224(3), 1108–1120.","ieee":"G. Puixeu Sala, M. Pickup, D. Field, and S. C. H. Barrett, “Variation in sexual dimorphism in a wind-pollinated plant: The influence of geographical context and life-cycle dynamics,” New Phytologist, vol. 224, no. 3. Wiley, pp. 1108–1120, 2019.","apa":"Puixeu Sala, G., Pickup, M., Field, D., & Barrett, S. C. H. (2019). Variation in sexual dimorphism in a wind-pollinated plant: The influence of geographical context and life-cycle dynamics. New Phytologist. Wiley. https://doi.org/10.1111/nph.16050"},"article_type":"original","page":"1108-1120","file_date_updated":"2020-07-14T12:47:42Z","ec_funded":1,"author":[{"first_name":"Gemma","last_name":"Puixeu Sala","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8330-1754","full_name":"Puixeu Sala, Gemma"},{"full_name":"Pickup, Melinda","first_name":"Melinda","last_name":"Pickup","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6118-0541"},{"last_name":"Field","first_name":"David","orcid":"0000-0002-4014-8478","full_name":"Field, David"},{"full_name":"Barrett, Spencer C.H.","first_name":"Spencer C.H.","last_name":"Barrett"}],"related_material":{"record":[{"relation":"research_data","status":"public","id":"9803"},{"id":"14058","status":"public","relation":"dissertation_contains"}]},"date_created":"2019-08-25T22:00:51Z","date_updated":"2023-08-29T07:17:07Z","volume":224,"year":"2019","publication_status":"published","department":[{"_id":"NiBa"},{"_id":"BeVi"}],"publisher":"Wiley","month":"11","publication_identifier":{"eissn":["1469-8137"]},"doi":"10.1111/nph.16050","language":[{"iso":"eng"}],"external_id":{"isi":["000481376500001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","isi":1,"project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}]},{"title":"Data from: Variation in sexual dimorphism in a wind-pollinated plant: the influence of geographical context and life-cycle dynamics","status":"public","publisher":"Dryad","department":[{"_id":"NiBa"},{"_id":"BeVi"}],"_id":"9803","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2019","date_updated":"2023-08-29T07:17:07Z","date_created":"2021-08-06T11:48:42Z","oa_version":"Published Version","author":[{"full_name":"Puixeu Sala, Gemma","first_name":"Gemma","last_name":"Puixeu Sala","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8330-1754"},{"id":"2C78037E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6118-0541","first_name":"Melinda","last_name":"Pickup","full_name":"Pickup, Melinda"},{"last_name":"Field","first_name":"David","full_name":"Field, David"},{"last_name":"Barrett","first_name":"Spencer C.H.","full_name":"Barrett, Spencer C.H."}],"related_material":{"record":[{"id":"14058","status":"public","relation":"used_in_publication"},{"id":"6831","status":"public","relation":"used_in_publication"}]},"type":"research_data_reference","abstract":[{"lang":"eng","text":"Understanding the mechanisms causing phenotypic differences between females and males has long fascinated evolutionary biologists. An extensive literature exists on animal sexual dimorphism but less is known about sex differences in plants, particularly the extent of geographical variation in sexual dimorphism and its life-cycle dynamics. Here, we investigate patterns of genetically-based sexual dimorphism in vegetative and reproductive traits of a wind-pollinated dioecious plant, Rumex hastatulus, across three life-cycle stages using open-pollinated families from 30 populations spanning the geographic range and chromosomal variation (XY and XY1Y2) of the species. The direction and degree of sexual dimorphism was highly variable among populations and life-cycle stages. Sex-specific differences in reproductive function explained a significant amount of temporal change in sexual dimorphism. For several traits, geographical variation in sexual dimorphism was associated with bioclimatic parameters, likely due to the differential responses of the sexes to climate. We found no systematic differences in sexual dimorphism between chromosome races. Sex-specific trait differences in dioecious plants largely result from a balance between sexual and natural selection on resource allocation. Our results indicate that abiotic factors associated with geographical context also play a role in modifying sexual dimorphism during the plant life cycle."}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.n1701c9"}],"oa":1,"citation":{"apa":"Puixeu Sala, G., Pickup, M., Field, D., & Barrett, S. C. H. (2019). Data from: Variation in sexual dimorphism in a wind-pollinated plant: the influence of geographical context and life-cycle dynamics. Dryad. https://doi.org/10.5061/dryad.n1701c9","ieee":"G. Puixeu Sala, M. Pickup, D. Field, and S. C. H. Barrett, “Data from: Variation in sexual dimorphism in a wind-pollinated plant: the influence of geographical context and life-cycle dynamics.” Dryad, 2019.","ista":"Puixeu Sala G, Pickup M, Field D, Barrett SCH. 2019. Data from: Variation in sexual dimorphism in a wind-pollinated plant: the influence of geographical context and life-cycle dynamics, Dryad, 10.5061/dryad.n1701c9.","ama":"Puixeu Sala G, Pickup M, Field D, Barrett SCH. Data from: Variation in sexual dimorphism in a wind-pollinated plant: the influence of geographical context and life-cycle dynamics. 2019. doi:10.5061/dryad.n1701c9","chicago":"Puixeu Sala, Gemma, Melinda Pickup, David Field, and Spencer C.H. Barrett. “Data from: Variation in Sexual Dimorphism in a Wind-Pollinated Plant: The Influence of Geographical Context and Life-Cycle Dynamics.” Dryad, 2019. https://doi.org/10.5061/dryad.n1701c9.","short":"G. Puixeu Sala, M. Pickup, D. Field, S.C.H. Barrett, (2019).","mla":"Puixeu Sala, Gemma, et al. Data from: Variation in Sexual Dimorphism in a Wind-Pollinated Plant: The Influence of Geographical Context and Life-Cycle Dynamics. Dryad, 2019, doi:10.5061/dryad.n1701c9."},"doi":"10.5061/dryad.n1701c9","date_published":"2019-07-22T00:00:00Z","day":"22","month":"07","article_processing_charge":"No"},{"abstract":[{"text":"Many traits of interest are highly heritable and genetically complex, meaning that much of the variation they exhibit arises from differences at numerous loci in the genome. Complex traits and their evolution have been studied for more than a century, but only in the last decade have genome-wide association studies (GWASs) in humans begun to reveal their genetic basis. Here, we bring these threads of research together to ask how findings from GWASs can further our understanding of the processes that give rise to heritable variation in complex traits and of the genetic basis of complex trait evolution in response to changing selection pressures (i.e., of polygenic adaptation). Conversely, we ask how evolutionary thinking helps us to interpret findings from GWASs and informs related efforts of practical importance.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"6862","checksum":"23d3978cf4739a89ce2c3e779f9305ca","date_created":"2019-09-09T07:22:12Z","date_updated":"2020-07-14T12:47:42Z","access_level":"open_access","file_name":"2019_AnnualReview_Sella.pdf","file_size":411491,"content_type":"application/pdf","creator":"dernst"}],"title":"Thinking about the evolution of complex traits in the era of genome-wide association studies","ddc":["576"],"status":"public","intvolume":" 20","_id":"6855","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","day":"05","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2019-07-05T00:00:00Z","page":"461-493","publication":"Annual Review of Genomics and Human Genetics","citation":{"ista":"Sella G, Barton NH. 2019. Thinking about the evolution of complex traits in the era of genome-wide association studies. Annual Review of Genomics and Human Genetics. 20, 461–493.","ieee":"G. Sella and N. H. Barton, “Thinking about the evolution of complex traits in the era of genome-wide association studies,” Annual Review of Genomics and Human Genetics, vol. 20. Annual Reviews, pp. 461–493, 2019.","apa":"Sella, G., & Barton, N. H. (2019). Thinking about the evolution of complex traits in the era of genome-wide association studies. Annual Review of Genomics and Human Genetics. Annual Reviews. https://doi.org/10.1146/annurev-genom-083115-022316","ama":"Sella G, Barton NH. Thinking about the evolution of complex traits in the era of genome-wide association studies. Annual Review of Genomics and Human Genetics. 2019;20:461-493. doi:10.1146/annurev-genom-083115-022316","chicago":"Sella, Guy, and Nicholas H Barton. “Thinking about the Evolution of Complex Traits in the Era of Genome-Wide Association Studies.” Annual Review of Genomics and Human Genetics. Annual Reviews, 2019. https://doi.org/10.1146/annurev-genom-083115-022316.","mla":"Sella, Guy, and Nicholas H. Barton. “Thinking about the Evolution of Complex Traits in the Era of Genome-Wide Association Studies.” Annual Review of Genomics and Human Genetics, vol. 20, Annual Reviews, 2019, pp. 461–93, doi:10.1146/annurev-genom-083115-022316.","short":"G. Sella, N.H. Barton, Annual Review of Genomics and Human Genetics 20 (2019) 461–493."},"file_date_updated":"2020-07-14T12:47:42Z","date_created":"2019-09-07T14:28:29Z","date_updated":"2023-08-29T07:49:38Z","volume":20,"author":[{"first_name":"Guy","last_name":"Sella","full_name":"Sella, Guy"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H"}],"publication_status":"published","publisher":"Annual Reviews","department":[{"_id":"NiBa"}],"year":"2019","pmid":1,"month":"07","publication_identifier":{"issn":["1527-8204"],"eissn":["1545-293X"]},"language":[{"iso":"eng"}],"doi":"10.1146/annurev-genom-083115-022316","isi":1,"quality_controlled":"1","external_id":{"pmid":["31283361"],"isi":["000485148400020"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1},{"date_updated":"2023-08-29T07:51:09Z","date_created":"2019-09-07T14:43:02Z","volume":6,"author":[{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"}],"publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Oxford University Press","year":"2019","file_date_updated":"2020-10-02T09:16:44Z","language":[{"iso":"eng"}],"doi":"10.1093/nsr/nwy113","quality_controlled":"1","isi":1,"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000467957400025"]},"month":"03","publication_identifier":{"eissn":["2053-714X"],"issn":["2095-5138"]},"file":[{"access_level":"open_access","file_name":"2019_NSR_Barton.pdf","file_size":106463,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"8595","checksum":"571d60fa21a568607d1fd04e119da88c","success":1,"date_created":"2020-10-02T09:16:44Z","date_updated":"2020-10-02T09:16:44Z"}],"oa_version":"Published Version","ddc":["570"],"status":"public","title":"Is speciation driven by cycles of mixing and isolation?","intvolume":" 6","_id":"6858","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"2","type":"journal_article","date_published":"2019-03-01T00:00:00Z","article_type":"review","page":"291-292","publication":"National Science Review","citation":{"ama":"Barton NH. Is speciation driven by cycles of mixing and isolation? National Science Review. 2019;6(2):291-292. doi:10.1093/nsr/nwy113","ista":"Barton NH. 2019. Is speciation driven by cycles of mixing and isolation? National Science Review. 6(2), 291–292.","apa":"Barton, N. H. (2019). Is speciation driven by cycles of mixing and isolation? National Science Review. Oxford University Press. https://doi.org/10.1093/nsr/nwy113","ieee":"N. H. Barton, “Is speciation driven by cycles of mixing and isolation?,” National Science Review, vol. 6, no. 2. Oxford University Press, pp. 291–292, 2019.","mla":"Barton, Nicholas H. “Is Speciation Driven by Cycles of Mixing and Isolation?” National Science Review, vol. 6, no. 2, Oxford University Press, 2019, pp. 291–92, doi:10.1093/nsr/nwy113.","short":"N.H. Barton, National Science Review 6 (2019) 291–292.","chicago":"Barton, Nicholas H. “Is Speciation Driven by Cycles of Mixing and Isolation?” National Science Review. Oxford University Press, 2019. https://doi.org/10.1093/nsr/nwy113."},"day":"01","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1"},{"scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"No","publication":"BioEssays","citation":{"ama":"Giese B, Friess JL, Schetelig MF, et al. Gene Drives: Dynamics and regulatory matters – A report from the workshop “Evaluation of spatial and temporal control of Gene Drives”, 4 – 5 April 2019, Vienna. BioEssays. 2019;41(11). doi:10.1002/bies.201900151","ista":"Giese B, Friess JL, Schetelig MF, Barton NH, Messer P, Debarre F, Meimberg H, Windbichler N, Boete C. 2019. Gene Drives: Dynamics and regulatory matters – A report from the workshop “Evaluation of spatial and temporal control of Gene Drives”, 4 – 5 April 2019, Vienna. BioEssays. 41(11), 1900151.","ieee":"B. Giese et al., “Gene Drives: Dynamics and regulatory matters – A report from the workshop ‘Evaluation of spatial and temporal control of Gene Drives’, 4 – 5 April 2019, Vienna,” BioEssays, vol. 41, no. 11. Wiley, 2019.","apa":"Giese, B., Friess, J. L., Schetelig, M. F., Barton, N. H., Messer, P., Debarre, F., … Boete, C. (2019). Gene Drives: Dynamics and regulatory matters – A report from the workshop “Evaluation of spatial and temporal control of Gene Drives”, 4 – 5 April 2019, Vienna. BioEssays. Wiley. https://doi.org/10.1002/bies.201900151","mla":"Giese, B., et al. “Gene Drives: Dynamics and Regulatory Matters – A Report from the Workshop ‘Evaluation of Spatial and Temporal Control of Gene Drives’, 4 – 5 April 2019, Vienna.” BioEssays, vol. 41, no. 11, 1900151, Wiley, 2019, doi:10.1002/bies.201900151.","short":"B. Giese, J.L. Friess, M.F. Schetelig, N.H. Barton, P. Messer, F. Debarre, H. Meimberg, N. Windbichler, C. Boete, BioEssays 41 (2019).","chicago":"Giese, B, J L Friess, M F Schetelig, Nicholas H Barton, Philip Messer, Florence Debarre, H Meimberg, N Windbichler, and C Boete. “Gene Drives: Dynamics and Regulatory Matters – A Report from the Workshop ‘Evaluation of Spatial and Temporal Control of Gene Drives’, 4 – 5 April 2019, Vienna.” BioEssays. Wiley, 2019. https://doi.org/10.1002/bies.201900151."},"article_type":"original","date_published":"2019-11-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Gene Drives are regarded as future tools with a high potential for population control. Due to their inherent ability to overcome the rules of Mendelian inheritance, gene drives (GD) may spread genes rapidly through populations of sexually reproducing organisms. A release of organisms carrying a GD would constitute a paradigm shift in the handling of genetically modified organisms because gene drive organisms (GDO) are designed to drive their transgenes into wild populations and thereby increase the number of GDOs. The rapid development in this field and its focus on wild populations demand a prospective risk assessment with a focus on exposure related aspects. Presently, it is unclear how adequate risk management could be guaranteed to limit the spread of GDs in time and space, in order to avoid potential adverse effects in socio‐ecological systems.\r\n\r\nThe recent workshop on the “Evaluation of Spatial and Temporal Control of Gene Drives” hosted by the Institute of Safety/Security and Risk Sciences (ISR) in Vienna aimed at gaining some insight into the potential population dynamic behavior of GDs and appropriate measures of control. Scientists from France, Germany, England, and the USA discussed both topics in this meeting on April 4–5, 2019. This article summarizes results of the workshop."}],"issue":"11","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6857","status":"public","title":"Gene Drives: Dynamics and regulatory matters – A report from the workshop “Evaluation of spatial and temporal control of Gene Drives”, 4 – 5 April 2019, Vienna","ddc":["570"],"intvolume":" 41","oa_version":"Published Version","file":[{"file_id":"6939","relation":"main_file","date_updated":"2020-07-14T12:47:42Z","date_created":"2019-10-11T06:59:26Z","checksum":"8cc7551bff70b2658f8d5630f228ee12","file_name":"2019_BioEssays_Giese.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":193248}],"month":"11","publication_identifier":{"eissn":["1521-1878"]},"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000489502000001"]},"isi":1,"quality_controlled":"1","doi":"10.1002/bies.201900151","language":[{"iso":"eng"}],"article_number":"1900151","file_date_updated":"2020-07-14T12:47:42Z","year":"2019","publication_status":"published","publisher":"Wiley","department":[{"_id":"NiBa"}],"author":[{"last_name":"Giese","first_name":"B","full_name":"Giese, B"},{"full_name":"Friess, J L","first_name":"J L","last_name":"Friess"},{"full_name":"Schetelig, M F ","last_name":"Schetelig","first_name":"M F "},{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"},{"full_name":"Messer, Philip","last_name":"Messer","first_name":"Philip"},{"full_name":"Debarre, Florence","first_name":"Florence","last_name":"Debarre"},{"full_name":"Meimberg, H","last_name":"Meimberg","first_name":"H"},{"last_name":"Windbichler","first_name":"N","full_name":"Windbichler, N"},{"last_name":"Boete","first_name":"C","full_name":"Boete, C"}],"date_updated":"2023-08-30T06:56:26Z","date_created":"2019-09-07T14:40:03Z","volume":41},{"type":"research_data_reference","abstract":[{"text":"Genetic incompatibilities contribute to reproductive isolation between many diverging populations, but it is still unclear to what extent they play a role if divergence happens with gene flow. In contact zones between the \"Crab\" and \"Wave\" ecotypes of the snail Littorina saxatilis divergent selection forms strong barriers to gene flow, while the role of postzygotic barriers due to selection against hybrids remains unclear. High embryo abortion rates in this species could indicate the presence of such barriers. Postzygotic barriers might include genetic incompatibilities (e.g. Dobzhansky-Muller incompatibilities) but also maladaptation, both expected to be most pronounced in contact zones. In addition, embryo abortion might reflect physiological stress on females and embryos independent of any genetic stress. We examined all embryos of >500 females sampled outside and inside contact zones of three populations in Sweden. Females' clutch size ranged from 0 to 1011 embryos (mean 130±123) and abortion rates varied between 0 and100% (mean 12%). We described female genotypes by using a hybrid index based on hundreds of SNPs differentiated between ecotypes with which we characterised female genotypes. We also calculated female SNP heterozygosity and inversion karyotype. Clutch size did not vary with female hybrid index and abortion rates were only weakly related to hybrid index in two sites but not at all in a third site. No additional variation in abortion rate was explained by female SNP heterozygosity, but increased female inversion heterozygosity added slightly to increased abortion. Our results show only weak and probably biologically insignificant postzygotic barriers contributing to ecotype divergence and the high and variable abortion rates were marginally, if at all, explained by hybrid index of females.","lang":"eng"}],"_id":"13067","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2019","publisher":"Dryad","department":[{"_id":"NiBa"}],"ddc":["570"],"status":"public","title":"Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes?","related_material":{"record":[{"id":"7205","relation":"used_in_publication","status":"public"}]},"author":[{"full_name":"Johannesson, Kerstin","first_name":"Kerstin","last_name":"Johannesson"},{"first_name":"Zuzanna","last_name":"Zagrodzka","full_name":"Zagrodzka, Zuzanna"},{"first_name":"Rui","last_name":"Faria","full_name":"Faria, Rui"},{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","first_name":"Anja M","last_name":"Westram","full_name":"Westram, Anja M"},{"full_name":"Butlin, Roger","last_name":"Butlin","first_name":"Roger"}],"oa_version":"Published Version","date_created":"2023-05-23T16:36:27Z","date_updated":"2023-09-06T14:48:57Z","article_processing_charge":"No","day":"02","month":"12","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.tb2rbnzwk"}],"citation":{"chicago":"Johannesson, Kerstin, Zuzanna Zagrodzka, Rui Faria, Anja M Westram, and Roger Butlin. “Data from: Is Embryo Abortion a Postzygotic Barrier to Gene Flow between Littorina Ecotypes?” Dryad, 2019. https://doi.org/10.5061/DRYAD.TB2RBNZWK.","mla":"Johannesson, Kerstin, et al. Data from: Is Embryo Abortion a Postzygotic Barrier to Gene Flow between Littorina Ecotypes? Dryad, 2019, doi:10.5061/DRYAD.TB2RBNZWK.","short":"K. Johannesson, Z. Zagrodzka, R. Faria, A.M. Westram, R. Butlin, (2019).","ista":"Johannesson K, Zagrodzka Z, Faria R, Westram AM, Butlin R. 2019. Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes?, Dryad, 10.5061/DRYAD.TB2RBNZWK.","apa":"Johannesson, K., Zagrodzka, Z., Faria, R., Westram, A. M., & Butlin, R. (2019). Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes? Dryad. https://doi.org/10.5061/DRYAD.TB2RBNZWK","ieee":"K. Johannesson, Z. Zagrodzka, R. Faria, A. M. Westram, and R. Butlin, “Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes?” Dryad, 2019.","ama":"Johannesson K, Zagrodzka Z, Faria R, Westram AM, Butlin R. Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes? 2019. doi:10.5061/DRYAD.TB2RBNZWK"},"doi":"10.5061/DRYAD.TB2RBNZWK","date_published":"2019-12-02T00:00:00Z"},{"article_processing_charge":"No","has_accepted_license":"1","day":"04","scopus_import":"1","date_published":"2019-12-04T00:00:00Z","citation":{"ista":"Morales HE, Faria R, Johannesson K, Larsson T, Panova M, Westram AM, Butlin RK. 2019. Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast. Science Advances. 5(12), eaav9963.","apa":"Morales, H. E., Faria, R., Johannesson, K., Larsson, T., Panova, M., Westram, A. M., & Butlin, R. K. (2019). Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast. Science Advances. AAAS. https://doi.org/10.1126/sciadv.aav9963","ieee":"H. E. Morales et al., “Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast,” Science Advances, vol. 5, no. 12. AAAS, 2019.","ama":"Morales HE, Faria R, Johannesson K, et al. Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast. Science Advances. 2019;5(12). doi:10.1126/sciadv.aav9963","chicago":"Morales, Hernán E., Rui Faria, Kerstin Johannesson, Tomas Larsson, Marina Panova, Anja M Westram, and Roger K. Butlin. “Genomic Architecture of Parallel Ecological Divergence: Beyond a Single Environmental Contrast.” Science Advances. AAAS, 2019. https://doi.org/10.1126/sciadv.aav9963.","mla":"Morales, Hernán E., et al. “Genomic Architecture of Parallel Ecological Divergence: Beyond a Single Environmental Contrast.” Science Advances, vol. 5, no. 12, eaav9963, AAAS, 2019, doi:10.1126/sciadv.aav9963.","short":"H.E. Morales, R. Faria, K. Johannesson, T. Larsson, M. Panova, A.M. Westram, R.K. Butlin, Science Advances 5 (2019)."},"publication":"Science Advances","article_type":"original","issue":"12","abstract":[{"lang":"eng","text":"The study of parallel ecological divergence provides important clues to the operation of natural selection. Parallel divergence often occurs in heterogeneous environments with different kinds of environmental gradients in different locations, but the genomic basis underlying this process is unknown. We investigated the genomics of rapid parallel adaptation in the marine snail Littorina saxatilis in response to two independent environmental axes (crab-predation versus wave-action and low-shore versus high-shore). Using pooled whole-genome resequencing, we show that sharing of genomic regions of high differentiation between environments is generally low but increases at smaller spatial scales. We identify different shared genomic regions of divergence for each environmental axis and show that most of these regions overlap with candidate chromosomal inversions. Several inversion regions are divergent and polymorphic across many localities. We argue that chromosomal inversions could store shared variation that fuels rapid parallel adaptation to heterogeneous environments, possibly as balanced polymorphism shared by adaptive gene flow."}],"type":"journal_article","oa_version":"Published Version","file":[{"date_created":"2020-02-03T13:33:25Z","date_updated":"2020-07-14T12:47:57Z","checksum":"af99a5dcdc66c6d6102051faf3be48d8","relation":"main_file","file_id":"7442","content_type":"application/pdf","file_size":1869449,"creator":"dernst","file_name":"2019_ScienceAdvances_Morales.pdf","access_level":"open_access"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"7393","intvolume":" 5","title":"Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast","ddc":["570"],"status":"public","publication_identifier":{"issn":["2375-2548"]},"month":"12","doi":"10.1126/sciadv.aav9963","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"external_id":{"pmid":["31840052"],"isi":["000505069600008"]},"project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"_id":"265B41B8-B435-11E9-9278-68D0E5697425","grant_number":"797747","call_identifier":"H2020","name":"Theoretical and empirical approaches to understanding Parallel Adaptation"}],"quality_controlled":"1","isi":1,"ec_funded":1,"file_date_updated":"2020-07-14T12:47:57Z","article_number":"eaav9963","author":[{"full_name":"Morales, Hernán E.","last_name":"Morales","first_name":"Hernán E."},{"full_name":"Faria, Rui","last_name":"Faria","first_name":"Rui"},{"last_name":"Johannesson","first_name":"Kerstin","full_name":"Johannesson, Kerstin"},{"last_name":"Larsson","first_name":"Tomas","full_name":"Larsson, Tomas"},{"last_name":"Panova","first_name":"Marina","full_name":"Panova, Marina"},{"orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","first_name":"Anja M","full_name":"Westram, Anja M"},{"first_name":"Roger K.","last_name":"Butlin","full_name":"Butlin, Roger K."}],"volume":5,"date_updated":"2023-09-06T15:35:56Z","date_created":"2020-01-29T15:58:27Z","pmid":1,"year":"2019","publisher":"AAAS","department":[{"_id":"NiBa"}],"publication_status":"published"},{"doi":"10.1002/9781119487845.ch4","language":[{"iso":"eng"}],"external_id":{"isi":["000261343000003"]},"isi":1,"quality_controlled":"1","month":"07","publication_identifier":{"isbn":["9781119429142"]},"author":[{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"full_name":"Etheridge, Alison","first_name":"Alison","last_name":"Etheridge"}],"edition":"4","date_updated":"2023-09-08T11:24:15Z","date_created":"2020-08-21T04:25:39Z","year":"2019","publication_status":"published","editor":[{"full_name":"Balding, David","first_name":"David","last_name":"Balding"},{"last_name":"Moltke","first_name":"Ida","full_name":"Moltke, Ida"},{"full_name":"Marioni, John","last_name":"Marioni","first_name":"John"}],"department":[{"_id":"NiBa"}],"publisher":"Wiley","date_published":"2019-07-29T00:00:00Z","publication":"Handbook of statistical genomics","citation":{"mla":"Barton, Nicholas H., and Alison Etheridge. “Mathematical Models in Population Genetics.” Handbook of Statistical Genomics, edited by David Balding et al., 4th ed., Wiley, 2019, pp. 115–44, doi:10.1002/9781119487845.ch4.","short":"N.H. Barton, A. Etheridge, in:, D. Balding, I. Moltke, J. Marioni (Eds.), Handbook of Statistical Genomics, 4th ed., Wiley, 2019, pp. 115–144.","chicago":"Barton, Nicholas H, and Alison Etheridge. “Mathematical Models in Population Genetics.” In Handbook of Statistical Genomics, edited by David Balding, Ida Moltke, and John Marioni, 4th ed., 115–44. Wiley, 2019. https://doi.org/10.1002/9781119487845.ch4.","ama":"Barton NH, Etheridge A. Mathematical models in population genetics. In: Balding D, Moltke I, Marioni J, eds. Handbook of Statistical Genomics. 4th ed. Wiley; 2019:115-144. doi:10.1002/9781119487845.ch4","ista":"Barton NH, Etheridge A. 2019.Mathematical models in population genetics. In: Handbook of statistical genomics. , 115–144.","ieee":"N. H. Barton and A. Etheridge, “Mathematical models in population genetics,” in Handbook of statistical genomics, 4th ed., D. Balding, I. Moltke, and J. Marioni, Eds. Wiley, 2019, pp. 115–144.","apa":"Barton, N. H., & Etheridge, A. (2019). Mathematical models in population genetics. In D. Balding, I. Moltke, & J. Marioni (Eds.), Handbook of statistical genomics (4th ed., pp. 115–144). Wiley. https://doi.org/10.1002/9781119487845.ch4"},"page":"115-144","day":"29","article_processing_charge":"No","oa_version":"None","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"8281","status":"public","title":"Mathematical models in population genetics","ddc":["576"],"abstract":[{"lang":"eng","text":"We review the history of population genetics, starting with its origins a century ago from the synthesis between Mendel and Darwin's ideas, through to the recent development of sophisticated schemes of inference from sequence data, based on the coalescent. We explain the close relation between the coalescent and a diffusion process, which we illustrate by their application to understand spatial structure. We summarise the powerful methods available for analysis of multiple loci, when linkage equilibrium can be assumed, and then discuss approaches to the more challenging case, where associations between alleles require that we follow genotype, rather than allele, frequencies. Though we can hardly cover the whole of population genetics, we give an overview of the current state of the subject, and future challenges to it."}],"type":"book_chapter"},{"status":"public","title":"Data from: The consequences of an introgression event","publisher":"Dryad","department":[{"_id":"NiBa"}],"year":"2019","_id":"9805","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-09-19T10:06:07Z","date_created":"2021-08-06T12:03:50Z","oa_version":"Published Version","author":[{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"}],"related_material":{"record":[{"id":"40","status":"public","relation":"used_in_publication"}]},"type":"research_data_reference","abstract":[{"lang":"eng","text":"The spread of adaptive alleles is fundamental to evolution, and in theory, this process is well‐understood. However, only rarely can we follow this process—whether it originates from the spread of a new mutation, or by introgression from another population. In this issue of Molecular Ecology, Hanemaaijer et al. (2018) report on a 25‐year long study of the mosquitoes Anopheles gambiae (Figure 1) and Anopheles coluzzi in Mali, based on genotypes at 15 single‐nucleotide polymorphism (SNP). The species are usually reproductively isolated from each other, but in 2002 and 2006, bursts of hybridization were observed, when F1 hybrids became abundant. Alleles backcrossed from A. gambiae into A. coluzzi, but after the first event, these declined over the following years. In contrast, after 2006, an insecticide resistance allele that had established in A. gambiae spread into A. coluzzi, and rose to high frequency there, over 6 years (~75 generations). Whole genome sequences of 74 individuals showed that A. gambiae SNP from across the genome had become common in the A. coluzzi population, but that most of these were clustered in 34 genes around the resistance locus. A new set of SNP from 25 of these genes were assayed over time; over the 4 years since near‐fixation of the resistance allele; some remained common, whereas others declined. What do these patterns tell us about this introgression event?"}],"main_file_link":[{"url":"https://doi.org/10.5061/dryad.2kb6fh4","open_access":"1"}],"oa":1,"citation":{"ista":"Barton NH. 2019. Data from: The consequences of an introgression event, Dryad, 10.5061/dryad.2kb6fh4.","apa":"Barton, N. H. (2019). Data from: The consequences of an introgression event. Dryad. https://doi.org/10.5061/dryad.2kb6fh4","ieee":"N. H. Barton, “Data from: The consequences of an introgression event.” Dryad, 2019.","ama":"Barton NH. Data from: The consequences of an introgression event. 2019. doi:10.5061/dryad.2kb6fh4","chicago":"Barton, Nicholas H. “Data from: The Consequences of an Introgression Event.” Dryad, 2019. https://doi.org/10.5061/dryad.2kb6fh4.","mla":"Barton, Nicholas H. Data from: The Consequences of an Introgression Event. Dryad, 2019, doi:10.5061/dryad.2kb6fh4.","short":"N.H. Barton, (2019)."},"date_published":"2019-01-09T00:00:00Z","doi":"10.5061/dryad.2kb6fh4","day":"09","month":"01","article_processing_charge":"No"},{"day":"11","article_processing_charge":"No","has_accepted_license":"1","date_published":"2019-03-11T00:00:00Z","citation":{"ista":"Prizak R. 2019. Coevolution of transcription factors and their binding sites in sequence space. Institute of Science and Technology Austria.","apa":"Prizak, R. (2019). Coevolution of transcription factors and their binding sites in sequence space. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:th6071","ieee":"R. Prizak, “Coevolution of transcription factors and their binding sites in sequence space,” Institute of Science and Technology Austria, 2019.","ama":"Prizak R. Coevolution of transcription factors and their binding sites in sequence space. 2019. doi:10.15479/at:ista:th6071","chicago":"Prizak, Roshan. “Coevolution of Transcription Factors and Their Binding Sites in Sequence Space.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/at:ista:th6071.","mla":"Prizak, Roshan. Coevolution of Transcription Factors and Their Binding Sites in Sequence Space. Institute of Science and Technology Austria, 2019, doi:10.15479/at:ista:th6071.","short":"R. Prizak, Coevolution of Transcription Factors and Their Binding Sites in Sequence Space, Institute of Science and Technology Austria, 2019."},"page":"189","abstract":[{"lang":"eng","text":"Transcription factors, by binding to specific sequences on the DNA, control the precise spatio-temporal expression of genes inside a cell. However, this specificity is limited, leading to frequent incorrect binding of transcription factors that might have deleterious consequences on the cell. By constructing a biophysical model of TF-DNA binding in the context of gene regulation, I will first explore how regulatory constraints can strongly shape the distribution of a population in sequence space. Then, by directly linking this to a picture of multiple types of transcription factors performing their functions simultaneously inside the cell, I will explore the extent of regulatory crosstalk -- incorrect binding interactions between transcription factors and binding sites that lead to erroneous regulatory states -- and understand the constraints this places on the design of regulatory systems. I will then develop a generic theoretical framework to investigate the coevolution of multiple transcription factors and multiple binding sites, in the context of a gene regulatory network that performs a certain function. As a particular tractable version of this problem, I will consider the evolution of two transcription factors when they transmit upstream signals to downstream target genes. Specifically, I will describe the evolutionary steady states and the evolutionary pathways involved, along with their timescales, of a system that initially undergoes a transcription factor duplication event. To connect this important theoretical model to the prominent biological event of transcription factor duplication giving rise to paralogous families, I will then describe a bioinformatics analysis of C2H2 Zn-finger transcription factors, a major family in humans, and focus on the patterns of evolution that paralogs have undergone in their various protein domains in the recent past. "}],"type":"dissertation","alternative_title":["ISTA Thesis"],"file":[{"file_id":"6072","relation":"main_file","checksum":"e60a72de35d270b31f1a23d50f224ec0","date_updated":"2020-07-14T12:47:18Z","date_created":"2019-03-06T16:05:07Z","access_level":"open_access","file_name":"Thesis_final_PDFA_RoshanPrizak.pdf","creator":"rprizak","file_size":20995465,"content_type":"application/pdf"},{"checksum":"67c2630333d05ebafef5f018863a8465","date_updated":"2020-07-14T12:47:18Z","date_created":"2019-03-06T16:09:39Z","title":"Latex files","file_id":"6073","relation":"source_file","creator":"rprizak","content_type":"application/zip","file_size":85705272,"access_level":"closed","file_name":"thesis_v2_merge.zip"}],"oa_version":"Published Version","_id":"6071","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","ddc":["576"],"title":"Coevolution of transcription factors and their binding sites in sequence space","month":"03","publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/at:ista:th6071","supervisor":[{"last_name":"Tkačik","first_name":"Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"oa":1,"project":[{"name":"Biophysics of information processing in gene regulation","call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425","grant_number":"P28844-B27"}],"file_date_updated":"2020-07-14T12:47:18Z","author":[{"first_name":"Roshan","last_name":"Prizak","id":"4456104E-F248-11E8-B48F-1D18A9856A87","full_name":"Prizak, Roshan"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"1358"},{"id":"955","status":"public","relation":"part_of_dissertation"}]},"date_updated":"2023-09-22T10:00:48Z","date_created":"2019-03-06T16:16:10Z","year":"2019","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GaTk"},{"_id":"NiBa"}]},{"abstract":[{"lang":"eng","text":"Plant mating systems play a key role in structuring genetic variation both within and between species. In hybrid zones, the outcomes and dynamics of hybridization are usually interpreted as the balance between gene flow and selection against hybrids. Yet, mating systems can introduce selective forces that alter these expectations; with diverse outcomes for the level and direction of gene flow depending on variation in outcrossing and whether the mating systems of the species pair are the same or divergent. We present a survey of hybridization in 133 species pairs from 41 plant families and examine how patterns of hybridization vary with mating system. We examine if hybrid zone mode, level of gene flow, asymmetries in gene flow and the frequency of reproductive isolating barriers vary in relation to mating system/s of the species pair. We combine these results with a simulation model and examples from the literature to address two general themes: (i) the two‐way interaction between introgression and the evolution of reproductive systems, and (ii) how mating system can facilitate or restrict interspecific gene flow. We conclude that examining mating system with hybridization provides unique opportunities to understand divergence and the processes underlying reproductive isolation."}],"issue":"3","type":"journal_article","file":[{"checksum":"21e4c95599bbcaf7c483b89954658672","date_created":"2019-11-13T08:15:05Z","date_updated":"2020-07-14T12:47:42Z","file_id":"7011","relation":"main_file","creator":"dernst","file_size":1511958,"content_type":"application/pdf","access_level":"open_access","file_name":"2019_NewPhytologist_Pickup.pdf"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6856","ddc":["570"],"title":"Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow","status":"public","intvolume":" 224","day":"01","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2019-11-01T00:00:00Z","publication":"New Phytologist","citation":{"short":"M. Pickup, N.H. Barton, Y. Brandvain, C. Fraisse, S. Yakimowski, T. Dixit, C. Lexer, E. Cereghetti, D. Field, New Phytologist 224 (2019) 1035–1047.","mla":"Pickup, Melinda, et al. “Mating System Variation in Hybrid Zones: Facilitation, Barriers and Asymmetries to Gene Flow.” New Phytologist, vol. 224, no. 3, Wiley, 2019, pp. 1035–47, doi:10.1111/nph.16180.","chicago":"Pickup, Melinda, Nicholas H Barton, Yaniv Brandvain, Christelle Fraisse, Sarah Yakimowski, Tanmay Dixit, Christian Lexer, Eva Cereghetti, and David Field. “Mating System Variation in Hybrid Zones: Facilitation, Barriers and Asymmetries to Gene Flow.” New Phytologist. Wiley, 2019. https://doi.org/10.1111/nph.16180.","ama":"Pickup M, Barton NH, Brandvain Y, et al. Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow. New Phytologist. 2019;224(3):1035-1047. doi:10.1111/nph.16180","ieee":"M. Pickup et al., “Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow,” New Phytologist, vol. 224, no. 3. Wiley, pp. 1035–1047, 2019.","apa":"Pickup, M., Barton, N. H., Brandvain, Y., Fraisse, C., Yakimowski, S., Dixit, T., … Field, D. (2019). Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow. New Phytologist. Wiley. https://doi.org/10.1111/nph.16180","ista":"Pickup M, Barton NH, Brandvain Y, Fraisse C, Yakimowski S, Dixit T, Lexer C, Cereghetti E, Field D. 2019. Mating system variation in hybrid zones: Facilitation, barriers and asymmetries to gene flow. New Phytologist. 224(3), 1035–1047."},"article_type":"original","page":"1035-1047","file_date_updated":"2020-07-14T12:47:42Z","ec_funded":1,"author":[{"full_name":"Pickup, Melinda","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6118-0541","first_name":"Melinda","last_name":"Pickup"},{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton"},{"full_name":"Brandvain, Yaniv","last_name":"Brandvain","first_name":"Yaniv"},{"first_name":"Christelle","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle"},{"first_name":"Sarah","last_name":"Yakimowski","full_name":"Yakimowski, Sarah"},{"last_name":"Dixit","first_name":"Tanmay","full_name":"Dixit, Tanmay"},{"full_name":"Lexer, Christian","last_name":"Lexer","first_name":"Christian"},{"full_name":"Cereghetti, Eva","last_name":"Cereghetti","first_name":"Eva","id":"71AA91B4-05ED-11EA-8BEB-F5833E63BD63"},{"full_name":"Field, David","last_name":"Field","first_name":"David","orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-10-18T08:47:08Z","date_created":"2019-09-07T14:35:40Z","volume":224,"year":"2019","pmid":1,"publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Wiley","month":"11","publication_identifier":{"eissn":["1469-8137"],"issn":["0028-646X"]},"doi":"10.1111/nph.16180","language":[{"iso":"eng"}],"external_id":{"pmid":["31505037"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","project":[{"_id":"25B36484-B435-11E9-9278-68D0E5697425","grant_number":"329960","name":"Mating system and the evolutionary dynamics of hybrid zones","call_identifier":"FP7"},{"call_identifier":"FWF","name":"Sex chromosomes and species barriers","grant_number":"M02463","_id":"2662AADE-B435-11E9-9278-68D0E5697425"}]},{"publication_identifier":{"issn":["0737-4038"],"eissn":["1537-1719"]},"month":"03","project":[{"_id":"250ED89C-B435-11E9-9278-68D0E5697425","grant_number":"P28842-B22","name":"Sex chromosome evolution under male- and female- heterogamety","call_identifier":"FWF"}],"isi":1,"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30590559"}],"external_id":{"pmid":["30590559"],"isi":["000462585100006"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1093/molbev/msy246","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"publisher":"Oxford University Press","publication_status":"published","pmid":1,"year":"2019","volume":36,"date_updated":"2024-02-21T13:59:17Z","date_created":"2019-03-10T22:59:19Z","related_material":{"record":[{"status":"public","relation":"popular_science","id":"5757"}]},"author":[{"full_name":"Fraisse, Christelle","last_name":"Fraisse","first_name":"Christelle","orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-8330-1754","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","last_name":"Puixeu Sala","first_name":"Gemma","full_name":"Puixeu Sala, Gemma"},{"orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","first_name":"Beatriz","full_name":"Vicoso, Beatriz"}],"scopus_import":"1","article_processing_charge":"No","day":"01","page":"500-515","citation":{"ieee":"C. Fraisse, G. Puixeu Sala, and B. Vicoso, “Pleiotropy modulates the efficacy of selection in drosophila melanogaster,” Molecular biology and evolution, vol. 36, no. 3. Oxford University Press, pp. 500–515, 2019.","apa":"Fraisse, C., Puixeu Sala, G., & Vicoso, B. (2019). Pleiotropy modulates the efficacy of selection in drosophila melanogaster. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msy246","ista":"Fraisse C, Puixeu Sala G, Vicoso B. 2019. Pleiotropy modulates the efficacy of selection in drosophila melanogaster. Molecular biology and evolution. 36(3), 500–515.","ama":"Fraisse C, Puixeu Sala G, Vicoso B. Pleiotropy modulates the efficacy of selection in drosophila melanogaster. Molecular biology and evolution. 2019;36(3):500-515. doi:10.1093/molbev/msy246","chicago":"Fraisse, Christelle, Gemma Puixeu Sala, and Beatriz Vicoso. “Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.” Molecular Biology and Evolution. Oxford University Press, 2019. https://doi.org/10.1093/molbev/msy246.","short":"C. Fraisse, G. Puixeu Sala, B. Vicoso, Molecular Biology and Evolution 36 (2019) 500–515.","mla":"Fraisse, Christelle, et al. “Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.” Molecular Biology and Evolution, vol. 36, no. 3, Oxford University Press, 2019, pp. 500–15, doi:10.1093/molbev/msy246."},"publication":"Molecular biology and evolution","date_published":"2019-03-01T00:00:00Z","type":"journal_article","issue":"3","abstract":[{"text":"Pleiotropy is the well-established idea that a single mutation affects multiple phenotypes. If a mutation has opposite effects on fitness when expressed in different contexts, then genetic conflict arises. Pleiotropic conflict is expected to reduce the efficacy of selection by limiting the fixation of beneficial mutations through adaptation, and the removal of deleterious mutations through purifying selection. Although this has been widely discussed, in particular in the context of a putative “gender load,” it has yet to be systematically quantified. In this work, we empirically estimate to which extent different pleiotropic regimes impede the efficacy of selection in Drosophila melanogaster. We use whole-genome polymorphism data from a single African population and divergence data from D. simulans to estimate the fraction of adaptive fixations (α), the rate of adaptation (ωA), and the direction of selection (DoS). After controlling for confounding covariates, we find that the different pleiotropic regimes have a relatively small, but significant, effect on selection efficacy. Specifically, our results suggest that pleiotropic sexual antagonism may restrict the efficacy of selection, but that this conflict can be resolved by limiting the expression of genes to the sex where they are beneficial. Intermediate levels of pleiotropy across tissues and life stages can also lead to maladaptation in D. melanogaster, due to inefficient purifying selection combined with low frequency of mutations that confer a selective advantage. Thus, our study highlights the need to consider the efficacy of selection in the context of antagonistic pleiotropy, and of genetic conflict in general.","lang":"eng"}],"intvolume":" 36","status":"public","title":"Pleiotropy modulates the efficacy of selection in drosophila melanogaster","_id":"6089","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Submitted Version"},{"oa_version":"Preprint","title":"Receptor crosstalk improves concentration sensing of multiple ligands","status":"public","intvolume":" 99","_id":"6090","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Cells need to reliably sense external ligand concentrations to achieve various biological functions such as chemotaxis or signaling. The molecular recognition of ligands by surface receptors is degenerate in many systems, leading to crosstalk between ligand-receptor pairs. Crosstalk is often thought of as a deviation from optimal specific recognition, as the binding of noncognate ligands can interfere with the detection of the receptor's cognate ligand, possibly leading to a false triggering of a downstream signaling pathway. Here we quantify the optimal precision of sensing the concentrations of multiple ligands by a collection of promiscuous receptors. We demonstrate that crosstalk can improve precision in concentration sensing and discrimination tasks. To achieve superior precision, the additional information about ligand concentrations contained in short binding events of the noncognate ligand should be exploited. We present a proofreading scheme to realize an approximate estimation of multiple ligand concentrations that reaches a precision close to the derived optimal bounds. Our results help rationalize the observed ubiquity of receptor crosstalk in molecular sensing.","lang":"eng"}],"issue":"2","type":"journal_article","date_published":"2019-02-26T00:00:00Z","publication":"Physical Review E","citation":{"short":"M. Carballo-Pacheco, J. Desponds, T. Gavrilchenko, A. Mayer, R. Prizak, G. Reddy, I. Nemenman, T. Mora, Physical Review E 99 (2019).","mla":"Carballo-Pacheco, Martín, et al. “Receptor Crosstalk Improves Concentration Sensing of Multiple Ligands.” Physical Review E, vol. 99, no. 2, 022423, American Physical Society, 2019, doi:10.1103/PhysRevE.99.022423.","chicago":"Carballo-Pacheco, Martín, Jonathan Desponds, Tatyana Gavrilchenko, Andreas Mayer, Roshan Prizak, Gautam Reddy, Ilya Nemenman, and Thierry Mora. “Receptor Crosstalk Improves Concentration Sensing of Multiple Ligands.” Physical Review E. American Physical Society, 2019. https://doi.org/10.1103/PhysRevE.99.022423.","ama":"Carballo-Pacheco M, Desponds J, Gavrilchenko T, et al. Receptor crosstalk improves concentration sensing of multiple ligands. Physical Review E. 2019;99(2). doi:10.1103/PhysRevE.99.022423","ieee":"M. Carballo-Pacheco et al., “Receptor crosstalk improves concentration sensing of multiple ligands,” Physical Review E, vol. 99, no. 2. American Physical Society, 2019.","apa":"Carballo-Pacheco, M., Desponds, J., Gavrilchenko, T., Mayer, A., Prizak, R., Reddy, G., … Mora, T. (2019). Receptor crosstalk improves concentration sensing of multiple ligands. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.99.022423","ista":"Carballo-Pacheco M, Desponds J, Gavrilchenko T, Mayer A, Prizak R, Reddy G, Nemenman I, Mora T. 2019. Receptor crosstalk improves concentration sensing of multiple ligands. Physical Review E. 99(2), 022423."},"day":"26","article_processing_charge":"No","scopus_import":"1","date_created":"2019-03-10T22:59:20Z","date_updated":"2024-02-28T13:12:06Z","volume":99,"author":[{"full_name":"Carballo-Pacheco, Martín","first_name":"Martín","last_name":"Carballo-Pacheco"},{"last_name":"Desponds","first_name":"Jonathan","full_name":"Desponds, Jonathan"},{"last_name":"Gavrilchenko","first_name":"Tatyana","full_name":"Gavrilchenko, Tatyana"},{"full_name":"Mayer, Andreas","last_name":"Mayer","first_name":"Andreas"},{"id":"4456104E-F248-11E8-B48F-1D18A9856A87","last_name":"Prizak","first_name":"Roshan","full_name":"Prizak, Roshan"},{"full_name":"Reddy, Gautam","first_name":"Gautam","last_name":"Reddy"},{"first_name":"Ilya","last_name":"Nemenman","full_name":"Nemenman, Ilya"},{"full_name":"Mora, Thierry","first_name":"Thierry","last_name":"Mora"}],"publication_status":"published","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"publisher":"American Physical Society","year":"2019","article_number":"022423","language":[{"iso":"eng"}],"doi":"10.1103/PhysRevE.99.022423","isi":1,"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/448118v1.abstract"}],"oa":1,"external_id":{"isi":["000459916500007"]},"month":"02"},{"article_processing_charge":"No","has_accepted_license":"1","day":"06","scopus_import":"1","date_published":"2019-06-06T00:00:00Z","citation":{"mla":"Castro, João Pl, et al. “An Integrative Genomic Analysis of the Longshanks Selection Experiment for Longer Limbs in Mice.” ELife, vol. 8, e42014, eLife Sciences Publications, 2019, doi:10.7554/eLife.42014.","short":"J.P. Castro, M.N. Yancoskie, M. Marchini, S. Belohlavy, L. Hiramatsu, M. Kučka, W.H. Beluch, R. Naumann, I. Skuplik, J. Cobb, N.H. Barton, C. Rolian, Y.F. Chan, ELife 8 (2019).","chicago":"Castro, João Pl, Michelle N. Yancoskie, Marta Marchini, Stefanie Belohlavy, Layla Hiramatsu, Marek Kučka, William H. Beluch, et al. “An Integrative Genomic Analysis of the Longshanks Selection Experiment for Longer Limbs in Mice.” ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/eLife.42014.","ama":"Castro JP, Yancoskie MN, Marchini M, et al. An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice. eLife. 2019;8. doi:10.7554/eLife.42014","ista":"Castro JP, Yancoskie MN, Marchini M, Belohlavy S, Hiramatsu L, Kučka M, Beluch WH, Naumann R, Skuplik I, Cobb J, Barton NH, Rolian C, Chan YF. 2019. An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice. eLife. 8, e42014.","ieee":"J. P. Castro et al., “An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice,” eLife, vol. 8. eLife Sciences Publications, 2019.","apa":"Castro, J. P., Yancoskie, M. N., Marchini, M., Belohlavy, S., Hiramatsu, L., Kučka, M., … Chan, Y. F. (2019). An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.42014"},"publication":"eLife","abstract":[{"text":"Evolutionary studies are often limited by missing data that are critical to understanding the history of selection. Selection experiments, which reproduce rapid evolution under controlled conditions, are excellent tools to study how genomes evolve under selection. Here we present a genomic dissection of the Longshanks selection experiment, in which mice were selectively bred over 20 generations for longer tibiae relative to body mass, resulting in 13% longer tibiae in two replicates. We synthesized evolutionary theory, genome sequences and molecular genetics to understand the selection response and found that it involved both polygenic adaptation and discrete loci of major effect, with the strongest loci tending to be selected in parallel between replicates. We show that selection may favor de-repression of bone growth through inactivating two limb enhancers of an inhibitor, Nkx3-2. Our integrative genomic analyses thus show that it is possible to connect individual base-pair changes to the overall selection response.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"file_id":"6721","relation":"main_file","date_created":"2019-07-29T07:41:18Z","date_updated":"2020-07-14T12:47:38Z","checksum":"fa0936fe58f0d9e3f8e75038570e5a17","file_name":"2019_eLife_Castro.pdf","access_level":"open_access","creator":"apreinsp","content_type":"application/pdf","file_size":6748249}],"intvolume":" 8","status":"public","ddc":["576"],"title":"An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"6713","month":"06","language":[{"iso":"eng"}],"doi":"10.7554/eLife.42014","isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"pmid":["31169497"],"isi":["000473588700001"]},"file_date_updated":"2020-07-14T12:47:38Z","article_number":"e42014","volume":8,"date_updated":"2024-03-28T23:30:23Z","date_created":"2019-07-28T21:59:17Z","related_material":{"record":[{"id":"9804","status":"public","relation":"research_data"},{"id":"11388","relation":"dissertation_contains","status":"public"}]},"author":[{"last_name":"Castro","first_name":"João Pl","full_name":"Castro, João Pl"},{"full_name":"Yancoskie, Michelle N.","last_name":"Yancoskie","first_name":"Michelle N."},{"full_name":"Marchini, Marta","last_name":"Marchini","first_name":"Marta"},{"first_name":"Stefanie","last_name":"Belohlavy","id":"43FE426A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9849-498X","full_name":"Belohlavy, Stefanie"},{"first_name":"Layla","last_name":"Hiramatsu","full_name":"Hiramatsu, Layla"},{"first_name":"Marek","last_name":"Kučka","full_name":"Kučka, Marek"},{"full_name":"Beluch, William H.","last_name":"Beluch","first_name":"William H."},{"full_name":"Naumann, Ronald","first_name":"Ronald","last_name":"Naumann"},{"full_name":"Skuplik, Isabella","first_name":"Isabella","last_name":"Skuplik"},{"full_name":"Cobb, John","first_name":"John","last_name":"Cobb"},{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"first_name":"Campbell","last_name":"Rolian","full_name":"Rolian, Campbell"},{"full_name":"Chan, Yingguang Frank","first_name":"Yingguang Frank","last_name":"Chan"}],"department":[{"_id":"NiBa"}],"publisher":"eLife Sciences Publications","publication_status":"published","pmid":1,"year":"2019"},{"publication_identifier":{"issn":["15449173"]},"month":"06","language":[{"iso":"eng"}],"doi":"10.1371/journal.pbio.2005372","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"publist_id":"7550","file_date_updated":"2020-07-14T12:46:01Z","article_number":"e2005372","volume":16,"date_created":"2018-12-11T11:45:46Z","date_updated":"2023-02-23T14:10:16Z","related_material":{"record":[{"relation":"research_data","status":"public","id":"9839"}]},"author":[{"orcid":"0000-0003-0951-3112","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","last_name":"Polechova","first_name":"Jitka","full_name":"Polechova, Jitka"}],"publisher":"Public Library of Science","department":[{"_id":"NiBa"}],"publication_status":"published","year":"2018","has_accepted_license":"1","day":"15","scopus_import":1,"date_published":"2018-06-15T00:00:00Z","citation":{"short":"J. Polechova, PLoS Biology 16 (2018).","mla":"Polechova, Jitka. “Is the Sky the Limit? On the Expansion Threshold of a Species’ Range.” PLoS Biology, vol. 16, no. 6, e2005372, Public Library of Science, 2018, doi:10.1371/journal.pbio.2005372.","chicago":"Polechova, Jitka. “Is the Sky the Limit? On the Expansion Threshold of a Species’ Range.” PLoS Biology. Public Library of Science, 2018. https://doi.org/10.1371/journal.pbio.2005372.","ama":"Polechova J. Is the sky the limit? On the expansion threshold of a species’ range. PLoS Biology. 2018;16(6). doi:10.1371/journal.pbio.2005372","apa":"Polechova, J. (2018). Is the sky the limit? On the expansion threshold of a species’ range. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2005372","ieee":"J. Polechova, “Is the sky the limit? On the expansion threshold of a species’ range,” PLoS Biology, vol. 16, no. 6. Public Library of Science, 2018.","ista":"Polechova J. 2018. Is the sky the limit? On the expansion threshold of a species’ range. PLoS Biology. 16(6), e2005372."},"publication":"PLoS Biology","issue":"6","abstract":[{"lang":"eng","text":"More than 100 years after Grigg’s influential analysis of species’ borders, the causes of limits to species’ ranges still represent a puzzle that has never been understood with clarity. The topic has become especially important recently as many scientists have become interested in the potential for species’ ranges to shift in response to climate change—and yet nearly all of those studies fail to recognise or incorporate evolutionary genetics in a way that relates to theoretical developments. I show that range margins can be understood based on just two measurable parameters: (i) the fitness cost of dispersal—a measure of environmental heterogeneity—and (ii) the strength of genetic drift, which reduces genetic diversity. Together, these two parameters define an ‘expansion threshold’: adaptation fails when genetic drift reduces genetic diversity below that required for adaptation to a heterogeneous environment. When the key parameters drop below this expansion threshold locally, a sharp range margin forms. When they drop below this threshold throughout the species’ range, adaptation collapses everywhere, resulting in either extinction or formation of a fragmented metapopulation. Because the effects of dispersal differ fundamentally with dimension, the second parameter—the strength of genetic drift—is qualitatively different compared to a linear habitat. In two-dimensional habitats, genetic drift becomes effectively independent of selection. It decreases with ‘neighbourhood size’—the number of individuals accessible by dispersal within one generation. Moreover, in contrast to earlier predictions, which neglected evolution of genetic variance and/or stochasticity in two dimensions, dispersal into small marginal populations aids adaptation. This is because the reduction of both genetic and demographic stochasticity has a stronger effect than the cost of dispersal through increased maladaptation. The expansion threshold thus provides a novel, theoretically justified, and testable prediction for formation of the range margin and collapse of the species’ range."}],"type":"journal_article","oa_version":"Published Version","file":[{"checksum":"908c52751bba30c55ed36789e5e4c84d","date_updated":"2020-07-14T12:46:01Z","date_created":"2019-01-22T08:30:03Z","relation":"main_file","file_id":"5870","file_size":6968201,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2017_PLOS_Polechova.pdf"}],"intvolume":" 16","title":"Is the sky the limit? On the expansion threshold of a species’ range","ddc":["576"],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"315"},{"article_processing_charge":"No","day":"09","month":"10","doi":"10.5061/dryad.72cg113","date_published":"2018-10-09T00:00:00Z","citation":{"ama":"Faria R, Chaube P, Morales HE, et al. Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. 2018. doi:10.5061/dryad.72cg113","apa":"Faria, R., Chaube, P., Morales, H. E., Larsson, T., Lemmon, A. R., Lemmon, E. M., … Butlin, R. K. (2018). Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. Dryad. https://doi.org/10.5061/dryad.72cg113","ieee":"R. Faria et al., “Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes.” Dryad, 2018.","ista":"Faria R, Chaube P, Morales HE, Larsson T, Lemmon AR, Lemmon EM, Rafajlović M, Panova M, Ravinet M, Johannesson K, Westram AM, Butlin RK. 2018. Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes, Dryad, 10.5061/dryad.72cg113.","short":"R. Faria, P. Chaube, H.E. Morales, T. Larsson, A.R. Lemmon, E.M. Lemmon, M. Rafajlović, M. Panova, M. Ravinet, K. Johannesson, A.M. Westram, R.K. Butlin, (2018).","mla":"Faria, Rui, et al. Data from: Multiple Chromosomal Rearrangements in a Hybrid Zone between Littorina Saxatilis Ecotypes. Dryad, 2018, doi:10.5061/dryad.72cg113.","chicago":"Faria, Rui, Pragya Chaube, Hernán E. Morales, Tomas Larsson, Alan R. Lemmon, Emily M. Lemmon, Marina Rafajlović, et al. “Data from: Multiple Chromosomal Rearrangements in a Hybrid Zone between Littorina Saxatilis Ecotypes.” Dryad, 2018. https://doi.org/10.5061/dryad.72cg113."},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.72cg113"}],"abstract":[{"text":"Both classical and recent studies suggest that chromosomal inversion polymorphisms are important in adaptation and speciation. However, biases in discovery and reporting of inversions make it difficult to assess their prevalence and biological importance. Here, we use an approach based on linkage disequilibrium among markers genotyped for samples collected across a transect between contrasting habitats to detect chromosomal rearrangements de novo. We report 17 polymorphic rearrangements in a single locality for the coastal marine snail, Littorina saxatilis. Patterns of diversity in the field and of recombination in controlled crosses provide strong evidence that at least the majority of these rearrangements are inversions. Most show clinal changes in frequency between habitats, suggestive of divergent selection, but only one appears to be fixed for different arrangements in the two habitats. Consistent with widespread evidence for balancing selection on inversion polymorphisms, we argue that a combination of heterosis and divergent selection can explain the observed patterns and should be considered in other systems spanning environmental gradients.","lang":"eng"}],"type":"research_data_reference","oa_version":"Published Version","date_created":"2021-08-09T12:46:39Z","date_updated":"2023-08-24T14:50:26Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"6095"}]},"author":[{"first_name":"Rui","last_name":"Faria","full_name":"Faria, Rui"},{"full_name":"Chaube, Pragya","last_name":"Chaube","first_name":"Pragya"},{"full_name":"Morales, Hernán E.","first_name":"Hernán E.","last_name":"Morales"},{"full_name":"Larsson, Tomas","first_name":"Tomas","last_name":"Larsson"},{"first_name":"Alan R.","last_name":"Lemmon","full_name":"Lemmon, Alan R."},{"full_name":"Lemmon, Emily M.","first_name":"Emily M.","last_name":"Lemmon"},{"first_name":"Marina","last_name":"Rafajlović","full_name":"Rafajlović, Marina"},{"full_name":"Panova, Marina","first_name":"Marina","last_name":"Panova"},{"first_name":"Mark","last_name":"Ravinet","full_name":"Ravinet, Mark"},{"first_name":"Kerstin","last_name":"Johannesson","full_name":"Johannesson, Kerstin"},{"full_name":"Westram, Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","first_name":"Anja M","last_name":"Westram"},{"first_name":"Roger K.","last_name":"Butlin","full_name":"Butlin, Roger K."}],"publisher":"Dryad","department":[{"_id":"NiBa"}],"status":"public","title":"Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes","_id":"9837","year":"2018","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf"},{"oa_version":"Published Version","file":[{"creator":"dernst","content_type":"application/pdf","file_size":3533881,"file_name":"2018_eLife_Payne.pdf","access_level":"open_access","date_updated":"2020-07-14T12:46:25Z","date_created":"2018-12-17T10:36:07Z","checksum":"447cf6e680bdc3c01062a8737d876569","file_id":"5689","relation":"main_file"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"423","title":"CRISPR-based herd immunity can limit phage epidemics in bacterial populations","ddc":["576"],"status":"public","intvolume":" 7","abstract":[{"text":"Herd immunity, a process in which resistant individuals limit the spread of a pathogen among susceptible hosts has been extensively studied in eukaryotes. Even though bacteria have evolved multiple immune systems against their phage pathogens, herd immunity in bacteria remains unexplored. Here we experimentally demonstrate that herd immunity arises during phage epidemics in structured and unstructured Escherichia coli populations consisting of differing frequencies of susceptible and resistant cells harboring CRISPR immunity. In addition, we develop a mathematical model that quantifies how herd immunity is affected by spatial population structure, bacterial growth rate, and phage replication rate. Using our model we infer a general epidemiological rule describing the relative speed of an epidemic in partially resistant spatially structured populations. Our experimental and theoretical findings indicate that herd immunity may be important in bacterial communities, allowing for stable coexistence of bacteria and their phages and the maintenance of polymorphism in bacterial immunity.","lang":"eng"}],"type":"journal_article","date_published":"2018-03-09T00:00:00Z","publication":"eLife","citation":{"mla":"Payne, Pavel, et al. “CRISPR-Based Herd Immunity Can Limit Phage Epidemics in Bacterial Populations.” ELife, vol. 7, e32035, eLife Sciences Publications, 2018, doi:10.7554/eLife.32035.","short":"P. Payne, L. Geyrhofer, N.H. Barton, J.P. Bollback, ELife 7 (2018).","chicago":"Payne, Pavel, Lukas Geyrhofer, Nicholas H Barton, and Jonathan P Bollback. “CRISPR-Based Herd Immunity Can Limit Phage Epidemics in Bacterial Populations.” ELife. eLife Sciences Publications, 2018. https://doi.org/10.7554/eLife.32035.","ama":"Payne P, Geyrhofer L, Barton NH, Bollback JP. CRISPR-based herd immunity can limit phage epidemics in bacterial populations. eLife. 2018;7. doi:10.7554/eLife.32035","ista":"Payne P, Geyrhofer L, Barton NH, Bollback JP. 2018. CRISPR-based herd immunity can limit phage epidemics in bacterial populations. eLife. 7, e32035.","ieee":"P. Payne, L. Geyrhofer, N. H. Barton, and J. P. Bollback, “CRISPR-based herd immunity can limit phage epidemics in bacterial populations,” eLife, vol. 7. eLife Sciences Publications, 2018.","apa":"Payne, P., Geyrhofer, L., Barton, N. H., & Bollback, J. P. (2018). CRISPR-based herd immunity can limit phage epidemics in bacterial populations. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.32035"},"day":"09","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","author":[{"last_name":"Payne","first_name":"Pavel","orcid":"0000-0002-2711-9453","id":"35F78294-F248-11E8-B48F-1D18A9856A87","full_name":"Payne, Pavel"},{"full_name":"Geyrhofer, Lukas","last_name":"Geyrhofer","first_name":"Lukas"},{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"first_name":"Jonathan P","last_name":"Bollback","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4624-4612","full_name":"Bollback, Jonathan P"}],"related_material":{"record":[{"relation":"research_data","status":"public","id":"9840"}]},"date_created":"2018-12-11T11:46:23Z","date_updated":"2023-09-11T12:49:17Z","volume":7,"acknowledgement":"We are grateful to Remy Chait for his help and assistance with establishing our experimental setups and to Tobias Bergmiller for valuable insights into some specific experimental details. We thank Luciano Marraffini for donating us the pCas9 plasmid used in this study. We also want to express our gratitude to Seth Barribeau, Andrea Betancourt, Călin Guet, Mato Lagator, Tiago Paixão and Maroš Pleška for valuable discussions on the manuscript. Finally, we would like to thank the \r\neditors and reviewers for their helpful comments and suggestions.","year":"2018","publication_status":"published","publisher":"eLife Sciences Publications","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"file_date_updated":"2020-07-14T12:46:25Z","publist_id":"7400","ec_funded":1,"article_number":"e32035","doi":"10.7554/eLife.32035","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000431035800001"]},"quality_controlled":"1","isi":1,"project":[{"grant_number":"648440","_id":"2578D616-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Selective Barriers to Horizontal Gene Transfer"}],"month":"03"},{"type":"research_data_reference","abstract":[{"text":"Herd immunity, a process in which resistant individuals limit the spread of a pathogen among susceptible hosts has been extensively studied in eukaryotes. Even though bacteria have evolved multiple immune systems against their phage pathogens, herd immunity in bacteria remains unexplored. Here we experimentally demonstrate that herd immunity arises during phage epidemics in structured and unstructured Escherichia coli populations consisting of differing frequencies of susceptible and resistant cells harboring CRISPR immunity. In addition, we develop a mathematical model that quantifies how herd immunity is affected by spatial population structure, bacterial growth rate, and phage replication rate. Using our model we infer a general epidemiological rule describing the relative speed of an epidemic in partially resistant spatially structured populations. Our experimental and theoretical findings indicate that herd immunity may be important in bacterial communities, allowing for stable coexistence of bacteria and their phages and the maintenance of polymorphism in bacterial immunity.","lang":"eng"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9840","year":"2018","publisher":"Dryad","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"title":"Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations","status":"public","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"423"}]},"author":[{"full_name":"Payne, Pavel","orcid":"0000-0002-2711-9453","id":"35F78294-F248-11E8-B48F-1D18A9856A87","last_name":"Payne","first_name":"Pavel"},{"last_name":"Geyrhofer","first_name":"Lukas","full_name":"Geyrhofer, Lukas"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"},{"orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","last_name":"Bollback","first_name":"Jonathan P","full_name":"Bollback, Jonathan P"}],"oa_version":"Published Version","date_created":"2021-08-09T13:10:02Z","date_updated":"2023-09-11T12:49:17Z","article_processing_charge":"No","month":"03","day":"12","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.42n44"}],"oa":1,"citation":{"ama":"Payne P, Geyrhofer L, Barton NH, Bollback JP. Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations. 2018. doi:10.5061/dryad.42n44","ista":"Payne P, Geyrhofer L, Barton NH, Bollback JP. 2018. Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations, Dryad, 10.5061/dryad.42n44.","apa":"Payne, P., Geyrhofer, L., Barton, N. H., & Bollback, J. P. (2018). Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations. Dryad. https://doi.org/10.5061/dryad.42n44","ieee":"P. Payne, L. Geyrhofer, N. H. Barton, and J. P. Bollback, “Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations.” Dryad, 2018.","mla":"Payne, Pavel, et al. Data from: CRISPR-Based Herd Immunity Limits Phage Epidemics in Bacterial Populations. Dryad, 2018, doi:10.5061/dryad.42n44.","short":"P. Payne, L. Geyrhofer, N.H. Barton, J.P. Bollback, (2018).","chicago":"Payne, Pavel, Lukas Geyrhofer, Nicholas H Barton, and Jonathan P Bollback. “Data from: CRISPR-Based Herd Immunity Limits Phage Epidemics in Bacterial Populations.” Dryad, 2018. https://doi.org/10.5061/dryad.42n44."},"doi":"10.5061/dryad.42n44","date_published":"2018-03-12T00:00:00Z"},{"has_accepted_license":"1","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2018-07-01T00:00:00Z","page":"110-127","article_type":"original","citation":{"ama":"Barton NH, Etheridge A. Establishment in a new habitat by polygenic adaptation. Theoretical Population Biology. 2018;122(7):110-127. doi:10.1016/j.tpb.2017.11.007","ieee":"N. H. Barton and A. Etheridge, “Establishment in a new habitat by polygenic adaptation,” Theoretical Population Biology, vol. 122, no. 7. Academic Press, pp. 110–127, 2018.","apa":"Barton, N. H., & Etheridge, A. (2018). Establishment in a new habitat by polygenic adaptation. Theoretical Population Biology. Academic Press. https://doi.org/10.1016/j.tpb.2017.11.007","ista":"Barton NH, Etheridge A. 2018. Establishment in a new habitat by polygenic adaptation. Theoretical Population Biology. 122(7), 110–127.","short":"N.H. Barton, A. Etheridge, Theoretical Population Biology 122 (2018) 110–127.","mla":"Barton, Nicholas H., and Alison Etheridge. “Establishment in a New Habitat by Polygenic Adaptation.” Theoretical Population Biology, vol. 122, no. 7, Academic Press, 2018, pp. 110–27, doi:10.1016/j.tpb.2017.11.007.","chicago":"Barton, Nicholas H, and Alison Etheridge. “Establishment in a New Habitat by Polygenic Adaptation.” Theoretical Population Biology. Academic Press, 2018. https://doi.org/10.1016/j.tpb.2017.11.007."},"publication":"Theoretical Population Biology","issue":"7","abstract":[{"lang":"eng","text":"Maladapted individuals can only colonise a new habitat if they can evolve a\r\npositive growth rate fast enough to avoid extinction, a process known as evolutionary\r\nrescue. We treat log fitness at low density in the new habitat as a\r\nsingle polygenic trait and thus use the infinitesimal model to follow the evolution\r\nof the growth rate; this assumes that the trait values of offspring of a\r\nsexual union are normally distributed around the mean of the parents’ trait\r\nvalues, with variance that depends only on the parents’ relatedness. The\r\nprobability that a single migrant can establish depends on just two parameters:\r\nthe mean and genetic variance of the trait in the source population.\r\nThe chance of success becomes small if migrants come from a population\r\nwith mean growth rate in the new habitat more than a few standard deviations\r\nbelow zero; this chance depends roughly equally on the probability\r\nthat the initial founder is unusually fit, and on the subsequent increase in\r\ngrowth rate of its offspring as a result of selection. The loss of genetic variation\r\nduring the founding event is substantial, but highly variable. With\r\ncontinued migration at rate M, establishment is inevitable; when migration\r\nis rare, the expected time to establishment decreases inversely with M.\r\nHowever, above a threshold migration rate, the population may be trapped\r\nin a ‘sink’ state, in which adaptation is held back by gene flow; above this\r\nthreshold, the expected time to establishment increases exponentially with M. This threshold behaviour is captured by a deterministic approximation,\r\nwhich assumes a Gaussian distribution of the trait in the founder population\r\nwith mean and variance evolving deterministically. By assuming a constant\r\ngenetic variance, we also develop a diffusion approximation for the joint distribution\r\nof population size and trait mean, which extends to include stabilising\r\nselection and density regulation. Divergence of the population from its\r\nancestors causes partial reproductive isolation, which we measure through\r\nthe reproductive value of migrants into the newly established population."}],"type":"journal_article","oa_version":"Submitted Version","file":[{"date_updated":"2020-07-14T12:47:09Z","date_created":"2019-12-21T09:36:39Z","checksum":"0b96f6db47e3e91b5e7d103b847c239d","file_id":"7199","relation":"main_file","creator":"nbarton","content_type":"application/pdf","file_size":2287682,"file_name":"bartonetheridge.pdf","access_level":"open_access"}],"intvolume":" 122","ddc":["519","576"],"title":"Establishment in a new habitat by polygenic adaptation","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"564","month":"07","language":[{"iso":"eng"}],"doi":"10.1016/j.tpb.2017.11.007","project":[{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000440392900014"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"ec_funded":1,"publist_id":"7250","file_date_updated":"2020-07-14T12:47:09Z","volume":122,"date_created":"2018-12-11T11:47:12Z","date_updated":"2023-09-11T13:41:22Z","related_material":{"record":[{"status":"public","relation":"research_data","id":"9842"}]},"author":[{"last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"},{"full_name":"Etheridge, Alison","last_name":"Etheridge","first_name":"Alison"}],"department":[{"_id":"NiBa"}],"publisher":"Academic Press","publication_status":"published","year":"2018"},{"type":"journal_article","abstract":[{"lang":"eng","text":"In continuous populations with local migration, nearby pairs of individuals have on average more similar genotypes\r\nthan geographically well separated pairs. A barrier to gene flow distorts this classical pattern of isolation by distance. Genetic similarity is decreased for sample pairs on different sides of the barrier and increased for pairs on the same side near the barrier. Here, we introduce an inference scheme that utilizes this signal to detect and estimate the strength of a linear barrier to gene flow in two-dimensions. We use a diffusion approximation to model the effects of a barrier on the geographical spread of ancestry backwards in time. This approach allows us to calculate the chance of recent coalescence and probability of identity by descent. We introduce an inference scheme that fits these theoretical results to the geographical covariance structure of bialleleic genetic markers. It can estimate the strength of the barrier as well as several demographic parameters. We investigate the power of our inference scheme to detect barriers by applying it to a wide range of simulated data. We also showcase an example application to a Antirrhinum majus (snapdragon) flower color hybrid zone, where we do not detect any signal of a strong genome wide barrier to gene flow."}],"issue":"3","title":"Estimating barriers to gene flow from distorted isolation-by-distance patterns","status":"public","intvolume":" 208","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"563","oa_version":"Preprint","scopus_import":"1","day":"01","article_processing_charge":"No","page":"1231-1245","publication":"Genetics","citation":{"ieee":"H. Ringbauer, A. Kolesnikov, D. Field, and N. H. Barton, “Estimating barriers to gene flow from distorted isolation-by-distance patterns,” Genetics, vol. 208, no. 3. Genetics Society of America, pp. 1231–1245, 2018.","apa":"Ringbauer, H., Kolesnikov, A., Field, D., & Barton, N. H. (2018). Estimating barriers to gene flow from distorted isolation-by-distance patterns. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.117.300638","ista":"Ringbauer H, Kolesnikov A, Field D, Barton NH. 2018. Estimating barriers to gene flow from distorted isolation-by-distance patterns. Genetics. 208(3), 1231–1245.","ama":"Ringbauer H, Kolesnikov A, Field D, Barton NH. Estimating barriers to gene flow from distorted isolation-by-distance patterns. Genetics. 2018;208(3):1231-1245. doi:10.1534/genetics.117.300638","chicago":"Ringbauer, Harald, Alexander Kolesnikov, David Field, and Nicholas H Barton. “Estimating Barriers to Gene Flow from Distorted Isolation-by-Distance Patterns.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.117.300638.","short":"H. Ringbauer, A. Kolesnikov, D. Field, N.H. Barton, Genetics 208 (2018) 1231–1245.","mla":"Ringbauer, Harald, et al. “Estimating Barriers to Gene Flow from Distorted Isolation-by-Distance Patterns.” Genetics, vol. 208, no. 3, Genetics Society of America, 2018, pp. 1231–45, doi:10.1534/genetics.117.300638."},"date_published":"2018-03-01T00:00:00Z","publist_id":"7251","publication_status":"published","department":[{"_id":"NiBa"},{"_id":"ChLa"}],"publisher":"Genetics Society of America","year":"2018","date_created":"2018-12-11T11:47:12Z","date_updated":"2023-09-11T13:42:38Z","volume":208,"author":[{"first_name":"Harald","last_name":"Ringbauer","id":"417FCFF4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4884-9682","full_name":"Ringbauer, Harald"},{"first_name":"Alexander","last_name":"Kolesnikov","id":"2D157DB6-F248-11E8-B48F-1D18A9856A87","full_name":"Kolesnikov, Alexander"},{"full_name":"Field, David","first_name":"David","last_name":"Field"},{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"200"}]},"month":"03","quality_controlled":"1","isi":1,"oa":1,"main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/205484v1","open_access":"1"}],"external_id":{"isi":["000426219600025"]},"language":[{"iso":"eng"}],"doi":"10.1534/genetics.117.300638"},{"ec_funded":1,"volume":209,"date_created":"2018-12-11T11:45:47Z","date_updated":"2023-09-11T13:57:43Z","related_material":{"link":[{"url":"https://ist.ac.at/en/news/recognizing-others-but-not-yourself-new-insights-into-the-evolution-of-plant-mating/","relation":"press_release","description":"News on IST Homepage"}],"record":[{"id":"9813","relation":"research_data","status":"public"}]},"author":[{"full_name":"Bodova, Katarina","first_name":"Katarina","last_name":"Bodova","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7214-0171"},{"full_name":"Priklopil, Tadeas","id":"3C869AA0-F248-11E8-B48F-1D18A9856A87","first_name":"Tadeas","last_name":"Priklopil"},{"full_name":"Field, David","first_name":"David","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478"},{"full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-6118-0541","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","last_name":"Pickup","first_name":"Melinda","full_name":"Pickup, Melinda"}],"department":[{"_id":"NiBa"},{"_id":"GaTk"}],"publisher":"Genetics Society of America","publication_status":"published","year":"2018","month":"07","language":[{"iso":"eng"}],"doi":"10.1534/genetics.118.300748","project":[{"grant_number":"329960","_id":"25B36484-B435-11E9-9278-68D0E5697425","name":"Mating system and the evolutionary dynamics of hybrid zones","call_identifier":"FP7"},{"_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation"},{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000437171700017"]},"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/node/80098.abstract"}],"oa":1,"issue":"3","abstract":[{"text":"Self-incompatibility (SI) is a genetically based recognition system that functions to prevent self-fertilization and mating among related plants. An enduring puzzle in SI is how the high diversity observed in nature arises and is maintained. Based on the underlying recognition mechanism, SI can be classified into two main groups: self- and non-self recognition. Most work has focused on diversification within self-recognition systems despite expected differences between the two groups in the evolutionary pathways and outcomes of diversification. Here, we use a deterministic population genetic model and stochastic simulations to investigate how novel S-haplotypes evolve in a gametophytic non-self recognition (SRNase/S Locus F-box (SLF)) SI system. For this model the pathways for diversification involve either the maintenance or breakdown of SI and can vary in the order of mutations of the female (SRNase) and male (SLF) components. We show analytically that diversification can occur with high inbreeding depression and self-pollination, but this varies with evolutionary pathway and level of completeness (which determines the number of potential mating partners in the population), and in general is more likely for lower haplotype number. The conditions for diversification are broader in stochastic simulations of finite population size. However, the number of haplotypes observed under high inbreeding and moderate to high self-pollination is less than that commonly observed in nature. Diversification was observed through pathways that maintain SI as well as through self-compatible intermediates. Yet the lifespan of diversified haplotypes was sensitive to their level of completeness. By examining diversification in a non-self recognition SI system, this model extends our understanding of the evolution and maintenance of haplotype diversity observed in a self recognition system common in flowering plants.","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","intvolume":" 209","status":"public","title":"Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"316","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2018-07-01T00:00:00Z","page":"861-883","article_type":"original","citation":{"ieee":"K. Bodova, T. Priklopil, D. Field, N. H. Barton, and M. Pickup, “Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system,” Genetics, vol. 209, no. 3. Genetics Society of America, pp. 861–883, 2018.","apa":"Bodova, K., Priklopil, T., Field, D., Barton, N. H., & Pickup, M. (2018). Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.118.300748","ista":"Bodova K, Priklopil T, Field D, Barton NH, Pickup M. 2018. Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system. Genetics. 209(3), 861–883.","ama":"Bodova K, Priklopil T, Field D, Barton NH, Pickup M. Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system. Genetics. 2018;209(3):861-883. doi:10.1534/genetics.118.300748","chicago":"Bodova, Katarina, Tadeas Priklopil, David Field, Nicholas H Barton, and Melinda Pickup. “Evolutionary Pathways for the Generation of New Self-Incompatibility Haplotypes in a Non-Self Recognition System.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.118.300748.","short":"K. Bodova, T. Priklopil, D. Field, N.H. Barton, M. Pickup, Genetics 209 (2018) 861–883.","mla":"Bodova, Katarina, et al. “Evolutionary Pathways for the Generation of New Self-Incompatibility Haplotypes in a Non-Self Recognition System.” Genetics, vol. 209, no. 3, Genetics Society of America, 2018, pp. 861–83, doi:10.1534/genetics.118.300748."},"publication":"Genetics"},{"article_processing_charge":"No","day":"30","month":"04","doi":"10.25386/genetics.6148304.v1","date_published":"2018-04-30T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.25386/genetics.6148304.v1"}],"oa":1,"citation":{"mla":"Bodova, Katarina, et al. Supplemental Material for Bodova et Al., 2018. Genetics Society of America, 2018, doi:10.25386/genetics.6148304.v1.","short":"K. Bodova, T. Priklopil, D. Field, N.H. Barton, M. Pickup, (2018).","chicago":"Bodova, Katarina, Tadeas Priklopil, David Field, Nicholas H Barton, and Melinda Pickup. “Supplemental Material for Bodova et Al., 2018.” Genetics Society of America, 2018. https://doi.org/10.25386/genetics.6148304.v1.","ama":"Bodova K, Priklopil T, Field D, Barton NH, Pickup M. Supplemental material for Bodova et al., 2018. 2018. doi:10.25386/genetics.6148304.v1","ista":"Bodova K, Priklopil T, Field D, Barton NH, Pickup M. 2018. Supplemental material for Bodova et al., 2018, Genetics Society of America, 10.25386/genetics.6148304.v1.","apa":"Bodova, K., Priklopil, T., Field, D., Barton, N. H., & Pickup, M. (2018). Supplemental material for Bodova et al., 2018. Genetics Society of America. https://doi.org/10.25386/genetics.6148304.v1","ieee":"K. Bodova, T. Priklopil, D. Field, N. H. Barton, and M. Pickup, “Supplemental material for Bodova et al., 2018.” Genetics Society of America, 2018."},"abstract":[{"lang":"eng","text":"File S1 contains figures that clarify the following features: (i) effect of population size on the average number/frequency of SI classes, (ii) changes in the minimal completeness deficit in time for a single class, and (iii) diversification diagrams for all studied pathways, including the summary figure for k = 8. File S2 contains the code required for a stochastic simulation of the SLF system with an example. This file also includes the output in the form of figures and tables."}],"type":"research_data_reference","oa_version":"Published Version","date_updated":"2023-09-11T13:57:42Z","date_created":"2021-08-06T13:04:32Z","related_material":{"record":[{"id":"316","relation":"used_in_publication","status":"public"}]},"author":[{"full_name":"Bod'ová, Katarína","orcid":"0000-0002-7214-0171","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","last_name":"Bod'ová","first_name":"Katarína"},{"full_name":"Priklopil, Tadeas","last_name":"Priklopil","first_name":"Tadeas","id":"3C869AA0-F248-11E8-B48F-1D18A9856A87"},{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478","first_name":"David","last_name":"Field","full_name":"Field, David"},{"last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"},{"full_name":"Pickup, Melinda","last_name":"Pickup","first_name":"Melinda","orcid":"0000-0001-6118-0541","id":"2C78037E-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"NiBa"},{"_id":"GaTk"}],"publisher":"Genetics Society of America","status":"public","title":"Supplemental material for Bodova et al., 2018","_id":"9813","year":"2018","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf"},{"publication":"Algorithmica","citation":{"chicago":"Oliveto, Pietro, Tiago Paixao, Jorge Pérez Heredia, Dirk Sudholt, and Barbora Trubenova. “How to Escape Local Optima in Black Box Optimisation When Non Elitism Outperforms Elitism.” Algorithmica. Springer, 2018. https://doi.org/10.1007/s00453-017-0369-2.","mla":"Oliveto, Pietro, et al. “How to Escape Local Optima in Black Box Optimisation When Non Elitism Outperforms Elitism.” Algorithmica, vol. 80, no. 5, Springer, 2018, pp. 1604–33, doi:10.1007/s00453-017-0369-2.","short":"P. Oliveto, T. Paixao, J. Pérez Heredia, D. Sudholt, B. Trubenova, Algorithmica 80 (2018) 1604–1633.","ista":"Oliveto P, Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. 2018. How to escape local optima in black box optimisation when non elitism outperforms elitism. Algorithmica. 80(5), 1604–1633.","apa":"Oliveto, P., Paixao, T., Pérez Heredia, J., Sudholt, D., & Trubenova, B. (2018). How to escape local optima in black box optimisation when non elitism outperforms elitism. Algorithmica. Springer. https://doi.org/10.1007/s00453-017-0369-2","ieee":"P. Oliveto, T. Paixao, J. Pérez Heredia, D. Sudholt, and B. Trubenova, “How to escape local optima in black box optimisation when non elitism outperforms elitism,” Algorithmica, vol. 80, no. 5. Springer, pp. 1604–1633, 2018.","ama":"Oliveto P, Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. How to escape local optima in black box optimisation when non elitism outperforms elitism. Algorithmica. 2018;80(5):1604-1633. doi:10.1007/s00453-017-0369-2"},"page":"1604 - 1633","date_published":"2018-05-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","has_accepted_license":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"723","ddc":["576"],"title":"How to escape local optima in black box optimisation when non elitism outperforms elitism","status":"public","intvolume":" 80","pubrep_id":"1014","oa_version":"Published Version","file":[{"creator":"system","file_size":691245,"content_type":"application/pdf","file_name":"IST-2018-1014-v1+1_2018_Paixao_Escape.pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:54Z","date_created":"2018-12-12T10:08:14Z","checksum":"7d92f5d7be81e387edeec4f06442791c","file_id":"4674","relation":"main_file"}],"type":"journal_article","abstract":[{"text":"Escaping local optima is one of the major obstacles to function optimisation. Using the metaphor of a fitness landscape, local optima correspond to hills separated by fitness valleys that have to be overcome. We define a class of fitness valleys of tunable difficulty by considering their length, representing the Hamming path between the two optima and their depth, the drop in fitness. For this function class we present a runtime comparison between stochastic search algorithms using different search strategies. The (1+1) EA is a simple and well-studied evolutionary algorithm that has to jump across the valley to a point of higher fitness because it does not accept worsening moves (elitism). In contrast, the Metropolis algorithm and the Strong Selection Weak Mutation (SSWM) algorithm, a famous process in population genetics, are both able to cross the fitness valley by accepting worsening moves. We show that the runtime of the (1+1) EA depends critically on the length of the valley while the runtimes of the non-elitist algorithms depend crucially on the depth of the valley. Moreover, we show that both SSWM and Metropolis can also efficiently optimise a rugged function consisting of consecutive valleys.","lang":"eng"}],"issue":"5","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000428239300010"]},"oa":1,"quality_controlled":"1","isi":1,"project":[{"_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","grant_number":"618091","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","call_identifier":"FP7"}],"doi":"10.1007/s00453-017-0369-2","language":[{"iso":"eng"}],"month":"05","year":"2018","publication_status":"published","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"publisher":"Springer","author":[{"full_name":"Oliveto, Pietro","first_name":"Pietro","last_name":"Oliveto"},{"full_name":"Paixao, Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2361-3953","first_name":"Tiago","last_name":"Paixao"},{"full_name":"Pérez Heredia, Jorge","first_name":"Jorge","last_name":"Pérez Heredia"},{"first_name":"Dirk","last_name":"Sudholt","full_name":"Sudholt, Dirk"},{"first_name":"Barbora","last_name":"Trubenova","id":"42302D54-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6873-2967","full_name":"Trubenova, Barbora"}],"date_updated":"2023-09-11T14:11:35Z","date_created":"2018-12-11T11:48:09Z","volume":80,"file_date_updated":"2020-07-14T12:47:54Z","ec_funded":1,"publist_id":"6957"},{"isi":1,"quality_controlled":"1","oa":1,"external_id":{"isi":["000440014100020"]},"main_file_link":[{"url":"https://www.biorxiv.org/content/early/2017/11/30/227082","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1534/genetics.118.301018","month":"08","department":[{"_id":"NiBa"}],"publisher":"Genetics Society of America","publication_status":"published","year":"2018","volume":209,"date_created":"2018-12-11T11:45:36Z","date_updated":"2023-09-13T08:22:32Z","author":[{"full_name":"Sachdeva, Himani","id":"42377A0A-F248-11E8-B48F-1D18A9856A87","last_name":"Sachdeva","first_name":"Himani"},{"full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"7617","page":"1279 - 1303","citation":{"ama":"Sachdeva H, Barton NH. Introgression of a block of genome under infinitesimal selection. Genetics. 2018;209(4):1279-1303. doi:10.1534/genetics.118.301018","ieee":"H. Sachdeva and N. H. Barton, “Introgression of a block of genome under infinitesimal selection,” Genetics, vol. 209, no. 4. Genetics Society of America, pp. 1279–1303, 2018.","apa":"Sachdeva, H., & Barton, N. H. (2018). Introgression of a block of genome under infinitesimal selection. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.118.301018","ista":"Sachdeva H, Barton NH. 2018. Introgression of a block of genome under infinitesimal selection. Genetics. 209(4), 1279–1303.","short":"H. Sachdeva, N.H. Barton, Genetics 209 (2018) 1279–1303.","mla":"Sachdeva, Himani, and Nicholas H. Barton. “Introgression of a Block of Genome under Infinitesimal Selection.” Genetics, vol. 209, no. 4, Genetics Society of America, 2018, pp. 1279–303, doi:10.1534/genetics.118.301018.","chicago":"Sachdeva, Himani, and Nicholas H Barton. “Introgression of a Block of Genome under Infinitesimal Selection.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.118.301018."},"publication":"Genetics","date_published":"2018-08-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"01","intvolume":" 209","title":"Introgression of a block of genome under infinitesimal selection","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"282","oa_version":"Submitted Version","type":"journal_article","issue":"4","abstract":[{"lang":"eng","text":"Adaptive introgression is common in nature and can be driven by selection acting on multiple, linked genes. We explore the effects of polygenic selection on introgression under the infinitesimal model with linkage. This model assumes that the introgressing block has an effectively infinite number of genes, each with an infinitesimal effect on the trait under selection. The block is assumed to introgress under directional selection within a native population that is genetically homogeneous. We use individual-based simulations and a branching process approximation to compute various statistics of the introgressing block, and explore how these depend on parameters such as the map length and initial trait value associated with the introgressing block, the genetic variability along the block, and the strength of selection. Our results show that the introgression dynamics of a block under infinitesimal selection is qualitatively different from the dynamics of neutral introgression. We also find that in the long run, surviving descendant blocks are likely to have intermediate lengths, and clarify how the length is shaped by the interplay between linkage and infinitesimal selection. Our results suggest that it may be difficult to distinguish introgression of single loci from that of genomic blocks with multiple, tightly linked and weakly selected loci."}]},{"day":"04","article_processing_charge":"No","scopus_import":"1","date_published":"2018-12-04T00:00:00Z","article_type":"original","page":"1411-1427","publication":"Genetics","citation":{"ama":"Sachdeva H, Barton NH. Replicability of introgression under linked, polygenic selection. Genetics. 2018;210(4):1411-1427. doi:10.1534/genetics.118.301429","ieee":"H. Sachdeva and N. H. Barton, “Replicability of introgression under linked, polygenic selection,” Genetics, vol. 210, no. 4. Genetics Society of America, pp. 1411–1427, 2018.","apa":"Sachdeva, H., & Barton, N. H. (2018). Replicability of introgression under linked, polygenic selection. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.118.301429","ista":"Sachdeva H, Barton NH. 2018. Replicability of introgression under linked, polygenic selection. Genetics. 210(4), 1411–1427.","short":"H. Sachdeva, N.H. Barton, Genetics 210 (2018) 1411–1427.","mla":"Sachdeva, Himani, and Nicholas H. Barton. “Replicability of Introgression under Linked, Polygenic Selection.” Genetics, vol. 210, no. 4, Genetics Society of America, 2018, pp. 1411–27, doi:10.1534/genetics.118.301429.","chicago":"Sachdeva, Himani, and Nicholas H Barton. “Replicability of Introgression under Linked, Polygenic Selection.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.118.301429."},"abstract":[{"text":"We study how a block of genome with a large number of weakly selected loci introgresses under directional selection into a genetically homogeneous population. We derive exact expressions for the expected rate of growth of any fragment of the introduced block during the initial phase of introgression, and show that the growth rate of a single-locus variant is largely insensitive to its own additive effect, but depends instead on the combined effect of all loci within a characteristic linkage scale. The expected growth rate of a fragment is highly correlated with its long-term introgression probability in populations of moderate size, and can hence identify variants that are likely to introgress across replicate populations. We clarify how the introgression probability of an individual variant is determined by the interplay between hitchhiking with relatively large fragments during the early phase of introgression and selection on fine-scale variation within these, which at longer times results in differential introgression probabilities for beneficial and deleterious loci within successful fragments. By simulating individuals, we also investigate how introgression probabilities at individual loci depend on the variance of fitness effects, the net fitness of the introduced block, and the size of the recipient population, and how this shapes the net advance under selection. Our work suggests that even highly replicable substitutions may be associated with a range of selective effects, which makes it challenging to fine map the causal loci that underlie polygenic adaptation.","lang":"eng"}],"issue":"4","type":"journal_article","oa_version":"Preprint","title":"Replicability of introgression under linked, polygenic selection","status":"public","intvolume":" 210","_id":"39","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","month":"12","publication_identifier":{"issn":["00166731"]},"language":[{"iso":"eng"}],"doi":"10.1534/genetics.118.301429","quality_controlled":"1","isi":1,"external_id":{"isi":["000452315900021"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/379578v1"}],"date_created":"2018-12-11T11:44:18Z","date_updated":"2023-09-18T08:10:29Z","volume":210,"author":[{"full_name":"Sachdeva, Himani","id":"42377A0A-F248-11E8-B48F-1D18A9856A87","last_name":"Sachdeva","first_name":"Himani"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"}],"publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Genetics Society of America","year":"2018"},{"author":[{"full_name":"Tavares, Hugo","first_name":"Hugo","last_name":"Tavares"},{"full_name":"Whitley, Annabel","last_name":"Whitley","first_name":"Annabel"},{"full_name":"Field, David","first_name":"David","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478"},{"full_name":"Bradley, Desmond","last_name":"Bradley","first_name":"Desmond"},{"full_name":"Couchman, Matthew","first_name":"Matthew","last_name":"Couchman"},{"full_name":"Copsey, Lucy","last_name":"Copsey","first_name":"Lucy"},{"last_name":"Elleouet","first_name":"Joane","full_name":"Elleouet, Joane"},{"last_name":"Burrus","first_name":"Monique","full_name":"Burrus, Monique"},{"full_name":"Andalo, Christophe","last_name":"Andalo","first_name":"Christophe"},{"full_name":"Li, Miaomiao","last_name":"Li","first_name":"Miaomiao"},{"first_name":"Qun","last_name":"Li","full_name":"Li, Qun"},{"last_name":"Xue","first_name":"Yongbiao","full_name":"Xue, Yongbiao"},{"last_name":"Rebocho","first_name":"Alexandra B","full_name":"Rebocho, Alexandra B"},{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"},{"full_name":"Coen, Enrico","last_name":"Coen","first_name":"Enrico"}],"date_created":"2018-12-11T11:44:18Z","date_updated":"2023-09-18T08:36:49Z","volume":115,"acknowledgement":" ERC Grant 201252 (to N.H.B.)","year":"2018","pmid":1,"publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"National Academy of Sciences","file_date_updated":"2020-07-14T12:46:16Z","publist_id":"8017","doi":"10.1073/pnas.1801832115","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"external_id":{"isi":["000448040500065"],"pmid":["30297406"]},"quality_controlled":"1","isi":1,"month":"10","publication_identifier":{"issn":["00278424"]},"file":[{"creator":"dernst","file_size":1911302,"content_type":"application/pdf","file_name":"11006.full.pdf","access_level":"open_access","date_created":"2018-12-17T08:44:03Z","date_updated":"2020-07-14T12:46:16Z","checksum":"d2305d0cc81dbbe4c1c677d64ad6f6d1","file_id":"5683","relation":"main_file"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"38","title":"Selection and gene flow shape genomic islands that control floral guides","status":"public","ddc":["570"],"intvolume":" 115","abstract":[{"text":"Genomes of closely-related species or populations often display localized regions of enhanced relative sequence divergence, termed genomic islands. It has been proposed that these islands arise through selective sweeps and/or barriers to gene flow. Here, we genetically dissect a genomic island that controls flower color pattern differences between two subspecies of Antirrhinum majus, A.m.striatum and A.m.pseudomajus, and relate it to clinal variation across a natural hybrid zone. We show that selective sweeps likely raised relative divergence at two tightly-linked MYB-like transcription factors, leading to distinct flower patterns in the two subspecies. The two patterns provide alternate floral guides and create a strong barrier to gene flow where populations come into contact. This barrier affects the selected flower color genes and tightlylinked loci, but does not extend outside of this domain, allowing gene flow to lower relative divergence for the rest of the chromosome. Thus, both selective sweeps and barriers to gene flow play a role in shaping genomic islands: sweeps cause elevation in relative divergence, while heterogeneous gene flow flattens the surrounding \"sea,\" making the island of divergence stand out. By showing how selective sweeps establish alternative adaptive phenotypes that lead to barriers to gene flow, our study sheds light on possible mechanisms leading to reproductive isolation and speciation.","lang":"eng"}],"issue":"43","type":"journal_article","date_published":"2018-10-23T00:00:00Z","publication":"PNAS","citation":{"apa":"Tavares, H., Whitley, A., Field, D., Bradley, D., Couchman, M., Copsey, L., … Coen, E. (2018). Selection and gene flow shape genomic islands that control floral guides. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1801832115","ieee":"H. Tavares et al., “Selection and gene flow shape genomic islands that control floral guides,” PNAS, vol. 115, no. 43. National Academy of Sciences, pp. 11006–11011, 2018.","ista":"Tavares H, Whitley A, Field D, Bradley D, Couchman M, Copsey L, Elleouet J, Burrus M, Andalo C, Li M, Li Q, Xue Y, Rebocho AB, Barton NH, Coen E. 2018. Selection and gene flow shape genomic islands that control floral guides. PNAS. 115(43), 11006–11011.","ama":"Tavares H, Whitley A, Field D, et al. Selection and gene flow shape genomic islands that control floral guides. PNAS. 2018;115(43):11006-11011. doi:10.1073/pnas.1801832115","chicago":"Tavares, Hugo, Annabel Whitley, David Field, Desmond Bradley, Matthew Couchman, Lucy Copsey, Joane Elleouet, et al. “Selection and Gene Flow Shape Genomic Islands That Control Floral Guides.” PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1801832115.","short":"H. Tavares, A. Whitley, D. Field, D. Bradley, M. Couchman, L. Copsey, J. Elleouet, M. Burrus, C. Andalo, M. Li, Q. Li, Y. Xue, A.B. Rebocho, N.H. Barton, E. Coen, PNAS 115 (2018) 11006–11011.","mla":"Tavares, Hugo, et al. “Selection and Gene Flow Shape Genomic Islands That Control Floral Guides.” PNAS, vol. 115, no. 43, National Academy of Sciences, 2018, pp. 11006–11, doi:10.1073/pnas.1801832115."},"page":"11006 - 11011","day":"23","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1"},{"date_published":"2018-12-31T00:00:00Z","citation":{"ama":"Barton NH. The consequences of an introgression event. Molecular Ecology. 2018;27(24):4973-4975. doi:10.1111/mec.14950","ista":"Barton NH. 2018. The consequences of an introgression event. Molecular Ecology. 27(24), 4973–4975.","ieee":"N. H. Barton, “The consequences of an introgression event,” Molecular Ecology, vol. 27, no. 24. Wiley, pp. 4973–4975, 2018.","apa":"Barton, N. H. (2018). The consequences of an introgression event. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.14950","mla":"Barton, Nicholas H. “The Consequences of an Introgression Event.” Molecular Ecology, vol. 27, no. 24, Wiley, 2018, pp. 4973–75, doi:10.1111/mec.14950.","short":"N.H. Barton, Molecular Ecology 27 (2018) 4973–4975.","chicago":"Barton, Nicholas H. “The Consequences of an Introgression Event.” Molecular Ecology. Wiley, 2018. https://doi.org/10.1111/mec.14950."},"publication":"Molecular Ecology","page":"4973-4975","article_type":"letter_note","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"31","scopus_import":"1","file":[{"date_updated":"2020-07-14T12:46:22Z","date_created":"2019-07-19T06:54:46Z","relation":"main_file","file_id":"6652","file_size":295452,"content_type":"application/pdf","creator":"apreinsp","access_level":"open_access","file_name":"2018_MolecularEcology_BartonNick.pdf"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"40","intvolume":" 27","title":"The consequences of an introgression event","ddc":["576"],"status":"public","issue":"24","abstract":[{"text":"Hanemaaijer et al. (Molecular Ecology, 27, 2018) describe the genetic consequences of the introgression of an insecticide resistance allele into a mosquito population. Linked alleles initially increased, but many of these later declined. It is hard to determine whether this decline was due to counter‐selection, rather than simply to chance.","lang":"eng"}],"type":"journal_article","doi":"10.1111/mec.14950","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000454600500001"],"pmid":["30599087"]},"quality_controlled":"1","isi":1,"publication_identifier":{"issn":["1365294X"]},"month":"12","related_material":{"record":[{"status":"public","relation":"research_data","id":"9805"}]},"author":[{"last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"}],"volume":27,"date_updated":"2023-09-19T10:06:08Z","date_created":"2018-12-11T11:44:18Z","pmid":1,"year":"2018","publisher":"Wiley","department":[{"_id":"NiBa"}],"publication_status":"published","publist_id":"8014","file_date_updated":"2020-07-14T12:46:22Z"},{"oa_version":"Published Version","title":"The spread of an inversion with migration and selection","status":"public","intvolume":" 208","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"565","abstract":[{"lang":"eng","text":"We re-examine the model of Kirkpatrick and Barton for the spread of an inversion into a local population. This model assumes that local selection maintains alleles at two or more loci, despite immigration of alternative alleles at these loci from another population. We show that an inversion is favored because it prevents the breakdown of linkage disequilibrium generated by migration; the selective advantage of an inversion is proportional to the amount of recombination between the loci involved, as in other cases where inversions are selected for. We derive expressions for the rate of spread of an inversion; when the loci covered by the inversion are tightly linked, these conditions deviate substantially from those proposed previously, and imply that an inversion can then have only a small advantage. "}],"issue":"1","type":"journal_article","date_published":"2018-01-01T00:00:00Z","article_type":"original","page":"377 - 382","publication":"Genetics","citation":{"apa":"Charlesworth, B., & Barton, N. H. (2018). The spread of an inversion with migration and selection. Genetics. Genetics . https://doi.org/10.1534/genetics.117.300426","ieee":"B. Charlesworth and N. H. Barton, “The spread of an inversion with migration and selection,” Genetics, vol. 208, no. 1. Genetics , pp. 377–382, 2018.","ista":"Charlesworth B, Barton NH. 2018. The spread of an inversion with migration and selection. Genetics. 208(1), 377–382.","ama":"Charlesworth B, Barton NH. The spread of an inversion with migration and selection. Genetics. 2018;208(1):377-382. doi:10.1534/genetics.117.300426","chicago":"Charlesworth, Brian, and Nicholas H Barton. “The Spread of an Inversion with Migration and Selection.” Genetics. Genetics , 2018. https://doi.org/10.1534/genetics.117.300426.","short":"B. Charlesworth, N.H. Barton, Genetics 208 (2018) 377–382.","mla":"Charlesworth, Brian, and Nicholas H. Barton. “The Spread of an Inversion with Migration and Selection.” Genetics, vol. 208, no. 1, Genetics , 2018, pp. 377–82, doi:10.1534/genetics.117.300426."},"day":"01","article_processing_charge":"No","scopus_import":"1","date_updated":"2023-09-19T10:12:31Z","date_created":"2018-12-11T11:47:12Z","volume":208,"author":[{"last_name":"Charlesworth","first_name":"Brian","full_name":"Charlesworth, Brian"},{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton"}],"publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Genetics ","year":"2018","pmid":1,"publist_id":"7249","language":[{"iso":"eng"}],"doi":"10.1534/genetics.117.300426","isi":1,"quality_controlled":"1","external_id":{"pmid":["29158424"],"isi":["000419356300025"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753870/"}],"month":"01"},{"day":"01","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2018-04-01T00:00:00Z","publication":"Genetics","citation":{"chicago":"Novembre, John, and Nicholas H Barton. “Tread Lightly Interpreting Polygenic Tests of Selection.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.118.300786.","short":"J. Novembre, N.H. Barton, Genetics 208 (2018) 1351–1355.","mla":"Novembre, John, and Nicholas H. Barton. “Tread Lightly Interpreting Polygenic Tests of Selection.” Genetics, vol. 208, no. 4, Genetics Society of America, 2018, pp. 1351–55, doi:10.1534/genetics.118.300786.","ieee":"J. Novembre and N. H. Barton, “Tread lightly interpreting polygenic tests of selection,” Genetics, vol. 208, no. 4. Genetics Society of America, pp. 1351–1355, 2018.","apa":"Novembre, J., & Barton, N. H. (2018). Tread lightly interpreting polygenic tests of selection. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.118.300786","ista":"Novembre J, Barton NH. 2018. Tread lightly interpreting polygenic tests of selection. Genetics. 208(4), 1351–1355.","ama":"Novembre J, Barton NH. Tread lightly interpreting polygenic tests of selection. Genetics. 2018;208(4):1351-1355. doi:10.1534/genetics.118.300786"},"page":"1351 - 1355","abstract":[{"lang":"eng","text":"In this issue of GENETICS, a new method for detecting natural selection on polygenic traits is developed and applied to sev- eral human examples ( Racimo et al. 2018 ). By de fi nition, many loci contribute to variation in polygenic traits, and a challenge for evolutionary ge neticists has been that these traits can evolve by small, nearly undetectable shifts in allele frequencies across each of many, typically unknown, loci. Recently, a helpful remedy has arisen. Genome-wide associ- ation studies (GWAS) have been illuminating sets of loci that can be interrogated jointly for c hanges in allele frequencies. By aggregating small signal s of change across many such loci, directional natural selection is now in principle detect- able using genetic data, even for highly polygenic traits. This is an exciting arena of progress – with these methods, tests can be made for selection associated with traits, and we can now study selection in what may be its most prevalent mode. The continuing fast pace of GWAS publications suggest there will be many more polygenic tests of selection in the near future, as every new GWAS is an opportunity for an accom- panying test of polygenic selection. However, it is important to be aware of complications th at arise in interpretation, especially given that these studies may easily be misinter- preted both in and outside the evolutionary genetics commu- nity. Here, we provide context for understanding polygenic tests and urge caution regarding how these results are inter- preted and reported upon more broadly."}],"issue":"4","type":"journal_article","pubrep_id":"1012","file":[{"date_created":"2018-12-12T10:12:40Z","date_updated":"2020-07-14T12:46:26Z","checksum":"3d838dc285df394376555b794b6a5ad1","file_id":"4958","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":500129,"file_name":"IST-2018-1012-v1+1_2018_Barton_Tread.pdf","access_level":"open_access"}],"oa_version":"Published Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"430","title":"Tread lightly interpreting polygenic tests of selection","status":"public","ddc":["576"],"intvolume":" 208","month":"04","doi":"10.1534/genetics.118.300786","language":[{"iso":"eng"}],"external_id":{"isi":["000429094400005"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","isi":1,"file_date_updated":"2020-07-14T12:46:26Z","publist_id":"7393","author":[{"full_name":"Novembre, John","last_name":"Novembre","first_name":"John"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"}],"date_created":"2018-12-11T11:46:26Z","date_updated":"2023-09-19T10:17:30Z","volume":208,"year":"2018","publication_status":"published","publisher":"Genetics Society of America","department":[{"_id":"NiBa"}]},{"language":[{"iso":"eng"}],"doi":"10.1016/j.physd.2017.10.015","quality_controlled":"1","isi":1,"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1704.08757","open_access":"1"}],"external_id":{"isi":["000437962900012"],"arxiv":["1704.08757"]},"month":"08","date_created":"2018-12-11T11:47:28Z","date_updated":"2023-09-19T10:38:34Z","volume":"376-377","author":[{"last_name":"Bodova","first_name":"Katarina","orcid":"0000-0002-7214-0171","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","full_name":"Bodova, Katarina"},{"full_name":"Haskovec, Jan","first_name":"Jan","last_name":"Haskovec"},{"full_name":"Markowich, Peter","first_name":"Peter","last_name":"Markowich"}],"publication_status":"published","publisher":"Elsevier","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"acknowledgement":"JH and PM are funded by KAUST baseline funds and grant no. 1000000193 .\r\nWe thank Nicholas Barton (IST Austria) for his useful comments and suggestions. \r\n\r\n","year":"2018","publist_id":"7198","date_published":"2018-08-01T00:00:00Z","page":"108-120","publication":"Physica D: Nonlinear Phenomena","citation":{"apa":"Bodova, K., Haskovec, J., & Markowich, P. (2018). Well posedness and maximum entropy approximation for the dynamics of quantitative traits. Physica D: Nonlinear Phenomena. Elsevier. https://doi.org/10.1016/j.physd.2017.10.015","ieee":"K. Bodova, J. Haskovec, and P. Markowich, “Well posedness and maximum entropy approximation for the dynamics of quantitative traits,” Physica D: Nonlinear Phenomena, vol. 376–377. Elsevier, pp. 108–120, 2018.","ista":"Bodova K, Haskovec J, Markowich P. 2018. Well posedness and maximum entropy approximation for the dynamics of quantitative traits. Physica D: Nonlinear Phenomena. 376–377, 108–120.","ama":"Bodova K, Haskovec J, Markowich P. Well posedness and maximum entropy approximation for the dynamics of quantitative traits. Physica D: Nonlinear Phenomena. 2018;376-377:108-120. doi:10.1016/j.physd.2017.10.015","chicago":"Bodova, Katarina, Jan Haskovec, and Peter Markowich. “Well Posedness and Maximum Entropy Approximation for the Dynamics of Quantitative Traits.” Physica D: Nonlinear Phenomena. Elsevier, 2018. https://doi.org/10.1016/j.physd.2017.10.015.","short":"K. Bodova, J. Haskovec, P. Markowich, Physica D: Nonlinear Phenomena 376–377 (2018) 108–120.","mla":"Bodova, Katarina, et al. “Well Posedness and Maximum Entropy Approximation for the Dynamics of Quantitative Traits.” Physica D: Nonlinear Phenomena, vol. 376–377, Elsevier, 2018, pp. 108–20, doi:10.1016/j.physd.2017.10.015."},"day":"01","article_processing_charge":"No","scopus_import":"1","oa_version":"Submitted Version","title":"Well posedness and maximum entropy approximation for the dynamics of quantitative traits","status":"public","_id":"607","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"lang":"eng","text":"We study the Fokker-Planck equation derived in the large system limit of the Markovian process describing the dynamics of quantitative traits. The Fokker-Planck equation is posed on a bounded domain and its transport and diffusion coefficients vanish on the domain's boundary. We first argue that, despite this degeneracy, the standard no-flux boundary condition is valid. We derive the weak formulation of the problem and prove the existence and uniqueness of its solutions by constructing the corresponding contraction semigroup on a suitable function space. Then, we prove that for the parameter regime with high enough mutation rate the problem exhibits a positive spectral gap, which implies exponential convergence to equilibrium.Next, we provide a simple derivation of the so-called Dynamic Maximum Entropy (DynMaxEnt) method for approximation of observables (moments) of the Fokker-Planck solution, which can be interpreted as a nonlinear Galerkin approximation. The limited applicability of the DynMaxEnt method inspires us to introduce its modified version that is valid for the whole range of admissible parameters. Finally, we present several numerical experiments to demonstrate the performance of both the original and modified DynMaxEnt methods. We observe that in the parameter regimes where both methods are valid, the modified one exhibits slightly better approximation properties compared to the original one."}],"type":"journal_article"},{"publication_identifier":{"issn":["2663-337X"]},"month":"02","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"language":[{"iso":"eng"}],"supervisor":[{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"}],"degree_awarded":"PhD","doi":"10.15479/AT:ISTA:th_963","publist_id":"7713","file_date_updated":"2020-07-14T12:45:23Z","department":[{"_id":"NiBa"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2018","date_updated":"2023-09-20T12:00:56Z","date_created":"2018-12-11T11:45:10Z","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"563"},{"id":"1074","status":"public","relation":"part_of_dissertation"}]},"author":[{"last_name":"Ringbauer","first_name":"Harald","orcid":"0000-0002-4884-9682","id":"417FCFF4-F248-11E8-B48F-1D18A9856A87","full_name":"Ringbauer, Harald"}],"has_accepted_license":"1","article_processing_charge":"No","day":"21","page":"146","citation":{"chicago":"Ringbauer, Harald. “Inferring Recent Demography from Spatial Genetic Structure.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_963.","short":"H. Ringbauer, Inferring Recent Demography from Spatial Genetic Structure, Institute of Science and Technology Austria, 2018.","mla":"Ringbauer, Harald. Inferring Recent Demography from Spatial Genetic Structure. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_963.","apa":"Ringbauer, H. (2018). Inferring recent demography from spatial genetic structure. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_963","ieee":"H. Ringbauer, “Inferring recent demography from spatial genetic structure,” Institute of Science and Technology Austria, 2018.","ista":"Ringbauer H. 2018. Inferring recent demography from spatial genetic structure. Institute of Science and Technology Austria.","ama":"Ringbauer H. Inferring recent demography from spatial genetic structure. 2018. doi:10.15479/AT:ISTA:th_963"},"date_published":"2018-02-21T00:00:00Z","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"This thesis is concerned with the inference of current population structure based on geo-referenced genetic data. The underlying idea is that population structure affects its spatial genetic structure. Therefore, genotype information can be utilized to estimate important demographic parameters such as migration rates. These indirect estimates of population structure have become very attractive, as genotype data is now widely available. However, there also has been much concern about these approaches. Importantly, genetic structure can be influenced by many complex patterns, which often cannot be disentangled. Moreover, many methods merely fit heuristic patterns of genetic structure, and do not build upon population genetics theory. Here, I describe two novel inference methods that address these shortcomings. In Chapter 2, I introduce an inference scheme based on a new type of signal, identity by descent (IBD) blocks. Recently, it has become feasible to detect such long blocks of genome shared between pairs of samples. These blocks are direct traces of recent coalescence events. As such, they contain ample signal for inferring recent demography. I examine sharing of IBD blocks in two-dimensional populations with local migration. Using a diffusion approximation, I derive formulas for an isolation by distance pattern of long IBD blocks and show that sharing of long IBD blocks approaches rapid exponential decay for growing sample distance. I describe an inference scheme based on these results. It can robustly estimate the dispersal rate and population density, which is demonstrated on simulated data. I also show an application to estimate mean migration and the rate of recent population growth within Eastern Europe. Chapter 3 is about a novel method to estimate barriers to gene flow in a two dimensional population. This inference scheme utilizes geographically localized allele frequency fluctuations - a classical isolation by distance signal. The strength of these local fluctuations increases on average next to a barrier, and there is less correlation across it. I again use a framework of diffusion of ancestral lineages to model this effect, and provide an efficient numerical implementation to fit the results to geo-referenced biallelic SNP data. This inference scheme is able to robustly estimate strong barriers to gene flow, as tests on simulated data confirm.","lang":"eng"}],"status":"public","title":"Inferring recent demography from spatial genetic structure","ddc":["576"],"_id":"200","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","file":[{"creator":"system","file_size":5792935,"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2018-963-v1+1_thesis.pdf","checksum":"8cc534d2b528ae017acf80874cce48c9","date_created":"2018-12-12T10:14:55Z","date_updated":"2020-07-14T12:45:23Z","file_id":"5111","relation":"main_file"},{"content_type":"application/zip","file_size":113365,"creator":"dernst","access_level":"closed","file_name":"2018_thesis_ringbauer_source.zip","checksum":"6af18d7e5a7e2728ceda2f41ee24f628","date_created":"2019-04-05T09:30:12Z","date_updated":"2020-07-14T12:45:23Z","relation":"source_file","file_id":"6224"}],"pubrep_id":"963"},{"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000440484800002"]},"isi":1,"quality_controlled":"1","doi":"10.7717/peerj.5198","language":[{"iso":"eng"}],"month":"07","year":"2018","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"publisher":"PeerJ","publication_status":"published","author":[{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075","first_name":"Christelle","last_name":"Fraisse","full_name":"Fraisse, Christelle"},{"first_name":"Camille","last_name":"Roux","full_name":"Roux, Camille"},{"full_name":"Gagnaire, Pierre","first_name":"Pierre","last_name":"Gagnaire"},{"last_name":"Romiguier","first_name":"Jonathan","full_name":"Romiguier, Jonathan"},{"full_name":"Faivre, Nicolas","last_name":"Faivre","first_name":"Nicolas"},{"first_name":"John","last_name":"Welch","full_name":"Welch, John"},{"first_name":"Nicolas","last_name":"Bierne","full_name":"Bierne, Nicolas"}],"volume":2018,"date_updated":"2023-10-17T12:25:28Z","date_created":"2018-12-11T11:44:50Z","article_number":"30083438","publist_id":"7784","file_date_updated":"2020-07-14T12:44:48Z","citation":{"mla":"Fraisse, Christelle, et al. “The Divergence History of European Blue Mussel Species Reconstructed from Approximate Bayesian Computation: The Effects of Sequencing Techniques and Sampling Strategies.” PeerJ, vol. 2018, no. 7, 30083438, PeerJ, 2018, doi:10.7717/peerj.5198.","short":"C. Fraisse, C. Roux, P. Gagnaire, J. Romiguier, N. Faivre, J. Welch, N. Bierne, PeerJ 2018 (2018).","chicago":"Fraisse, Christelle, Camille Roux, Pierre Gagnaire, Jonathan Romiguier, Nicolas Faivre, John Welch, and Nicolas Bierne. “The Divergence History of European Blue Mussel Species Reconstructed from Approximate Bayesian Computation: The Effects of Sequencing Techniques and Sampling Strategies.” PeerJ. PeerJ, 2018. https://doi.org/10.7717/peerj.5198.","ama":"Fraisse C, Roux C, Gagnaire P, et al. The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies. PeerJ. 2018;2018(7). doi:10.7717/peerj.5198","ista":"Fraisse C, Roux C, Gagnaire P, Romiguier J, Faivre N, Welch J, Bierne N. 2018. The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies. PeerJ. 2018(7), 30083438.","apa":"Fraisse, C., Roux, C., Gagnaire, P., Romiguier, J., Faivre, N., Welch, J., & Bierne, N. (2018). The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies. PeerJ. PeerJ. https://doi.org/10.7717/peerj.5198","ieee":"C. Fraisse et al., “The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies,” PeerJ, vol. 2018, no. 7. PeerJ, 2018."},"publication":"PeerJ","date_published":"2018-07-30T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"30","_id":"139","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 2018","status":"public","ddc":["576"],"title":"The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies","file":[{"checksum":"7d55ae22598a1c70759cd671600cff53","date_created":"2018-12-18T09:42:11Z","date_updated":"2020-07-14T12:44:48Z","file_id":"5739","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":1480792,"access_level":"open_access","file_name":"2018_PeerJ_Fraisse.pdf"}],"oa_version":"Published Version","type":"journal_article","issue":"7","abstract":[{"lang":"eng","text":"Genome-scale diversity data are increasingly available in a variety of biological systems, and can be used to reconstruct the past evolutionary history of species divergence. However, extracting the full demographic information from these data is not trivial, and requires inferential methods that account for the diversity of coalescent histories throughout the genome. Here, we evaluate the potential and limitations of one such approach. We reexamine a well-known system of mussel sister species, using the joint site frequency spectrum (jSFS) of synonymousmutations computed either fromexome capture or RNA-seq, in an Approximate Bayesian Computation (ABC) framework. We first assess the best sampling strategy (number of: individuals, loci, and bins in the jSFS), and show that model selection is robust to variation in the number of individuals and loci. In contrast, different binning choices when summarizing the jSFS, strongly affect the results: including classes of low and high frequency shared polymorphisms can more effectively reveal recent migration events. We then take advantage of the flexibility of ABC to compare more realistic models of speciation, including variation in migration rates through time (i.e., periodic connectivity) and across genes (i.e., genome-wide heterogeneity in migration rates). We show that these models were consistently selected as the most probable, suggesting that mussels have experienced a complex history of gene flow during divergence and that the species boundary is semi-permeable. Our work provides a comprehensive evaluation of ABC demographic inference in mussels based on the coding jSFS, and supplies guidelines for employing different sequencing techniques and sampling strategies. We emphasize, perhaps surprisingly, that inferences are less limited by the volume of data, than by the way in which they are analyzed."}]},{"article_number":"e5325","file_date_updated":"2020-07-14T12:46:06Z","publist_id":"8022","year":"2018","acknowledgement":"Johanna Bertl was supported by the Vienna Graduate School of Population Genetics (Austrian Science Fund (FWF): W1225-B20) and worked on this project while employed at the Department of Statistics and Operations Research, University of Vienna, Austria. This article was developed in the framework of the Grenoble Alpes Data Institute, which is supported by the French National Research Agency under the “Investissments d’avenir” program (ANR-15-IDEX-02).","pmid":1,"publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"PeerJ","author":[{"full_name":"Bertl, Johanna","last_name":"Bertl","first_name":"Johanna"},{"id":"417FCFF4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4884-9682","first_name":"Harald","last_name":"Ringbauer","full_name":"Ringbauer, Harald"},{"last_name":"Blum","first_name":"Michaël","full_name":"Blum, Michaël"}],"date_created":"2018-12-11T11:44:16Z","date_updated":"2023-10-17T12:24:43Z","volume":2018,"month":"10","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000447204400001"],"pmid":["30294507"]},"isi":1,"quality_controlled":"1","doi":"10.7717/peerj.5325","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Secondary contact is the reestablishment of gene flow between sister populations that have diverged. For instance, at the end of the Quaternary glaciations in Europe, secondary contact occurred during the northward expansion of the populations which had found refugia in the southern peninsulas. With the advent of multi-locus markers, secondary contact can be investigated using various molecular signatures including gradients of allele frequency, admixture clines, and local increase of genetic differentiation. We use coalescent simulations to investigate if molecular data provide enough information to distinguish between secondary contact following range expansion and an alternative evolutionary scenario consisting of a barrier to gene flow in an isolation-by-distance model. We find that an excess of linkage disequilibrium and of genetic diversity at the suture zone is a unique signature of secondary contact. We also find that the directionality index ψ, which was proposed to study range expansion, is informative to distinguish between the two hypotheses. However, although evidence for secondary contact is usually conveyed by statistics related to admixture coefficients, we find that they can be confounded by isolation-by-distance. We recommend to account for the spatial repartition of individuals when investigating secondary contact in order to better reflect the complex spatio-temporal evolution of populations and species."}],"issue":"10","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"33","ddc":["576"],"title":"Can secondary contact following range expansion be distinguished from barriers to gene flow?","status":"public","intvolume":" 2018","file":[{"date_updated":"2020-07-14T12:46:06Z","date_created":"2018-12-17T10:46:06Z","checksum":"3334886c4b39678db4c4b74299ca14ba","relation":"main_file","file_id":"5692","file_size":1328344,"content_type":"application/pdf","creator":"dernst","file_name":"2018_PeerJ_Bertl.pdf","access_level":"open_access"}],"oa_version":"Published Version","scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"No","publication":"PeerJ","citation":{"mla":"Bertl, Johanna, et al. “Can Secondary Contact Following Range Expansion Be Distinguished from Barriers to Gene Flow?” PeerJ, vol. 2018, no. 10, e5325, PeerJ, 2018, doi:10.7717/peerj.5325.","short":"J. Bertl, H. Ringbauer, M. Blum, PeerJ 2018 (2018).","chicago":"Bertl, Johanna, Harald Ringbauer, and Michaël Blum. “Can Secondary Contact Following Range Expansion Be Distinguished from Barriers to Gene Flow?” PeerJ. PeerJ, 2018. https://doi.org/10.7717/peerj.5325.","ama":"Bertl J, Ringbauer H, Blum M. Can secondary contact following range expansion be distinguished from barriers to gene flow? PeerJ. 2018;2018(10). doi:10.7717/peerj.5325","ista":"Bertl J, Ringbauer H, Blum M. 2018. Can secondary contact following range expansion be distinguished from barriers to gene flow? PeerJ. 2018(10), e5325.","ieee":"J. Bertl, H. Ringbauer, and M. Blum, “Can secondary contact following range expansion be distinguished from barriers to gene flow?,” PeerJ, vol. 2018, no. 10. PeerJ, 2018.","apa":"Bertl, J., Ringbauer, H., & Blum, M. (2018). Can secondary contact following range expansion be distinguished from barriers to gene flow? PeerJ. PeerJ. https://doi.org/10.7717/peerj.5325"},"date_published":"2018-10-01T00:00:00Z"},{"publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Wiley","year":"2018","acknowledgement":"ERC, Grant/Award Number: 250152","date_updated":"2024-02-21T13:45:00Z","date_created":"2018-12-11T11:45:37Z","volume":18,"author":[{"orcid":"0000-0002-8511-0254","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","last_name":"Ellis","first_name":"Thomas","full_name":"Ellis, Thomas"},{"full_name":"Field, David","orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field","first_name":"David"},{"last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"}],"related_material":{"record":[{"id":"5583","relation":"popular_science","status":"public"}]},"ec_funded":1,"isi":1,"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["000441753000007"]},"language":[{"iso":"eng"}],"doi":"10.1111/1755-0998.12782","month":"09","title":"Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering","status":"public","intvolume":" 18","_id":"286","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"None","type":"journal_article","abstract":[{"text":"Pedigree and sibship reconstruction are important methods in quantifying relationships and fitness of individuals in natural populations. Current methods employ a Markov chain-based algorithm to explore plausible possible pedigrees iteratively. This provides accurate results, but is time-consuming. Here, we develop a method to infer sibship and paternity relationships from half-sibling arrays of known maternity using hierarchical clustering. Given 50 or more unlinked SNP markers and empirically derived error rates, the method performs as well as the widely used package Colony, but is faster by two orders of magnitude. Using simulations, we show that the method performs well across contrasting mating scenarios, even when samples are large. We then apply the method to open-pollinated arrays of the snapdragon Antirrhinum majus and find evidence for a high degree of multiple mating. Although we focus on diploid SNP data, the method does not depend on marker type and as such has broad applications in nonmodel systems. ","lang":"eng"}],"issue":"5","page":"988 - 999","publication":"Molecular Ecology Resources","citation":{"short":"T. Ellis, D. Field, N.H. Barton, Molecular Ecology Resources 18 (2018) 988–999.","mla":"Ellis, Thomas, et al. “Efficient Inference of Paternity and Sibship Inference given Known Maternity via Hierarchical Clustering.” Molecular Ecology Resources, vol. 18, no. 5, Wiley, 2018, pp. 988–99, doi:10.1111/1755-0998.12782.","chicago":"Ellis, Thomas, David Field, and Nicholas H Barton. “Efficient Inference of Paternity and Sibship Inference given Known Maternity via Hierarchical Clustering.” Molecular Ecology Resources. Wiley, 2018. https://doi.org/10.1111/1755-0998.12782.","ama":"Ellis T, Field D, Barton NH. Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering. Molecular Ecology Resources. 2018;18(5):988-999. doi:10.1111/1755-0998.12782","apa":"Ellis, T., Field, D., & Barton, N. H. (2018). Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering. Molecular Ecology Resources. Wiley. https://doi.org/10.1111/1755-0998.12782","ieee":"T. Ellis, D. Field, and N. H. Barton, “Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering,” Molecular Ecology Resources, vol. 18, no. 5. Wiley, pp. 988–999, 2018.","ista":"Ellis T, Field D, Barton NH. 2018. Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering. Molecular Ecology Resources. 18(5), 988–999."},"date_published":"2018-09-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No"},{"datarep_id":"95","type":"research_data","abstract":[{"text":"Data and scripts are provided in support of the manuscript \"Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering\", and the associated Python package FAPS, available from www.github.com/ellisztamas/faps.\r\n\r\nSimulation scripts cover:\r\n1. Performance under different mating scenarios.\r\n2. Comparison with Colony2.\r\n3. Effect of changing the number of Monte Carlo draws\r\n\r\nThe final script covers the analysis of half-sib arrays from wild-pollinated seed in an Antirrhinum majus hybrid zone.","lang":"eng"}],"file_date_updated":"2020-07-14T12:47:07Z","_id":"5583","year":"2018","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Data and Python scripts supporting Python package FAPS","publisher":"Institute of Science and Technology Austria","department":[{"_id":"NiBa"}],"author":[{"first_name":"Thomas","last_name":"Ellis","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8511-0254","full_name":"Ellis, Thomas"}],"contributor":[{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field","first_name":"David"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"}],"related_material":{"record":[{"id":"286","relation":"research_paper","status":"public"}]},"date_created":"2018-12-12T12:31:39Z","date_updated":"2024-02-21T13:45:01Z","file":[{"creator":"system","file_size":122048,"content_type":"text/csv","file_name":"IST-2018-95-v1+1_amajus_GPS_2012.csv","access_level":"open_access","date_created":"2018-12-12T13:02:41Z","date_updated":"2020-07-14T12:47:07Z","checksum":"fc6aab51439f2622ba6df8632e66fd4f","file_id":"5606","relation":"main_file"},{"relation":"main_file","file_id":"5607","date_created":"2018-12-12T13:02:42Z","date_updated":"2020-07-14T12:47:07Z","checksum":"92347586ae4f8a6eb7c04354797bf314","file_name":"IST-2018-95-v1+2_offspring_SNPs_2012.csv","access_level":"open_access","content_type":"text/csv","file_size":235980,"creator":"system"},{"checksum":"3300813645a54e6c5c39f41917228354","date_updated":"2020-07-14T12:47:07Z","date_created":"2018-12-12T13:02:43Z","file_id":"5608","relation":"main_file","creator":"system","file_size":311712,"content_type":"text/csv","access_level":"open_access","file_name":"IST-2018-95-v1+3_parents_SNPs_2012.csv"},{"file_id":"5609","relation":"main_file","checksum":"e739fc473567fd8f39438b445fc46147","date_created":"2018-12-12T13:02:44Z","date_updated":"2020-07-14T12:47:07Z","access_level":"open_access","file_name":"IST-2018-95-v1+4_faps_scripts.zip","creator":"system","content_type":"application/zip","file_size":342090}],"oa_version":"Published Version","day":"12","month":"02","article_processing_charge":"No","has_accepted_license":"1","citation":{"ama":"Ellis T. Data and Python scripts supporting Python package FAPS. 2018. doi:10.15479/AT:ISTA:95","ista":"Ellis T. 2018. Data and Python scripts supporting Python package FAPS, Institute of Science and Technology Austria, 10.15479/AT:ISTA:95.","ieee":"T. Ellis, “Data and Python scripts supporting Python package FAPS.” Institute of Science and Technology Austria, 2018.","apa":"Ellis, T. (2018). Data and Python scripts supporting Python package FAPS. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:95","mla":"Ellis, Thomas. Data and Python Scripts Supporting Python Package FAPS. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:95.","short":"T. Ellis, (2018).","chicago":"Ellis, Thomas. “Data and Python Scripts Supporting Python Package FAPS.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:95."},"tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"oa":1,"doi":"10.15479/AT:ISTA:95","date_published":"2018-02-12T00:00:00Z"},{"doi":"10.15479/at:ista:/5757","date_published":"2018-12-19T00:00:00Z","citation":{"ista":"Fraisse C. 2018. Supplementary Files for ‘Pleiotropy modulates the efficacy of selection in Drosophila melanogaster’, Institute of Science and Technology Austria, 10.15479/at:ista:/5757.","ieee":"C. Fraisse, “Supplementary Files for ‘Pleiotropy modulates the efficacy of selection in Drosophila melanogaster.’” Institute of Science and Technology Austria, 2018.","apa":"Fraisse, C. (2018). Supplementary Files for “Pleiotropy modulates the efficacy of selection in Drosophila melanogaster.” Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:/5757","ama":"Fraisse C. Supplementary Files for “Pleiotropy modulates the efficacy of selection in Drosophila melanogaster.” 2018. doi:10.15479/at:ista:/5757","chicago":"Fraisse, Christelle. “Supplementary Files for ‘Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.’” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/at:ista:/5757.","mla":"Fraisse, Christelle. Supplementary Files for “Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.” Institute of Science and Technology Austria, 2018, doi:10.15479/at:ista:/5757.","short":"C. Fraisse, (2018)."},"oa":1,"project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"article_processing_charge":"No","has_accepted_license":"1","month":"12","day":"19","keyword":["(mal)adaptation","pleiotropy","selective constraint","evo-devo","gene expression","Drosophila melanogaster"],"contributor":[{"first_name":"Christelle","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Puixeu Sala","first_name":"Gemma","id":"33AB266C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306"}],"related_material":{"record":[{"id":"6089","status":"public","relation":"research_paper"}]},"author":[{"full_name":"Fraisse, Christelle","orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse","first_name":"Christelle"}],"file":[{"checksum":"aed7ee9ca3f4dc07d8a66945f68e13cd","date_created":"2018-12-19T14:19:52Z","date_updated":"2020-07-14T12:47:11Z","relation":"main_file","file_id":"5758","file_size":369837892,"content_type":"application/zip","creator":"cfraisse","access_level":"open_access","file_name":"FileS1.zip"},{"checksum":"3592e467b4d8206650860b612d6e12f3","date_created":"2018-12-19T14:19:49Z","date_updated":"2020-07-14T12:47:11Z","relation":"main_file","file_id":"5759","file_size":84856909,"content_type":"application/zip","creator":"cfraisse","access_level":"open_access","file_name":"FileS2.zip"},{"access_level":"open_access","file_name":"FileS3.txt","creator":"cfraisse","content_type":"text/plain","file_size":881133,"file_id":"5760","relation":"main_file","checksum":"c37ac5d5437c457338afc128c1240655","date_created":"2018-12-19T14:19:49Z","date_updated":"2020-07-14T12:47:11Z"},{"file_name":"FileS4.txt","access_level":"open_access","content_type":"text/plain","file_size":883742,"creator":"cfraisse","relation":"main_file","file_id":"5761","date_created":"2018-12-19T14:19:49Z","date_updated":"2020-07-14T12:47:11Z","checksum":"943dfd14da61817441e33e3e3cb8cdb9"},{"file_name":"FileS5.txt","access_level":"open_access","file_size":2495437,"content_type":"text/plain","creator":"cfraisse","relation":"main_file","file_id":"5762","date_updated":"2020-07-14T12:47:11Z","date_created":"2018-12-19T14:19:49Z","checksum":"1c669b6c4690ec1bbca3e2da9f566d17"},{"file_name":"FileS6.txt","access_level":"open_access","file_size":15913457,"content_type":"text/plain","creator":"cfraisse","relation":"main_file","file_id":"5763","date_updated":"2020-07-14T12:47:11Z","date_created":"2018-12-19T14:19:50Z","checksum":"f40f661b987ca6fb6b47f650cbbb04e6"},{"access_level":"open_access","file_name":"FileS7.txt","file_size":2584120,"content_type":"text/plain","creator":"cfraisse","relation":"main_file","file_id":"5764","checksum":"25f41e5b8a075669c6c88d4c6713bf6f","date_created":"2018-12-19T14:19:50Z","date_updated":"2020-07-14T12:47:11Z"},{"checksum":"f6c0bd3e63e14ddf5445bd69b43a9152","date_updated":"2020-07-14T12:47:11Z","date_created":"2018-12-19T14:19:50Z","relation":"main_file","file_id":"5765","file_size":2446059,"content_type":"text/plain","creator":"cfraisse","access_level":"open_access","file_name":"FileS8.txt"},{"file_name":"FileS9.txt","access_level":"open_access","file_size":100737,"content_type":"text/plain","creator":"cfraisse","relation":"main_file","file_id":"5766","date_updated":"2020-07-14T12:47:11Z","date_created":"2018-12-19T14:19:50Z","checksum":"0fe7a58a030b11bf3b9c8ff7a7addcae"}],"oa_version":"Published Version","date_created":"2018-12-19T14:22:35Z","date_updated":"2024-02-21T13:59:18Z","_id":"5757","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2018","publisher":"Institute of Science and Technology Austria","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"status":"public","ddc":["576"],"title":"Supplementary Files for \"Pleiotropy modulates the efficacy of selection in Drosophila melanogaster\"","ec_funded":1,"file_date_updated":"2020-07-14T12:47:11Z","abstract":[{"text":"File S1. Variant Calling Format file of the ingroup: 197 haploid sequences of D. melanogaster from Zambia (Africa) aligned to the D. melanogaster 5.57 reference genome.\r\n\r\nFile S2. Variant Calling Format file of the outgroup: 1 haploid sequence of D. simulans aligned to the D. melanogaster 5.57 reference genome.\r\n\r\nFile S3. Annotations of each transcript in coding regions with SNPeff: Ps (# of synonymous polymorphic sites); Pn (# of non-synonymous polymorphic sites); Ds (# of synonymous divergent sites); Dn (# of non-synonymous divergent sites); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S4. Annotations of each transcript in non-coding regions with SNPeff: Ps (# of synonymous polymorphic sites); Pu (# of UTR polymorphic sites); Ds (# of synonymous divergent sites); Du (# of UTR divergent sites); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S5. Annotations of each transcript in coding regions with SNPGenie: Ps (# of synonymous polymorphic sites); πs (synonymous diversity); Ss_p (total # of synonymous sites in the polymorphism data); Pn (# of non-synonymous polymorphic sites); πn (non-synonymous diversity); Sn_p (total # of non-synonymous sites in the polymorphism data); Ds (# of synonymous divergent sites); ks (synonymous evolutionary rate); Ss_d (total # of synonymous sites in the divergence data); Dn (# of non-synonymous divergent sites); kn (non-synonymous evolutionary rate); Sn_d (total # of non-\r\nsynonymous sites in the divergence data); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S6. Gene expression values (RPKM summed over all transcripts) for each sample. Values were quantile-normalized across all samples.\r\n\r\nFile S7. Final dataset with all covariates, ⍺ MK , ωA MK and DoS for coding sites, excluding variants below 5% frequency.\r\n\r\nFile S8. Final dataset with all covariates, ⍺ MK , ωA MK and DoS for non-coding sites, excluding variants below 5%\r\nfrequency.\r\n\r\nFile S9. Final dataset with all covariates, ⍺ EWK , ωA EWK and deleterious SFS for coding sites obtained with the Eyre-Walker and Keightley method on binned data and using all variants.","lang":"eng"}],"type":"research_data"},{"date_published":"2017-01-12T00:00:00Z","doi":"10.1145/3040718.3040729","conference":{"end_date":"2017-01-15","location":"Copenhagen, Denmark","start_date":"2017-01-12","name":"FOGA: Foundations of Genetic Algorithms"},"language":[{"iso":"eng"}],"citation":{"mla":"Paixao, Tiago, and Jorge Pérez Heredia. “An Application of Stochastic Differential Equations to Evolutionary Algorithms.” Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms, ACM, 2017, pp. 3–11, doi:10.1145/3040718.3040729.","short":"T. Paixao, J. Pérez Heredia, in:, Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms, ACM, 2017, pp. 3–11.","chicago":"Paixao, Tiago, and Jorge Pérez Heredia. “An Application of Stochastic Differential Equations to Evolutionary Algorithms.” In Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms, 3–11. ACM, 2017. https://doi.org/10.1145/3040718.3040729.","ama":"Paixao T, Pérez Heredia J. An application of stochastic differential equations to evolutionary algorithms. In: Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms. ACM; 2017:3-11. doi:10.1145/3040718.3040729","ista":"Paixao T, Pérez Heredia J. 2017. An application of stochastic differential equations to evolutionary algorithms. Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms. FOGA: Foundations of Genetic Algorithms, 3–11.","ieee":"T. Paixao and J. Pérez Heredia, “An application of stochastic differential equations to evolutionary algorithms,” in Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms, Copenhagen, Denmark, 2017, pp. 3–11.","apa":"Paixao, T., & Pérez Heredia, J. (2017). An application of stochastic differential equations to evolutionary algorithms. In Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms (pp. 3–11). Copenhagen, Denmark: ACM. https://doi.org/10.1145/3040718.3040729"},"publication":"Proceedings of the 14th ACM/SIGEVO Conference on Foundations of Genetic Algorithms","page":"3 - 11","quality_controlled":"1","publication_identifier":{"isbn":["978-145034651-1"]},"day":"12","month":"01","scopus_import":1,"author":[{"id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2361-3953","first_name":"Tiago","last_name":"Paixao","full_name":"Paixao, Tiago"},{"full_name":"Pérez Heredia, Jorge","first_name":"Jorge","last_name":"Pérez Heredia"}],"oa_version":"None","date_created":"2018-12-11T11:50:12Z","date_updated":"2021-01-12T06:48:22Z","year":"2017","_id":"1112","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"NiBa"}],"publisher":"ACM","title":"An application of stochastic differential equations to evolutionary algorithms","publication_status":"published","status":"public","publist_id":"6255","abstract":[{"text":"There has been renewed interest in modelling the behaviour of evolutionary algorithms by more traditional mathematical objects, such as ordinary differential equations or Markov chains. The advantage is that the analysis becomes greatly facilitated due to the existence of well established methods. However, this typically comes at the cost of disregarding information about the process. Here, we introduce the use of stochastic differential equations (SDEs) for the study of EAs. SDEs can produce simple analytical results for the dynamics of stochastic processes, unlike Markov chains which can produce rigorous but unwieldy expressions about the dynamics. On the other hand, unlike ordinary differential equations (ODEs), they do not discard information about the stochasticity of the process. We show that these are especially suitable for the analysis of fixed budget scenarios and present analogs of the additive and multiplicative drift theorems for SDEs. We exemplify the use of these methods for two model algorithms ((1+1) EA and RLS) on two canonical problems(OneMax and LeadingOnes).","lang":"eng"}],"type":"conference"},{"language":[{"iso":"eng"}],"doi":"10.1007/s11538-016-0244-3","project":[{"name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","call_identifier":"FP7","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","grant_number":"618091"},{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1607.00944"}],"oa":1,"month":"03","volume":79,"date_updated":"2021-01-12T06:48:58Z","date_created":"2018-12-11T11:50:38Z","author":[{"last_name":"Kollár","first_name":"Richard","full_name":"Kollár, Richard"},{"full_name":"Novak, Sebastian","last_name":"Novak","first_name":"Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"NiBa"}],"publisher":"Springer","publication_status":"published","year":"2017","acknowledgement":"We thank Nick Barton, Katarína Bod’ová, and Sr\r\n-\r\ndan Sarikas for constructive feed-\r\nback and support. Furthermore, we would like to express our deep gratitude to the anonymous referees (one\r\nof whom, Jimmy Garnier, agreed to reveal his identity) and the editor Max Souza, for very helpful and\r\ndetailed comments and suggestions that significantly helped us to improve the manuscript. This project has\r\nreceived funding from the European Union’s Seventh Framework Programme for research, technological\r\ndevelopment and demonstration under Grant Agreement 618091 Speed of Adaptation in Population Genet-\r\nics and Evolutionary Computation (SAGE) and the European Research Council (ERC) Grant No. 250152\r\n(SN), from the Scientific Grant Agency of the Slovak Republic under the Grant 1/0459/13 and by the Slovak\r\nResearch and Development Agency under the Contract No. APVV-14-0378 (RK). RK would also like to\r\nthank IST Austria for its hospitality during the work on this project.","publist_id":"6160","ec_funded":1,"date_published":"2017-03-01T00:00:00Z","page":"525-559","citation":{"ieee":"R. Kollár and S. Novak, “Existence of traveling waves for the generalized F–KPP equation,” Bulletin of Mathematical Biology, vol. 79, no. 3. Springer, pp. 525–559, 2017.","apa":"Kollár, R., & Novak, S. (2017). Existence of traveling waves for the generalized F–KPP equation. Bulletin of Mathematical Biology. Springer. https://doi.org/10.1007/s11538-016-0244-3","ista":"Kollár R, Novak S. 2017. Existence of traveling waves for the generalized F–KPP equation. Bulletin of Mathematical Biology. 79(3), 525–559.","ama":"Kollár R, Novak S. Existence of traveling waves for the generalized F–KPP equation. Bulletin of Mathematical Biology. 2017;79(3):525-559. doi:10.1007/s11538-016-0244-3","chicago":"Kollár, Richard, and Sebastian Novak. “Existence of Traveling Waves for the Generalized F–KPP Equation.” Bulletin of Mathematical Biology. Springer, 2017. https://doi.org/10.1007/s11538-016-0244-3.","short":"R. Kollár, S. Novak, Bulletin of Mathematical Biology 79 (2017) 525–559.","mla":"Kollár, Richard, and Sebastian Novak. “Existence of Traveling Waves for the Generalized F–KPP Equation.” Bulletin of Mathematical Biology, vol. 79, no. 3, Springer, 2017, pp. 525–59, doi:10.1007/s11538-016-0244-3."},"publication":"Bulletin of Mathematical Biology","day":"01","scopus_import":1,"oa_version":"Preprint","intvolume":" 79","status":"public","title":"Existence of traveling waves for the generalized F–KPP equation","_id":"1191","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","issue":"3","abstract":[{"lang":"eng","text":"Variation in genotypes may be responsible for differences in dispersal rates, directional biases, and growth rates of individuals. These traits may favor certain genotypes and enhance their spatiotemporal spreading into areas occupied by the less advantageous genotypes. We study how these factors influence the speed of spreading in the case of two competing genotypes under the assumption that spatial variation of the total population is small compared to the spatial variation of the frequencies of the genotypes in the population. In that case, the dynamics of the frequency of one of the genotypes is approximately described by a generalized Fisher–Kolmogorov–Petrovskii–Piskunov (F–KPP) equation. This generalized F–KPP equation with (nonlinear) frequency-dependent diffusion and advection terms admits traveling wave solutions that characterize the invasion of the dominant genotype. Our existence results generalize the classical theory for traveling waves for the F–KPP with constant coefficients. Moreover, in the particular case of the quadratic (monostable) nonlinear growth–decay rate in the generalized F–KPP we study in detail the influence of the variance in diffusion and mean displacement rates of the two genotypes on the minimal wave propagation speed."}],"type":"journal_article"},{"date_updated":"2021-01-12T08:03:15Z","date_created":"2018-12-11T11:47:14Z","volume":6,"author":[{"full_name":"Lagator, Mato","id":"345D25EC-F248-11E8-B48F-1D18A9856A87","last_name":"Lagator","first_name":"Mato"},{"full_name":"Sarikas, Srdjan","last_name":"Sarikas","first_name":"Srdjan","id":"35F0286E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Acar, Hande","id":"2DDF136A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1986-9753","first_name":"Hande","last_name":"Acar"},{"first_name":"Jonathan P","last_name":"Bollback","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4624-4612","full_name":"Bollback, Jonathan P"},{"last_name":"Guet","first_name":"Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C"}],"publication_status":"published","department":[{"_id":"CaGu"},{"_id":"JoBo"},{"_id":"NiBa"}],"publisher":"eLife Sciences Publications","year":"2017","file_date_updated":"2020-07-14T12:47:10Z","publist_id":"7244","ec_funded":1,"article_number":"e28921","language":[{"iso":"eng"}],"doi":"10.7554/eLife.28921","quality_controlled":"1","project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"name":"Selective Barriers to Horizontal Gene Transfer","call_identifier":"H2020","_id":"2578D616-B435-11E9-9278-68D0E5697425","grant_number":"648440"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"month":"11","publication_identifier":{"issn":["2050084X"]},"file":[{"file_name":"IST-2017-918-v1+1_elife-28921-figures-v3.pdf","access_level":"open_access","creator":"system","file_size":8453470,"content_type":"application/pdf","file_id":"5096","relation":"main_file","date_created":"2018-12-12T10:14:42Z","date_updated":"2020-07-14T12:47:10Z","checksum":"273ab17f33305e4eaafd911ff88e7c5b"},{"file_name":"IST-2017-918-v1+2_elife-28921-v3.pdf","access_level":"open_access","file_size":1953221,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"5097","date_created":"2018-12-12T10:14:43Z","date_updated":"2020-07-14T12:47:10Z","checksum":"b433f90576c7be597cd43367946f8e7f"}],"oa_version":"Published Version","pubrep_id":"918","ddc":["576"],"title":"Regulatory network structure determines patterns of intermolecular epistasis","status":"public","intvolume":" 6","_id":"570","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Most phenotypes are determined by molecular systems composed of specifically interacting molecules. However, unlike for individual components, little is known about the distributions of mutational effects of molecular systems as a whole. We ask how the distribution of mutational effects of a transcriptional regulatory system differs from the distributions of its components, by first independently, and then simultaneously, mutating a transcription factor and the associated promoter it represses. We find that the system distribution exhibits increased phenotypic variation compared to individual component distributions - an effect arising from intermolecular epistasis between the transcription factor and its DNA-binding site. In large part, this epistasis can be qualitatively attributed to the structure of the transcriptional regulatory system and could therefore be a common feature in prokaryotes. Counter-intuitively, intermolecular epistasis can alleviate the constraints of individual components, thereby increasing phenotypic variation that selection could act on and facilitating adaptive evolution. "}],"type":"journal_article","date_published":"2017-11-13T00:00:00Z","publication":"eLife","citation":{"chicago":"Lagator, Mato, Srdjan Sarikas, Hande Acar, Jonathan P Bollback, and Calin C Guet. “Regulatory Network Structure Determines Patterns of Intermolecular Epistasis.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/eLife.28921.","mla":"Lagator, Mato, et al. “Regulatory Network Structure Determines Patterns of Intermolecular Epistasis.” ELife, vol. 6, e28921, eLife Sciences Publications, 2017, doi:10.7554/eLife.28921.","short":"M. Lagator, S. Sarikas, H. Acar, J.P. Bollback, C.C. Guet, ELife 6 (2017).","ista":"Lagator M, Sarikas S, Acar H, Bollback JP, Guet CC. 2017. Regulatory network structure determines patterns of intermolecular epistasis. eLife. 6, e28921.","ieee":"M. Lagator, S. Sarikas, H. Acar, J. P. Bollback, and C. C. Guet, “Regulatory network structure determines patterns of intermolecular epistasis,” eLife, vol. 6. eLife Sciences Publications, 2017.","apa":"Lagator, M., Sarikas, S., Acar, H., Bollback, J. P., & Guet, C. C. (2017). Regulatory network structure determines patterns of intermolecular epistasis. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.28921","ama":"Lagator M, Sarikas S, Acar H, Bollback JP, Guet CC. Regulatory network structure determines patterns of intermolecular epistasis. eLife. 2017;6. doi:10.7554/eLife.28921"},"day":"13","has_accepted_license":"1","scopus_import":1},{"scopus_import":1,"publication_identifier":{"issn":["00368075"]},"day":"17","month":"11","page":"925 - 928","quality_controlled":"1","citation":{"ama":"Bradley D, Xu P, Mohorianu I, et al. Evolution of flower color pattern through selection on regulatory small RNAs. Science. 2017;358(6365):925-928. doi:10.1126/science.aao3526","ista":"Bradley D, Xu P, Mohorianu I, Whibley A, Field D, Tavares H, Couchman M, Copsey L, Carpenter R, Li M, Li Q, Xue Y, Dalmay T, Coen E. 2017. Evolution of flower color pattern through selection on regulatory small RNAs. Science. 358(6365), 925–928.","apa":"Bradley, D., Xu, P., Mohorianu, I., Whibley, A., Field, D., Tavares, H., … Coen, E. (2017). Evolution of flower color pattern through selection on regulatory small RNAs. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aao3526","ieee":"D. Bradley et al., “Evolution of flower color pattern through selection on regulatory small RNAs,” Science, vol. 358, no. 6365. American Association for the Advancement of Science, pp. 925–928, 2017.","mla":"Bradley, Desmond, et al. “Evolution of Flower Color Pattern through Selection on Regulatory Small RNAs.” Science, vol. 358, no. 6365, American Association for the Advancement of Science, 2017, pp. 925–28, doi:10.1126/science.aao3526.","short":"D. Bradley, P. Xu, I. Mohorianu, A. Whibley, D. Field, H. Tavares, M. Couchman, L. Copsey, R. Carpenter, M. Li, Q. Li, Y. Xue, T. Dalmay, E. Coen, Science 358 (2017) 925–928.","chicago":"Bradley, Desmond, Ping Xu, Irina Mohorianu, Annabel Whibley, David Field, Hugo Tavares, Matthew Couchman, et al. “Evolution of Flower Color Pattern through Selection on Regulatory Small RNAs.” Science. American Association for the Advancement of Science, 2017. https://doi.org/10.1126/science.aao3526."},"publication":"Science","language":[{"iso":"eng"}],"date_published":"2017-11-17T00:00:00Z","doi":"10.1126/science.aao3526","type":"journal_article","issue":"6365","publist_id":"7193","abstract":[{"text":"Small RNAs (sRNAs) regulate genes in plants and animals. Here, we show that population-wide differences in color patterns in snapdragon flowers are caused by an inverted duplication that generates sRNAs. The complexity and size of the transcripts indicate that the duplication represents an intermediate on the pathway to microRNA evolution. The sRNAs repress a pigment biosynthesis gene, creating a yellow highlight at the site of pollinator entry. The inverted duplication exhibits steep clines in allele frequency in a natural hybrid zone, showing that the allele is under selection. Thus, regulatory interactions of evolutionarily recent sRNAs can be acted upon by selection and contribute to the evolution of phenotypic diversity.","lang":"eng"}],"publisher":"American Association for the Advancement of Science","department":[{"_id":"NiBa"}],"intvolume":" 358","title":"Evolution of flower color pattern through selection on regulatory small RNAs","publication_status":"published","status":"public","_id":"611","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2017","volume":358,"oa_version":"None","date_created":"2018-12-11T11:47:29Z","date_updated":"2021-01-12T08:06:10Z","author":[{"first_name":"Desmond","last_name":"Bradley","full_name":"Bradley, Desmond"},{"full_name":"Xu, Ping","first_name":"Ping","last_name":"Xu"},{"last_name":"Mohorianu","first_name":"Irina","full_name":"Mohorianu, Irina"},{"last_name":"Whibley","first_name":"Annabel","full_name":"Whibley, Annabel"},{"full_name":"Field, David","last_name":"Field","first_name":"David","orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tavares, Hugo","last_name":"Tavares","first_name":"Hugo"},{"last_name":"Couchman","first_name":"Matthew","full_name":"Couchman, Matthew"},{"full_name":"Copsey, Lucy","first_name":"Lucy","last_name":"Copsey"},{"first_name":"Rosemary","last_name":"Carpenter","full_name":"Carpenter, Rosemary"},{"full_name":"Li, Miaomiao","first_name":"Miaomiao","last_name":"Li"},{"last_name":"Li","first_name":"Qun","full_name":"Li, Qun"},{"last_name":"Xue","first_name":"Yongbiao","full_name":"Xue, Yongbiao"},{"full_name":"Dalmay, Tamas","last_name":"Dalmay","first_name":"Tamas"},{"last_name":"Coen","first_name":"Enrico","full_name":"Coen, Enrico"}]},{"publication":"Theoretical Population Biology","citation":{"ista":"Barton NH, Etheridge A, Véber A. 2017. The infinitesimal model: Definition derivation and implications. Theoretical Population Biology. 118, 50–73.","apa":"Barton, N. H., Etheridge, A., & Véber, A. (2017). The infinitesimal model: Definition derivation and implications. Theoretical Population Biology. Academic Press. https://doi.org/10.1016/j.tpb.2017.06.001","ieee":"N. H. Barton, A. Etheridge, and A. Véber, “The infinitesimal model: Definition derivation and implications,” Theoretical Population Biology, vol. 118. Academic Press, pp. 50–73, 2017.","ama":"Barton NH, Etheridge A, Véber A. The infinitesimal model: Definition derivation and implications. Theoretical Population Biology. 2017;118:50-73. doi:10.1016/j.tpb.2017.06.001","chicago":"Barton, Nicholas H, Alison Etheridge, and Amandine Véber. “The Infinitesimal Model: Definition Derivation and Implications.” Theoretical Population Biology. Academic Press, 2017. https://doi.org/10.1016/j.tpb.2017.06.001.","mla":"Barton, Nicholas H., et al. “The Infinitesimal Model: Definition Derivation and Implications.” Theoretical Population Biology, vol. 118, Academic Press, 2017, pp. 50–73, doi:10.1016/j.tpb.2017.06.001.","short":"N.H. Barton, A. Etheridge, A. Véber, Theoretical Population Biology 118 (2017) 50–73."},"page":"50 - 73","date_published":"2017-12-01T00:00:00Z","scopus_import":1,"day":"01","has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"626","ddc":["576"],"title":"The infinitesimal model: Definition derivation and implications","status":"public","intvolume":" 118","pubrep_id":"908","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"IST-2017-908-v1+1_1-s2.0-S0040580917300886-main_1_.pdf","creator":"system","content_type":"application/pdf","file_size":1133924,"file_id":"4964","relation":"main_file","checksum":"7dd02bfcfe8f244f4a6c19091aedf2c8","date_updated":"2020-07-14T12:47:25Z","date_created":"2018-12-12T10:12:45Z"}],"type":"journal_article","abstract":[{"text":"Our focus here is on the infinitesimal model. In this model, one or several quantitative traits are described as the sum of a genetic and a non-genetic component, the first being distributed within families as a normal random variable centred at the average of the parental genetic components, and with a variance independent of the parental traits. Thus, the variance that segregates within families is not perturbed by selection, and can be predicted from the variance components. This does not necessarily imply that the trait distribution across the whole population should be Gaussian, and indeed selection or population structure may have a substantial effect on the overall trait distribution. One of our main aims is to identify some general conditions on the allelic effects for the infinitesimal model to be accurate. We first review the long history of the infinitesimal model in quantitative genetics. Then we formulate the model at the phenotypic level in terms of individual trait values and relationships between individuals, but including different evolutionary processes: genetic drift, recombination, selection, mutation, population structure, …. We give a range of examples of its application to evolutionary questions related to stabilising selection, assortative mating, effective population size and response to selection, habitat preference and speciation. We provide a mathematical justification of the model as the limit as the number M of underlying loci tends to infinity of a model with Mendelian inheritance, mutation and environmental noise, when the genetic component of the trait is purely additive. We also show how the model generalises to include epistatic effects. We prove in particular that, within each family, the genetic components of the individual trait values in the current generation are indeed normally distributed with a variance independent of ancestral traits, up to an error of order 1∕M. Simulations suggest that in some cases the convergence may be as fast as 1∕M.","lang":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","project":[{"name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152"}],"doi":"10.1016/j.tpb.2017.06.001","language":[{"iso":"eng"}],"month":"12","publication_identifier":{"issn":["00405809"]},"year":"2017","publication_status":"published","publisher":"Academic Press","department":[{"_id":"NiBa"}],"author":[{"full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Etheridge, Alison","first_name":"Alison","last_name":"Etheridge"},{"full_name":"Véber, Amandine","first_name":"Amandine","last_name":"Véber"}],"date_created":"2018-12-11T11:47:34Z","date_updated":"2021-01-12T08:06:50Z","volume":118,"file_date_updated":"2020-07-14T12:47:25Z","ec_funded":1,"publist_id":"7169"},{"citation":{"ieee":"M. Lukacisinova, S. Novak, and T. Paixao, “Modelling and simulation details.” Public Library of Science, 2017.","apa":"Lukacisinova, M., Novak, S., & Paixao, T. (2017). Modelling and simulation details. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005609.s001","ista":"Lukacisinova M, Novak S, Paixao T. 2017. Modelling and simulation details, Public Library of Science, 10.1371/journal.pcbi.1005609.s001.","ama":"Lukacisinova M, Novak S, Paixao T. Modelling and simulation details. 2017. doi:10.1371/journal.pcbi.1005609.s001","chicago":"Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Modelling and Simulation Details.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005609.s001.","short":"M. Lukacisinova, S. Novak, T. Paixao, (2017).","mla":"Lukacisinova, Marta, et al. Modelling and Simulation Details. Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005609.s001."},"doi":"10.1371/journal.pcbi.1005609.s001","date_published":"2017-07-18T00:00:00Z","day":"18","month":"07","article_processing_charge":"No","_id":"9849","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2017","title":"Modelling and simulation details","status":"public","department":[{"_id":"ToBo"},{"_id":"NiBa"},{"_id":"CaGu"}],"publisher":"Public Library of Science","author":[{"full_name":"Lukacisinova, Marta","last_name":"Lukacisinova","first_name":"Marta","orcid":"0000-0002-2519-8004","id":"4342E402-F248-11E8-B48F-1D18A9856A87"},{"id":"461468AE-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian","last_name":"Novak","full_name":"Novak, Sebastian"},{"orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","last_name":"Paixao","first_name":"Tiago","full_name":"Paixao, Tiago"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"696"}]},"date_updated":"2023-02-23T12:55:39Z","date_created":"2021-08-09T14:02:34Z","oa_version":"Published Version","type":"research_data_reference","abstract":[{"text":"This text provides additional information about the model, a derivation of the analytic results in Eq (4), and details about simulations of an additional parameter set.","lang":"eng"}]},{"citation":{"mla":"Lukacisinova, Marta, et al. Extensions of the Model. Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005609.s002.","short":"M. Lukacisinova, S. Novak, T. Paixao, (2017).","chicago":"Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Extensions of the Model.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005609.s002.","ama":"Lukacisinova M, Novak S, Paixao T. Extensions of the model. 2017. doi:10.1371/journal.pcbi.1005609.s002","ista":"Lukacisinova M, Novak S, Paixao T. 2017. Extensions of the model, Public Library of Science, 10.1371/journal.pcbi.1005609.s002.","apa":"Lukacisinova, M., Novak, S., & Paixao, T. (2017). Extensions of the model. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005609.s002","ieee":"M. Lukacisinova, S. Novak, and T. Paixao, “Extensions of the model.” Public Library of Science, 2017."},"date_published":"2017-07-18T00:00:00Z","doi":"10.1371/journal.pcbi.1005609.s002","article_processing_charge":"No","day":"18","month":"07","department":[{"_id":"ToBo"},{"_id":"CaGu"},{"_id":"NiBa"}],"publisher":"Public Library of Science","title":"Extensions of the model","status":"public","year":"2017","_id":"9850","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa_version":"Published Version","date_created":"2021-08-09T14:05:24Z","date_updated":"2023-02-23T12:55:39Z","related_material":{"record":[{"id":"696","status":"public","relation":"used_in_publication"}]},"author":[{"full_name":"Lukacisinova, Marta","id":"4342E402-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2519-8004","first_name":"Marta","last_name":"Lukacisinova"},{"last_name":"Novak","first_name":"Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87","full_name":"Novak, Sebastian"},{"full_name":"Paixao, Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2361-3953","first_name":"Tiago","last_name":"Paixao"}],"type":"research_data_reference","abstract":[{"lang":"eng","text":"In this text, we discuss how a cost of resistance and the possibility of lethal mutations impact our model."}]},{"doi":"10.1371/journal.pcbi.1005609.s003","date_published":"2017-07-18T00:00:00Z","citation":{"chicago":"Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Heuristic Prediction for Multiple Stresses.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005609.s003.","short":"M. Lukacisinova, S. Novak, T. Paixao, (2017).","mla":"Lukacisinova, Marta, et al. Heuristic Prediction for Multiple Stresses. Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005609.s003.","ieee":"M. Lukacisinova, S. Novak, and T. Paixao, “Heuristic prediction for multiple stresses.” Public Library of Science, 2017.","apa":"Lukacisinova, M., Novak, S., & Paixao, T. (2017). Heuristic prediction for multiple stresses. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005609.s003","ista":"Lukacisinova M, Novak S, Paixao T. 2017. Heuristic prediction for multiple stresses, Public Library of Science, 10.1371/journal.pcbi.1005609.s003.","ama":"Lukacisinova M, Novak S, Paixao T. Heuristic prediction for multiple stresses. 2017. doi:10.1371/journal.pcbi.1005609.s003"},"day":"18","month":"07","article_processing_charge":"No","date_updated":"2023-02-23T12:55:39Z","date_created":"2021-08-09T14:08:14Z","oa_version":"Published Version","author":[{"id":"4342E402-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2519-8004","first_name":"Marta","last_name":"Lukacisinova","full_name":"Lukacisinova, Marta"},{"full_name":"Novak, Sebastian","last_name":"Novak","first_name":"Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Paixao, Tiago","last_name":"Paixao","first_name":"Tiago","orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"696"}]},"status":"public","title":"Heuristic prediction for multiple stresses","department":[{"_id":"ToBo"},{"_id":"CaGu"},{"_id":"NiBa"}],"publisher":"Public Library of Science","_id":"9851","year":"2017","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","abstract":[{"lang":"eng","text":"Based on the intuitive derivation of the dynamics of SIM allele frequency pM in the main text, we present a heuristic prediction for the long-term SIM allele frequencies with χ > 1 stresses and compare it to numerical simulations."}],"type":"research_data_reference"},{"type":"research_data_reference","abstract":[{"text":"We show how different combination strategies affect the fraction of individuals that are multi-resistant.","lang":"eng"}],"status":"public","title":"Resistance frequencies for different combination strategies","publisher":"Public Library of Science","department":[{"_id":"ToBo"},{"_id":"CaGu"},{"_id":"NiBa"}],"year":"2017","_id":"9852","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-02-23T12:55:39Z","date_created":"2021-08-09T14:11:40Z","oa_version":"Published Version","author":[{"full_name":"Lukacisinova, Marta","id":"4342E402-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2519-8004","first_name":"Marta","last_name":"Lukacisinova"},{"first_name":"Sebastian","last_name":"Novak","id":"461468AE-F248-11E8-B48F-1D18A9856A87","full_name":"Novak, Sebastian"},{"first_name":"Tiago","last_name":"Paixao","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2361-3953","full_name":"Paixao, Tiago"}],"related_material":{"record":[{"id":"696","relation":"used_in_publication","status":"public"}]},"day":"18","month":"07","article_processing_charge":"No","citation":{"mla":"Lukacisinova, Marta, et al. Resistance Frequencies for Different Combination Strategies. Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005609.s004.","short":"M. Lukacisinova, S. Novak, T. Paixao, (2017).","chicago":"Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Resistance Frequencies for Different Combination Strategies.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pcbi.1005609.s004.","ama":"Lukacisinova M, Novak S, Paixao T. Resistance frequencies for different combination strategies. 2017. doi:10.1371/journal.pcbi.1005609.s004","ista":"Lukacisinova M, Novak S, Paixao T. 2017. Resistance frequencies for different combination strategies, Public Library of Science, 10.1371/journal.pcbi.1005609.s004.","apa":"Lukacisinova, M., Novak, S., & Paixao, T. (2017). Resistance frequencies for different combination strategies. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005609.s004","ieee":"M. Lukacisinova, S. Novak, and T. Paixao, “Resistance frequencies for different combination strategies.” Public Library of Science, 2017."},"date_published":"2017-07-18T00:00:00Z","doi":"10.1371/journal.pcbi.1005609.s004"},{"page":"83","citation":{"chicago":"Payne, Pavel. “Bacterial Herd and Social Immunity to Phages.” Institute of Science and Technology Austria, 2017.","mla":"Payne, Pavel. Bacterial Herd and Social Immunity to Phages. Institute of Science and Technology Austria, 2017.","short":"P. Payne, Bacterial Herd and Social Immunity to Phages, Institute of Science and Technology Austria, 2017.","ista":"Payne P. 2017. Bacterial herd and social immunity to phages. Institute of Science and Technology Austria.","apa":"Payne, P. (2017). Bacterial herd and social immunity to phages. Institute of Science and Technology Austria.","ieee":"P. Payne, “Bacterial herd and social immunity to phages,” Institute of Science and Technology Austria, 2017.","ama":"Payne P. Bacterial herd and social immunity to phages. 2017."},"oa":1,"supervisor":[{"full_name":"Bollback, Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4624-4612","first_name":"Jonathan P","last_name":"Bollback"},{"full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"date_published":"2017-02-01T00:00:00Z","day":"01","month":"02","article_processing_charge":"No","has_accepted_license":"1","publication_identifier":{"issn":["2663-337X"]},"status":"public","publication_status":"published","title":"Bacterial herd and social immunity to phages","ddc":["570"],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"_id":"6291","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","year":"2017","date_created":"2019-04-09T15:16:45Z","date_updated":"2023-09-07T12:00:00Z","file":[{"file_id":"6292","relation":"main_file","date_updated":"2020-07-14T12:47:27Z","date_created":"2019-04-09T15:15:32Z","checksum":"a0fc5c26a89c0ea759947ffba87d0d8f","file_name":"thesis_pavel_payne_final_w_signature_page.pdf","access_level":"closed","creator":"dernst","content_type":"application/pdf","file_size":3025175},{"date_updated":"2021-02-22T13:45:59Z","date_created":"2021-02-22T13:45:59Z","checksum":"af531e921a7f64a9e0af4cd8783b2226","success":1,"relation":"main_file","file_id":"9187","file_size":3111536,"content_type":"application/pdf","creator":"dernst","file_name":"2017_Payne_Thesis.pdf","access_level":"open_access"}],"oa_version":"Published Version","author":[{"full_name":"Payne, Pavel","id":"35F78294-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2711-9453","first_name":"Pavel","last_name":"Payne"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"Bacteria and their pathogens – phages – are the most abundant living entities on Earth. Throughout their coevolution, bacteria have evolved multiple immune systems to overcome the ubiquitous threat from the phages. Although the molecu- lar details of these immune systems’ functions are relatively well understood, their epidemiological consequences for the phage-bacterial communities have been largely neglected. In this thesis we employed both experimental and theoretical methods to explore whether herd and social immunity may arise in bacterial popu- lations. Using our experimental system consisting of Escherichia coli strains with a CRISPR based immunity to the T7 phage we show that herd immunity arises in phage-bacterial communities and that it is accentuated when the populations are spatially structured. By fitting a mathematical model, we inferred expressions for the herd immunity threshold and the velocity of spread of a phage epidemic in partially resistant bacterial populations, which both depend on the bacterial growth rate, phage burst size and phage latent period. We also investigated the poten- tial for social immunity in Streptococcus thermophilus and its phage 2972 using a bioinformatic analysis of potentially coding short open reading frames with a signalling signature, encoded within the CRISPR associated genes. Subsequently, we tested one identified potentially signalling peptide and found that its addition to a phage-challenged culture increases probability of survival of bacteria two fold, although the results were only marginally significant. Together, these results demonstrate that the ubiquitous arms races between bacteria and phages have further consequences at the level of the population.","lang":"eng"}],"file_date_updated":"2021-02-22T13:45:59Z"},{"oa_version":"Published Version","date_created":"2021-08-09T13:18:55Z","date_updated":"2023-09-11T13:41:21Z","related_material":{"record":[{"id":"564","relation":"used_in_publication","status":"public"}]},"author":[{"full_name":"Etheridge, Alison","first_name":"Alison","last_name":"Etheridge"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H"}],"department":[{"_id":"NiBa"}],"publisher":"Mendeley Data","status":"public","title":"Data for: Establishment in a new habitat by polygenic adaptation","year":"2017","_id":"9842","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","abstract":[{"text":"Mathematica notebooks used to generate figures.","lang":"eng"}],"type":"research_data_reference","doi":"10.17632/nw68fxzjpm.1","date_published":"2017-12-29T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.17632/nw68fxzjpm.1"}],"citation":{"chicago":"Etheridge, Alison, and Nicholas H Barton. “Data for: Establishment in a New Habitat by Polygenic Adaptation.” Mendeley Data, 2017. https://doi.org/10.17632/nw68fxzjpm.1.","mla":"Etheridge, Alison, and Nicholas H. Barton. Data for: Establishment in a New Habitat by Polygenic Adaptation. Mendeley Data, 2017, doi:10.17632/nw68fxzjpm.1.","short":"A. Etheridge, N.H. Barton, (2017).","ista":"Etheridge A, Barton NH. 2017. Data for: Establishment in a new habitat by polygenic adaptation, Mendeley Data, 10.17632/nw68fxzjpm.1.","ieee":"A. Etheridge and N. H. Barton, “Data for: Establishment in a new habitat by polygenic adaptation.” Mendeley Data, 2017.","apa":"Etheridge, A., & Barton, N. H. (2017). Data for: Establishment in a new habitat by polygenic adaptation. Mendeley Data. https://doi.org/10.17632/nw68fxzjpm.1","ama":"Etheridge A, Barton NH. Data for: Establishment in a new habitat by polygenic adaptation. 2017. doi:10.17632/nw68fxzjpm.1"},"oa":1,"article_processing_charge":"No","month":"12","day":"29"},{"type":"journal_article","issue":"8","abstract":[{"lang":"eng","text":"The behaviour of gene regulatory networks (GRNs) is typically analysed using simulation-based statistical testing-like methods. In this paper, we demonstrate that we can replace this approach by a formal verification-like method that gives higher assurance and scalability. We focus on Wagner’s weighted GRN model with varying weights, which is used in evolutionary biology. In the model, weight parameters represent the gene interaction strength that may change due to genetic mutations. For a property of interest, we synthesise the constraints over the parameter space that represent the set of GRNs satisfying the property. We experimentally show that our parameter synthesis procedure computes the mutational robustness of GRNs—an important problem of interest in evolutionary biology—more efficiently than the classical simulation method. We specify the property in linear temporal logic. We employ symbolic bounded model checking and SMT solving to compute the space of GRNs that satisfy the property, which amounts to synthesizing a set of linear constraints on the weights."}],"intvolume":" 54","status":"public","title":"Model checking the evolution of gene regulatory networks","ddc":["006","576"],"_id":"1351","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"date_created":"2019-01-17T15:57:29Z","date_updated":"2020-07-14T12:44:46Z","checksum":"4e661d9135d7f8c342e8e258dee76f3e","relation":"main_file","file_id":"5841","file_size":755241,"content_type":"application/pdf","creator":"dernst","file_name":"2017_ActaInformatica_Giacobbe.pdf","access_level":"open_access"}],"oa_version":"Published Version","pubrep_id":"649","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"01","page":"765 - 787","citation":{"ama":"Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. Model checking the evolution of gene regulatory networks. Acta Informatica. 2017;54(8):765-787. doi:10.1007/s00236-016-0278-x","ieee":"M. Giacobbe, C. C. Guet, A. Gupta, T. A. Henzinger, T. Paixao, and T. Petrov, “Model checking the evolution of gene regulatory networks,” Acta Informatica, vol. 54, no. 8. Springer, pp. 765–787, 2017.","apa":"Giacobbe, M., Guet, C. C., Gupta, A., Henzinger, T. A., Paixao, T., & Petrov, T. (2017). Model checking the evolution of gene regulatory networks. Acta Informatica. Springer. https://doi.org/10.1007/s00236-016-0278-x","ista":"Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. 2017. Model checking the evolution of gene regulatory networks. Acta Informatica. 54(8), 765–787.","short":"M. Giacobbe, C.C. Guet, A. Gupta, T.A. Henzinger, T. Paixao, T. Petrov, Acta Informatica 54 (2017) 765–787.","mla":"Giacobbe, Mirco, et al. “Model Checking the Evolution of Gene Regulatory Networks.” Acta Informatica, vol. 54, no. 8, Springer, 2017, pp. 765–87, doi:10.1007/s00236-016-0278-x.","chicago":"Giacobbe, Mirco, Calin C Guet, Ashutosh Gupta, Thomas A Henzinger, Tiago Paixao, and Tatjana Petrov. “Model Checking the Evolution of Gene Regulatory Networks.” Acta Informatica. Springer, 2017. https://doi.org/10.1007/s00236-016-0278-x."},"publication":"Acta Informatica","date_published":"2017-12-01T00:00:00Z","ec_funded":1,"publist_id":"5898","file_date_updated":"2020-07-14T12:44:46Z","publisher":"Springer","department":[{"_id":"ToHe"},{"_id":"CaGu"},{"_id":"NiBa"}],"publication_status":"published","year":"2017","volume":54,"date_updated":"2023-09-20T11:06:03Z","date_created":"2018-12-11T11:51:32Z","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"1835"}]},"author":[{"full_name":"Giacobbe, Mirco","first_name":"Mirco","last_name":"Giacobbe","id":"3444EA5E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8180-0904"},{"last_name":"Guet","first_name":"Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C"},{"id":"335E5684-F248-11E8-B48F-1D18A9856A87","last_name":"Gupta","first_name":"Ashutosh","full_name":"Gupta, Ashutosh"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A"},{"last_name":"Paixao","first_name":"Tiago","orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","full_name":"Paixao, Tiago"},{"full_name":"Petrov, Tatjana","orcid":"0000-0002-9041-0905","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","last_name":"Petrov","first_name":"Tatjana"}],"publication_identifier":{"issn":["00015903"]},"month":"12","project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","call_identifier":"FP7","name":"Quantitative Reactive Modeling"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","call_identifier":"FWF","name":"The Wittgenstein Prize"},{"call_identifier":"FP7","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","grant_number":"618091"},{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"},{"_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"}],"isi":1,"quality_controlled":"1","external_id":{"isi":["000414343200003"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/s00236-016-0278-x"},{"type":"journal_article","abstract":[{"lang":"eng","text":"Evolutionary algorithms (EAs) form a popular optimisation paradigm inspired by natural evolution. In recent years the field of evolutionary computation has developed a rigorous analytical theory to analyse the runtimes of EAs on many illustrative problems. Here we apply this theory to a simple model of natural evolution. In the Strong Selection Weak Mutation (SSWM) evolutionary regime the time between occurrences of new mutations is much longer than the time it takes for a mutated genotype to take over the population. In this situation, the population only contains copies of one genotype and evolution can be modelled as a stochastic process evolving one genotype by means of mutation and selection between the resident and the mutated genotype. The probability of accepting the mutated genotype then depends on the change in fitness. We study this process, SSWM, from an algorithmic perspective, quantifying its expected optimisation time for various parameters and investigating differences to a similar evolutionary algorithm, the well-known (1+1) EA. We show that SSWM can have a moderate advantage over the (1+1) EA at crossing fitness valleys and study an example where SSWM outperforms the (1+1) EA by taking advantage of information on the fitness gradient."}],"issue":"2","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"1336","title":"Towards a runtime comparison of natural and artificial evolution","ddc":["576"],"status":"public","intvolume":" 78","pubrep_id":"658","oa_version":"Published Version","file":[{"file_size":710206,"content_type":"application/pdf","creator":"system","access_level":"open_access","file_name":"IST-2016-658-v1+1_s00453-016-0212-1.pdf","checksum":"7873f665a0c598ac747c908f34cb14b9","date_created":"2018-12-12T10:10:19Z","date_updated":"2020-07-14T12:44:44Z","relation":"main_file","file_id":"4805"}],"scopus_import":"1","day":"01","article_processing_charge":"No","has_accepted_license":"1","publication":"Algorithmica","citation":{"ama":"Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. Towards a runtime comparison of natural and artificial evolution. Algorithmica. 2017;78(2):681-713. doi:10.1007/s00453-016-0212-1","ista":"Paixao T, Pérez Heredia J, Sudholt D, Trubenova B. 2017. Towards a runtime comparison of natural and artificial evolution. Algorithmica. 78(2), 681–713.","apa":"Paixao, T., Pérez Heredia, J., Sudholt, D., & Trubenova, B. (2017). Towards a runtime comparison of natural and artificial evolution. Algorithmica. Springer. https://doi.org/10.1007/s00453-016-0212-1","ieee":"T. Paixao, J. Pérez Heredia, D. Sudholt, and B. Trubenova, “Towards a runtime comparison of natural and artificial evolution,” Algorithmica, vol. 78, no. 2. Springer, pp. 681–713, 2017.","mla":"Paixao, Tiago, et al. “Towards a Runtime Comparison of Natural and Artificial Evolution.” Algorithmica, vol. 78, no. 2, Springer, 2017, pp. 681–713, doi:10.1007/s00453-016-0212-1.","short":"T. Paixao, J. Pérez Heredia, D. Sudholt, B. Trubenova, Algorithmica 78 (2017) 681–713.","chicago":"Paixao, Tiago, Jorge Pérez Heredia, Dirk Sudholt, and Barbora Trubenova. “Towards a Runtime Comparison of Natural and Artificial Evolution.” Algorithmica. Springer, 2017. https://doi.org/10.1007/s00453-016-0212-1."},"page":"681 - 713","date_published":"2017-06-01T00:00:00Z","file_date_updated":"2020-07-14T12:44:44Z","ec_funded":1,"publist_id":"5931","year":"2017","publication_status":"published","publisher":"Springer","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"author":[{"full_name":"Paixao, Tiago","orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","last_name":"Paixao","first_name":"Tiago"},{"full_name":"Pérez Heredia, Jorge","first_name":"Jorge","last_name":"Pérez Heredia"},{"last_name":"Sudholt","first_name":"Dirk","full_name":"Sudholt, Dirk"},{"full_name":"Trubenova, Barbora","id":"42302D54-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6873-2967","first_name":"Barbora","last_name":"Trubenova"}],"date_created":"2018-12-11T11:51:27Z","date_updated":"2023-09-20T11:14:42Z","volume":78,"month":"06","publication_identifier":{"issn":["01784617"]},"external_id":{"isi":["000400379500013"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","isi":1,"project":[{"grant_number":"618091","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation"}],"doi":"10.1007/s00453-016-0212-1","language":[{"iso":"eng"}]},{"date_published":"2017-01-01T00:00:00Z","page":"96 - 109","publication":"Heredity","citation":{"chicago":"Barton, Nicholas H. “How Does Epistasis Influence the Response to Selection?” Heredity. Nature Publishing Group, 2017. https://doi.org/10.1038/hdy.2016.109.","short":"N.H. Barton, Heredity 118 (2017) 96–109.","mla":"Barton, Nicholas H. “How Does Epistasis Influence the Response to Selection?” Heredity, vol. 118, Nature Publishing Group, 2017, pp. 96–109, doi:10.1038/hdy.2016.109.","ieee":"N. H. Barton, “How does epistasis influence the response to selection?,” Heredity, vol. 118. Nature Publishing Group, pp. 96–109, 2017.","apa":"Barton, N. H. (2017). How does epistasis influence the response to selection? Heredity. Nature Publishing Group. https://doi.org/10.1038/hdy.2016.109","ista":"Barton NH. 2017. How does epistasis influence the response to selection? Heredity. 118, 96–109.","ama":"Barton NH. How does epistasis influence the response to selection? Heredity. 2017;118:96-109. doi:10.1038/hdy.2016.109"},"day":"01","article_processing_charge":"No","scopus_import":"1","oa_version":"Submitted Version","title":"How does epistasis influence the response to selection?","status":"public","intvolume":" 118","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"1199","abstract":[{"lang":"eng","text":"Much of quantitative genetics is based on the ‘infinitesimal model’, under which selection has a negligible effect on the genetic variance. This is typically justified by assuming a very large number of loci with additive effects. However, it applies even when genes interact, provided that the number of loci is large enough that selection on each of them is weak relative to random drift. In the long term, directional selection will change allele frequencies, but even then, the effects of epistasis on the ultimate change in trait mean due to selection may be modest. Stabilising selection can maintain many traits close to their optima, even when the underlying alleles are weakly selected. However, the number of traits that can be optimised is apparently limited to ~4Ne by the ‘drift load’, and this is hard to reconcile with the apparent complexity of many organisms. Just as for the mutation load, this limit can be evaded by a particular form of negative epistasis. A more robust limit is set by the variance in reproductive success. This suggests that selection accumulates information most efficiently in the infinitesimal regime, when selection on individual alleles is weak, and comparable with random drift. A review of evidence on selection strength suggests that although most variance in fitness may be because of alleles with large Nes, substantial amounts of adaptation may be because of alleles in the infinitesimal regime, in which epistasis has modest effects."}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1038/hdy.2016.109","quality_controlled":"1","isi":1,"project":[{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152"}],"external_id":{"isi":["000392229100011"]},"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5176114/","open_access":"1"}],"oa":1,"month":"01","date_created":"2018-12-11T11:50:40Z","date_updated":"2023-09-20T11:17:47Z","volume":118,"author":[{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"}],"related_material":{"record":[{"id":"9710","status":"public","relation":"research_data"}]},"publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Nature Publishing Group","year":"2017","ec_funded":1,"publist_id":"6151"},{"type":"journal_article","abstract":[{"text":"Dispersal is a crucial factor in natural evolution, since it determines the habitat experienced by any population and defines the spatial scale of interactions between individuals. There is compelling evidence for systematic differences in dispersal characteristics within the same population, i.e., genotype-dependent dispersal. The consequences of genotype-dependent dispersal on other evolutionary phenomena, however, are poorly understood. In this article we investigate the effect of genotype-dependent dispersal on spatial gene frequency patterns, using a generalization of the classical diffusion model of selection and dispersal. Dispersal is characterized by the variance of dispersal (diffusion coefficient) and the mean displacement (directional advection term). We demonstrate that genotype-dependent dispersal may change the qualitative behavior of Fisher waves, which change from being “pulled” to being “pushed” wave fronts as the discrepancy in dispersal between genotypes increases. The speed of any wave is partitioned into components due to selection, genotype-dependent variance of dispersal, and genotype-dependent mean displacement. We apply our findings to wave fronts maintained by selection against heterozygotes. Furthermore, we identify a benefit of increased variance of dispersal, quantify its effect on the speed of the wave, and discuss the implications for the evolution of dispersal strategies.","lang":"eng"}],"issue":"1","_id":"1169","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ddc":["576"],"status":"public","title":"Spatial gene frequency waves under genotype dependent dispersal","intvolume":" 205","pubrep_id":"727","oa_version":"Submitted Version","file":[{"file_size":361500,"content_type":"application/pdf","creator":"system","file_name":"IST-2016-727-v1+1_SFC_Genetics_final.pdf","access_level":"open_access","date_updated":"2020-07-14T12:44:37Z","date_created":"2018-12-12T10:10:43Z","checksum":"7c8ab79cda1f92760bbbbe0f53175bfc","relation":"main_file","file_id":"4833"}],"scopus_import":"1","day":"01","article_processing_charge":"No","has_accepted_license":"1","publication":"Genetics","citation":{"ista":"Novak S, Kollár R. 2017. Spatial gene frequency waves under genotype dependent dispersal. Genetics. 205(1), 367–374.","apa":"Novak, S., & Kollár, R. (2017). Spatial gene frequency waves under genotype dependent dispersal. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.116.193946","ieee":"S. Novak and R. Kollár, “Spatial gene frequency waves under genotype dependent dispersal,” Genetics, vol. 205, no. 1. Genetics Society of America, pp. 367–374, 2017.","ama":"Novak S, Kollár R. Spatial gene frequency waves under genotype dependent dispersal. Genetics. 2017;205(1):367-374. doi:10.1534/genetics.116.193946","chicago":"Novak, Sebastian, and Richard Kollár. “Spatial Gene Frequency Waves under Genotype Dependent Dispersal.” Genetics. Genetics Society of America, 2017. https://doi.org/10.1534/genetics.116.193946.","mla":"Novak, Sebastian, and Richard Kollár. “Spatial Gene Frequency Waves under Genotype Dependent Dispersal.” Genetics, vol. 205, no. 1, Genetics Society of America, 2017, pp. 367–74, doi:10.1534/genetics.116.193946.","short":"S. Novak, R. Kollár, Genetics 205 (2017) 367–374."},"page":"367 - 374","date_published":"2017-01-01T00:00:00Z","file_date_updated":"2020-07-14T12:44:37Z","publist_id":"6188","ec_funded":1,"year":"2017","publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Genetics Society of America","author":[{"full_name":"Novak, Sebastian","orcid":"0000-0002-2519-824X","id":"461468AE-F248-11E8-B48F-1D18A9856A87","last_name":"Novak","first_name":"Sebastian"},{"full_name":"Kollár, Richard","last_name":"Kollár","first_name":"Richard"}],"date_updated":"2023-09-20T11:24:21Z","date_created":"2018-12-11T11:50:31Z","volume":205,"month":"01","publication_identifier":{"issn":["00166731"]},"external_id":{"isi":["000393677300025"]},"oa":1,"quality_controlled":"1","isi":1,"project":[{"name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","call_identifier":"FP7","grant_number":"618091","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425"},{"_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation"}],"doi":"10.1534/genetics.116.193946","language":[{"iso":"eng"}]},{"date_published":"2017-02-01T00:00:00Z","citation":{"ista":"Heredia J, Trubenova B, Sudholt D, Paixao T. 2017. Selection limits to adaptive walks on correlated landscapes. Genetics. 205(2), 803–825.","apa":"Heredia, J., Trubenova, B., Sudholt, D., & Paixao, T. (2017). Selection limits to adaptive walks on correlated landscapes. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.116.189340","ieee":"J. Heredia, B. Trubenova, D. Sudholt, and T. Paixao, “Selection limits to adaptive walks on correlated landscapes,” Genetics, vol. 205, no. 2. Genetics Society of America, pp. 803–825, 2017.","ama":"Heredia J, Trubenova B, Sudholt D, Paixao T. Selection limits to adaptive walks on correlated landscapes. Genetics. 2017;205(2):803-825. doi:10.1534/genetics.116.189340","chicago":"Heredia, Jorge, Barbora Trubenova, Dirk Sudholt, and Tiago Paixao. “Selection Limits to Adaptive Walks on Correlated Landscapes.” Genetics. Genetics Society of America, 2017. https://doi.org/10.1534/genetics.116.189340.","mla":"Heredia, Jorge, et al. “Selection Limits to Adaptive Walks on Correlated Landscapes.” Genetics, vol. 205, no. 2, Genetics Society of America, 2017, pp. 803–25, doi:10.1534/genetics.116.189340.","short":"J. Heredia, B. Trubenova, D. Sudholt, T. Paixao, Genetics 205 (2017) 803–825."},"publication":"Genetics","page":"803 - 825","article_type":"original","article_processing_charge":"No","day":"01","scopus_import":"1","oa_version":"Published Version","_id":"1111","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 205","title":"Selection limits to adaptive walks on correlated landscapes","status":"public","issue":"2","abstract":[{"text":"Adaptation depends critically on the effects of new mutations and their dependency on the genetic background in which they occur. These two factors can be summarized by the fitness landscape. However, it would require testing all mutations in all backgrounds, making the definition and analysis of fitness landscapes mostly inaccessible. Instead of postulating a particular fitness landscape, we address this problem by considering general classes of landscapes and calculating an upper limit for the time it takes for a population to reach a fitness peak, circumventing the need to have full knowledge about the fitness landscape. We analyze populations in the weak-mutation regime and characterize the conditions that enable them to quickly reach the fitness peak as a function of the number of sites under selection. We show that for additive landscapes there is a critical selection strength enabling populations to reach high-fitness genotypes, regardless of the distribution of effects. This threshold scales with the number of sites under selection, effectively setting a limit to adaptation, and results from the inevitable increase in deleterious mutational pressure as the population adapts in a space of discrete genotypes. Furthermore, we show that for the class of all unimodal landscapes this condition is sufficient but not necessary for rapid adaptation, as in some highly epistatic landscapes the critical strength does not depend on the number of sites under selection; effectively removing this barrier to adaptation.","lang":"eng"}],"type":"journal_article","doi":"10.1534/genetics.116.189340","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1534/genetics.116.189340"}],"external_id":{"pmid":["27881471"],"isi":["000394144900025"]},"project":[{"name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","call_identifier":"FP7","grant_number":"618091","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"publication_identifier":{"issn":["00166731"]},"month":"02","author":[{"first_name":"Jorge","last_name":"Heredia","full_name":"Heredia, Jorge"},{"first_name":"Barbora","last_name":"Trubenova","id":"42302D54-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6873-2967","full_name":"Trubenova, Barbora"},{"last_name":"Sudholt","first_name":"Dirk","full_name":"Sudholt, Dirk"},{"full_name":"Paixao, Tiago","first_name":"Tiago","last_name":"Paixao","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2361-3953"}],"volume":205,"date_created":"2018-12-11T11:50:12Z","date_updated":"2023-09-20T11:35:03Z","pmid":1,"year":"2017","publisher":"Genetics Society of America","department":[{"_id":"NiBa"}],"publication_status":"published","ec_funded":1,"publist_id":"6256"},{"abstract":[{"lang":"eng","text":"Viral capsids are structurally constrained by interactions among the amino acids (AAs) of their constituent proteins. Therefore, epistasis is expected to evolve among physically interacting sites and to influence the rates of substitution. To study the evolution of epistasis, we focused on the major structural protein of the fX174 phage family by first reconstructing the ancestral protein sequences of 18 species using a Bayesian statistical framework. The inferred ancestral reconstruction differed at eight AAs, for a total of 256 possible ancestral haplotypes. For each ancestral haplotype and the extant species, we estimated, in silico, the distribution of free energies and epistasis of the capsid structure. We found that free energy has not significantly increased but epistasis has. We decomposed epistasis up to fifth order and found that higher-order epistasis sometimes compensates pairwise interactions making the free energy seem additive. The dN/dS ratio is low, suggesting strong purifying selection, and that structure is under stabilizing selection. We synthesized phages carrying ancestral haplotypes of the coat protein gene and measured their fitness experimentally. Our findings indicate that stabilizing mutations can have higher fitness, and that fitness optima do not necessarily coincide with energy minima."}],"issue":"126","type":"journal_article","file":[{"file_size":1092015,"content_type":"application/pdf","creator":"dernst","file_name":"2017_JRSI_Redondo.pdf","access_level":"open_access","date_created":"2019-01-18T09:14:02Z","date_updated":"2019-01-18T09:14:02Z","success":1,"relation":"main_file","file_id":"5843"}],"oa_version":"Published Version","title":"Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family","status":"public","ddc":["570"],"intvolume":" 14","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"1077","day":"04","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","scopus_import":"1","date_published":"2017-01-04T00:00:00Z","publication":"Journal of the Royal Society Interface","citation":{"apa":"Fernandes Redondo, R. A., de Vladar, H., Włodarski, T., & Bollback, J. P. (2017). Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. Journal of the Royal Society Interface. Royal Society of London. https://doi.org/10.1098/rsif.2016.0139","ieee":"R. A. Fernandes Redondo, H. de Vladar, T. Włodarski, and J. P. Bollback, “Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family,” Journal of the Royal Society Interface, vol. 14, no. 126. Royal Society of London, 2017.","ista":"Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. 2017. Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. Journal of the Royal Society Interface. 14(126), 20160139.","ama":"Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. Journal of the Royal Society Interface. 2017;14(126). doi:10.1098/rsif.2016.0139","chicago":"Fernandes Redondo, Rodrigo A, Harold de Vladar, Tomasz Włodarski, and Jonathan P Bollback. “Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family.” Journal of the Royal Society Interface. Royal Society of London, 2017. https://doi.org/10.1098/rsif.2016.0139.","short":"R.A. Fernandes Redondo, H. de Vladar, T. Włodarski, J.P. Bollback, Journal of the Royal Society Interface 14 (2017).","mla":"Fernandes Redondo, Rodrigo A., et al. “Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family.” Journal of the Royal Society Interface, vol. 14, no. 126, 20160139, Royal Society of London, 2017, doi:10.1098/rsif.2016.0139."},"file_date_updated":"2019-01-18T09:14:02Z","publist_id":"6303","ec_funded":1,"article_number":"20160139","date_created":"2018-12-11T11:50:01Z","date_updated":"2023-09-20T11:56:34Z","volume":14,"author":[{"first_name":"Rodrigo A","last_name":"Fernandes Redondo","id":"409D5C96-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5837-2793","full_name":"Fernandes Redondo, Rodrigo A"},{"id":"2A181218-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5985-7653","first_name":"Harold","last_name":"Vladar","full_name":"Vladar, Harold"},{"full_name":"Włodarski, Tomasz","first_name":"Tomasz","last_name":"Włodarski"},{"orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","last_name":"Bollback","first_name":"Jonathan P","full_name":"Bollback, Jonathan P"}],"related_material":{"record":[{"relation":"research_data","status":"public","id":"9864"}]},"publication_status":"published","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"publisher":"Royal Society of London","year":"2017","month":"01","publication_identifier":{"issn":["17425689"]},"language":[{"iso":"eng"}],"doi":"10.1098/rsif.2016.0139","isi":1,"quality_controlled":"1","project":[{"grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation"},{"name":"Selective Barriers to Horizontal Gene Transfer","call_identifier":"H2020","grant_number":"648440","_id":"2578D616-B435-11E9-9278-68D0E5697425"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000393380400001"]},"oa":1},{"oa":1,"main_file_link":[{"open_access":"1","url":"http://www.biorxiv.org/content/early/2016/09/23/076810"}],"external_id":{"isi":["000395807200023"]},"quality_controlled":"1","isi":1,"project":[{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152"}],"doi":"10.1534/genetics.116.196220","language":[{"iso":"eng"}],"month":"03","publication_identifier":{"issn":["00166731"]},"year":"2017","publication_status":"published","publisher":"Genetics Society of America","department":[{"_id":"NiBa"}],"author":[{"full_name":"Ringbauer, Harald","id":"417FCFF4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4884-9682","first_name":"Harald","last_name":"Ringbauer"},{"full_name":"Coop, Graham","last_name":"Coop","first_name":"Graham"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"200"}]},"date_created":"2018-12-11T11:50:00Z","date_updated":"2023-09-20T12:00:56Z","volume":205,"ec_funded":1,"publist_id":"6307","publication":"Genetics","citation":{"ista":"Ringbauer H, Coop G, Barton NH. 2017. Inferring recent demography from isolation by distance of long shared sequence blocks. Genetics. 205(3), 1335–1351.","apa":"Ringbauer, H., Coop, G., & Barton, N. H. (2017). Inferring recent demography from isolation by distance of long shared sequence blocks. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.116.196220","ieee":"H. Ringbauer, G. Coop, and N. H. Barton, “Inferring recent demography from isolation by distance of long shared sequence blocks,” Genetics, vol. 205, no. 3. Genetics Society of America, pp. 1335–1351, 2017.","ama":"Ringbauer H, Coop G, Barton NH. Inferring recent demography from isolation by distance of long shared sequence blocks. Genetics. 2017;205(3):1335-1351. doi:10.1534/genetics.116.196220","chicago":"Ringbauer, Harald, Graham Coop, and Nicholas H Barton. “Inferring Recent Demography from Isolation by Distance of Long Shared Sequence Blocks.” Genetics. Genetics Society of America, 2017. https://doi.org/10.1534/genetics.116.196220.","mla":"Ringbauer, Harald, et al. “Inferring Recent Demography from Isolation by Distance of Long Shared Sequence Blocks.” Genetics, vol. 205, no. 3, Genetics Society of America, 2017, pp. 1335–51, doi:10.1534/genetics.116.196220.","short":"H. Ringbauer, G. Coop, N.H. Barton, Genetics 205 (2017) 1335–1351."},"page":"1335 - 1351","date_published":"2017-03-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"1074","status":"public","title":"Inferring recent demography from isolation by distance of long shared sequence blocks","intvolume":" 205","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"Recently it has become feasible to detect long blocks of nearly identical sequence shared between pairs of genomes. These IBD blocks are direct traces of recent coalescence events and, as such, contain ample signal to infer recent demography. Here, we examine sharing of such blocks in two-dimensional populations with local migration. Using a diffusion approximation to trace genetic ancestry, we derive analytical formulae for patterns of isolation by distance of IBD blocks, which can also incorporate recent population density changes. We introduce an inference scheme that uses a composite likelihood approach to fit these formulae. We then extensively evaluate our theory and inference method on a range of scenarios using simulated data. We first validate the diffusion approximation by showing that the theoretical results closely match the simulated block sharing patterns. We then demonstrate that our inference scheme can accurately and robustly infer dispersal rate and effective density, as well as bounds on recent dynamics of population density. To demonstrate an application, we use our estimation scheme to explore the fit of a diffusion model to Eastern European samples in the POPRES data set. We show that ancestry diffusing with a rate of σ ≈ 50–100 km/√gen during the last centuries, combined with accelerating population growth, can explain the observed exponential decay of block sharing with increasing pairwise sample distance.","lang":"eng"}],"issue":"3"},{"article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2017-04-01T00:00:00Z","citation":{"apa":"Uecker, H. (2017). Evolutionary rescue in randomly mating, selfing, and clonal populations. Evolution. Wiley-Blackwell. https://doi.org/10.1111/evo.13191","ieee":"H. Uecker, “Evolutionary rescue in randomly mating, selfing, and clonal populations,” Evolution, vol. 71, no. 4. Wiley-Blackwell, pp. 845–858, 2017.","ista":"Uecker H. 2017. Evolutionary rescue in randomly mating, selfing, and clonal populations. Evolution. 71(4), 845–858.","ama":"Uecker H. Evolutionary rescue in randomly mating, selfing, and clonal populations. Evolution. 2017;71(4):845-858. doi:10.1111/evo.13191","chicago":"Uecker, Hildegard. “Evolutionary Rescue in Randomly Mating, Selfing, and Clonal Populations.” Evolution. Wiley-Blackwell, 2017. https://doi.org/10.1111/evo.13191.","short":"H. Uecker, Evolution 71 (2017) 845–858.","mla":"Uecker, Hildegard. “Evolutionary Rescue in Randomly Mating, Selfing, and Clonal Populations.” Evolution, vol. 71, no. 4, Wiley-Blackwell, 2017, pp. 845–58, doi:10.1111/evo.13191."},"publication":"Evolution","page":"845 - 858","issue":"4","abstract":[{"text":"Severe environmental change can drive a population extinct unless the population adapts in time to the new conditions (“evolutionary rescue”). How does biparental sexual reproduction influence the chances of population persistence compared to clonal reproduction or selfing? In this article, we set up a one‐locus two‐allele model for adaptation in diploid species, where rescue is contingent on the establishment of the mutant homozygote. Reproduction can occur by random mating, selfing, or clonally. Random mating generates and destroys the rescue mutant; selfing is efficient at generating it but at the same time depletes the heterozygote, which can lead to a low mutant frequency in the standing genetic variation. Due to these (and other) antagonistic effects, we find a nontrivial dependence of population survival on the rate of sex/selfing, which is strongly influenced by the dominance coefficient of the mutation before and after the environmental change. Importantly, since mating with the wild‐type breaks the mutant homozygote up, a slow decay of the wild‐type population size can impede rescue in randomly mating populations.","lang":"eng"}],"type":"journal_article","oa_version":"Submitted Version","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"1063","intvolume":" 71","status":"public","title":"Evolutionary rescue in randomly mating, selfing, and clonal populations","publication_identifier":{"issn":["00143820"]},"month":"04","doi":"10.1111/evo.13191","language":[{"iso":"eng"}],"main_file_link":[{"url":"http://biorxiv.org/content/early/2016/10/14/081042","open_access":"1"}],"external_id":{"isi":["000398545200003"]},"oa":1,"project":[{"name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152"}],"quality_controlled":"1","isi":1,"ec_funded":1,"publist_id":"6327","author":[{"id":"2DB8F68A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9435-2813","first_name":"Hildegard","last_name":"Uecker","full_name":"Uecker, Hildegard"}],"volume":71,"date_updated":"2023-09-20T12:10:32Z","date_created":"2018-12-11T11:49:57Z","year":"2017","publisher":"Wiley-Blackwell","department":[{"_id":"NiBa"}],"publication_status":"published"},{"volume":71,"date_created":"2018-12-11T11:49:34Z","date_updated":"2023-09-22T09:55:13Z","author":[{"first_name":"Himani","last_name":"Sachdeva","id":"42377A0A-F248-11E8-B48F-1D18A9856A87","full_name":"Sachdeva, Himani"},{"full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"NiBa"}],"publisher":"Wiley-Blackwell","publication_status":"published","pmid":1,"year":"2017","ec_funded":1,"publist_id":"6409","file_date_updated":"2020-07-14T12:48:18Z","language":[{"iso":"eng"}],"doi":"10.1111/evo.13252","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"},{"name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152"}],"quality_controlled":"1","isi":1,"oa":1,"external_id":{"pmid":["28419447"],"isi":["000403014800005"]},"publication_identifier":{"issn":["00143820"]},"month":"06","oa_version":"Submitted Version","file":[{"checksum":"6d4c38cb1347fd43620d1736c6df5c79","date_created":"2019-04-17T07:37:04Z","date_updated":"2020-07-14T12:48:18Z","relation":"main_file","file_id":"6329","content_type":"application/pdf","file_size":625260,"creator":"dernst","access_level":"open_access","file_name":"2017_Evolution_Sachdeva_supplement.pdf"},{"checksum":"f1d90dd8831b44baf49b4dd176f263af","date_created":"2019-04-17T07:37:04Z","date_updated":"2020-07-14T12:48:18Z","file_id":"6330","relation":"main_file","creator":"dernst","file_size":520110,"content_type":"application/pdf","access_level":"open_access","file_name":"2017_Evolution_Sachdeva_article.pdf"}],"pubrep_id":"977","intvolume":" 71","title":"Divergence and evolution of assortative mating in a polygenic trait model of speciation with gene flow","status":"public","ddc":["576"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"990","issue":"6","abstract":[{"text":"Assortative mating is an important driver of speciation in populations with gene flow and is predicted to evolve under certain conditions in few-locus models. However, the evolution of assortment is less understood for mating based on quantitative traits, which are often characterized by high genetic variability and extensive linkage disequilibrium between trait loci. We explore this scenario for a two-deme model with migration, by considering a single polygenic trait subject to divergent viability selection across demes, as well as assortative mating and sexual selection within demes, and investigate how trait divergence is shaped by various evolutionary forces. Our analysis reveals the existence of sharp thresholds of assortment strength, at which divergence increases dramatically. We also study the evolution of assortment via invasion of modifiers of mate discrimination and show that the ES assortment strength has an intermediate value under a range of migration-selection parameters, even in diverged populations, due to subtle effects which depend sensitively on the extent of phenotypic variation within these populations. The evolutionary dynamics of the polygenic trait is studied using the hypergeometric and infinitesimal models. We further investigate the sensitivity of our results to the assumptions of the hypergeometric model, using individual-based simulations.","lang":"eng"}],"type":"journal_article","date_published":"2017-06-01T00:00:00Z","page":"1478 - 1493 ","citation":{"ista":"Sachdeva H, Barton NH. 2017. Divergence and evolution of assortative mating in a polygenic trait model of speciation with gene flow. Evolution; International Journal of Organic Evolution. 71(6), 1478–1493.","ieee":"H. Sachdeva and N. H. Barton, “Divergence and evolution of assortative mating in a polygenic trait model of speciation with gene flow,” Evolution; International Journal of Organic Evolution, vol. 71, no. 6. Wiley-Blackwell, pp. 1478–1493, 2017.","apa":"Sachdeva, H., & Barton, N. H. (2017). Divergence and evolution of assortative mating in a polygenic trait model of speciation with gene flow. Evolution; International Journal of Organic Evolution. Wiley-Blackwell. https://doi.org/10.1111/evo.13252","ama":"Sachdeva H, Barton NH. Divergence and evolution of assortative mating in a polygenic trait model of speciation with gene flow. Evolution; International Journal of Organic Evolution. 2017;71(6):1478-1493. doi:10.1111/evo.13252","chicago":"Sachdeva, Himani, and Nicholas H Barton. “Divergence and Evolution of Assortative Mating in a Polygenic Trait Model of Speciation with Gene Flow.” Evolution; International Journal of Organic Evolution. Wiley-Blackwell, 2017. https://doi.org/10.1111/evo.13252.","mla":"Sachdeva, Himani, and Nicholas H. Barton. “Divergence and Evolution of Assortative Mating in a Polygenic Trait Model of Speciation with Gene Flow.” Evolution; International Journal of Organic Evolution, vol. 71, no. 6, Wiley-Blackwell, 2017, pp. 1478–93, doi:10.1111/evo.13252.","short":"H. Sachdeva, N.H. Barton, Evolution; International Journal of Organic Evolution 71 (2017) 1478–1493."},"publication":"Evolution; International Journal of Organic Evolution","article_processing_charge":"No","has_accepted_license":"1","day":"01","scopus_import":"1"},{"citation":{"mla":"Lagator, Mato, et al. “On the Mechanistic Nature of Epistasis in a Canonical Cis-Regulatory Element.” ELife, vol. 6, e25192, eLife Sciences Publications, 2017, doi:10.7554/eLife.25192.","short":"M. Lagator, T. Paixao, N.H. Barton, J.P. Bollback, C.C. Guet, ELife 6 (2017).","chicago":"Lagator, Mato, Tiago Paixao, Nicholas H Barton, Jonathan P Bollback, and Calin C Guet. “On the Mechanistic Nature of Epistasis in a Canonical Cis-Regulatory Element.” ELife. eLife Sciences Publications, 2017. https://doi.org/10.7554/eLife.25192.","ama":"Lagator M, Paixao T, Barton NH, Bollback JP, Guet CC. On the mechanistic nature of epistasis in a canonical cis-regulatory element. eLife. 2017;6. doi:10.7554/eLife.25192","ista":"Lagator M, Paixao T, Barton NH, Bollback JP, Guet CC. 2017. On the mechanistic nature of epistasis in a canonical cis-regulatory element. eLife. 6, e25192.","apa":"Lagator, M., Paixao, T., Barton, N. H., Bollback, J. P., & Guet, C. C. (2017). On the mechanistic nature of epistasis in a canonical cis-regulatory element. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.25192","ieee":"M. Lagator, T. Paixao, N. H. Barton, J. P. Bollback, and C. C. Guet, “On the mechanistic nature of epistasis in a canonical cis-regulatory element,” eLife, vol. 6. eLife Sciences Publications, 2017."},"publication":"eLife","date_published":"2017-05-18T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes","day":"18","intvolume":" 6","status":"public","ddc":["576"],"title":"On the mechanistic nature of epistasis in a canonical cis-regulatory element","_id":"954","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"date_created":"2018-12-12T10:17:49Z","date_updated":"2020-07-14T12:48:16Z","checksum":"59cdd4400fb41280122d414fea971546","relation":"main_file","file_id":"5306","content_type":"application/pdf","file_size":2441529,"creator":"system","file_name":"IST-2017-841-v1+1_elife-25192-v2.pdf","access_level":"open_access"},{"checksum":"b69024880558b858eb8c5d47a92b6377","date_updated":"2020-07-14T12:48:16Z","date_created":"2018-12-12T10:17:50Z","file_id":"5307","relation":"main_file","creator":"system","file_size":3752660,"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2017-841-v1+2_elife-25192-figures-v2.pdf"}],"oa_version":"Published Version","pubrep_id":"841","type":"journal_article","abstract":[{"lang":"eng","text":"Understanding the relation between genotype and phenotype remains a major challenge. The difficulty of predicting individual mutation effects, and particularly the interactions between them, has prevented the development of a comprehensive theory that links genotypic changes to their phenotypic effects. We show that a general thermodynamic framework for gene regulation, based on a biophysical understanding of protein-DNA binding, accurately predicts the sign of epistasis in a canonical cis-regulatory element consisting of overlapping RNA polymerase and repressor binding sites. Sign and magnitude of individual mutation effects are sufficient to predict the sign of epistasis and its environmental dependence. Thus, the thermodynamic model offers the correct null prediction for epistasis between mutations across DNA-binding sites. Our results indicate that a predictive theory for the effects of cis-regulatory mutations is possible from first principles, as long as the essential molecular mechanisms and the constraints these impose on a biological system are accounted for."}],"project":[{"name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","call_identifier":"FP7","grant_number":"618091","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425"},{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"},{"_id":"2578D616-B435-11E9-9278-68D0E5697425","grant_number":"648440","call_identifier":"H2020","name":"Selective Barriers to Horizontal Gene Transfer"}],"quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000404024800001"]},"language":[{"iso":"eng"}],"doi":"10.7554/eLife.25192","publication_identifier":{"issn":["2050084X"]},"month":"05","department":[{"_id":"CaGu"},{"_id":"NiBa"},{"_id":"JoBo"}],"publisher":"eLife Sciences Publications","publication_status":"published","year":"2017","volume":6,"date_created":"2018-12-11T11:49:23Z","date_updated":"2023-09-22T10:01:17Z","author":[{"last_name":"Lagator","first_name":"Mato","id":"345D25EC-F248-11E8-B48F-1D18A9856A87","full_name":"Lagator, Mato"},{"last_name":"Paixao","first_name":"Tiago","orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","full_name":"Paixao, Tiago"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"},{"full_name":"Bollback, Jonathan P","orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","last_name":"Bollback","first_name":"Jonathan P"},{"full_name":"Guet, Calin C","last_name":"Guet","first_name":"Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"}],"article_number":"e25192","ec_funded":1,"publist_id":"6460","file_date_updated":"2020-07-14T12:48:16Z"},{"month":"08","publication_identifier":{"issn":["20411723"]},"isi":1,"quality_controlled":"1","project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation"},{"_id":"254E9036-B435-11E9-9278-68D0E5697425","grant_number":"P28844-B27","call_identifier":"FWF","name":"Biophysics of information processing in gene regulation"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000407198800005"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1038/s41467-017-00238-8","article_number":"216","file_date_updated":"2020-07-14T12:48:16Z","ec_funded":1,"publist_id":"6459","publication_status":"published","publisher":"Nature Publishing Group","department":[{"_id":"GaTk"},{"_id":"NiBa"}],"year":"2017","date_created":"2018-12-11T11:49:23Z","date_updated":"2023-09-22T10:00:49Z","volume":8,"author":[{"first_name":"Tamar","last_name":"Friedlander","id":"36A5845C-F248-11E8-B48F-1D18A9856A87","full_name":"Friedlander, Tamar"},{"id":"4456104E-F248-11E8-B48F-1D18A9856A87","last_name":"Prizak","first_name":"Roshan","full_name":"Prizak, Roshan"},{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"},{"full_name":"Tkacik, Gasper","last_name":"Tkacik","first_name":"Gasper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"6071"}]},"scopus_import":"1","day":"09","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","publication":"Nature Communications","citation":{"chicago":"Friedlander, Tamar, Roshan Prizak, Nicholas H Barton, and Gašper Tkačik. “Evolution of New Regulatory Functions on Biophysically Realistic Fitness Landscapes.” Nature Communications. Nature Publishing Group, 2017. https://doi.org/10.1038/s41467-017-00238-8.","short":"T. Friedlander, R. Prizak, N.H. Barton, G. Tkačik, Nature Communications 8 (2017).","mla":"Friedlander, Tamar, et al. “Evolution of New Regulatory Functions on Biophysically Realistic Fitness Landscapes.” Nature Communications, vol. 8, no. 1, 216, Nature Publishing Group, 2017, doi:10.1038/s41467-017-00238-8.","apa":"Friedlander, T., Prizak, R., Barton, N. H., & Tkačik, G. (2017). Evolution of new regulatory functions on biophysically realistic fitness landscapes. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-017-00238-8","ieee":"T. Friedlander, R. Prizak, N. H. Barton, and G. Tkačik, “Evolution of new regulatory functions on biophysically realistic fitness landscapes,” Nature Communications, vol. 8, no. 1. Nature Publishing Group, 2017.","ista":"Friedlander T, Prizak R, Barton NH, Tkačik G. 2017. Evolution of new regulatory functions on biophysically realistic fitness landscapes. Nature Communications. 8(1), 216.","ama":"Friedlander T, Prizak R, Barton NH, Tkačik G. Evolution of new regulatory functions on biophysically realistic fitness landscapes. Nature Communications. 2017;8(1). doi:10.1038/s41467-017-00238-8"},"date_published":"2017-08-09T00:00:00Z","type":"journal_article","abstract":[{"text":"Gene expression is controlled by networks of regulatory proteins that interact specifically with external signals and DNA regulatory sequences. These interactions force the network components to co-evolve so as to continually maintain function. Yet, existing models of evolution mostly focus on isolated genetic elements. In contrast, we study the essential process by which regulatory networks grow: the duplication and subsequent specialization of network components. We synthesize a biophysical model of molecular interactions with the evolutionary framework to find the conditions and pathways by which new regulatory functions emerge. We show that specialization of new network components is usually slow, but can be drastically accelerated in the presence of regulatory crosstalk and mutations that promote promiscuous interactions between network components.","lang":"eng"}],"issue":"1","status":"public","title":"Evolution of new regulatory functions on biophysically realistic fitness landscapes","ddc":["539","576"],"intvolume":" 8","_id":"955","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","file":[{"file_name":"IST-2017-864-v1+1_s41467-017-00238-8.pdf","access_level":"open_access","creator":"system","file_size":998157,"content_type":"application/pdf","file_id":"5064","relation":"main_file","date_created":"2018-12-12T10:14:14Z","date_updated":"2020-07-14T12:48:16Z","checksum":"29a1b5db458048d3bd5c67e0e2a56818"},{"date_updated":"2020-07-14T12:48:16Z","date_created":"2018-12-12T10:14:15Z","checksum":"7b78401e52a576cf3e6bbf8d0abadc17","file_id":"5065","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":9715993,"file_name":"IST-2017-864-v1+2_41467_2017_238_MOESM1_ESM.pdf","access_level":"open_access"}],"pubrep_id":"864"},{"month":"05","language":[{"iso":"eng"}],"doi":"10.1098/rspb.2016.2864","isi":1,"quality_controlled":"1","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5454256/","open_access":"1"}],"oa":1,"external_id":{"pmid":["28566483"],"isi":["000405148800021"]},"publist_id":"6462","article_number":"20162864","volume":284,"date_updated":"2023-09-22T10:01:48Z","date_created":"2018-12-11T11:49:23Z","author":[{"last_name":"Charlesworth","first_name":"Deborah","full_name":"Charlesworth, Deborah"},{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton"},{"first_name":"Brian","last_name":"Charlesworth","full_name":"Charlesworth, Brian"}],"publisher":"Royal Society, The","department":[{"_id":"NiBa"}],"publication_status":"published","pmid":1,"year":"2017","article_processing_charge":"No","day":"31","scopus_import":"1","date_published":"2017-05-31T00:00:00Z","citation":{"chicago":"Charlesworth, Deborah, Nicholas H Barton, and Brian Charlesworth. “The Sources of Adaptive Evolution.” Proceedings of the Royal Society of London Series B Biological Sciences. Royal Society, The, 2017. https://doi.org/10.1098/rspb.2016.2864.","mla":"Charlesworth, Deborah, et al. “The Sources of Adaptive Evolution.” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 284, no. 1855, 20162864, Royal Society, The, 2017, doi:10.1098/rspb.2016.2864.","short":"D. Charlesworth, N.H. Barton, B. Charlesworth, Proceedings of the Royal Society of London Series B Biological Sciences 284 (2017).","ista":"Charlesworth D, Barton NH, Charlesworth B. 2017. The sources of adaptive evolution. Proceedings of the Royal Society of London Series B Biological Sciences. 284(1855), 20162864.","apa":"Charlesworth, D., Barton, N. H., & Charlesworth, B. (2017). The sources of adaptive evolution. Proceedings of the Royal Society of London Series B Biological Sciences. Royal Society, The. https://doi.org/10.1098/rspb.2016.2864","ieee":"D. Charlesworth, N. H. Barton, and B. Charlesworth, “The sources of adaptive evolution,” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 284, no. 1855. Royal Society, The, 2017.","ama":"Charlesworth D, Barton NH, Charlesworth B. The sources of adaptive evolution. Proceedings of the Royal Society of London Series B Biological Sciences. 2017;284(1855). doi:10.1098/rspb.2016.2864"},"publication":"Proceedings of the Royal Society of London Series B Biological Sciences","issue":"1855","abstract":[{"text":"The role of natural selection in the evolution of adaptive phenotypes has undergone constant probing by evolutionary biologists, employing both theoretical and empirical approaches. As Darwin noted, natural selection can act together with other processes, including random changes in the frequencies of phenotypic differences that are not under strong selection, and changes in the environment, which may reflect evolutionary changes in the organisms themselves. As understanding of genetics developed after 1900, the new genetic discoveries were incorporated into evolutionary biology. The resulting general principles were summarized by Julian Huxley in his 1942 book Evolution: the modern synthesis. Here, we examine how recent advances in genetics, developmental biology and molecular biology, including epigenetics, relate to today's understanding of the evolution of adaptations. We illustrate how careful genetic studies have repeatedly shown that apparently puzzling results in a wide diversity of organisms involve processes that are consistent with neo-Darwinism. They do not support important roles in adaptation for processes such as directed mutation or the inheritance of acquired characters, and therefore no radical revision of our understanding of the mechanism of adaptive evolution is needed.","lang":"eng"}],"type":"journal_article","oa_version":"Submitted Version","intvolume":" 284","status":"public","title":"The sources of adaptive evolution","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"953"},{"date_updated":"2023-09-22T10:02:21Z","date_created":"2018-12-11T11:49:22Z","volume":115,"author":[{"full_name":"Turelli, Michael","first_name":"Michael","last_name":"Turelli"},{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"}],"publication_status":"published","publisher":"Elsevier","department":[{"_id":"NiBa"}],"year":"2017","pmid":1,"file_date_updated":"2020-07-14T12:48:16Z","publist_id":"6463","language":[{"iso":"eng"}],"doi":"10.1016/j.tpb.2017.03.003","quality_controlled":"1","external_id":{"pmid":["28411063"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"month":"06","publication_identifier":{"issn":["00405809"]},"oa_version":"Submitted Version","file":[{"creator":"dernst","content_type":"application/pdf","file_size":2073856,"file_name":"2017_TheoreticalPopulationBio_Turelli.pdf","access_level":"open_access","date_created":"2019-04-17T06:39:45Z","date_updated":"2020-07-14T12:48:16Z","checksum":"9aeff86fa7de69f7a15cf4fc60d57d01","file_id":"6327","relation":"main_file"}],"pubrep_id":"972","ddc":["576"],"status":"public","title":"Deploying dengue-suppressing Wolbachia: Robust models predict slow but effective spatial spread in Aedes aegypti","intvolume":" 115","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"952","abstract":[{"lang":"eng","text":"A novel strategy for controlling the spread of arboviral diseases such as dengue, Zika and chikungunya is to transform mosquito populations with virus-suppressing Wolbachia. In general, Wolbachia transinfected into mosquitoes induce fitness costs through lower viability or fecundity. These maternally inherited bacteria also produce a frequency-dependent advantage for infected females by inducing cytoplasmic incompatibility (CI), which kills the embryos produced by uninfected females mated to infected males. These competing effects, a frequency-dependent advantage and frequency-independent costs, produce bistable Wolbachia frequency dynamics. Above a threshold frequency, denoted pˆ, CI drives fitness-decreasing Wolbachia transinfections through local populations; but below pˆ, infection frequencies tend to decline to zero. If pˆ is not too high, CI also drives spatial spread once infections become established over sufficiently large areas. We illustrate how simple models provide testable predictions concerning the spatial and temporal dynamics of Wolbachia introductions, focusing on rate of spatial spread, the shape of spreading waves, and the conditions for initiating spread from local introductions. First, we consider the robustness of diffusion-based predictions to incorporating two important features of wMel-Aedes aegypti biology that may be inconsistent with the diffusion approximations, namely fast local dynamics induced by complete CI (i.e., all embryos produced from incompatible crosses die) and long-tailed, non-Gaussian dispersal. With complete CI, our numerical analyses show that long-tailed dispersal changes wave-width predictions only slightly; but it can significantly reduce wave speed relative to the diffusion prediction; it also allows smaller local introductions to initiate spatial spread. Second, we use approximations for pˆ and dispersal distances to predict the outcome of 2013 releases of wMel-infected Aedes aegypti in Cairns, Australia, Third, we describe new data from Ae. aegypti populations near Cairns, Australia that demonstrate long-distance dispersal and provide an approximate lower bound on pˆ for wMel in northeastern Australia. Finally, we apply our analyses to produce operational guidelines for efficient transformation of vector populations over large areas. We demonstrate that even very slow spatial spread, on the order of 10-20 m/month (as predicted), can produce area-wide population transformation within a few years following initial releases covering about 20-30% of the target area."}],"type":"journal_article","date_published":"2017-06-01T00:00:00Z","page":"45 - 60","publication":"Theoretical Population Biology","citation":{"ieee":"M. Turelli and N. H. Barton, “Deploying dengue-suppressing Wolbachia: Robust models predict slow but effective spatial spread in Aedes aegypti,” Theoretical Population Biology, vol. 115. Elsevier, pp. 45–60, 2017.","apa":"Turelli, M., & Barton, N. H. (2017). Deploying dengue-suppressing Wolbachia: Robust models predict slow but effective spatial spread in Aedes aegypti. Theoretical Population Biology. Elsevier. https://doi.org/10.1016/j.tpb.2017.03.003","ista":"Turelli M, Barton NH. 2017. Deploying dengue-suppressing Wolbachia: Robust models predict slow but effective spatial spread in Aedes aegypti. Theoretical Population Biology. 115, 45–60.","ama":"Turelli M, Barton NH. Deploying dengue-suppressing Wolbachia: Robust models predict slow but effective spatial spread in Aedes aegypti. Theoretical Population Biology. 2017;115:45-60. doi:10.1016/j.tpb.2017.03.003","chicago":"Turelli, Michael, and Nicholas H Barton. “Deploying Dengue-Suppressing Wolbachia: Robust Models Predict Slow but Effective Spatial Spread in Aedes Aegypti.” Theoretical Population Biology. Elsevier, 2017. https://doi.org/10.1016/j.tpb.2017.03.003.","short":"M. Turelli, N.H. Barton, Theoretical Population Biology 115 (2017) 45–60.","mla":"Turelli, Michael, and Nicholas H. Barton. “Deploying Dengue-Suppressing Wolbachia: Robust Models Predict Slow but Effective Spatial Spread in Aedes Aegypti.” Theoretical Population Biology, vol. 115, Elsevier, 2017, pp. 45–60, doi:10.1016/j.tpb.2017.03.003."},"day":"01","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1"},{"_id":"951","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":" 15","title":"Local introduction and heterogeneous spatial spread of dengue-suppressing Wolbachia through an urban population of Aedes Aegypti","status":"public","ddc":["576"],"pubrep_id":"843","file":[{"file_id":"4691","relation":"main_file","date_created":"2018-12-12T10:08:30Z","date_updated":"2020-07-14T12:48:16Z","checksum":"107d290bd1159ec77b734eb2824b01c8","file_name":"IST-2017-843-v1+1_journal.pbio.2001894.pdf","access_level":"open_access","creator":"system","file_size":5541206,"content_type":"application/pdf"}],"oa_version":"Published Version","type":"journal_article","issue":"5","abstract":[{"lang":"eng","text":"Dengue-suppressing Wolbachia strains are promising tools for arbovirus control, particularly as they have the potential to self-spread following local introductions. To test this, we followed the frequency of the transinfected Wolbachia strain wMel through Ae. aegypti in Cairns, Australia, following releases at 3 nonisolated locations within the city in early 2013. Spatial spread was analysed graphically using interpolation and by fitting a statistical model describing the position and width of the wave. For the larger 2 of the 3 releases (covering 0.97 km2 and 0.52 km2), we observed slow but steady spatial spread, at about 100–200 m per year, roughly consistent with theoretical predictions. In contrast, the smallest release (0.11 km2) produced erratic temporal and spatial dynamics, with little evidence of spread after 2 years. This is consistent with the prediction concerning fitness-decreasing Wolbachia transinfections that a minimum release area is needed to achieve stable local establishment and spread in continuous habitats. Our graphical and likelihood analyses produced broadly consistent estimates of wave speed and wave width. Spread at all sites was spatially heterogeneous, suggesting that environmental heterogeneity will affect large-scale Wolbachia transformations of urban mosquito populations. The persistence and spread of Wolbachia in release areas meeting minimum area requirements indicates the promise of successful large-scale population transfo"}],"citation":{"ama":"Schmidt T, Barton NH, Rasic G, et al. Local introduction and heterogeneous spatial spread of dengue-suppressing Wolbachia through an urban population of Aedes Aegypti. PLoS Biology. 2017;15(5). doi:10.1371/journal.pbio.2001894","apa":"Schmidt, T., Barton, N. H., Rasic, G., Turley, A., Montgomery, B., Iturbe Ormaetxe, I., … Turelli, M. (2017). Local introduction and heterogeneous spatial spread of dengue-suppressing Wolbachia through an urban population of Aedes Aegypti. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2001894","ieee":"T. Schmidt et al., “Local introduction and heterogeneous spatial spread of dengue-suppressing Wolbachia through an urban population of Aedes Aegypti,” PLoS Biology, vol. 15, no. 5. Public Library of Science, 2017.","ista":"Schmidt T, Barton NH, Rasic G, Turley A, Montgomery B, Iturbe Ormaetxe I, Cook P, Ryan P, Ritchie S, Hoffmann A, O’Neill S, Turelli M. 2017. Local introduction and heterogeneous spatial spread of dengue-suppressing Wolbachia through an urban population of Aedes Aegypti. PLoS Biology. 15(5), e2001894.","short":"T. Schmidt, N.H. Barton, G. Rasic, A. Turley, B. Montgomery, I. Iturbe Ormaetxe, P. Cook, P. Ryan, S. Ritchie, A. Hoffmann, S. O’Neill, M. Turelli, PLoS Biology 15 (2017).","mla":"Schmidt, Tom, et al. “Local Introduction and Heterogeneous Spatial Spread of Dengue-Suppressing Wolbachia through an Urban Population of Aedes Aegypti.” PLoS Biology, vol. 15, no. 5, e2001894, Public Library of Science, 2017, doi:10.1371/journal.pbio.2001894.","chicago":"Schmidt, Tom, Nicholas H Barton, Gordana Rasic, Andrew Turley, Brian Montgomery, Inaki Iturbe Ormaetxe, Peter Cook, et al. “Local Introduction and Heterogeneous Spatial Spread of Dengue-Suppressing Wolbachia through an Urban Population of Aedes Aegypti.” PLoS Biology. Public Library of Science, 2017. https://doi.org/10.1371/journal.pbio.2001894."},"publication":"PLoS Biology","date_published":"2017-05-30T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"30","year":"2017","department":[{"_id":"NiBa"}],"publisher":"Public Library of Science","publication_status":"published","related_material":{"record":[{"id":"9856","relation":"research_data","status":"public"},{"status":"public","relation":"research_data","id":"9857"},{"id":"9858","status":"public","relation":"research_data"}]},"author":[{"last_name":"Schmidt","first_name":"Tom","full_name":"Schmidt, Tom"},{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"},{"full_name":"Rasic, Gordana","first_name":"Gordana","last_name":"Rasic"},{"last_name":"Turley","first_name":"Andrew","full_name":"Turley, Andrew"},{"first_name":"Brian","last_name":"Montgomery","full_name":"Montgomery, Brian"},{"full_name":"Iturbe Ormaetxe, Inaki","last_name":"Iturbe Ormaetxe","first_name":"Inaki"},{"full_name":"Cook, Peter","first_name":"Peter","last_name":"Cook"},{"full_name":"Ryan, Peter","last_name":"Ryan","first_name":"Peter"},{"first_name":"Scott","last_name":"Ritchie","full_name":"Ritchie, Scott"},{"full_name":"Hoffmann, Ary","first_name":"Ary","last_name":"Hoffmann"},{"first_name":"Scott","last_name":"O’Neill","full_name":"O’Neill, Scott"},{"full_name":"Turelli, Michael","last_name":"Turelli","first_name":"Michael"}],"volume":15,"date_updated":"2023-09-22T10:02:52Z","date_created":"2018-12-11T11:49:22Z","article_number":"e2001894","publist_id":"6464","file_date_updated":"2020-07-14T12:48:16Z","external_id":{"isi":["000402520000012"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","isi":1,"doi":"10.1371/journal.pbio.2001894","language":[{"iso":"eng"}],"publication_identifier":{"issn":["15449173"]},"month":"05"},{"day":"30","month":"05","article_processing_charge":"No","date_published":"2017-05-30T00:00:00Z","doi":"10.1371/journal.pbio.2001894.s016","citation":{"ista":"Schmidt T, Barton NH, Rasic G, Turley A, Montgomery B, Iturbe Ormaetxe I, Cook P, Ryan P, Ritchie S, Hoffmann A, O’Neill S, Turelli M. 2017. Excel file with data on mosquito densities, Wolbachia infection status and housing characteristics, Public Library of Science, 10.1371/journal.pbio.2001894.s016.","ieee":"T. Schmidt et al., “Excel file with data on mosquito densities, Wolbachia infection status and housing characteristics.” Public Library of Science, 2017.","apa":"Schmidt, T., Barton, N. H., Rasic, G., Turley, A., Montgomery, B., Iturbe Ormaetxe, I., … Turelli, M. (2017). Excel file with data on mosquito densities, Wolbachia infection status and housing characteristics. Public Library of Science. https://doi.org/10.1371/journal.pbio.2001894.s016","ama":"Schmidt T, Barton NH, Rasic G, et al. Excel file with data on mosquito densities, Wolbachia infection status and housing characteristics. 2017. doi:10.1371/journal.pbio.2001894.s016","chicago":"Schmidt, Tom, Nicholas H Barton, Gordana Rasic, Andrew Turley, Brian Montgomery, Inaki Iturbe Ormaetxe, Peter Cook, et al. “Excel File with Data on Mosquito Densities, Wolbachia Infection Status and Housing Characteristics.” Public Library of Science, 2017. https://doi.org/10.1371/journal.pbio.2001894.s016.","mla":"Schmidt, Tom, et al. Excel File with Data on Mosquito Densities, Wolbachia Infection Status and Housing Characteristics. Public Library of Science, 2017, doi:10.1371/journal.pbio.2001894.s016.","short":"T. Schmidt, N.H. Barton, G. Rasic, A. Turley, B. Montgomery, I. Iturbe Ormaetxe, P. Cook, P. Ryan, S. Ritchie, A. Hoffmann, S. O’Neill, M. Turelli, (2017)."},"type":"research_data_reference","author":[{"first_name":"Tom","last_name":"Schmidt","full_name":"Schmidt, Tom"},{"last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"},{"full_name":"Rasic, Gordana","first_name":"Gordana","last_name":"Rasic"},{"full_name":"Turley, Andrew","last_name":"Turley","first_name":"Andrew"},{"last_name":"Montgomery","first_name":"Brian","full_name":"Montgomery, Brian"},{"last_name":"Iturbe Ormaetxe","first_name":"Inaki","full_name":"Iturbe Ormaetxe, Inaki"},{"full_name":"Cook, Peter","first_name":"Peter","last_name":"Cook"},{"full_name":"Ryan, Peter","first_name":"Peter","last_name":"Ryan"},{"full_name":"Ritchie, Scott","first_name":"Scott","last_name":"Ritchie"},{"first_name":"Ary","last_name":"Hoffmann","full_name":"Hoffmann, Ary"},{"full_name":"O’Neill, Scott","first_name":"Scott","last_name":"O’Neill"},{"last_name":"Turelli","first_name":"Michael","full_name":"Turelli, Michael"}],"related_material":{"record":[{"id":"951","status":"public","relation":"used_in_publication"}]},"date_created":"2021-08-10T07:47:07Z","date_updated":"2023-09-22T10:02:51Z","oa_version":"Published Version","year":"2017","_id":"9858","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","status":"public","title":"Excel file with data on mosquito densities, Wolbachia infection status and housing characteristics","department":[{"_id":"NiBa"}],"publisher":"Public Library of Science"},{"_id":"9857","year":"2017","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","status":"public","title":"Supporting information concerning observed wMel frequencies and analyses of habitat variables","department":[{"_id":"NiBa"}],"publisher":"Public Library of Science ","author":[{"first_name":"Tom","last_name":"Schmidt","full_name":"Schmidt, Tom"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"},{"first_name":"Gordana","last_name":"Rasic","full_name":"Rasic, Gordana"},{"first_name":"Andrew","last_name":"Turley","full_name":"Turley, Andrew"},{"full_name":"Montgomery, Brian","first_name":"Brian","last_name":"Montgomery"},{"last_name":"Iturbe Ormaetxe","first_name":"Inaki","full_name":"Iturbe Ormaetxe, Inaki"},{"first_name":"Peter","last_name":"Cook","full_name":"Cook, Peter"},{"full_name":"Ryan, Peter","last_name":"Ryan","first_name":"Peter"},{"full_name":"Ritchie, Scott","last_name":"Ritchie","first_name":"Scott"},{"last_name":"Hoffmann","first_name":"Ary","full_name":"Hoffmann, Ary"},{"full_name":"O’Neill, Scott","first_name":"Scott","last_name":"O’Neill"},{"full_name":"Turelli, Michael","last_name":"Turelli","first_name":"Michael"}],"related_material":{"record":[{"id":"951","relation":"used_in_publication","status":"public"}]},"date_updated":"2023-09-22T10:02:51Z","date_created":"2021-08-10T07:41:52Z","oa_version":"Published Version","type":"research_data_reference","citation":{"ieee":"T. Schmidt et al., “Supporting information concerning observed wMel frequencies and analyses of habitat variables.” Public Library of Science , 2017.","apa":"Schmidt, T., Barton, N. H., Rasic, G., Turley, A., Montgomery, B., Iturbe Ormaetxe, I., … Turelli, M. (2017). Supporting information concerning observed wMel frequencies and analyses of habitat variables. Public Library of Science . https://doi.org/10.1371/journal.pbio.2001894.s015","ista":"Schmidt T, Barton NH, Rasic G, Turley A, Montgomery B, Iturbe Ormaetxe I, Cook P, Ryan P, Ritchie S, Hoffmann A, O’Neill S, Turelli M. 2017. Supporting information concerning observed wMel frequencies and analyses of habitat variables, Public Library of Science , 10.1371/journal.pbio.2001894.s015.","ama":"Schmidt T, Barton NH, Rasic G, et al. Supporting information concerning observed wMel frequencies and analyses of habitat variables. 2017. doi:10.1371/journal.pbio.2001894.s015","chicago":"Schmidt, Tom, Nicholas H Barton, Gordana Rasic, Andrew Turley, Brian Montgomery, Inaki Iturbe Ormaetxe, Peter Cook, et al. “Supporting Information Concerning Observed WMel Frequencies and Analyses of Habitat Variables.” Public Library of Science , 2017. https://doi.org/10.1371/journal.pbio.2001894.s015.","short":"T. Schmidt, N.H. Barton, G. Rasic, A. Turley, B. Montgomery, I. Iturbe Ormaetxe, P. Cook, P. Ryan, S. Ritchie, A. Hoffmann, S. O’Neill, M. Turelli, (2017).","mla":"Schmidt, Tom, et al. Supporting Information Concerning Observed WMel Frequencies and Analyses of Habitat Variables. Public Library of Science , 2017, doi:10.1371/journal.pbio.2001894.s015."},"doi":"10.1371/journal.pbio.2001894.s015","date_published":"2017-05-30T00:00:00Z","month":"05","day":"30","article_processing_charge":"No"}]