[{"license":"https://creativecommons.org/licenses/by-nc/4.0/","file_date_updated":"2024-01-23T08:10:00Z","article_number":"kzad002","volume":2,"date_updated":"2024-01-23T08:13:43Z","date_created":"2024-01-18T07:54:10Z","author":[{"full_name":"Stankowski, Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","last_name":"Stankowski","first_name":"Sean"},{"first_name":"Zuzanna B","last_name":"Zagrodzka","full_name":"Zagrodzka, Zuzanna B"},{"last_name":"Galindo","first_name":"Juan","full_name":"Galindo, Juan"},{"last_name":"Montaño-Rendón","first_name":"Mauricio","full_name":"Montaño-Rendón, Mauricio"},{"full_name":"Faria, Rui","last_name":"Faria","first_name":"Rui"},{"full_name":"Mikhailova, Natalia","last_name":"Mikhailova","first_name":"Natalia"},{"full_name":"Blakeslee, April M H","last_name":"Blakeslee","first_name":"April M H"},{"last_name":"Arnason","first_name":"Einar","full_name":"Arnason, Einar"},{"first_name":"Thomas","last_name":"Broquet","full_name":"Broquet, Thomas"},{"full_name":"Morales, Hernán E","first_name":"Hernán E","last_name":"Morales"},{"full_name":"Grahame, John W","last_name":"Grahame","first_name":"John W"},{"first_name":"Anja M","last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M"},{"full_name":"Johannesson, Kerstin","first_name":"Kerstin","last_name":"Johannesson"},{"full_name":"Butlin, Roger K","last_name":"Butlin","first_name":"Roger K"}],"department":[{"_id":"NiBa"}],"publisher":"Oxford University Press","publication_status":"published","year":"2023","acknowledgement":"Isobel Eyres, Richard Turney, Graciela Sotelo, Jenny Larson, and Stéphane Loisel helped with the collection and processing of samples. Petri Kemppainen kindly provided samples from Trondheim Fjord. Mark Dunning helped with the development of bioinformatic pipelines. The analysis of genomic data was conducted on the University of Sheffield high-performance computing cluster, ShARC. Funding was provided by the Natural Environment Research Council (NERC) and the European Research Council (ERC). J.G. was funded by a Juntas Industriales y Navales (JIN) project (Ministerio de Ciencia, Innovación y Universidades, code RTI2018-101274-J-I00).","publication_identifier":{"eissn":["2752-938X"]},"month":"08","language":[{"iso":"eng"}],"doi":"10.1093/evolinnean/kzad002","quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"issue":"1","abstract":[{"text":"Understanding the factors that have shaped the current distributions and diversity of species is a central and longstanding aim of evolutionary biology. The recent inclusion of genomic data into phylogeographic studies has dramatically improved our understanding in organisms where evolutionary relationships have been challenging to infer. We used whole-genome sequences to study the phylogeography of the intertidal snail Littorina saxatilis, which has successfully colonized and diversified across a broad range of coastal environments in the Northern Hemisphere amid repeated cycles of glaciation. Building on past studies based on short DNA sequences, we used genome-wide data to provide a clearer picture of the relationships among samples spanning most of the species natural range. Our results confirm the trans-Atlantic colonization of North America from Europe, and have allowed us to identify rough locations of glacial refugia and to infer likely routes of colonization within Europe. We also investigated the signals in different datasets to account for the effects of genomic architecture and non-neutral evolution, which provides new insights about diversification of four ecotypes of L. saxatilis (the crab, wave, barnacle, and brackish ecotypes) at different spatial scales. Overall, we provide a much clearer picture of the biogeography of L. saxatilis, providing a foundation for more detailed phylogenomic and demographic studies.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"creator":"dernst","file_size":3408944,"content_type":"application/pdf","access_level":"open_access","file_name":"2023_EvolJourLinneanSociety_Stankowski.pdf","success":1,"checksum":"ba6f9102d3a9fe6631c4fa398c5e4313","date_updated":"2024-01-23T08:10:00Z","date_created":"2024-01-23T08:10:00Z","file_id":"14875","relation":"main_file"}],"intvolume":" 2","ddc":["570"],"title":"Whole-genome phylogeography of the intertidal snail Littorina saxatilis","status":"public","_id":"14833","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"17","date_published":"2023-08-17T00:00:00Z","article_type":"original","citation":{"chicago":"Stankowski, Sean, Zuzanna B Zagrodzka, Juan Galindo, Mauricio Montaño-Rendón, Rui Faria, Natalia Mikhailova, April M H Blakeslee, et al. “Whole-Genome Phylogeography of the Intertidal Snail Littorina Saxatilis.” Evolutionary Journal of the Linnean Society. Oxford University Press, 2023. https://doi.org/10.1093/evolinnean/kzad002.","mla":"Stankowski, Sean, et al. “Whole-Genome Phylogeography of the Intertidal Snail Littorina Saxatilis.” Evolutionary Journal of the Linnean Society, vol. 2, no. 1, kzad002, Oxford University Press, 2023, doi:10.1093/evolinnean/kzad002.","short":"S. Stankowski, Z.B. Zagrodzka, J. Galindo, M. Montaño-Rendón, R. Faria, N. Mikhailova, A.M.H. Blakeslee, E. Arnason, T. Broquet, H.E. Morales, J.W. Grahame, A.M. Westram, K. Johannesson, R.K. Butlin, Evolutionary Journal of the Linnean Society 2 (2023).","ista":"Stankowski S, Zagrodzka ZB, Galindo J, Montaño-Rendón M, Faria R, Mikhailova N, Blakeslee AMH, Arnason E, Broquet T, Morales HE, Grahame JW, Westram AM, Johannesson K, Butlin RK. 2023. Whole-genome phylogeography of the intertidal snail Littorina saxatilis. Evolutionary Journal of the Linnean Society. 2(1), kzad002.","ieee":"S. Stankowski et al., “Whole-genome phylogeography of the intertidal snail Littorina saxatilis,” Evolutionary Journal of the Linnean Society, vol. 2, no. 1. Oxford University Press, 2023.","apa":"Stankowski, S., Zagrodzka, Z. B., Galindo, J., Montaño-Rendón, M., Faria, R., Mikhailova, N., … Butlin, R. K. (2023). Whole-genome phylogeography of the intertidal snail Littorina saxatilis. Evolutionary Journal of the Linnean Society. Oxford University Press. https://doi.org/10.1093/evolinnean/kzad002","ama":"Stankowski S, Zagrodzka ZB, Galindo J, et al. Whole-genome phylogeography of the intertidal snail Littorina saxatilis. Evolutionary Journal of the Linnean Society. 2023;2(1). doi:10.1093/evolinnean/kzad002"},"publication":"Evolutionary Journal of the Linnean Society"},{"year":"2023","_id":"14732","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","status":"public","title":"Genetic load, eco-evolutionary feedback and extinction in a metapopulation","publication_status":"submitted","department":[{"_id":"NiBa"},{"_id":"JaMa"}],"author":[{"full_name":"Olusanya, Oluwafunmilola O","last_name":"Olusanya","first_name":"Oluwafunmilola O","orcid":"0000-0003-1971-8314","id":"41AD96DC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Khudiakova, Kseniia","id":"4E6DC800-AE37-11E9-AC72-31CAE5697425","orcid":"0000-0002-6246-1465","first_name":"Kseniia","last_name":"Khudiakova"},{"last_name":"Sachdeva","first_name":"Himani","id":"42377A0A-F248-11E8-B48F-1D18A9856A87","full_name":"Sachdeva, Himani"}],"related_material":{"record":[{"id":"14711","relation":"dissertation_contains","status":"public"}]},"date_created":"2024-01-04T09:35:54Z","date_updated":"2024-01-26T12:00:53Z","oa_version":"Preprint","type":"preprint","abstract":[{"text":"Fragmented landscapes pose a significant threat to the persistence of species as they are highly susceptible to heightened risk of extinction due to the combined effects of genetic and demographic factors such as genetic drift and demographic stochasticity. This paper explores the intricate interplay between genetic load and extinction risk within metapopulations with a focus on understanding the impact of eco-evolutionary feedback mechanisms. We distinguish between two models of selection: soft selection, characterised by subpopulations maintaining carrying capacity despite load, and hard selection, where load can significantly affect population size. Within the soft selection framework, we investigate the impact of gene flow on genetic load at a single locus, while also considering the effect of selection strength and dominance coefficient. We subsequently build on this to examine how gene flow influences both population size and load under hard selection as well as identify critical thresholds for metapopulation persistence. Our analysis employs the diffusion, semi-deterministic and effective migration approximations. Our findings reveal that under soft selection, even modest levels of migration can significantly alleviate the burden of load. In sharp contrast, with hard selection, a much higher degree of gene flow is required to mitigate load and prevent the collapse of the metapopulation. Overall, this study sheds light into the crucial role migration plays in shaping the dynamics of genetic load and extinction risk in fragmented landscapes, offering valuable insights for conservation strategies and the preservation of diversity in a changing world.","lang":"eng"}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","publication":"bioRxiv","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2023.12.02.569702v1"}],"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"},"citation":{"chicago":"Olusanya, Oluwafunmilola O, Kseniia Khudiakova, and Himani Sachdeva. “Genetic Load, Eco-Evolutionary Feedback and Extinction in a Metapopulation.” BioRxiv, n.d. https://doi.org/10.1101/2023.12.02.569702.","mla":"Olusanya, Oluwafunmilola O., et al. “Genetic Load, Eco-Evolutionary Feedback and Extinction in a Metapopulation.” BioRxiv, doi:10.1101/2023.12.02.569702.","short":"O.O. Olusanya, K. Khudiakova, H. Sachdeva, BioRxiv (n.d.).","ista":"Olusanya OO, Khudiakova K, Sachdeva H. Genetic load, eco-evolutionary feedback and extinction in a metapopulation. bioRxiv, 10.1101/2023.12.02.569702.","apa":"Olusanya, O. O., Khudiakova, K., & Sachdeva, H. (n.d.). Genetic load, eco-evolutionary feedback and extinction in a metapopulation. bioRxiv. https://doi.org/10.1101/2023.12.02.569702","ieee":"O. O. Olusanya, K. Khudiakova, and H. Sachdeva, “Genetic load, eco-evolutionary feedback and extinction in a metapopulation,” bioRxiv. .","ama":"Olusanya OO, Khudiakova K, Sachdeva H. Genetic load, eco-evolutionary feedback and extinction in a metapopulation. bioRxiv. doi:10.1101/2023.12.02.569702"},"oa":1,"project":[{"grant_number":"P32896","_id":"c08d3278-5a5b-11eb-8a69-fdb09b55f4b8","name":"Causes and consequences of population fragmentation"},{"grant_number":"26293","_id":"34d33d68-11ca-11ed-8bc3-ec13763c0ca8","name":"The impact of deleterious mutations on small populations"},{"grant_number":"26380","_id":"34c872fe-11ca-11ed-8bc3-8534b82131e6","name":"Polygenic Adaptation in a Metapopulation"}],"date_published":"2023-12-04T00:00:00Z","doi":"10.1101/2023.12.02.569702","language":[{"iso":"eng"}],"day":"04","month":"12","article_processing_charge":"No"},{"month":"09","day":"05","has_accepted_license":"1","article_processing_charge":"No","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.8318995"}],"citation":{"ista":"Stankowski S. 2023. Data and code for: The genetic architecture of a recent transition to live-bearing in marine snails, Zenodo, 10.5281/ZENODO.8318995.","apa":"Stankowski, S. (2023). Data and code for: The genetic architecture of a recent transition to live-bearing in marine snails. Zenodo. https://doi.org/10.5281/ZENODO.8318995","ieee":"S. Stankowski, “Data and code for: The genetic architecture of a recent transition to live-bearing in marine snails.” Zenodo, 2023.","ama":"Stankowski S. Data and code for: The genetic architecture of a recent transition to live-bearing in marine snails. 2023. doi:10.5281/ZENODO.8318995","chicago":"Stankowski, Sean. “Data and Code for: The Genetic Architecture of a Recent Transition to Live-Bearing in Marine Snails.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8318995.","mla":"Stankowski, Sean. Data and Code for: The Genetic Architecture of a Recent Transition to Live-Bearing in Marine Snails. Zenodo, 2023, doi:10.5281/ZENODO.8318995.","short":"S. Stankowski, (2023)."},"date_published":"2023-09-05T00:00:00Z","doi":"10.5281/ZENODO.8318995","type":"research_data_reference","abstract":[{"text":"This repository contains the code and VCF files needed to conduct the analyses in our MS. Each folder contains a readMe document explaining the nature of each file and dataset and the results and analyses that they relate to. The same anlaysis code (but not VCF files) is also available at https://github.com/seanstankowski/Littorina_reproductive_mode","lang":"eng"}],"license":"https://creativecommons.org/licenses/by/4.0/","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14812","year":"2023","ddc":["570"],"title":"Data and code for: The genetic architecture of a recent transition to live-bearing in marine snails","status":"public","department":[{"_id":"NiBa"}],"publisher":"Zenodo","author":[{"first_name":"Sean","last_name":"Stankowski","id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean"}],"contributor":[{"first_name":"Zusanna","last_name":"Zagrodzka"},{"last_name":"Garlovsky","first_name":"Martin"},{"last_name":"Pal","first_name":"Arka","orcid":"0000-0002-4530-8469","id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425"},{"id":"428A94B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1145-9226","first_name":"Daria","last_name":"Shipilina"},{"id":"ae681a14-dc74-11ea-a0a7-c6ef18161701","first_name":"Diego Fernando","last_name":"Garcia Castillo"},{"last_name":"Lifchitz","first_name":"Hila","id":"d6ab5470-2fb3-11ed-8633-986a9b84edac"},{"last_name":"Le Moan","first_name":"Alan"},{"first_name":"Erica","last_name":"Leder"},{"first_name":"James","last_name":"Reeve"},{"last_name":"Johannesson","first_name":"Kerstin"},{"first_name":"Anja M","last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969"},{"last_name":"Butlin","first_name":"Roger"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"14796"}]},"date_created":"2024-01-16T10:23:01Z","date_updated":"2024-03-05T09:35:25Z","oa_version":"Published Version"},{"year":"2023","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"publisher":"Institute of Science and Technology Austria","author":[{"id":"1cf464b2-dc7d-11ea-9b2f-f9b1aa9417d1","first_name":"Mara","last_name":"Julseth","full_name":"Julseth, Mara"}],"date_updated":"2023-06-02T22:30:05Z","date_created":"2023-04-04T18:57:11Z","file_date_updated":"2023-06-02T22:30:04Z","oa":1,"doi":"10.15479/at:ista:12800","degree_awarded":"MS","supervisor":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H"}],"language":[{"iso":"eng"}],"month":"04","publication_identifier":{"issn":["2791-4585"]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"12800","status":"public","title":"The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone","ddc":["576"],"oa_version":"Published Version","file":[{"relation":"supplementary_material","file_id":"12805","date_updated":"2023-06-02T22:30:04Z","date_created":"2023-04-06T06:09:40Z","checksum":"b76cf6d69f2093d8248f6a3f9d4654a4","embargo_to":"open_access","file_name":"Dispersaldata.xlsx","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet","file_size":52795,"creator":"mjulseth"},{"creator":"mjulseth","content_type":"application/vnd.wolfram.nb","file_size":787239,"file_name":"2023_MSc_ThesisMaraJulseth_Notebook.nb","access_level":"open_access","date_created":"2023-04-06T06:11:27Z","date_updated":"2023-06-02T22:30:04Z","checksum":"5a13b6d204371572e249f03795bc0d04","file_id":"12806","embargo":"2023-06-01","relation":"supplementary_material"},{"creator":"mjulseth","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":1061763,"file_name":"ThesisMaraJulseth_04_23.docx","embargo_to":"open_access","access_level":"closed","date_created":"2023-04-06T08:26:12Z","date_updated":"2023-06-02T22:30:04Z","checksum":"c3ec842839ed1e66bf2618ae33047df8","file_id":"12812","relation":"source_file"},{"file_id":"12813","embargo":"2023-06-01","relation":"main_file","date_created":"2023-04-06T08:26:37Z","date_updated":"2023-06-02T22:30:04Z","checksum":"3132cc998fbe3ae2a3a83c2a69367f37","file_name":"ThesisMaraJulseth_04_23.pdf","access_level":"open_access","creator":"mjulseth","file_size":1741364,"content_type":"application/pdf"}],"type":"dissertation","alternative_title":["ISTA Master's Thesis"],"abstract":[{"lang":"eng","text":"The evolutionary processes that brought about today’s plethora of living species and the many billions more ancient ones all underlie biology. Evolutionary pathways are neither directed nor deterministic, but rather an interplay between selection, migration, mutation, genetic drift and other environmental factors. Hybrid zones, as natural crossing experiments, offer a great opportunity to use cline analysis to deduce different evolutionary processes - for example, selection strength. Theoretical cline models, largely assuming uniform distribution of individuals, often lack the capability of incorporating population structure. Since in reality organisms mostly live in patchy distributions and their dispersal is hardly ever Gaussian, it is necessary to unravel the effect of these different elements of population structure on cline parameters and shape. In this thesis, I develop a simulation inspired by the A. majus hybrid zone of a single selected locus under frequency dependent selection. This simulation enables us to untangle the effects of different elements of population structure as for example a low-density center and long-range dispersal. This thesis is therefore a first step towards theoretically untangling the effects of different elements of population structure on cline parameters and shape. "}],"citation":{"ama":"Julseth M. The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone. 2023. doi:10.15479/at:ista:12800","apa":"Julseth, M. (2023). The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12800","ieee":"M. Julseth, “The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone,” Institute of Science and Technology Austria, 2023.","ista":"Julseth M. 2023. The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone. Institute of Science and Technology Austria.","short":"M. Julseth, The Effect of Local Population Structure on Genetic Variation at Selected Loci in the A. Majus Hybrid Zone, Institute of Science and Technology Austria, 2023.","mla":"Julseth, Mara. The Effect of Local Population Structure on Genetic Variation at Selected Loci in the A. Majus Hybrid Zone. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12800.","chicago":"Julseth, Mara. “The Effect of Local Population Structure on Genetic Variation at Selected Loci in the A. Majus Hybrid Zone.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12800."},"page":"21","date_published":"2023-04-05T00:00:00Z","day":"05","has_accepted_license":"1","article_processing_charge":"No"},{"date_published":"2022-07-18T00:00:00Z","article_type":"original","citation":{"chicago":"Barton, Nicholas H. “The ‘New Synthesis.’” Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences, 2022. https://doi.org/10.1073/pnas.2122147119.","short":"N.H. Barton, Proceedings of the National Academy of Sciences of the United States of America 119 (2022).","mla":"Barton, Nicholas H. “The ‘New Synthesis.’” Proceedings of the National Academy of Sciences of the United States of America, vol. 119, no. 30, e2122147119, Proceedings of the National Academy of Sciences, 2022, doi:10.1073/pnas.2122147119.","ieee":"N. H. Barton, “The ‘New Synthesis,’” Proceedings of the National Academy of Sciences of the United States of America, vol. 119, no. 30. Proceedings of the National Academy of Sciences, 2022.","apa":"Barton, N. H. (2022). The “New Synthesis.” Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2122147119","ista":"Barton NH. 2022. The ‘New Synthesis’. Proceedings of the National Academy of Sciences of the United States of America. 119(30), e2122147119.","ama":"Barton NH. The “New Synthesis.” Proceedings of the National Academy of Sciences of the United States of America. 2022;119(30). doi:10.1073/pnas.2122147119"},"publication":"Proceedings of the National Academy of Sciences of the United States of America","has_accepted_license":"1","article_processing_charge":"No","day":"18","scopus_import":"1","oa_version":"Published Version","file":[{"file_name":"2022_PNAS_Barton.pdf","access_level":"open_access","creator":"dernst","file_size":848511,"content_type":"application/pdf","file_id":"11716","relation":"main_file","date_created":"2022-08-01T10:58:28Z","date_updated":"2022-08-01T10:58:28Z","success":1,"checksum":"06c866196a8957f0c37b8a121771c885"}],"intvolume":" 119","ddc":["570"],"status":"public","title":"The \"New Synthesis\"","_id":"11702","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"30","abstract":[{"text":"When Mendel’s work was rediscovered in 1900, and extended to establish classical genetics, it was initially seen in opposition to Darwin’s theory of evolution by natural selection on continuous variation, as represented by the biometric research program that was the foundation of quantitative genetics. As Fisher, Haldane, and Wright established a century ago, Mendelian inheritance is exactly what is needed for natural selection to work efficiently. Yet, the synthesis remains unfinished. We do not understand why sexual reproduction and a fair meiosis predominate in eukaryotes, or how far these are responsible for their diversity and complexity. Moreover, although quantitative geneticists have long known that adaptive variation is highly polygenic, and that this is essential for efficient selection, this is only now becoming appreciated by molecular biologists—and we still do not have a good framework for understanding polygenic variation or diffuse function.","lang":"eng"}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1073/pnas.2122147119","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["35858408"]},"oa":1,"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"month":"07","volume":119,"date_updated":"2022-08-01T11:00:25Z","date_created":"2022-07-31T22:01:47Z","author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H"}],"publisher":"Proceedings of the National Academy of Sciences","department":[{"_id":"NiBa"}],"publication_status":"published","pmid":1,"acknowledgement":"I thank Laura Hayward, Jitka Polechova, and Anja Westram for discussions and comments.","year":"2022","file_date_updated":"2022-08-01T10:58:28Z","article_number":"e2122147119"},{"file_date_updated":"2022-04-07T08:11:51Z","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"publication_status":"published","year":"2022","date_created":"2022-04-07T08:19:54Z","date_updated":"2023-06-23T06:26:41Z","author":[{"last_name":"Matejovicova","first_name":"Lenka","id":"2DFDEC72-F248-11E8-B48F-1D18A9856A87","full_name":"Matejovicova, Lenka"}],"publication_identifier":{"isbn":["978-3-99078-016-9"],"issn":["2663-337X"]},"month":"04","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"},"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"}],"degree_awarded":"PhD","supervisor":[{"last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"}],"doi":"10.15479/at:ista:11128","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"lang":"eng","text":"Although we often see studies focusing on simple or even discrete traits in studies of colouration,\r\nthe variation of “appearance” phenotypes found in nature is often more complex, continuous\r\nand high-dimensional. Therefore, we developed automated methods suitable for large datasets\r\nof genomes and images, striving to account for their complex nature, while minimising human\r\nbias. We used these methods on a dataset of more than 20, 000 plant SNP genomes and\r\ncorresponding fower images from a hybrid zone of two subspecies of Antirrhinum majus with\r\ndistinctly coloured fowers to improve our understanding of the genetic nature of the fower\r\ncolour in our study system.\r\nFirstly, we use the advantage of large numbers of genotyped plants to estimate the haplotypes in\r\nthe main fower colour regulating region. We study colour- and geography-related characteristics\r\nof the estimated haplotypes and how they connect to their relatedness. We show discrepancies\r\nfrom the expected fower colour distributions given the genotype and identify particular\r\nhaplotypes leading to unexpected phenotypes. We also confrm a signifcant defcit of the\r\ndouble recessive recombinant and quite surprisingly, we show that haplotypes of the most\r\nfrequent parental type are much less variable than others.\r\nSecondly, we introduce our pipeline capable of processing tens of thousands of full fower\r\nimages without human interaction and summarising each image into a set of informative scores.\r\nWe show the compatibility of these machine-measured fower colour scores with the previously\r\nused manual scores and study impact of external efect on the resulting scores. Finally, we use\r\nthe machine-measured fower colour scores to ft and examine a phenotype cline across the\r\nhybrid zone in Planoles using full fower images as opposed to discrete, manual scores and\r\ncompare it with the genotypic cline."}],"ddc":["576","582"],"title":"Genetic basis of flower colour as a model for adaptive evolution","status":"public","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"11128","oa_version":"Published Version","file":[{"file_name":"LenkaPhD_Official_PDFA.pdf","access_level":"open_access","creator":"cchlebak","file_size":11906472,"content_type":"application/pdf","file_id":"11129","relation":"main_file","date_updated":"2022-04-07T08:11:34Z","date_created":"2022-04-07T08:11:34Z","checksum":"e9609bc4e8f8e20146fc1125fd4f1bf7"},{"access_level":"closed","file_name":"LenkaPhD Official_source.zip","creator":"cchlebak","file_size":23036766,"content_type":"application/x-zip-compressed","file_id":"11130","relation":"source_file","checksum":"99d67040432fd07a225643a212ee8588","date_updated":"2022-04-07T08:11:51Z","date_created":"2022-04-07T08:11:51Z"}],"article_processing_charge":"No","has_accepted_license":"1","day":"06","page":"112","citation":{"ama":"Matejovicova L. Genetic basis of flower colour as a model for adaptive evolution. 2022. doi:10.15479/at:ista:11128","ieee":"L. Matejovicova, “Genetic basis of flower colour as a model for adaptive evolution,” Institute of Science and Technology Austria, 2022.","apa":"Matejovicova, L. (2022). Genetic basis of flower colour as a model for adaptive evolution. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11128","ista":"Matejovicova L. 2022. Genetic basis of flower colour as a model for adaptive evolution. Institute of Science and Technology Austria.","short":"L. Matejovicova, Genetic Basis of Flower Colour as a Model for Adaptive Evolution, Institute of Science and Technology Austria, 2022.","mla":"Matejovicova, Lenka. Genetic Basis of Flower Colour as a Model for Adaptive Evolution. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11128.","chicago":"Matejovicova, Lenka. “Genetic Basis of Flower Colour as a Model for Adaptive Evolution.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11128."},"date_published":"2022-04-06T00:00:00Z"},{"article_processing_charge":"No","has_accepted_license":"1","day":"01","keyword":["genetics","ecology","evolution","behavior and systematics"],"date_published":"2022-02-01T00:00:00Z","page":"92-105","article_type":"original","citation":{"ista":"Turelli M, Barton NH. 2022. Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics, and disease control. Evolution Letters. 6(1), 92–105.","apa":"Turelli, M., & Barton, N. H. (2022). Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics, and disease control. Evolution Letters. Wiley. https://doi.org/10.1002/evl3.270","ieee":"M. Turelli and N. H. Barton, “Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics, and disease control,” Evolution Letters, vol. 6, no. 1. Wiley, pp. 92–105, 2022.","ama":"Turelli M, Barton NH. Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics, and disease control. Evolution Letters. 2022;6(1):92-105. doi:10.1002/evl3.270","chicago":"Turelli, Michael, and Nicholas H Barton. “Why Did the Wolbachia Transinfection Cross the Road? Drift, Deterministic Dynamics, and Disease Control.” Evolution Letters. Wiley, 2022. https://doi.org/10.1002/evl3.270.","mla":"Turelli, Michael, and Nicholas H. Barton. “Why Did the Wolbachia Transinfection Cross the Road? Drift, Deterministic Dynamics, and Disease Control.” Evolution Letters, vol. 6, no. 1, Wiley, 2022, pp. 92–105, doi:10.1002/evl3.270.","short":"M. Turelli, N.H. Barton, Evolution Letters 6 (2022) 92–105."},"publication":"Evolution Letters","issue":"1","abstract":[{"lang":"eng","text":"Maternally inherited Wolbachia transinfections are being introduced into natural mosquito populations to reduce the transmission of dengue, Zika, and other arboviruses. Wolbachia-induced cytoplasmic incompatibility provides a frequency-dependent reproductive advantage to infected females that can spread transinfections within and among populations. However, because transinfections generally reduce host fitness, they tend to spread within populations only after their frequency exceeds a critical threshold. This produces bistability with stable equilibrium frequencies at both 0 and 1, analogous to the bistability produced by underdominance between alleles or karyotypes and by population dynamics under Allee effects. Here, we analyze how stochastic frequency variation produced by finite population size can facilitate the local spread of variants with bistable dynamics into areas where invasion is unexpected from deterministic models. Our exemplar is the establishment of wMel Wolbachia in the Aedes aegypti population of Pyramid Estates (PE), a small community in far north Queensland, Australia. In 2011, wMel was stably introduced into Gordonvale, separated from PE by barriers to A. aegypti dispersal. After nearly 6 years during which wMel was observed only at low frequencies in PE, corresponding to an apparent equilibrium between immigration and selection, wMel rose to fixation by 2018. Using analytic approximations and statistical analyses, we demonstrate that the observed fixation of wMel at PE is consistent with both stochastic transition past an unstable threshold frequency and deterministic transformation produced by steady immigration at a rate just above the threshold required for deterministic invasion. The indeterminacy results from a delicate balance of parameters needed to produce the delayed transition observed. Our analyses suggest that once Wolbachia transinfections are established locally through systematic introductions, stochastic “threshold crossing” is likely to only minimally enhance spatial spread, providing a local ratchet that slightly—but systematically—aids area-wide transformation of disease-vector populations in heterogeneous landscapes."}],"type":"journal_article","file":[{"file_id":"11689","relation":"main_file","success":1,"checksum":"7e9a37e3b65b480cd7014a6a4a7e460a","date_created":"2022-07-29T06:59:10Z","date_updated":"2022-07-29T06:59:10Z","access_level":"open_access","file_name":"2022_EvolutionLetters_Turelli.pdf","creator":"dernst","file_size":2435185,"content_type":"application/pdf"}],"oa_version":"Published Version","intvolume":" 6","status":"public","ddc":["570"],"title":"Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics, and disease control","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10604","publication_identifier":{"eissn":["2056-3744"]},"month":"02","language":[{"iso":"eng"}],"doi":"10.1002/evl3.270","isi":1,"quality_controlled":"1","oa":1,"external_id":{"isi":["000754412600008"]},"file_date_updated":"2022-07-29T06:59:10Z","volume":6,"date_created":"2022-01-09T09:45:17Z","date_updated":"2023-08-02T13:50:09Z","related_material":{"record":[{"relation":"research_data","status":"public","id":"11686"}]},"author":[{"first_name":"Michael","last_name":"Turelli","full_name":"Turelli, Michael"},{"full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"NiBa"}],"publisher":"Wiley","publication_status":"published","year":"2022","acknowledgement":"We thank S. O'Neill, C. Simmons, and the World Mosquito Project for providing access to unpublished data. S. Ritchie provided valuable insights into Aedes aegypti biology and the literature describing A. aegypti populations near Cairns. We thank B. Cooper for help with the figures and D. Shropshire, S. O'Neill, S. Ritchie, A. Hoffmann, B. Cooper, and members of the Cooper lab for comments on an earlier draft. Comments from three reviewers greatly improved our presentation."},{"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"10604"}]},"author":[{"full_name":"Turelli, Michael","first_name":"Michael","last_name":"Turelli"},{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton"}],"oa_version":"Published Version","date_created":"2022-07-29T06:45:41Z","date_updated":"2023-08-02T13:50:08Z","year":"2022","_id":"11686","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","acknowledgement":"Bill and Melinda Gates Foundation, Award: OPP1180815","department":[{"_id":"NiBa"}],"publisher":"Dryad","status":"public","title":"Wolbachia frequency data from: Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics and disease control","ddc":["570"],"abstract":[{"lang":"eng","text":"Maternally inherited Wolbachia transinfections are being introduced into natural mosquito populations to reduce the transmission of dengue, Zika and other arboviruses. Wolbachia-induced cytoplasmic incompatibility provides a frequency-dependent reproductive advantage to infected females that can spread transinfections within and among populations. However, because transinfections generally reduce host fitness, they tend to spread within populations only after their frequency exceeds a critical threshold. This produces bistability with stable equilibrium frequencies at both 0 and 1, analogous to the bistability produced by underdominance between alleles or karyotypes and by population dynamics under Allee effects. Here, we analyze how stochastic frequency variation produced by finite population size can facilitate the local spread of variants with bistable dynamics into areas where invasion is unexpected from deterministic models. Our exemplar is the establishment of wMel Wolbachia in the Aedes aegypti population of Pyramid Estates (PE), a small community in far north Queensland, Australia. In 2011, wMel was stably introduced into Gordonvale, separated from PE by barriers to Ae. aegypti dispersal. After nearly six years during which wMel was observed only at low frequencies in PE, corresponding to an apparent equilibrium between immigration and selection, wMel rose to fixation by 2018. Using analytic approximations and statistical analyses, we demonstrate that the observed fixation of wMel at PE is consistent with both stochastic transition past an unstable threshold frequency and deterministic transformation produced by steady immigration at a rate just above the threshold required for deterministic invasion. The indeterminacy results from a delicate balance of parameters needed to produce the delayed transition observed. Our analyses suggest that once Wolbachia transinfections are established locally through systematic introductions, stochastic “threshold crossing” is likely to only minimally enhance spatial spread, providing a local ratchet that slightly – but systematically – aids area-wide transformation of disease-vector populations in heterogeneous landscapes."}],"license":"https://creativecommons.org/publicdomain/zero/1.0/","type":"research_data_reference","date_published":"2022-01-06T00:00:00Z","doi":"10.25338/B81931","main_file_link":[{"open_access":"1","url":"https://doi.org/10.25338/B81931"}],"tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"oa":1,"citation":{"chicago":"Turelli, Michael, and Nicholas H Barton. “Wolbachia Frequency Data from: Why Did the Wolbachia Transinfection Cross the Road? Drift, Deterministic Dynamics and Disease Control.” Dryad, 2022. https://doi.org/10.25338/B81931.","short":"M. Turelli, N.H. Barton, (2022).","mla":"Turelli, Michael, and Nicholas H. Barton. Wolbachia Frequency Data from: Why Did the Wolbachia Transinfection Cross the Road? Drift, Deterministic Dynamics and Disease Control. Dryad, 2022, doi:10.25338/B81931.","apa":"Turelli, M., & Barton, N. H. (2022). Wolbachia frequency data from: Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics and disease control. Dryad. https://doi.org/10.25338/B81931","ieee":"M. Turelli and N. H. Barton, “Wolbachia frequency data from: Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics and disease control.” Dryad, 2022.","ista":"Turelli M, Barton NH. 2022. Wolbachia frequency data from: Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics and disease control, Dryad, 10.25338/B81931.","ama":"Turelli M, Barton NH. Wolbachia frequency data from: Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics and disease control. 2022. doi:10.25338/B81931"},"article_processing_charge":"No","day":"06","month":"01","keyword":["Biological sciences"]},{"abstract":[{"lang":"eng","text":"Predicting function from sequence is a central problem of biology. Currently, this is possible only locally in a narrow mutational neighborhood around a wildtype sequence rather than globally from any sequence. Using random mutant libraries, we developed a biophysical model that accounts for multiple features of σ70 binding bacterial promoters to predict constitutive gene expression levels from any sequence. We experimentally and theoretically estimated that 10–20% of random sequences lead to expression and ~80% of non-expressing sequences are one mutation away from a functional promoter. The potential for generating expression from random sequences is so pervasive that selection acts against σ70-RNA polymerase binding sites even within inter-genic, promoter-containing regions. This pervasiveness of σ70-binding sites implies that emergence of promoters is not the limiting step in gene regulatory evolution. Ultimately, the inclusion of novel features of promoter function into a mechanistic model enabled not only more accurate predictions of gene expression levels, but also identified that promoters evolve more rapidly than previously thought."}],"type":"journal_article","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"10739","date_updated":"2022-02-07T07:14:09Z","date_created":"2022-02-07T07:14:09Z","checksum":"decdcdf600ff51e9a9703b49ca114170","success":1,"file_name":"2022_ELife_Lagator.pdf","access_level":"open_access","file_size":5604343,"content_type":"application/pdf","creator":"cchlebak"}],"_id":"10736","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Predicting bacterial promoter function and evolution from random sequences","ddc":["576"],"status":"public","intvolume":" 11","day":"26","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2022-01-26T00:00:00Z","publication":"eLife","citation":{"ama":"Lagator M, Sarikas S, Steinrueck M, et al. Predicting bacterial promoter function and evolution from random sequences. eLife. 2022;11. doi:10.7554/eLife.64543","ieee":"M. Lagator et al., “Predicting bacterial promoter function and evolution from random sequences,” eLife, vol. 11. eLife Sciences Publications, 2022.","apa":"Lagator, M., Sarikas, S., Steinrueck, M., Toledo-Aparicio, D., Bollback, J. P., Guet, C. C., & Tkačik, G. (2022). Predicting bacterial promoter function and evolution from random sequences. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.64543","ista":"Lagator M, Sarikas S, Steinrueck M, Toledo-Aparicio D, Bollback JP, Guet CC, Tkačik G. 2022. Predicting bacterial promoter function and evolution from random sequences. eLife. 11, e64543.","short":"M. Lagator, S. Sarikas, M. Steinrueck, D. Toledo-Aparicio, J.P. Bollback, C.C. Guet, G. Tkačik, ELife 11 (2022).","mla":"Lagator, Mato, et al. “Predicting Bacterial Promoter Function and Evolution from Random Sequences.” ELife, vol. 11, e64543, eLife Sciences Publications, 2022, doi:10.7554/eLife.64543.","chicago":"Lagator, Mato, Srdjan Sarikas, Magdalena Steinrueck, David Toledo-Aparicio, Jonathan P Bollback, Calin C Guet, and Gašper Tkačik. “Predicting Bacterial Promoter Function and Evolution from Random Sequences.” ELife. eLife Sciences Publications, 2022. https://doi.org/10.7554/eLife.64543."},"article_type":"original","file_date_updated":"2022-02-07T07:14:09Z","ec_funded":1,"article_number":"e64543","author":[{"id":"345D25EC-F248-11E8-B48F-1D18A9856A87","first_name":"Mato","last_name":"Lagator","full_name":"Lagator, Mato"},{"id":"35F0286E-F248-11E8-B48F-1D18A9856A87","last_name":"Sarikas","first_name":"Srdjan","full_name":"Sarikas, Srdjan"},{"first_name":"Magdalena","last_name":"Steinrueck","full_name":"Steinrueck, Magdalena"},{"first_name":"David","last_name":"Toledo-Aparicio","full_name":"Toledo-Aparicio, David"},{"last_name":"Bollback","first_name":"Jonathan P","orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","full_name":"Bollback, Jonathan P"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","first_name":"Calin C","last_name":"Guet","full_name":"Guet, Calin C"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","first_name":"Gašper","last_name":"Tkačik","full_name":"Tkačik, Gašper"}],"date_updated":"2023-08-02T14:09:02Z","date_created":"2022-02-06T23:01:32Z","volume":11,"year":"2022","acknowledgement":"We thank Hande Acar, Nicholas H Barton, Rok Grah, Tiago Paixao, Maros Pleska, Anna Staron, and Murat Tugrul for insightful comments and input on the manuscript. This work was supported by: Sir Henry Dale Fellowship jointly funded by the Wellcome Trust and the Royal Society (grant number 216779/Z/19/Z) to ML; IPC Grant from IST Austria to ML and SS; European Research Council Funding Programme 7 (2007–2013, grant agreement number 648440) to JPB.","pmid":1,"publication_status":"published","publisher":"eLife Sciences Publications","department":[{"_id":"CaGu"},{"_id":"GaTk"},{"_id":"NiBa"}],"month":"01","publication_identifier":{"eissn":["2050-084X"]},"doi":"10.7554/eLife.64543","language":[{"iso":"eng"}],"external_id":{"pmid":["35080492"],"isi":["000751104400001"]},"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","project":[{"_id":"2578D616-B435-11E9-9278-68D0E5697425","grant_number":"648440","call_identifier":"H2020","name":"Selective Barriers to Horizontal Gene Transfer"}]},{"type":"journal_article","abstract":[{"text":"Hybridization is a common evolutionary process with multiple possible outcomes. In vertebrates, interspecific hybridization has repeatedly generated parthenogenetic hybrid species. However, it is unknown whether the generation of parthenogenetic hybrids is a rare outcome of frequent hybridization between sexual species within a genus or the typical outcome of rare hybridization events. Darevskia is a genus of rock lizards with both hybrid parthenogenetic and sexual species. Using capture sequencing, we estimate phylogenetic relationships and gene flow among the sexual species, to determine how introgressive hybridization relates to the origins of parthenogenetic hybrids. We find evidence for widespread hybridization with gene flow, both between recently diverged species and deep branches. Surprisingly, we find no signal of gene flow between parental species of the parthenogenetic hybrids, suggesting that the parental pairs were either reproductively or geographically isolated early in their divergence. The generation of parthenogenetic hybrids in Darevskia is, then, a rare outcome of the total occurrence of hybridization within the genus, but the typical outcome when specific species pairs hybridize. Our results question the conventional view that parthenogenetic lineages are generated by hybridization in a window of divergence. Instead, they suggest that some lineages possess specific properties that underpin successful parthenogenetic reproduction.","lang":"eng"}],"issue":"5","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"11334","title":"Parthenogenesis in Darevskia lizards: A rare outcome of common hybridization, not a common outcome of rare hybridization","ddc":["570"],"status":"public","intvolume":" 76","file":[{"file_name":"2022_Evolution_Freitas.pdf","access_level":"open_access","content_type":"application/pdf","file_size":2855214,"creator":"dernst","relation":"main_file","file_id":"11729","date_created":"2022-08-05T06:19:28Z","date_updated":"2022-08-05T06:19:28Z","checksum":"c27c025ae9afcf6c804d46a909775ee5","success":1}],"oa_version":"Published Version","scopus_import":"1","day":"01","article_processing_charge":"No","has_accepted_license":"1","publication":"Evolution","citation":{"ama":"Freitas S, Westram AM, Schwander T, et al. Parthenogenesis in Darevskia lizards: A rare outcome of common hybridization, not a common outcome of rare hybridization. Evolution. 2022;76(5):899-914. doi:10.1111/evo.14462","ieee":"S. Freitas et al., “Parthenogenesis in Darevskia lizards: A rare outcome of common hybridization, not a common outcome of rare hybridization,” Evolution, vol. 76, no. 5. Wiley, pp. 899–914, 2022.","apa":"Freitas, S., Westram, A. M., Schwander, T., Arakelyan, M., Ilgaz, Ç., Kumlutas, Y., … Butlin, R. K. (2022). Parthenogenesis in Darevskia lizards: A rare outcome of common hybridization, not a common outcome of rare hybridization. Evolution. Wiley. https://doi.org/10.1111/evo.14462","ista":"Freitas S, Westram AM, Schwander T, Arakelyan M, Ilgaz Ç, Kumlutas Y, Harris DJ, Carretero MA, Butlin RK. 2022. Parthenogenesis in Darevskia lizards: A rare outcome of common hybridization, not a common outcome of rare hybridization. Evolution. 76(5), 899–914.","short":"S. Freitas, A.M. Westram, T. Schwander, M. Arakelyan, Ç. Ilgaz, Y. Kumlutas, D.J. Harris, M.A. Carretero, R.K. Butlin, Evolution 76 (2022) 899–914.","mla":"Freitas, Susana, et al. “Parthenogenesis in Darevskia Lizards: A Rare Outcome of Common Hybridization, Not a Common Outcome of Rare Hybridization.” Evolution, vol. 76, no. 5, Wiley, 2022, pp. 899–914, doi:10.1111/evo.14462.","chicago":"Freitas, Susana, Anja M Westram, Tanja Schwander, Marine Arakelyan, Çetin Ilgaz, Yusuf Kumlutas, David James Harris, Miguel A. Carretero, and Roger K. Butlin. “Parthenogenesis in Darevskia Lizards: A Rare Outcome of Common Hybridization, Not a Common Outcome of Rare Hybridization.” Evolution. Wiley, 2022. https://doi.org/10.1111/evo.14462."},"article_type":"original","page":"899-914","date_published":"2022-05-01T00:00:00Z","file_date_updated":"2022-08-05T06:19:28Z","ec_funded":1,"year":"2022","acknowledgement":"The authors thank A. van der Meijden and F. Ahmadzadeh for providing specimens and tissue samples, and A. Vardanyan, C. Corti, F. Jorge, and S. Drovetski for support during field work. The authors also thank S. Qiu for assistance with python scripting, S. Rocha for her support in BEAST analysis, and B. Wielstra for his comments on\r\na previous version of the manuscript. SF was funded by FCT grant SFRH/BD/81483/2011 (a PhD individual grant). AMW was funded by the European Union’s Horizon 2020 research and innovation programme under Marie Skłodowska-Curie grant agreement no. 797747. TS acknowledges funding from the Swiss National Science Foundation (grants\r\nPP00P3_170627 and 31003A_182495). The work was carried out under financial support of the projects “Preserving Armenian biodiversity: Joint Portuguese – Armenian program for training in modern conservation biology” of Gulbenkian Foundation (Portugal) and PTDC/BIABEC/101256/2008 of Fundação para a Ciência e a Tecnologia (FCT, Portugal).","pmid":1,"publication_status":"published","department":[{"_id":"NiBa"},{"_id":"BeVi"}],"publisher":"Wiley","author":[{"full_name":"Freitas, Susana","first_name":"Susana","last_name":"Freitas"},{"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":"Tanja","last_name":"Schwander","full_name":"Schwander, Tanja"},{"full_name":"Arakelyan, Marine","last_name":"Arakelyan","first_name":"Marine"},{"full_name":"Ilgaz, Çetin","first_name":"Çetin","last_name":"Ilgaz"},{"full_name":"Kumlutas, Yusuf","first_name":"Yusuf","last_name":"Kumlutas"},{"last_name":"Harris","first_name":"David James","full_name":"Harris, David James"},{"first_name":"Miguel A.","last_name":"Carretero","full_name":"Carretero, Miguel A."},{"full_name":"Butlin, Roger K.","first_name":"Roger K.","last_name":"Butlin"}],"date_updated":"2023-08-03T07:00:28Z","date_created":"2022-04-24T22:01:44Z","volume":76,"month":"05","publication_identifier":{"issn":["0014-3820"],"eissn":["1558-5646"]},"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"external_id":{"pmid":["35323995"],"isi":["000781632500001"]},"isi":1,"quality_controlled":"1","project":[{"grant_number":"797747","_id":"265B41B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Theoretical and empirical approaches to understanding Parallel Adaptation"}],"doi":"10.1111/evo.14462","language":[{"iso":"eng"}]},{"article_type":"original","publication":"Bulletin of Mathematical Biology","citation":{"chicago":"Saona Urmeneta, Raimundo J, Fyodor Kondrashov, and Kseniia Khudiakova. “Relation between the Number of Peaks and the Number of Reciprocal Sign Epistatic Interactions.” Bulletin of Mathematical Biology. Springer Nature, 2022. https://doi.org/10.1007/s11538-022-01029-z.","mla":"Saona Urmeneta, Raimundo J., et al. “Relation between the Number of Peaks and the Number of Reciprocal Sign Epistatic Interactions.” Bulletin of Mathematical Biology, vol. 84, no. 8, 74, Springer Nature, 2022, doi:10.1007/s11538-022-01029-z.","short":"R.J. Saona Urmeneta, F. Kondrashov, K. Khudiakova, Bulletin of Mathematical Biology 84 (2022).","ista":"Saona Urmeneta RJ, Kondrashov F, Khudiakova K. 2022. Relation between the number of peaks and the number of reciprocal sign epistatic interactions. Bulletin of Mathematical Biology. 84(8), 74.","ieee":"R. J. Saona Urmeneta, F. Kondrashov, and K. Khudiakova, “Relation between the number of peaks and the number of reciprocal sign epistatic interactions,” Bulletin of Mathematical Biology, vol. 84, no. 8. Springer Nature, 2022.","apa":"Saona Urmeneta, R. J., Kondrashov, F., & Khudiakova, K. (2022). Relation between the number of peaks and the number of reciprocal sign epistatic interactions. Bulletin of Mathematical Biology. Springer Nature. https://doi.org/10.1007/s11538-022-01029-z","ama":"Saona Urmeneta RJ, Kondrashov F, Khudiakova K. Relation between the number of peaks and the number of reciprocal sign epistatic interactions. Bulletin of Mathematical Biology. 2022;84(8). doi:10.1007/s11538-022-01029-z"},"date_published":"2022-06-17T00:00:00Z","keyword":["Computational Theory and Mathematics","General Agricultural and Biological Sciences","Pharmacology","General Environmental Science","General Biochemistry","Genetics and Molecular Biology","General Mathematics","Immunology","General Neuroscience"],"scopus_import":"1","day":"17","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","title":"Relation between the number of peaks and the number of reciprocal sign epistatic interactions","ddc":["510","570"],"status":"public","intvolume":" 84","_id":"11447","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","file":[{"file_id":"11455","relation":"main_file","success":1,"checksum":"05a1fe7d10914a00c2bca9b447993a65","date_updated":"2022-06-20T07:51:32Z","date_created":"2022-06-20T07:51:32Z","access_level":"open_access","file_name":"2022_BulletinMathBiology_Saona.pdf","creator":"dernst","file_size":463025,"content_type":"application/pdf"}],"type":"journal_article","abstract":[{"text":"Empirical essays of fitness landscapes suggest that they may be rugged, that is having multiple fitness peaks. Such fitness landscapes, those that have multiple peaks, necessarily have special local structures, called reciprocal sign epistasis (Poelwijk et al. in J Theor Biol 272:141–144, 2011). Here, we investigate the quantitative relationship between the number of fitness peaks and the number of reciprocal sign epistatic interactions. Previously, it has been shown (Poelwijk et al. in J Theor Biol 272:141–144, 2011) that pairwise reciprocal sign epistasis is a necessary but not sufficient condition for the existence of multiple peaks. Applying discrete Morse theory, which to our knowledge has never been used in this context, we extend this result by giving the minimal number of reciprocal sign epistatic interactions required to create a given number of peaks.","lang":"eng"}],"issue":"8","isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Characterizing the fitness landscape on population and global scales","grant_number":"771209","_id":"26580278-B435-11E9-9278-68D0E5697425"},{"_id":"c098eddd-5a5b-11eb-8a69-abe27170a68f","grant_number":"I05127","name":"Evolutionary analysis of 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"},"oa":1,"external_id":{"isi":["000812509800001"]},"language":[{"iso":"eng"}],"doi":"10.1007/s11538-022-01029-z","month":"06","publication_identifier":{"issn":["0092-8240"],"eissn":["1522-9602"]},"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"JaMa"}],"acknowledgement":"We are grateful to Herbert Edelsbrunner and Jeferson Zapata for helpful discussions. Open access funding provided by Austrian Science Fund (FWF). Partially supported by the ERC Consolidator (771209–CharFL) and the FWF Austrian Science Fund (I5127-B) grants to FAK.","year":"2022","date_created":"2022-06-17T16:16:15Z","date_updated":"2023-08-03T07:20:53Z","volume":84,"author":[{"full_name":"Saona Urmeneta, Raimundo J","orcid":"0000-0001-5103-038X","id":"BD1DF4C4-D767-11E9-B658-BC13E6697425","last_name":"Saona Urmeneta","first_name":"Raimundo J"},{"full_name":"Kondrashov, Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","first_name":"Fyodor","last_name":"Kondrashov"},{"full_name":"Khudiakova, Kseniia","orcid":"0000-0002-6246-1465","id":"4E6DC800-AE37-11E9-AC72-31CAE5697425","last_name":"Khudiakova","first_name":"Kseniia"}],"related_material":{"link":[{"url":"https://doi.org/10.1007/s11538-022-01118-z","relation":"erratum"}]},"article_number":"74","file_date_updated":"2022-06-20T07:51:32Z","ec_funded":1},{"publication_status":"published","publisher":"Royal Society of London","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"year":"2022","acknowledgement":"We thank the editor and two anonymous reviewers for their helpful and interesting comments on this manuscript.","date_created":"2022-07-08T11:41:56Z","date_updated":"2023-08-03T11:55:42Z","volume":377,"author":[{"full_name":"Westram, Anja M","last_name":"Westram","first_name":"Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Faria, Rui","last_name":"Faria","first_name":"Rui"},{"first_name":"Kerstin","last_name":"Johannesson","full_name":"Johannesson, Kerstin"},{"full_name":"Butlin, Roger","last_name":"Butlin","first_name":"Roger"},{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton"}],"article_number":"20210203","file_date_updated":"2023-02-02T08:20:29Z","isi":1,"quality_controlled":"1","project":[{"grant_number":"P32166","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","name":"The maintenance of alternative adaptive peaks in snapdragons"}],"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":["000812317300005"]},"language":[{"iso":"eng"}],"doi":"10.1098/rstb.2021.0203","month":"08","publication_identifier":{"issn":["0962-8436"],"eissn":["1471-2970"]},"ddc":["570"],"title":"Inversions and parallel evolution","status":"public","intvolume":" 377","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"11546","file":[{"date_updated":"2023-02-02T08:20:29Z","date_created":"2023-02-02T08:20:29Z","checksum":"49f69428f3dcf5ce3ff281f7d199e9df","success":1,"relation":"main_file","file_id":"12479","content_type":"application/pdf","file_size":920304,"creator":"dernst","file_name":"2022_PhilosophicalTransactionsB_Westram.pdf","access_level":"open_access"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Local adaptation leads to differences between populations within a species. In many systems, similar environmental contrasts occur repeatedly, sometimes driving parallel phenotypic evolution. Understanding the genomic basis of local adaptation and parallel evolution is a major goal of evolutionary genomics. It is now known that by preventing the break-up of favourable combinations of alleles across multiple loci, genetic architectures that reduce recombination, like chromosomal inversions, can make an important contribution to local adaptation. However, little is known about whether inversions also contribute disproportionately to parallel evolution. Our aim here is to highlight this knowledge gap, to showcase existing studies, and to illustrate the differences between genomic architectures with and without inversions using simple models. We predict that by generating stronger effective selection, inversions can sometimes speed up the parallel adaptive process or enable parallel adaptation where it would be impossible otherwise, but this is highly dependent on the spatial setting. We highlight that further empirical work is needed, in particular to cover a broader taxonomic range and to understand the relative importance of inversions compared to genomic regions without inversions.","lang":"eng"}],"issue":"1856","article_type":"original","publication":"Philosophical Transactions of the Royal Society B: Biological Sciences","citation":{"ista":"Westram AM, Faria R, Johannesson K, Butlin R, Barton NH. 2022. Inversions and parallel evolution. Philosophical Transactions of the Royal Society B: Biological Sciences. 377(1856), 20210203.","apa":"Westram, A. M., Faria, R., Johannesson, K., Butlin, R., & Barton, N. H. (2022). Inversions and parallel evolution. Philosophical Transactions of the Royal Society B: Biological Sciences. Royal Society of London. https://doi.org/10.1098/rstb.2021.0203","ieee":"A. M. Westram, R. Faria, K. Johannesson, R. Butlin, and N. H. Barton, “Inversions and parallel evolution,” Philosophical Transactions of the Royal Society B: Biological Sciences, vol. 377, no. 1856. Royal Society of London, 2022.","ama":"Westram AM, Faria R, Johannesson K, Butlin R, Barton NH. Inversions and parallel evolution. Philosophical Transactions of the Royal Society B: Biological Sciences. 2022;377(1856). doi:10.1098/rstb.2021.0203","chicago":"Westram, Anja M, Rui Faria, Kerstin Johannesson, Roger Butlin, and Nicholas H Barton. “Inversions and Parallel Evolution.” Philosophical Transactions of the Royal Society B: Biological Sciences. Royal Society of London, 2022. https://doi.org/10.1098/rstb.2021.0203.","mla":"Westram, Anja M., et al. “Inversions and Parallel Evolution.” Philosophical Transactions of the Royal Society B: Biological Sciences, vol. 377, no. 1856, 20210203, Royal Society of London, 2022, doi:10.1098/rstb.2021.0203.","short":"A.M. Westram, R. Faria, K. Johannesson, R. Butlin, N.H. Barton, Philosophical Transactions of the Royal Society B: Biological Sciences 377 (2022)."},"date_published":"2022-08-01T00:00:00Z","keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology"],"scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)"},{"oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":6431779,"creator":"dernst","file_name":"2022_MolecularEcologyRes_Szep.pdf","access_level":"open_access","date_created":"2023-02-02T08:11:23Z","date_updated":"2023-02-02T08:11:23Z","checksum":"3102e203e77b884bffffdbe8e548da88","success":1,"relation":"main_file","file_id":"12477"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"11640","intvolume":" 22","title":"Using gridCoal to assess whether standard population genetic theory holds in the presence of spatio-temporal heterogeneity in population size","ddc":["570"],"status":"public","issue":"8","abstract":[{"lang":"eng","text":"Spatially explicit population genetic models have long been developed, yet have rarely been used to test hypotheses about the spatial distribution of genetic diversity or the genetic divergence between populations. Here, we use spatially explicit coalescence simulations to explore the properties of the island and the two-dimensional stepping stone models under a wide range of scenarios with spatio-temporal variation in deme size. We avoid the simulation of genetic data, using the fact that under the studied models, summary statistics of genetic diversity and divergence can be approximated from coalescence times. We perform the simulations using gridCoal, a flexible spatial wrapper for the software msprime (Kelleher et al., 2016, Theoretical Population Biology, 95, 13) developed herein. In gridCoal, deme sizes can change arbitrarily across space and time, as well as migration rates between individual demes. We identify different factors that can cause a deviation from theoretical expectations, such as the simulation time in comparison to the effective deme size and the spatio-temporal autocorrelation across the grid. Our results highlight that FST, a measure of the strength of population structure, principally depends on recent demography, which makes it robust to temporal variation in deme size. In contrast, the amount of genetic diversity is dependent on the distant past when Ne is large, therefore longer run times are needed to estimate Ne than FST. Finally, we illustrate the use of gridCoal on a real-world example, the range expansion of silver fir (Abies alba Mill.) since the last glacial maximum, using different degrees of spatio-temporal variation in deme size."}],"type":"journal_article","date_published":"2022-11-01T00:00:00Z","citation":{"short":"E. Szep, B. Trubenova, K. Csilléry, Molecular Ecology Resources 22 (2022) 2941–2955.","mla":"Szep, Eniko, et al. “Using GridCoal to Assess Whether Standard Population Genetic Theory Holds in the Presence of Spatio-Temporal Heterogeneity in Population Size.” Molecular Ecology Resources, vol. 22, no. 8, Wiley, 2022, pp. 2941–55, doi:10.1111/1755-0998.13676.","chicago":"Szep, Eniko, Barbora Trubenova, and Katalin Csilléry. “Using GridCoal to Assess Whether Standard Population Genetic Theory Holds in the Presence of Spatio-Temporal Heterogeneity in Population Size.” Molecular Ecology Resources. Wiley, 2022. https://doi.org/10.1111/1755-0998.13676.","ama":"Szep E, Trubenova B, Csilléry K. Using gridCoal to assess whether standard population genetic theory holds in the presence of spatio-temporal heterogeneity in population size. Molecular Ecology Resources. 2022;22(8):2941-2955. doi:10.1111/1755-0998.13676","apa":"Szep, E., Trubenova, B., & Csilléry, K. (2022). Using gridCoal to assess whether standard population genetic theory holds in the presence of spatio-temporal heterogeneity in population size. Molecular Ecology Resources. Wiley. https://doi.org/10.1111/1755-0998.13676","ieee":"E. Szep, B. Trubenova, and K. Csilléry, “Using gridCoal to assess whether standard population genetic theory holds in the presence of spatio-temporal heterogeneity in population size,” Molecular Ecology Resources, vol. 22, no. 8. Wiley, pp. 2941–2955, 2022.","ista":"Szep E, Trubenova B, Csilléry K. 2022. Using gridCoal to assess whether standard population genetic theory holds in the presence of spatio-temporal heterogeneity in population size. Molecular Ecology Resources. 22(8), 2941–2955."},"publication":"Molecular Ecology Resources","page":"2941-2955","article_type":"original","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"01","scopus_import":"1","author":[{"id":"485BB5A4-F248-11E8-B48F-1D18A9856A87","first_name":"Eniko","last_name":"Szep","full_name":"Szep, Eniko"},{"full_name":"Trubenova, Barbora","last_name":"Trubenova","first_name":"Barbora","orcid":"0000-0002-6873-2967","id":"42302D54-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Csilléry, Katalin","first_name":"Katalin","last_name":"Csilléry"}],"volume":22,"date_created":"2022-07-24T22:01:43Z","date_updated":"2023-08-03T12:11:01Z","year":"2022","acknowledgement":"ES was supported by an IST studentship provided by IST Austria. BT was funded by the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Independent Fellowship (704172, RACE). This project received further funding awarded to KC from the Swiss National Science Foundation (SNSF CRSK-3_190288) and the Swiss Federal Research Institute WSL. We thank Nick Barton for many invaluable discussions and his comments on the thesis chapter and this manuscript. We thank Peter Ralph and Jerome Kelleher for useful discussions and Bisschop Gertjan for comments on this manuscript. We thank Fortunat Joos for providing us with the raw data from the LPX-Bern model for silver fir, and Willy Tinner for helpful insights about the demographic history of silver fir. We also thank the editor Alana Alexander for useful comments and advice on the manuscript. Open access funding provided by Eidgenossische Technische Hochschule Zurich.","publisher":"Wiley","department":[{"_id":"NiBa"}],"publication_status":"published","ec_funded":1,"file_date_updated":"2023-02-02T08:11:23Z","doi":"10.1111/1755-0998.13676","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"external_id":{"isi":["000825873600001"]},"project":[{"call_identifier":"H2020","name":"Rate of Adaptation in Changing Environment","_id":"25AEDD42-B435-11E9-9278-68D0E5697425","grant_number":"704172"}],"quality_controlled":"1","isi":1,"publication_identifier":{"issn":["1755-098X"],"eissn":["1755-0998"]},"month":"11"},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000839621100001"]},"quality_controlled":"1","isi":1,"doi":"10.1002/evl3.295","language":[{"iso":"eng"}],"month":"10","publication_identifier":{"eissn":["2056-3744"]},"acknowledgement":"We thank A. Wright and four anonymous reviewers for valuable comments on an earlier draft of this manuscript and all members of the Littorina group for helpful discussions. This work was supported by a European Research Council grant to RKB and by a Natural Environment Research Council studentship to KEH through the ACCE doctoral training program. KJ acknowledges support from the Swedish Science Research Council VR (Vetenskaprådet) (2017-03798). RF was supported by an FCT CEEC (Fundação para a Ciênca e a Tecnologia, Concurso Estímulo ao Emprego Científico) contract (2020.00275.CEECIND).","year":"2022","publication_status":"published","publisher":"Oxford Academic","department":[{"_id":"NiBa"}],"author":[{"full_name":"Hearn, Katherine E.","first_name":"Katherine E.","last_name":"Hearn"},{"full_name":"Koch, Eva L.","last_name":"Koch","first_name":"Eva L."},{"last_name":"Stankowski","first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean"},{"last_name":"Butlin","first_name":"Roger K.","full_name":"Butlin, Roger K."},{"full_name":"Faria, Rui","last_name":"Faria","first_name":"Rui"},{"last_name":"Johannesson","first_name":"Kerstin","full_name":"Johannesson, Kerstin"},{"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":"2022-08-28T22:02:02Z","date_updated":"2023-08-03T13:18:17Z","volume":6,"file_date_updated":"2023-02-27T07:17:42Z","publication":"Evolution Letters","citation":{"ama":"Hearn KE, Koch EL, Stankowski S, et al. Differing associations between sex determination and sex-linked inversions in two ecotypes of Littorina saxatilis. Evolution Letters. 2022;6(5):358-374. doi:10.1002/evl3.295","ieee":"K. E. Hearn et al., “Differing associations between sex determination and sex-linked inversions in two ecotypes of Littorina saxatilis,” Evolution Letters, vol. 6, no. 5. Oxford Academic, pp. 358–374, 2022.","apa":"Hearn, K. E., Koch, E. L., Stankowski, S., Butlin, R. K., Faria, R., Johannesson, K., & Westram, A. M. (2022). Differing associations between sex determination and sex-linked inversions in two ecotypes of Littorina saxatilis. Evolution Letters. Oxford Academic. https://doi.org/10.1002/evl3.295","ista":"Hearn KE, Koch EL, Stankowski S, Butlin RK, Faria R, Johannesson K, Westram AM. 2022. Differing associations between sex determination and sex-linked inversions in two ecotypes of Littorina saxatilis. Evolution Letters. 6(5), 358–374.","short":"K.E. Hearn, E.L. Koch, S. Stankowski, R.K. Butlin, R. Faria, K. Johannesson, A.M. Westram, Evolution Letters 6 (2022) 358–374.","mla":"Hearn, Katherine E., et al. “Differing Associations between Sex Determination and Sex-Linked Inversions in Two Ecotypes of Littorina Saxatilis.” Evolution Letters, vol. 6, no. 5, Oxford Academic, 2022, pp. 358–74, doi:10.1002/evl3.295.","chicago":"Hearn, Katherine E., Eva L. Koch, Sean Stankowski, Roger K. Butlin, Rui Faria, Kerstin Johannesson, and Anja M Westram. “Differing Associations between Sex Determination and Sex-Linked Inversions in Two Ecotypes of Littorina Saxatilis.” Evolution Letters. Oxford Academic, 2022. https://doi.org/10.1002/evl3.295."},"article_type":"original","page":"358-374","date_published":"2022-10-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"Yes","has_accepted_license":"1","_id":"12001","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["570"],"title":"Differing associations between sex determination and sex-linked inversions in two ecotypes of Littorina saxatilis","status":"public","intvolume":" 6","oa_version":"Published Version","file":[{"date_updated":"2023-02-27T07:17:42Z","date_created":"2023-02-27T07:17:42Z","success":1,"checksum":"2dcd06186a11b7d1be4cddc6b189f8fb","file_id":"12686","relation":"main_file","creator":"dernst","file_size":2368965,"content_type":"application/pdf","file_name":"2022_EvolutionLetters_Hearn.pdf","access_level":"open_access"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Sexual antagonism is a common hypothesis for driving the evolution of sex chromosomes, whereby recombination suppression is favored between sexually antagonistic loci and the sex-determining locus to maintain beneficial combinations of alleles. This results in the formation of a sex-determining region. Chromosomal inversions may contribute to recombination suppression but their precise role in sex chromosome evolution remains unclear. Because local adaptation is frequently facilitated through the suppression of recombination between adaptive loci by chromosomal inversions, there is potential for inversions that cover sex-determining regions to be involved in local adaptation as well, particularly if habitat variation creates environment-dependent sexual antagonism. With these processes in mind, we investigated sex determination in a well-studied example of local adaptation within a species: the intertidal snail, Littorina saxatilis. Using SNP data from a Swedish hybrid zone, we find novel evidence for a female-heterogametic sex determination system that is restricted to one ecotype. Our results suggest that four putative chromosomal inversions, two previously described and two newly discovered, span the putative sex chromosome pair. We determine their differing associations with sex, which suggest distinct strata of differing ages. The same inversions are found in the second ecotype but do not show any sex association. The striking disparity in inversion-sex associations between ecotypes that are connected by gene flow across a habitat transition that is just a few meters wide indicates a difference in selective regime that has produced a distinct barrier to the spread of the newly discovered sex-determining region between ecotypes. Such sex chromosome-environment interactions have not previously been uncovered in L. saxatilis and are known in few other organisms. A combination of both sex-specific selection and divergent natural selection is required to explain these highly unusual patterns."}],"issue":"5"},{"article_type":"original","citation":{"mla":"Hayward, Laura, and Guy Sella. “Polygenic Adaptation after a Sudden Change in Environment.” ELife, vol. 11, 66697, eLife Sciences Publications, 2022, doi:10.7554/elife.66697.","short":"L. Hayward, G. Sella, ELife 11 (2022).","chicago":"Hayward, Laura, and Guy Sella. “Polygenic Adaptation after a Sudden Change in Environment.” ELife. eLife Sciences Publications, 2022. https://doi.org/10.7554/elife.66697.","ama":"Hayward L, Sella G. Polygenic adaptation after a sudden change in environment. eLife. 2022;11. doi:10.7554/elife.66697","ista":"Hayward L, Sella G. 2022. Polygenic adaptation after a sudden change in environment. eLife. 11, 66697.","apa":"Hayward, L., & Sella, G. (2022). Polygenic adaptation after a sudden change in environment. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.66697","ieee":"L. Hayward and G. Sella, “Polygenic adaptation after a sudden change in environment,” eLife, vol. 11. eLife Sciences Publications, 2022."},"publication":"eLife","date_published":"2022-09-26T00:00:00Z","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"26","intvolume":" 11","title":"Polygenic adaptation after a sudden change in environment","ddc":["570"],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12157","file":[{"file_size":18935612,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2022_eLife_Hayward.pdf","checksum":"28de155b231ac1c8d4501c98b2fb359a","success":1,"date_created":"2023-01-24T12:21:32Z","date_updated":"2023-01-24T12:21:32Z","relation":"main_file","file_id":"12363"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Polygenic adaptation is thought to be ubiquitous, yet remains poorly understood. Here, we model this process analytically, in the plausible setting of a highly polygenic, quantitative trait that experiences a sudden shift in the fitness optimum. We show how the mean phenotype changes over time, depending on the effect sizes of loci that contribute to variance in the trait, and characterize the allele dynamics at these loci. Notably, we describe the two phases of the allele dynamics: The first is a rapid phase, in which directional selection introduces small frequency differences between alleles whose effects are aligned with or opposed to the shift, ultimately leading to small differences in their probability of fixation during a second, longer phase, governed by stabilizing selection. As we discuss, key results should hold in more general settings and have important implications for efforts to identify the genetic basis of adaptation in humans and other species.","lang":"eng"}],"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000890735600001"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.7554/elife.66697","publication_identifier":{"eissn":["2050-084X"]},"month":"09","department":[{"_id":"NiBa"}],"publisher":"eLife Sciences Publications","publication_status":"published","year":"2022","acknowledgement":"We thank Guy Amster, Jeremy Berg, Nick Barton, Yuval Simons and Molly Przeworski for many helpful discussions, and Jeremy Berg, Graham Coop, Joachim Hermisson, Guillaume Martin, Will Milligan, Peter Ralph, Yuval Simons, Leo Speidel and Molly Przeworski for comments on the manuscript.\r\nNational Institutes of Health GM115889 Laura Katharine Hayward Guy Sella \r\nNational Institutes of Health GM121372 Laura Katharine Hayward","volume":11,"date_created":"2023-01-12T12:09:00Z","date_updated":"2023-08-04T09:04:58Z","author":[{"id":"fc885ee5-24bf-11eb-ad7b-bcc5104c0c1b","last_name":"Hayward","first_name":"Laura","full_name":"Hayward, Laura"},{"first_name":"Guy","last_name":"Sella","full_name":"Sella, Guy"}],"article_number":"66697","file_date_updated":"2023-01-24T12:21:32Z"},{"day":"28","article_processing_charge":"No","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"scopus_import":"1","date_published":"2022-11-28T00:00:00Z","article_type":"letter_note","page":"26-29","publication":"Molecular Ecology","citation":{"chicago":"Westram, Anja M, and Roger Butlin. “Professor Kerstin Johannesson–Winner of the 2022 Molecular Ecology Prize.” Molecular Ecology. Wiley, 2022. https://doi.org/10.1111/mec.16779.","short":"A.M. Westram, R. Butlin, Molecular Ecology 32 (2022) 26–29.","mla":"Westram, Anja M., and Roger Butlin. “Professor Kerstin Johannesson–Winner of the 2022 Molecular Ecology Prize.” Molecular Ecology, vol. 32, no. 1, Wiley, 2022, pp. 26–29, doi:10.1111/mec.16779.","ieee":"A. M. Westram and R. Butlin, “Professor Kerstin Johannesson–winner of the 2022 Molecular Ecology Prize,” Molecular Ecology, vol. 32, no. 1. Wiley, pp. 26–29, 2022.","apa":"Westram, A. M., & Butlin, R. (2022). Professor Kerstin Johannesson–winner of the 2022 Molecular Ecology Prize. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.16779","ista":"Westram AM, Butlin R. 2022. Professor Kerstin Johannesson–winner of the 2022 Molecular Ecology Prize. Molecular Ecology. 32(1), 26–29.","ama":"Westram AM, Butlin R. Professor Kerstin Johannesson–winner of the 2022 Molecular Ecology Prize. Molecular Ecology. 2022;32(1):26-29. doi:10.1111/mec.16779"},"abstract":[{"lang":"eng","text":"Kerstin Johannesson is a marine ecologist and evolutionary biologist based at the Tjärnö Marine Laboratory of the University of Gothenburg, which is situated in the beautiful Kosterhavet National Park on the Swedish west coast. Her work, using marine periwinkles (especially Littorina saxatilis and L. fabalis) as main model systems, has made a remarkable contribution to marine evolutionary biology and our understanding of local adaptation and its genetic underpinnings."}],"issue":"1","type":"journal_article","oa_version":"Published Version","status":"public","title":"Professor Kerstin Johannesson–winner of the 2022 Molecular Ecology Prize","intvolume":" 32","_id":"12166","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"11","publication_identifier":{"issn":["0962-1083"],"eissn":["1365-294X"]},"language":[{"iso":"eng"}],"doi":"10.1111/mec.16779","isi":1,"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/mec.16779"}],"external_id":{"isi":["000892168800001"]},"oa":1,"date_created":"2023-01-12T12:10:28Z","date_updated":"2023-08-04T09:09:15Z","volume":32,"author":[{"full_name":"Westram, Anja M","first_name":"Anja M","last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969"},{"full_name":"Butlin, Roger","first_name":"Roger","last_name":"Butlin"}],"publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Wiley","year":"2022"},{"date_published":"2022-11-01T00:00:00Z","publication":"Evolution","citation":{"mla":"Stankowski, Sean. “Digest: On the Origin of a Possible Hybrid Species.” Evolution, vol. 76, no. 11, Wiley, 2022, pp. 2784–85, doi:10.1111/evo.14632.","short":"S. Stankowski, Evolution 76 (2022) 2784–2785.","chicago":"Stankowski, Sean. “Digest: On the Origin of a Possible Hybrid Species.” Evolution. Wiley, 2022. https://doi.org/10.1111/evo.14632.","ama":"Stankowski S. Digest: On the origin of a possible hybrid species. Evolution. 2022;76(11):2784-2785. doi:10.1111/evo.14632","ista":"Stankowski S. 2022. Digest: On the origin of a possible hybrid species. Evolution. 76(11), 2784–2785.","ieee":"S. Stankowski, “Digest: On the origin of a possible hybrid species,” Evolution, vol. 76, no. 11. Wiley, pp. 2784–2785, 2022.","apa":"Stankowski, S. (2022). Digest: On the origin of a possible hybrid species. Evolution. Wiley. https://doi.org/10.1111/evo.14632"},"article_type":"original","page":"2784-2785","day":"01","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","scopus_import":"1","keyword":["General Agricultural and Biological Sciences","Genetics","Ecology","Evolution","Behavior and Systematics"],"file":[{"creator":"dernst","file_size":287282,"content_type":"application/pdf","access_level":"open_access","file_name":"2022_Evolution_Stankowski.pdf","success":1,"checksum":"4c0f05083b414ac0323a1b9ee1abc275","date_updated":"2023-01-27T11:28:38Z","date_created":"2023-01-27T11:28:38Z","file_id":"12425","relation":"main_file"}],"oa_version":"Published Version","_id":"12234","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","ddc":["570"],"title":"Digest: On the origin of a possible hybrid species","intvolume":" 76","abstract":[{"text":"Hybrid speciation—the origin of new species resulting from the hybridization of genetically divergent lineages—was once considered rare, but genomic data suggest that it may occur more often than once thought. In this study, Noguerales and Ortego found genomic evidence supporting the hybrid origin of a grasshopper that is able to exploit a broader range of host plants than either of its putative parents.","lang":"eng"}],"issue":"11","type":"journal_article","doi":"10.1111/evo.14632","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"isi":["000855751600001"]},"oa":1,"quality_controlled":"1","isi":1,"month":"11","publication_identifier":{"eissn":["1558-5646"],"issn":["0014-3820"]},"author":[{"id":"43161670-5719-11EA-8025-FABC3DDC885E","first_name":"Sean","last_name":"Stankowski","full_name":"Stankowski, Sean"}],"date_created":"2023-01-16T09:50:48Z","date_updated":"2023-08-04T09:35:48Z","volume":76,"year":"2022","publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Wiley","file_date_updated":"2023-01-27T11:28:38Z"},{"has_accepted_license":"1","article_processing_charge":"No","day":"01","scopus_import":"1","keyword":["General Agricultural and Biological Sciences","Genetics","Ecology","Evolution","Behavior and Systematics"],"date_published":"2022-10-01T00:00:00Z","citation":{"mla":"Koch, Eva L., et al. “Genetic Architecture of Repeated Phenotypic Divergence in Littorina Saxatilis Evolution.” Evolution, vol. 76, no. 10, Wiley, 2022, pp. 2332–46, doi:10.1111/evo.14602.","short":"E.L. Koch, M. Ravinet, A.M. Westram, K. Johannesson, R.K. Butlin, Evolution 76 (2022) 2332–2346.","chicago":"Koch, Eva L., Mark Ravinet, Anja M Westram, Kerstin Johannesson, and Roger K. Butlin. “Genetic Architecture of Repeated Phenotypic Divergence in Littorina Saxatilis Evolution.” Evolution. Wiley, 2022. https://doi.org/10.1111/evo.14602.","ama":"Koch EL, Ravinet M, Westram AM, Johannesson K, Butlin RK. Genetic architecture of repeated phenotypic divergence in Littorina saxatilis evolution. Evolution. 2022;76(10):2332-2346. doi:10.1111/evo.14602","ista":"Koch EL, Ravinet M, Westram AM, Johannesson K, Butlin RK. 2022. Genetic architecture of repeated phenotypic divergence in Littorina saxatilis evolution. Evolution. 76(10), 2332–2346.","ieee":"E. L. Koch, M. Ravinet, A. M. Westram, K. Johannesson, and R. K. Butlin, “Genetic architecture of repeated phenotypic divergence in Littorina saxatilis evolution,” Evolution, vol. 76, no. 10. Wiley, pp. 2332–2346, 2022.","apa":"Koch, E. L., Ravinet, M., Westram, A. M., Johannesson, K., & Butlin, R. K. (2022). Genetic architecture of repeated phenotypic divergence in Littorina saxatilis evolution. Evolution. Wiley. https://doi.org/10.1111/evo.14602"},"publication":"Evolution","page":"2332-2346","article_type":"original","issue":"10","abstract":[{"text":"Chromosomal inversions have been shown to play a major role in a local adaptation by suppressing recombination between alternative arrangements and maintaining beneficial allele combinations. However, so far, their importance relative to the remaining genome remains largely unknown. Understanding the genetic architecture of adaptation requires better estimates of how loci of different effect sizes contribute to phenotypic variation. Here, we used three Swedish islands where the marine snail Littorina saxatilis has repeatedly evolved into two distinct ecotypes along a habitat transition. We estimated the contribution of inversion polymorphisms to phenotypic divergence while controlling for polygenic effects in the remaining genome using a quantitative genetics framework. We confirmed the importance of inversions but showed that contributions of loci outside inversions are of similar magnitude, with variable proportions dependent on the trait and the population. Some inversions showed consistent effects across all sites, whereas others exhibited site-specific effects, indicating that the genomic basis for replicated phenotypic divergence is only partly shared. The contributions of sexual dimorphism as well as environmental factors to phenotypic variation were significant but minor compared to inversions and polygenic background. Overall, this integrated approach provides insight into the multiple mechanisms contributing to parallel phenotypic divergence.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","file":[{"creator":"dernst","file_size":2990581,"content_type":"application/pdf","access_level":"open_access","file_name":"2022_Evolution_Koch.pdf","success":1,"checksum":"defd8a4bea61cf00a3c88d4a30e2728c","date_updated":"2023-01-30T08:45:35Z","date_created":"2023-01-30T08:45:35Z","file_id":"12439","relation":"main_file"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12247","intvolume":" 76","title":"Genetic architecture of repeated phenotypic divergence in Littorina saxatilis evolution","status":"public","ddc":["570"],"publication_identifier":{"eissn":["1558-5646"],"issn":["0014-3820"]},"month":"10","doi":"10.1111/evo.14602","language":[{"iso":"eng"}],"external_id":{"isi":["000848449100001"],"pmid":["35994296"]},"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","file_date_updated":"2023-01-30T08:45:35Z","related_material":{"record":[{"status":"public","relation":"research_data","id":"13066"}]},"author":[{"full_name":"Koch, Eva L.","last_name":"Koch","first_name":"Eva L."},{"full_name":"Ravinet, Mark","last_name":"Ravinet","first_name":"Mark"},{"last_name":"Westram","first_name":"Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","full_name":"Westram, Anja M"},{"last_name":"Johannesson","first_name":"Kerstin","full_name":"Johannesson, Kerstin"},{"full_name":"Butlin, Roger K.","last_name":"Butlin","first_name":"Roger K."}],"volume":76,"date_updated":"2023-08-04T09:42:11Z","date_created":"2023-01-16T09:54:15Z","pmid":1,"acknowledgement":"We thank everyone who helped with fieldwork, snail processing, and DNA extractions, particularly Laura Brettell, Mårten Duvetorp, Juan Galindo, Anne-Lise Liabot, Irena Senčić, and Zuzanna Zagrodzka. We also thank Rui Faria and Jenny Larsson for their contributions, with inversions and shell shape respectively. KJ was funded by the Swedish research council Vetenskapsrådet, grant number 2017-03798. R.K.B. and E.K. were funded by the European Research Council (ERC-2015-AdG-693030-BARRIERS). R.K.B. was also funded by the Natural Environment Research Council and the Swedish Research Council Vetenskapsrådet.","year":"2022","publisher":"Wiley","department":[{"_id":"NiBa"}],"publication_status":"published"},{"month":"07","day":"28","article_processing_charge":"No","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"citation":{"chicago":"Koch, Eva, Mark Ravinet, Anja M Westram, Kerstin Jonannesson, and Roger Butlin. “Data from: Genetic Architecture of Repeated Phenotypic Divergence in Littorina Saxatilis Ecotype Evolution.” Dryad, 2022. https://doi.org/10.5061/DRYAD.M905QFV4B.","short":"E. Koch, M. Ravinet, A.M. Westram, K. Jonannesson, R. Butlin, (2022).","mla":"Koch, Eva, et al. Data from: Genetic Architecture of Repeated Phenotypic Divergence in Littorina Saxatilis Ecotype Evolution. Dryad, 2022, doi:10.5061/DRYAD.M905QFV4B.","apa":"Koch, E., Ravinet, M., Westram, A. M., Jonannesson, K., & Butlin, R. (2022). Data from: Genetic architecture of repeated phenotypic divergence in Littorina saxatilis ecotype evolution. Dryad. https://doi.org/10.5061/DRYAD.M905QFV4B","ieee":"E. Koch, M. Ravinet, A. M. Westram, K. Jonannesson, and R. Butlin, “Data from: Genetic architecture of repeated phenotypic divergence in Littorina saxatilis ecotype evolution.” Dryad, 2022.","ista":"Koch E, Ravinet M, Westram AM, Jonannesson K, Butlin R. 2022. Data from: Genetic architecture of repeated phenotypic divergence in Littorina saxatilis ecotype evolution, Dryad, 10.5061/DRYAD.M905QFV4B.","ama":"Koch E, Ravinet M, Westram AM, Jonannesson K, Butlin R. Data from: Genetic architecture of repeated phenotypic divergence in Littorina saxatilis ecotype evolution. 2022. doi:10.5061/DRYAD.M905QFV4B"},"main_file_link":[{"url":"https://doi.org/10.5061/dryad.m905qfv4b","open_access":"1"}],"oa":1,"doi":"10.5061/DRYAD.M905QFV4B","date_published":"2022-07-28T00:00:00Z","type":"research_data_reference","abstract":[{"lang":"eng","text":"Chromosomal inversions have been shown to play a major role in local adaptation by suppressing recombination between alternative arrangements and maintaining beneficial allele combinations. However, so far, their importance relative to the remaining genome remains largely unknown. Understanding the genetic architecture of adaptation requires better estimates of how loci of different effect sizes contribute to phenotypic variation. Here, we used three Swedish islands where the marine snail Littorina saxatilis has repeatedly evolved into two distinct ecotypes along a habitat transition. We estimated the contribution of inversion polymorphisms to phenotypic divergence while controlling for polygenic effects in the remaining genome using a quantitative genetics framework. We confirmed the importance of inversions but showed that contributions of loci outside inversions are of similar magnitude, with variable proportions dependent on the trait and the population. Some inversions showed consistent effects across all sites, whereas others exhibited site-specific effects, indicating that the genomic basis for replicated phenotypic divergence is only partly shared. The contributions of sexual dimorphism as well as environmental factors to phenotypic variation were significant but minor compared to inversions and polygenic background. Overall, this integrated approach provides insight into the multiple mechanisms contributing to parallel phenotypic divergence."}],"_id":"13066","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2022","ddc":["570"],"title":"Data from: Genetic architecture of repeated phenotypic divergence in Littorina saxatilis ecotype evolution","status":"public","department":[{"_id":"NiBa"}],"publisher":"Dryad","author":[{"last_name":"Koch","first_name":"Eva","full_name":"Koch, Eva"},{"full_name":"Ravinet, Mark","last_name":"Ravinet","first_name":"Mark"},{"orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","first_name":"Anja M","full_name":"Westram, Anja M"},{"first_name":"Kerstin","last_name":"Jonannesson","full_name":"Jonannesson, Kerstin"},{"first_name":"Roger","last_name":"Butlin","full_name":"Butlin, Roger"}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"12247"}]},"date_created":"2023-05-23T16:33:12Z","date_updated":"2023-08-04T09:42:10Z","oa_version":"Published Version"},{"file":[{"file_name":"2022_JourEvoBiology_Westram.pdf","access_level":"open_access","creator":"dernst","file_size":3146793,"content_type":"application/pdf","file_id":"12448","relation":"main_file","date_created":"2023-01-30T10:05:31Z","date_updated":"2023-01-30T10:05:31Z","success":1,"checksum":"f08de57112330a7ee88d2e1b20576a1e"}],"oa_version":"Published Version","intvolume":" 35","status":"public","ddc":["570"],"title":"What is reproductive isolation?","_id":"12264","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"9","abstract":[{"lang":"eng","text":"Reproductive isolation (RI) is a core concept in evolutionary biology. It has been the central focus of speciation research since the modern synthesis and is the basis by which biological species are defined. Despite this, the term is used in seemingly different ways, and attempts to quantify RI have used very different approaches. After showing that the field lacks a clear definition of the term, we attempt to clarify key issues, including what RI is, how it can be quantified in principle, and how it can be measured in practice. Following other definitions with a genetic focus, we propose that RI is a quantitative measure of the effect that genetic differences between populations have on gene flow. Specifically, RI compares the flow of neutral alleles in the presence of these genetic differences to the flow without any such differences. RI is thus greater than zero when genetic differences between populations reduce the flow of neutral alleles between populations. We show how RI can be quantified in a range of scenarios. A key conclusion is that RI depends strongly on circumstances—including the spatial, temporal and genomic context—making it difficult to compare across systems. After reviewing methods for estimating RI from data, we conclude that it is difficult to measure in practice. We discuss our findings in light of the goals of speciation research and encourage the use of methods for estimating RI that integrate organismal and genetic approaches."}],"type":"journal_article","date_published":"2022-09-01T00:00:00Z","page":"1143-1164","article_type":"review","citation":{"ieee":"A. M. Westram, S. Stankowski, P. Surendranadh, and N. H. Barton, “What is reproductive isolation?,” Journal of Evolutionary Biology, vol. 35, no. 9. Wiley, pp. 1143–1164, 2022.","apa":"Westram, A. M., Stankowski, S., Surendranadh, P., & Barton, N. H. (2022). What is reproductive isolation? Journal of Evolutionary Biology. Wiley. https://doi.org/10.1111/jeb.14005","ista":"Westram AM, Stankowski S, Surendranadh P, Barton NH. 2022. What is reproductive isolation? Journal of Evolutionary Biology. 35(9), 1143–1164.","ama":"Westram AM, Stankowski S, Surendranadh P, Barton NH. What is reproductive isolation? Journal of Evolutionary Biology. 2022;35(9):1143-1164. doi:10.1111/jeb.14005","chicago":"Westram, Anja M, Sean Stankowski, Parvathy Surendranadh, and Nicholas H Barton. “What Is Reproductive Isolation?” Journal of Evolutionary Biology. Wiley, 2022. https://doi.org/10.1111/jeb.14005.","short":"A.M. Westram, S. Stankowski, P. Surendranadh, N.H. Barton, Journal of Evolutionary Biology 35 (2022) 1143–1164.","mla":"Westram, Anja M., et al. “What Is Reproductive Isolation?” Journal of Evolutionary Biology, vol. 35, no. 9, Wiley, 2022, pp. 1143–64, doi:10.1111/jeb.14005."},"publication":"Journal of Evolutionary Biology","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"01","keyword":["Ecology","Evolution","Behavior and Systematics"],"scopus_import":"1","volume":35,"date_created":"2023-01-16T09:59:24Z","date_updated":"2023-08-04T09:53:40Z","related_material":{"record":[{"id":"12265","status":"public","relation":"other"}]},"author":[{"orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","first_name":"Anja M","full_name":"Westram, Anja M"},{"full_name":"Stankowski, Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","last_name":"Stankowski","first_name":"Sean"},{"full_name":"Surendranadh, Parvathy","id":"455235B8-F248-11E8-B48F-1D18A9856A87","last_name":"Surendranadh","first_name":"Parvathy"},{"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","publication_status":"published","pmid":1,"year":"2022","acknowledgement":"We are grateful to the participants of the ESEB satellite symposium ‘Understanding reproductive isolation: bridging conceptual barriers in speciation research’ in 2021 for the interesting discussions that helped us clarify the thoughts presented in this article. We thank Roger Butlin, Michael Turelli and two anonymous reviewers for their thoughtful comments on this manuscript. We are also very grateful to Roger Butlin and the Barton Group for the continued conversa-tions about RI. In addition, we thank all participants of the speciation survey. Part of this work was funded by the Austrian Science Fund FWF (grant P 32166)","file_date_updated":"2023-01-30T10:05:31Z","language":[{"iso":"eng"}],"doi":"10.1111/jeb.14005","project":[{"name":"The maintenance of alternative adaptive peaks in snapdragons","grant_number":"P32166","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E"}],"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":{"pmid":["36063156"],"isi":["000849851100002"]},"publication_identifier":{"eissn":["1420-9101"],"issn":["1010-061X"]},"month":"09"},{"issue":"9","type":"journal_article","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"12449","checksum":"27268009e5eec030bc10667a4ac5ed4c","success":1,"date_updated":"2023-01-30T10:14:09Z","date_created":"2023-01-30T10:14:09Z","access_level":"open_access","file_name":"2022_JourEvoBiology_Westram_Response.pdf","content_type":"application/pdf","file_size":349603,"creator":"dernst"}],"title":"Reproductive isolation, speciation, and the value of disagreement: A reply to the commentaries on ‘What is reproductive isolation?’","ddc":["570"],"status":"public","intvolume":" 35","_id":"12265","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","day":"01","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","keyword":["Ecology","Evolution","Behavior and Systematics"],"scopus_import":"1","date_published":"2022-09-01T00:00:00Z","article_type":"letter_note","page":"1200-1205","publication":"Journal of Evolutionary Biology","citation":{"ama":"Westram AM, Stankowski S, Surendranadh P, Barton NH. Reproductive isolation, speciation, and the value of disagreement: A reply to the commentaries on ‘What is reproductive isolation?’ Journal of Evolutionary Biology. 2022;35(9):1200-1205. doi:10.1111/jeb.14082","ieee":"A. M. Westram, S. Stankowski, P. Surendranadh, and N. H. Barton, “Reproductive isolation, speciation, and the value of disagreement: A reply to the commentaries on ‘What is reproductive isolation?,’” Journal of Evolutionary Biology, vol. 35, no. 9. Wiley, pp. 1200–1205, 2022.","apa":"Westram, A. M., Stankowski, S., Surendranadh, P., & Barton, N. H. (2022). Reproductive isolation, speciation, and the value of disagreement: A reply to the commentaries on ‘What is reproductive isolation?’ Journal of Evolutionary Biology. Wiley. https://doi.org/10.1111/jeb.14082","ista":"Westram AM, Stankowski S, Surendranadh P, Barton NH. 2022. Reproductive isolation, speciation, and the value of disagreement: A reply to the commentaries on ‘What is reproductive isolation?’ Journal of Evolutionary Biology. 35(9), 1200–1205.","short":"A.M. Westram, S. Stankowski, P. Surendranadh, N.H. Barton, Journal of Evolutionary Biology 35 (2022) 1200–1205.","mla":"Westram, Anja M., et al. “Reproductive Isolation, Speciation, and the Value of Disagreement: A Reply to the Commentaries on ‘What Is Reproductive Isolation?’” Journal of Evolutionary Biology, vol. 35, no. 9, Wiley, 2022, pp. 1200–05, doi:10.1111/jeb.14082.","chicago":"Westram, Anja M, Sean Stankowski, Parvathy Surendranadh, and Nicholas H Barton. “Reproductive Isolation, Speciation, and the Value of Disagreement: A Reply to the Commentaries on ‘What Is Reproductive Isolation?’” Journal of Evolutionary Biology. Wiley, 2022. https://doi.org/10.1111/jeb.14082."},"file_date_updated":"2023-01-30T10:14:09Z","date_updated":"2023-08-04T09:53:41Z","date_created":"2023-01-16T09:59:37Z","volume":35,"author":[{"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":"Sean","last_name":"Stankowski","id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean"},{"first_name":"Parvathy","last_name":"Surendranadh","id":"455235B8-F248-11E8-B48F-1D18A9856A87","full_name":"Surendranadh, Parvathy"},{"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":[{"id":"12264","status":"public","relation":"other"}]},"publication_status":"published","publisher":"Wiley","department":[{"_id":"NiBa"}],"year":"2022","acknowledgement":"We are very grateful to the authors of the commentaries for the interesting discussion and to Luke Holman for handling this set of manuscripts. Part of this work was funded by the Austrian Science Fund FWF (grant P 32166).","month":"09","publication_identifier":{"eissn":["1420-9101"],"issn":["1010-061X"]},"language":[{"iso":"eng"}],"doi":"10.1111/jeb.14082","quality_controlled":"1","isi":1,"project":[{"name":"The maintenance of alternative adaptive peaks in snapdragons","grant_number":"P32166","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E"}],"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":["000849851100009"]},"oa":1},{"keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology"],"scopus_import":"1","day":"11","article_processing_charge":"No","has_accepted_license":"1","article_type":"original","publication":"Philosophical Transactions of the Royal Society B: Biological Sciences","citation":{"mla":"Barton, Nicholas H., and Oluwafunmilola O. Olusanya. “The Response of a Metapopulation to a Changing Environment.” Philosophical Transactions of the Royal Society B: Biological Sciences, vol. 377, no. 1848, The Royal Society, 2022, doi:10.1098/rstb.2021.0009.","short":"N.H. Barton, O.O. Olusanya, Philosophical Transactions of the Royal Society B: Biological Sciences 377 (2022).","chicago":"Barton, Nicholas H, and Oluwafunmilola O Olusanya. “The Response of a Metapopulation to a Changing Environment.” Philosophical Transactions of the Royal Society B: Biological Sciences. The Royal Society, 2022. https://doi.org/10.1098/rstb.2021.0009.","ama":"Barton NH, Olusanya OO. The response of a metapopulation to a changing environment. Philosophical Transactions of the Royal Society B: Biological Sciences. 2022;377(1848). doi:10.1098/rstb.2021.0009","ista":"Barton NH, Olusanya OO. 2022. The response of a metapopulation to a changing environment. Philosophical Transactions of the Royal Society B: Biological Sciences. 377(1848).","ieee":"N. H. Barton and O. O. Olusanya, “The response of a metapopulation to a changing environment,” Philosophical Transactions of the Royal Society B: Biological Sciences, vol. 377, no. 1848. The Royal Society, 2022.","apa":"Barton, N. H., & Olusanya, O. O. (2022). The response of a metapopulation to a changing environment. Philosophical Transactions of the Royal Society B: Biological Sciences. The Royal Society. https://doi.org/10.1098/rstb.2021.0009"},"date_published":"2022-04-11T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"A species distributed across diverse environments may adapt to local conditions. We ask how quickly such a species changes its range in response to changed conditions. Szép et al. (Szép E, Sachdeva H, Barton NH. 2021 Polygenic local adaptation in metapopulations: a stochastic eco-evolutionary model. Evolution75, 1030–1045 (doi:10.1111/evo.14210)) used the infinite island model to find the stationary distribution of allele frequencies and deme sizes. We extend this to find how a metapopulation responds to changes in carrying capacity, selection strength, or migration rate when deme sizes are fixed. We further develop a ‘fixed-state’ approximation. Under this approximation, polymorphism is only possible for a narrow range of habitat proportions when selection is weak compared to drift, but for a much wider range otherwise. When rates of selection or migration relative to drift change in a single deme of the metapopulation, the population takes a time of order m−1 to reach the new equilibrium. However, even with many loci, there can be substantial fluctuations in net adaptation, because at each locus, alleles randomly get lost or fixed. Thus, in a finite metapopulation, variation may gradually be lost by chance, even if it would persist in an infinite metapopulation. When conditions change across the whole metapopulation, there can be rapid change, which is predicted well by the fixed-state approximation. This work helps towards an understanding of how metapopulations extend their range across diverse environments.\r\nThis article is part of the theme issue ‘Species’ ranges in the face of changing environments (Part II)’."}],"issue":"1848","title":"The response of a metapopulation to a changing environment","status":"public","ddc":["570"],"intvolume":" 377","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"10787","oa_version":"Published Version","file":[{"file_id":"11719","relation":"main_file","date_updated":"2022-08-02T06:14:32Z","date_created":"2022-08-02T06:14:32Z","success":1,"checksum":"3b0243738f01bf3c07e0d7e8dc64f71d","file_name":"2022_PhilosophicalTransactionsRSB_Barton.pdf","access_level":"open_access","creator":"dernst","file_size":1349672,"content_type":"application/pdf"}],"month":"04","publication_identifier":{"issn":["0962-8436"],"eissn":["1471-2970"]},"isi":1,"quality_controlled":"1","project":[{"_id":"c08d3278-5a5b-11eb-8a69-fdb09b55f4b8","grant_number":"P32896","name":"Causes and consequences of population fragmentation"}],"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":["000758140300001"],"pmid":["35184588"]},"language":[{"iso":"eng"}],"doi":"10.1098/rstb.2021.0009","file_date_updated":"2022-08-02T06:14:32Z","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"publisher":"The Royal Society","year":"2022","acknowledgement":"This research was partly funded by the Austrian Science Fund (FWF) [FWF P-32896B].","pmid":1,"date_updated":"2024-01-26T12:00:53Z","date_created":"2022-02-21T16:08:10Z","volume":377,"author":[{"full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Olusanya, Oluwafunmilola O","last_name":"Olusanya","first_name":"Oluwafunmilola O","orcid":"0000-0003-1971-8314","id":"41AD96DC-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"id":"14711","relation":"dissertation_contains","status":"public"}]}},{"ddc":["576"],"title":"Genetic load and extinction in peripheral populations: The roles of migration, drift and demographic stochasticity","status":"public","intvolume":" 377","_id":"10658","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"relation":"main_file","file_id":"10659","checksum":"04ca9e2f0e344d680b947f2457df8d0a","date_updated":"2022-01-24T10:34:45Z","date_created":"2022-01-24T10:34:45Z","access_level":"open_access","file_name":"rstb.2021.0010.pdf","content_type":"application/pdf","file_size":1845792,"creator":"oolusany"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"We analyse how migration from a large mainland influences genetic load and population numbers on an island, in a scenario where fitness-affecting variants are unconditionally deleterious, and where numbers decline with increasing load. Our analysis shows that migration can have qualitatively different effects, depending on the total mutation target and fitness effects of deleterious variants. In particular, we find that populations exhibit a genetic Allee effect across a wide range of parameter combinations, when variants are partially recessive, cycling between low-load (large-population) and high-load (sink) states. Increased migration reduces load in the sink state (by increasing heterozygosity) but further inflates load in the large-population state (by hindering purging). We identify various critical parameter thresholds at which one or other stable state collapses, and discuss how these thresholds are influenced by the genetic versus demographic effects of migration. Our analysis is based on a ‘semi-deterministic’ analysis, which accounts for genetic drift but neglects demographic stochasticity. We also compare against simulations which account for both demographic stochasticity and drift. Our results clarify the importance of gene flow as a key determinant of extinction risk in peripheral populations, even in the absence of ecological gradients. This article is part of the theme issue ‘Species’ ranges in the face of changing environments (part I)’.","lang":"eng"}],"issue":"1846","article_type":"original","publication":"Philosophical Transactions of the Royal Society B","citation":{"ista":"Sachdeva H, Olusanya OO, Barton NH. 2022. Genetic load and extinction in peripheral populations: The roles of migration, drift and demographic stochasticity. Philosophical Transactions of the Royal Society B. 377(1846), 20210010.","apa":"Sachdeva, H., Olusanya, O. O., & Barton, N. H. (2022). Genetic load and extinction in peripheral populations: The roles of migration, drift and demographic stochasticity. Philosophical Transactions of the Royal Society B. The Royal Society. https://doi.org/10.1098/rstb.2021.0010","ieee":"H. Sachdeva, O. O. Olusanya, and N. H. Barton, “Genetic load and extinction in peripheral populations: The roles of migration, drift and demographic stochasticity,” Philosophical Transactions of the Royal Society B, vol. 377, no. 1846. The Royal Society, 2022.","ama":"Sachdeva H, Olusanya OO, Barton NH. Genetic load and extinction in peripheral populations: The roles of migration, drift and demographic stochasticity. Philosophical Transactions of the Royal Society B. 2022;377(1846). doi:10.1098/rstb.2021.0010","chicago":"Sachdeva, Himani, Oluwafunmilola O Olusanya, and Nicholas H Barton. “Genetic Load and Extinction in Peripheral Populations: The Roles of Migration, Drift and Demographic Stochasticity.” Philosophical Transactions of the Royal Society B. The Royal Society, 2022. https://doi.org/10.1098/rstb.2021.0010.","mla":"Sachdeva, Himani, et al. “Genetic Load and Extinction in Peripheral Populations: The Roles of Migration, Drift and Demographic Stochasticity.” Philosophical Transactions of the Royal Society B, vol. 377, no. 1846, 20210010, The Royal Society, 2022, doi:10.1098/rstb.2021.0010.","short":"H. Sachdeva, O.O. Olusanya, N.H. Barton, Philosophical Transactions of the Royal Society B 377 (2022)."},"date_published":"2022-01-24T00:00:00Z","day":"24","has_accepted_license":"1","article_processing_charge":"No","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"publisher":"The Royal Society","acknowledgement":"This research was partly funded by the Austrian Science Fund (FWF) (grant no. P-32896B).","year":"2022","pmid":1,"date_created":"2022-01-24T10:34:53Z","date_updated":"2024-01-26T12:00:53Z","volume":377,"author":[{"full_name":"Sachdeva, Himani","last_name":"Sachdeva","first_name":"Himani"},{"orcid":"0000-0003-1971-8314","id":"41AD96DC-F248-11E8-B48F-1D18A9856A87","last_name":"Olusanya","first_name":"Oluwafunmilola O","full_name":"Olusanya, Oluwafunmilola O"},{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton"}],"related_material":{"link":[{"url":"https://doi.org/10.1101/2021.08.05.455207","relation":"earlier_version"}],"record":[{"id":"14711","relation":"dissertation_contains","status":"public"}]},"article_number":"20210010","file_date_updated":"2022-01-24T10:34:45Z","isi":1,"quality_controlled":"1","project":[{"name":"Causes and consequences of population fragmentation","grant_number":"P32896","_id":"c08d3278-5a5b-11eb-8a69-fdb09b55f4b8"}],"external_id":{"isi":["000745854300008"],"pmid":["35067097"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1098/rstb.2021.0010","month":"01","publication_identifier":{"issn":["0962-8436"],"eissn":["1471-2970"]}},{"issue":"3","abstract":[{"text":"Many studies have quantified the distribution of heterozygosity and relatedness in natural populations, but few have examined the demographic processes driving these patterns. In this study, we take a novel approach by studying how population structure affects both pairwise identity and the distribution of heterozygosity in a natural population of the self-incompatible plant Antirrhinum majus. Excess variance in heterozygosity between individuals is due to identity disequilibrium, which reflects the variance in inbreeding between individuals; it is measured by the statistic g2. We calculated g2 together with FST and pairwise relatedness (Fij) using 91 SNPs in 22,353 individuals collected over 11 years. We find that pairwise Fij declines rapidly over short spatial scales, and the excess variance in heterozygosity between individuals reflects significant variation in inbreeding. Additionally, we detect an excess of individuals with around half the average heterozygosity, indicating either selfing or matings between close relatives. We use 2 types of simulation to ask whether variation in heterozygosity is consistent with fine-scale spatial population structure. First, by simulating offspring using parents drawn from a range of spatial scales, we show that the known pollen dispersal kernel explains g2. Second, we simulate a 1,000-generation pedigree using the known dispersal and spatial distribution and find that the resulting g2 is consistent with that observed from the field data. In contrast, a simulated population with uniform density underestimates g2, indicating that heterogeneous density promotes identity disequilibrium. Our study shows that heterogeneous density and leptokurtic dispersal can together explain the distribution of heterozygosity.","lang":"eng"}],"type":"journal_article","oa_version":"Submitted Version","file":[{"file_name":"Manuscript.pdf","access_level":"open_access","content_type":"application/pdf","file_size":885374,"creator":"larathoo","relation":"main_file","file_id":"11412","date_updated":"2022-05-26T12:48:15Z","date_created":"2022-05-26T12:48:15Z","checksum":"cc2d56deb608bd53c5cc02f03a875107","success":1},{"content_type":"application/pdf","file_size":1401704,"creator":"larathoo","file_name":"SupplementalMaterial.pdf","access_level":"open_access","date_created":"2022-05-26T12:48:21Z","date_updated":"2022-05-26T12:48:21Z","checksum":"693742595b6c7ed809423be01460d083","success":1,"relation":"main_file","file_id":"11413"}],"intvolume":" 221","status":"public","title":"Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus","ddc":["576"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"11411","has_accepted_license":"1","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2022-07-01T00:00:00Z","article_type":"original","citation":{"ieee":"P. Surendranadh, L. S. Arathoon, C. Baskett, D. Field, M. Pickup, and N. H. Barton, “Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus,” Genetics, vol. 221, no. 3. Oxford University Press, 2022.","apa":"Surendranadh, P., Arathoon, L. S., Baskett, C., Field, D., Pickup, M., & Barton, N. H. (2022). Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. Genetics. Oxford University Press. https://doi.org/10.1093/genetics/iyac083","ista":"Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. 2022. Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. Genetics. 221(3), iyac083.","ama":"Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. Genetics. 2022;221(3). doi:10.1093/genetics/iyac083","chicago":"Surendranadh, Parvathy, Louise S Arathoon, Carina Baskett, David Field, Melinda Pickup, and Nicholas H Barton. “Effects of Fine-Scale Population Structure on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus.” Genetics. Oxford University Press, 2022. https://doi.org/10.1093/genetics/iyac083.","short":"P. Surendranadh, L.S. Arathoon, C. Baskett, D. Field, M. Pickup, N.H. Barton, Genetics 221 (2022).","mla":"Surendranadh, Parvathy, et al. “Effects of Fine-Scale Population Structure on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus.” Genetics, vol. 221, no. 3, iyac083, Oxford University Press, 2022, doi:10.1093/genetics/iyac083."},"publication":"Genetics","file_date_updated":"2022-05-26T12:48:21Z","article_number":"iyac083","volume":221,"date_created":"2022-05-26T13:44:50Z","date_updated":"2024-02-21T12:38:33Z","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"14651"},{"relation":"research_data","status":"public","id":"11321"},{"id":"9192","relation":"research_data","status":"public"}]},"author":[{"full_name":"Surendranadh, Parvathy","id":"455235B8-F248-11E8-B48F-1D18A9856A87","last_name":"Surendranadh","first_name":"Parvathy"},{"first_name":"Louise S","last_name":"Arathoon","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1771-714X","full_name":"Arathoon, Louise S"},{"first_name":"Carina","last_name":"Baskett","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7354-8574","full_name":"Baskett, Carina"},{"full_name":"Field, David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478","first_name":"David","last_name":"Field"},{"full_name":"Pickup, Melinda","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6118-0541","first_name":"Melinda","last_name":"Pickup"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H"}],"publisher":"Oxford University Press","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"publication_status":"published","pmid":1,"acknowledgement":"Part of this work was funded by Marie Curie COFUND Doctoral Fellowship and Austrian Science Fund FWF (grant P32166).\r\nWe thank the many volunteers and friends who have contributed to data collection in the field site over the years, in particular those who have managed field seasons: Barbora Trubenova, Maria Clara Melo, Tom Ellis, Eva Cereghetti, Lenka Matejovicova, Beatriz Pablo Carmona. Frederic Ferrer and Eva Salmerón Mateu have been immensely helpful with logistics at our informal field station, El Serrat de Planoles. We thank Sean Stankowski for technical help in\r\nproducing figure 1. This research was also supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing (SciComp).","year":"2022","publication_identifier":{"eissn":["1943-2631"]},"month":"07","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"doi":"10.1093/genetics/iyac083","project":[{"grant_number":"P32166","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","name":"The maintenance of alternative adaptive peaks in snapdragons"}],"quality_controlled":"1","isi":1,"oa":1,"external_id":{"isi":["000803735800001"],"pmid":["35639938"]}},{"abstract":[{"lang":"eng","text":"Here are the research data underlying the publication \"Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus\" Further information are summed up in the README document. "}],"file_date_updated":"2022-04-22T09:39:03Z","type":"research_data","oa_version":"Published Version","file":[{"checksum":"96c1b86cdf25481f2a52972fcc45ca7f","success":1,"date_updated":"2022-04-22T09:39:03Z","date_created":"2022-04-22T09:39:03Z","relation":"main_file","file_id":"11326","content_type":"application/x-zip-compressed","file_size":13260571,"creator":"larathoo","access_level":"open_access","file_name":"Data_Code.zip"}],"date_updated":"2024-02-21T12:41:09Z","date_created":"2022-04-22T09:42:24Z","contributor":[{"contributor_type":"project_member","last_name":"Arathoon","first_name":"Louise S","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Carina","contributor_type":"project_member","last_name":"Baskett","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7354-8574"},{"first_name":"David","contributor_type":"project_member","last_name":"Field","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","contributor_type":"project_member","last_name":"Pickup"},{"first_name":"Nicholas H","contributor_type":"project_member","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"},{"id":"9192","relation":"earlier_version","status":"public"},{"relation":"earlier_version","status":"public","id":"8254"}]},"author":[{"last_name":"Surendranadh","first_name":"Parvathy","id":"455235B8-F248-11E8-B48F-1D18A9856A87","full_name":"Surendranadh, Parvathy"},{"orcid":"0000-0003-1771-714X","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","last_name":"Arathoon","first_name":"Louise S","full_name":"Arathoon, Louise S"},{"full_name":"Baskett, Carina","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7354-8574","first_name":"Carina","last_name":"Baskett"},{"last_name":"Field","first_name":"David","orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87","full_name":"Field, David"},{"full_name":"Pickup, Melinda","orcid":"0000-0001-6118-0541","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","last_name":"Pickup","first_name":"Melinda"},{"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":"GradSch"},{"_id":"NiBa"}],"publisher":"Institute of Science and Technology Austria","ddc":["570"],"status":"public","title":"Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus","year":"2022","_id":"11321","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","article_processing_charge":"No","month":"04","day":"28","date_published":"2022-04-28T00:00:00Z","doi":"10.15479/at:ista:11321","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. 2022. doi:10.15479/at:ista:11321","ista":"Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. 2022. Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus, Institute of Science and Technology Austria, 10.15479/at:ista:11321.","apa":"Surendranadh, P., Arathoon, L. S., Baskett, C., Field, D., Pickup, M., & Barton, N. H. (2022). Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11321","ieee":"P. Surendranadh, L. S. Arathoon, C. Baskett, D. Field, M. Pickup, and N. H. Barton, “Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus.” Institute of Science and Technology Austria, 2022.","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, 2022, doi:10.15479/at:ista:11321.","short":"P. Surendranadh, L.S. Arathoon, C. Baskett, D. Field, M. Pickup, N.H. Barton, (2022).","chicago":"Surendranadh, Parvathy, Louise S Arathoon, Carina Baskett, David Field, Melinda Pickup, and Nicholas H Barton. “Effects of Fine-Scale Population Structure on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11321."}},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12081","status":"public","title":"Accumulation and maintenance of information in evolution","ddc":["570"],"intvolume":" 119","oa_version":"Published Version","file":[{"date_updated":"2022-09-12T08:08:12Z","date_created":"2022-09-12T08:08:12Z","checksum":"6dec51f6567da9039982a571508a8e4d","success":1,"relation":"main_file","file_id":"12091","file_size":2165752,"content_type":"application/pdf","creator":"dernst","file_name":"2022_PNAS_Hledik.pdf","access_level":"open_access"}],"type":"journal_article","abstract":[{"text":"Selection accumulates information in the genome—it guides stochastically evolving populations toward states (genotype frequencies) that would be unlikely under neutrality. This can be quantified as the Kullback–Leibler (KL) divergence between the actual distribution of genotype frequencies and the corresponding neutral distribution. First, we show that this population-level information sets an upper bound on the information at the level of genotype and phenotype, limiting how precisely they can be specified by selection. Next, we study how the accumulation and maintenance of information is limited by the cost of selection, measured as the genetic load or the relative fitness variance, both of which we connect to the control-theoretic KL cost of control. The information accumulation rate is upper bounded by the population size times the cost of selection. This bound is very general, and applies across models (Wright–Fisher, Moran, diffusion) and to arbitrary forms of selection, mutation, and recombination. Finally, the cost of maintaining information depends on how it is encoded: Specifying a single allele out of two is expensive, but one bit encoded among many weakly specified loci (as in a polygenic trait) is cheap.","lang":"eng"}],"issue":"36","publication":"Proceedings of the National Academy of Sciences","citation":{"chicago":"Hledik, Michal, Nicholas H Barton, and Gašper Tkačik. “Accumulation and Maintenance of Information in Evolution.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2022. https://doi.org/10.1073/pnas.2123152119.","mla":"Hledik, Michal, et al. “Accumulation and Maintenance of Information in Evolution.” Proceedings of the National Academy of Sciences, vol. 119, no. 36, e2123152119, Proceedings of the National Academy of Sciences, 2022, doi:10.1073/pnas.2123152119.","short":"M. Hledik, N.H. Barton, G. Tkačik, Proceedings of the National Academy of Sciences 119 (2022).","ista":"Hledik M, Barton NH, Tkačik G. 2022. Accumulation and maintenance of information in evolution. Proceedings of the National Academy of Sciences. 119(36), e2123152119.","ieee":"M. Hledik, N. H. Barton, and G. Tkačik, “Accumulation and maintenance of information in evolution,” Proceedings of the National Academy of Sciences, vol. 119, no. 36. Proceedings of the National Academy of Sciences, 2022.","apa":"Hledik, M., Barton, N. H., & Tkačik, G. (2022). Accumulation and maintenance of information in evolution. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2123152119","ama":"Hledik M, Barton NH, Tkačik G. Accumulation and maintenance of information in evolution. Proceedings of the National Academy of Sciences. 2022;119(36). doi:10.1073/pnas.2123152119"},"article_type":"original","date_published":"2022-08-29T00:00:00Z","scopus_import":"1","day":"29","has_accepted_license":"1","article_processing_charge":"No","year":"2022","acknowledgement":"We thank Ksenia Khudiakova, Wiktor Młynarski, Sean Stankowski, and two anonymous reviewers for discussions and comments on the manuscript. G.T. and M.H. acknowledge funding from the Human Frontier Science Program Grant RGP0032/2018. N.B. acknowledges funding from ERC Grant 250152 “Information and Evolution.”","pmid":1,"publication_status":"published","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"publisher":"Proceedings of the National Academy of Sciences","author":[{"id":"4171253A-F248-11E8-B48F-1D18A9856A87","last_name":"Hledik","first_name":"Michal","full_name":"Hledik, Michal"},{"full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"1","first_name":"Gašper","last_name":"Tkačik","full_name":"Tkačik, Gašper"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"15020"}]},"date_created":"2022-09-11T22:01:55Z","date_updated":"2024-03-06T14:22:51Z","volume":119,"article_number":"e2123152119","file_date_updated":"2022-09-12T08:08:12Z","ec_funded":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":["000889278400014"],"pmid":["36037343"]},"quality_controlled":"1","isi":1,"project":[{"grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation"},{"grant_number":"RGP0034/2018","_id":"2665AAFE-B435-11E9-9278-68D0E5697425","name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?"}],"doi":"10.1073/pnas.2123152119","language":[{"iso":"eng"}],"month":"08","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]}},{"file":[{"access_level":"open_access","file_name":"thesis_sb_final_pdfa.pdf","creator":"sbelohla","content_type":"application/pdf","file_size":8247240,"file_id":"11398","embargo":"2023-05-19","relation":"main_file","checksum":"4d75e6a619df7e8a9d6e840aee182380","date_created":"2022-05-19T13:03:13Z","date_updated":"2023-05-20T22:30:03Z"},{"access_level":"closed","embargo_to":"open_access","file_name":"thesis_sb_final.zip","file_size":7094,"content_type":"application/x-zip-compressed","creator":"sbelohla","relation":"source_file","file_id":"11399","checksum":"7a5d8b6dd0ca00784f860075b0a7d8f0","date_updated":"2023-05-20T22:30:03Z","date_created":"2022-05-19T13:07:47Z"}],"oa_version":"Published Version","status":"public","ddc":["576"],"title":"The genetic basis of complex traits studied via analysis of evolve and resequence experiments","_id":"11388","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","abstract":[{"lang":"eng","text":"In evolve and resequence experiments, a population is sequenced, subjected to selection and\r\nthen sequenced again, so that genetic changes before and after selection can be observed at\r\nthe genetic level. Here, I use these studies to better understand the genetic basis of complex\r\ntraits - traits which depend on more than a few genes.\r\nIn the first chapter, I discuss the first evolve and resequence experiment, in which a population\r\nof mice, the so-called \"Longshanks\" mice, were selected for tibia length while their body mass\r\nwas kept constant. The full pedigree is known. We observed a selection response on all\r\nchromosomes and used the infinitesimal model with linkage, a model which assumes an infinite\r\nnumber of genes with infinitesimally small effect sizes, as a null model. Results implied a very\r\npolygenic basis with a few loci of major effect standing out and changing in parallel. There\r\nwas large variability between the different chromosomes in this study, probably due to LD.\r\nIn chapter two, I go on to discuss the impact of LD, on the variability in an allele-frequency\r\nbased summary statistic, giving an equation based on the initial allele frequencies, average\r\npairwise LD, and the first four moments of the haplotype block copy number distribution. I\r\ndescribe this distribution by referring back to the founder generation. I then demonstrate\r\nhow to infer selection via a maximum likelihood scheme on the example of a single locus and\r\ndiscuss how to extend this to more realistic scenarios.\r\nIn chapter three, I discuss the second evolve and resequence experiment, in which a small\r\npopulation of Drosophila melanogaster was selected for increased pupal case size over 6\r\ngenerations. The experiment was highly replicated with 27 lines selected within family and a\r\nknown pedigree. We observed a phenotypic selection response of over one standard deviation.\r\nI describe the patterns in allele frequency data, including allele frequency changes and patterns\r\nof heterozygosity, and give ideas for future work."}],"alternative_title":["ISTA Thesis"],"type":"dissertation","date_published":"2022-05-18T00:00:00Z","page":"98","citation":{"chicago":"Belohlavy, Stefanie. “The Genetic Basis of Complex Traits Studied via Analysis of Evolve and Resequence Experiments.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11388.","mla":"Belohlavy, Stefanie. The Genetic Basis of Complex Traits Studied via Analysis of Evolve and Resequence Experiments. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11388.","short":"S. Belohlavy, The Genetic Basis of Complex Traits Studied via Analysis of Evolve and Resequence Experiments, Institute of Science and Technology Austria, 2022.","ista":"Belohlavy S. 2022. The genetic basis of complex traits studied via analysis of evolve and resequence experiments. Institute of Science and Technology Austria.","apa":"Belohlavy, S. (2022). The genetic basis of complex traits studied via analysis of evolve and resequence experiments. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11388","ieee":"S. Belohlavy, “The genetic basis of complex traits studied via analysis of evolve and resequence experiments,” Institute of Science and Technology Austria, 2022.","ama":"Belohlavy S. The genetic basis of complex traits studied via analysis of evolve and resequence experiments. 2022. doi:10.15479/at:ista:11388"},"has_accepted_license":"1","article_processing_charge":"No","day":"18","date_updated":"2023-08-29T06:41:51Z","date_created":"2022-05-16T16:49:18Z","related_material":{"record":[{"id":"6713","relation":"part_of_dissertation","status":"public"}]},"author":[{"first_name":"Stefanie","last_name":"Belohlavy","id":"43FE426A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9849-498X","full_name":"Belohlavy, Stefanie"}],"department":[{"_id":"GradSch"},{"_id":"NiBa"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2022","file_date_updated":"2023-05-20T22:30:03Z","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"}],"doi":"10.15479/at:ista:11388","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"},"publication_identifier":{"isbn":["978-3-99078-018-3"]},"month":"05"},{"article_number":"e1009661","file_date_updated":"2022-05-16T08:53:11Z","pmid":1,"year":"2021","acknowledgement":"Computational resources for the study were provided by the Institute of Science and Technology, Austria.\r\nKB received funding from the Scientific Grant Agency of the Slovak Republic under the Grants Nos. 1/0755/19 and 1/0521/20.","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"publisher":"Public Library of Science","publication_status":"published","author":[{"last_name":"Bod'ová","first_name":"Katarína","orcid":"0000-0002-7214-0171","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","full_name":"Bod'ová, Katarína"},{"first_name":"Eniko","last_name":"Szep","id":"485BB5A4-F248-11E8-B48F-1D18A9856A87","full_name":"Szep, Eniko"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H"}],"volume":17,"date_updated":"2022-08-01T10:48:04Z","date_created":"2021-12-12T23:01:27Z","publication_identifier":{"issn":["1553-734X"],"eissn":["1553-7358"]},"month":"12","external_id":{"pmid":["34851948"],"arxiv":["2102.03669"]},"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","doi":"10.1371/journal.pcbi.1009661","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"type":"journal_article","issue":"12","abstract":[{"text":"Realistic models of biological processes typically involve interacting components on multiple scales, driven by changing environment and inherent stochasticity. Such models are often analytically and numerically intractable. We revisit a dynamic maximum entropy method that combines a static maximum entropy with a quasi-stationary approximation. This allows us to reduce stochastic non-equilibrium dynamics expressed by the Fokker-Planck equation to a simpler low-dimensional deterministic dynamics, without the need to track microscopic details. Although the method has been previously applied to a few (rather complicated) applications in population genetics, our main goal here is to explain and to better understand how the method works. We demonstrate the usefulness of the method for two widely studied stochastic problems, highlighting its accuracy in capturing important macroscopic quantities even in rapidly changing non-stationary conditions. For the Ornstein-Uhlenbeck process, the method recovers the exact dynamics whilst for a stochastic island model with migration from other habitats, the approximation retains high macroscopic accuracy under a wide range of scenarios in a dynamic environment.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"10535","intvolume":" 17","ddc":["570"],"title":"Dynamic maximum entropy provides accurate approximation of structured population dynamics","status":"public","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":2299486,"creator":"dernst","file_name":"2021_PLOsComBio_Bodova.pdf","access_level":"open_access","date_created":"2022-05-16T08:53:11Z","date_updated":"2022-05-16T08:53:11Z","checksum":"dcd185d4f7e0acee25edf1d6537f447e","success":1,"relation":"main_file","file_id":"11383"}],"scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"01","citation":{"chicago":"Bodova, Katarina, Eniko Szep, and Nicholas H Barton. “Dynamic Maximum Entropy Provides Accurate Approximation of Structured Population Dynamics.” PLoS Computational Biology. Public Library of Science, 2021. https://doi.org/10.1371/journal.pcbi.1009661.","mla":"Bodova, Katarina, et al. “Dynamic Maximum Entropy Provides Accurate Approximation of Structured Population Dynamics.” PLoS Computational Biology, vol. 17, no. 12, e1009661, Public Library of Science, 2021, doi:10.1371/journal.pcbi.1009661.","short":"K. Bodova, E. Szep, N.H. Barton, PLoS Computational Biology 17 (2021).","ista":"Bodova K, Szep E, Barton NH. 2021. Dynamic maximum entropy provides accurate approximation of structured population dynamics. PLoS Computational Biology. 17(12), e1009661.","ieee":"K. Bodova, E. Szep, and N. H. Barton, “Dynamic maximum entropy provides accurate approximation of structured population dynamics,” PLoS Computational Biology, vol. 17, no. 12. Public Library of Science, 2021.","apa":"Bodova, K., Szep, E., & Barton, N. H. (2021). Dynamic maximum entropy provides accurate approximation of structured population dynamics. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1009661","ama":"Bodova K, Szep E, Barton NH. Dynamic maximum entropy provides accurate approximation of structured population dynamics. PLoS Computational Biology. 2021;17(12). doi:10.1371/journal.pcbi.1009661"},"publication":"PLoS Computational Biology","article_type":"original","date_published":"2021-12-01T00:00:00Z"},{"title":"How do species barriers decay? Concordance and local introgression in mosaic hybrid zones of mussels","status":"public","intvolume":" 34","_id":"8708","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint","type":"journal_article","abstract":[{"lang":"eng","text":"The Mytilus complex of marine mussel species forms a mosaic of hybrid zones, found across temperate regions of the globe. This allows us to study ‘replicated’ instances of secondary contact between closely related species. Previous work on this complex has shown that local introgression is both widespread and highly heterogeneous, and has identified SNPs that are outliers of differentiation between lineages. Here, we developed an ancestry‐informative panel of such SNPs. We then compared their frequencies in newly sampled populations, including samples from within the hybrid zones, and parental populations at different distances from the contact. Results show that close to the hybrid zones, some outlier loci are near to fixation for the heterospecific allele, suggesting enhanced local introgression, or the local sweep of a shared ancestral allele. Conversely, genomic cline analyses, treating local parental populations as the reference, reveal a globally high concordance among loci, albeit with a few signals of asymmetric introgression. Enhanced local introgression at specific loci is consistent with the early transfer of adaptive variants after contact, possibly including asymmetric bi‐stable variants (Dobzhansky‐Muller incompatibilities), or haplotypes loaded with fewer deleterious mutations. Having escaped one barrier, however, these variants can be trapped or delayed at the next barrier, confining the introgression locally. These results shed light on the decay of species barriers during phases of contact."}],"issue":"1","article_type":"original","page":"208-223","publication":"Journal of Evolutionary Biology","citation":{"short":"A. Simon, C. Fraisse, T. El Ayari, C. Liautard‐Haag, P. Strelkov, J.J. Welch, N. Bierne, Journal of Evolutionary Biology 34 (2021) 208–223.","mla":"Simon, Alexis, et al. “How Do Species Barriers Decay? Concordance and Local Introgression in Mosaic Hybrid Zones of Mussels.” Journal of Evolutionary Biology, vol. 34, no. 1, Wiley, 2021, pp. 208–23, doi:10.1111/jeb.13709.","chicago":"Simon, Alexis, Christelle Fraisse, Tahani El Ayari, Cathy Liautard‐Haag, Petr Strelkov, John J Welch, and Nicolas Bierne. “How Do Species Barriers Decay? Concordance and Local Introgression in Mosaic Hybrid Zones of Mussels.” Journal of Evolutionary Biology. Wiley, 2021. https://doi.org/10.1111/jeb.13709.","ama":"Simon A, Fraisse C, El Ayari T, et al. How do species barriers decay? Concordance and local introgression in mosaic hybrid zones of mussels. Journal of Evolutionary Biology. 2021;34(1):208-223. doi:10.1111/jeb.13709","apa":"Simon, A., Fraisse, C., El Ayari, T., Liautard‐Haag, C., Strelkov, P., Welch, J. J., & Bierne, N. (2021). How do species barriers decay? Concordance and local introgression in mosaic hybrid zones of mussels. Journal of Evolutionary Biology. Wiley. https://doi.org/10.1111/jeb.13709","ieee":"A. Simon et al., “How do species barriers decay? Concordance and local introgression in mosaic hybrid zones of mussels,” Journal of Evolutionary Biology, vol. 34, no. 1. Wiley, pp. 208–223, 2021.","ista":"Simon A, Fraisse C, El Ayari T, Liautard‐Haag C, Strelkov P, Welch JJ, Bierne N. 2021. How do species barriers decay? Concordance and local introgression in mosaic hybrid zones of mussels. Journal of Evolutionary Biology. 34(1), 208–223."},"date_published":"2021-01-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","publication_status":"published","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"publisher":"Wiley","year":"2021","acknowledgement":"Data used in this work were partly produced through the genotyping and sequencing facilities of ISEM and LabEx CeMEB, an ANR ‘Investissements d'avenir’ program (ANR‐10‐LABX‐04‐01) This project benefited from the Montpellier Bioinformatics Biodiversity platform supported by the LabEx CeMEB. We thank Norah Saarman, Grant Pogson, Célia Gosset and Pierre‐Alexandre Gagnaire for providing samples. This work was funded by a Languedoc‐Roussillon ‘Chercheur(se)s d'Avenir’ grant (Connect7 project). P. Strelkov was supported by the Russian Science Foundation project 19‐74‐20024. This is article 2020‐240 of Institut des Sciences de l'Evolution de Montpellier.","pmid":1,"date_created":"2020-10-25T23:01:20Z","date_updated":"2023-08-04T11:04:11Z","volume":34,"author":[{"full_name":"Simon, Alexis","first_name":"Alexis","last_name":"Simon"},{"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","last_name":"El Ayari","first_name":"Tahani"},{"full_name":"Liautard‐Haag, Cathy","last_name":"Liautard‐Haag","first_name":"Cathy"},{"first_name":"Petr","last_name":"Strelkov","full_name":"Strelkov, Petr"},{"first_name":"John J","last_name":"Welch","full_name":"Welch, John J"},{"full_name":"Bierne, Nicolas","first_name":"Nicolas","last_name":"Bierne"}],"related_material":{"record":[{"id":"13073","relation":"research_data","status":"public"}]},"quality_controlled":"1","isi":1,"oa":1,"main_file_link":[{"url":"https://doi.org/10.1101/818559","open_access":"1"}],"external_id":{"pmid":["33045123"],"isi":["000579599700001"]},"language":[{"iso":"eng"}],"doi":"10.1111/jeb.13709","month":"01","publication_identifier":{"eissn":["14209101"],"issn":["1010061X"]}},{"publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Wiley","year":"2021","acknowledgement":"This work was financed by the Spanish Agencia Estatal de Investigación (CGL2017‐85718‐P), awarded to BCE, and co‐financed by FEDER. It was also supported by the Spanish Ministerio de Ciencia, Innovación y Universidades (EQC2018‐004418‐P), awarded to BCE. AS‐C was funded by the Spanish Ministerio de Ciencia, Innovación y Universidades through an FPU PhD fellowship (FPU014/02948). The authors thank Instituto Tecnológico y de Energías Renovables (ITER), S.A for providing access to the Teide High‐Performance Computing facility (Teide‐HPC). Fieldwork was supported by collecting permit AFF 107/17 (sigma number 2017‐00572) kindly provided by the Cabildo of Tenerife. The authors wish to thank the following for field work and sample sorting and identification: A. J. Pérez‐Delgado, H. López, and C. Andújar. We also thank V. García‐Olivares for assistance with laboratory and bioinformatic work.","pmid":1,"date_updated":"2023-08-04T11:09:49Z","date_created":"2020-11-08T23:01:26Z","volume":75,"author":[{"full_name":"Salces-Castellano, Antonia","last_name":"Salces-Castellano","first_name":"Antonia"},{"id":"43161670-5719-11EA-8025-FABC3DDC885E","last_name":"Stankowski","first_name":"Sean","full_name":"Stankowski, Sean"},{"last_name":"Arribas","first_name":"Paula","full_name":"Arribas, Paula"},{"full_name":"Patino, Jairo","last_name":"Patino","first_name":"Jairo"},{"first_name":"Dirk N. ","last_name":"Karger","full_name":"Karger, Dirk N. "},{"last_name":"Butlin","first_name":"Roger","full_name":"Butlin, Roger"},{"full_name":"Emerson, Brent C.","first_name":"Brent C.","last_name":"Emerson"}],"related_material":{"link":[{"url":"https://doi.org/10.1111/evo.14225","relation":"erratum"}]},"month":"02","publication_identifier":{"issn":["0014-3820"],"eissn":["1558-5646"]},"isi":1,"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"http://hdl.handle.net/10261/223937"}],"external_id":{"isi":["000583190600001"],"pmid":["33078844"]},"language":[{"iso":"eng"}],"doi":"10.1111/evo.14111","type":"journal_article","abstract":[{"lang":"eng","text":"Montane cloud forests are areas of high endemism, and are one of the more vulnerable terrestrial ecosystems to climate change. Thus, understanding how they both contribute to the generation of biodiversity, and will respond to ongoing climate change, are important and related challenges. The widely accepted model for montane cloud forest dynamics involves upslope forcing of their range limits with global climate warming. However, limited climate data provides some support for an alternative model, where range limits are forced downslope with climate warming. Testing between these two models is challenging, due to the inherent limitations of climate and pollen records. We overcome this with an alternative source of historical information, testing between competing model predictions using genomic data and demographic analyses for a species of beetle tightly associated to an oceanic island cloud forest. Results unequivocally support the alternative model: populations that were isolated at higher elevation peaks during the Last Glacial Maximum are now in contact and hybridizing at lower elevations. Our results suggest that genomic data are a rich source of information to further understand how montane cloud forest biodiversity originates, and how it is likely to be impacted by ongoing climate change."}],"issue":"2","title":"Long-term cloud forest response to climate warming revealed by insect speciation history","status":"public","intvolume":" 75","_id":"8743","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Submitted Version","scopus_import":"1","day":"01","article_processing_charge":"No","article_type":"original","page":"231-244","publication":"Evolution","citation":{"ama":"Salces-Castellano A, Stankowski S, Arribas P, et al. Long-term cloud forest response to climate warming revealed by insect speciation history. Evolution. 2021;75(2):231-244. doi:10.1111/evo.14111","apa":"Salces-Castellano, A., Stankowski, S., Arribas, P., Patino, J., Karger, D. N., Butlin, R., & Emerson, B. C. (2021). Long-term cloud forest response to climate warming revealed by insect speciation history. Evolution. Wiley. https://doi.org/10.1111/evo.14111","ieee":"A. Salces-Castellano et al., “Long-term cloud forest response to climate warming revealed by insect speciation history,” Evolution, vol. 75, no. 2. Wiley, pp. 231–244, 2021.","ista":"Salces-Castellano A, Stankowski S, Arribas P, Patino J, Karger DN, Butlin R, Emerson BC. 2021. Long-term cloud forest response to climate warming revealed by insect speciation history. Evolution. 75(2), 231–244.","short":"A. Salces-Castellano, S. Stankowski, P. Arribas, J. Patino, D.N. Karger, R. Butlin, B.C. Emerson, Evolution 75 (2021) 231–244.","mla":"Salces-Castellano, Antonia, et al. “Long-Term Cloud Forest Response to Climate Warming Revealed by Insect Speciation History.” Evolution, vol. 75, no. 2, Wiley, 2021, pp. 231–44, doi:10.1111/evo.14111.","chicago":"Salces-Castellano, Antonia, Sean Stankowski, Paula Arribas, Jairo Patino, Dirk N. Karger, Roger Butlin, and Brent C. Emerson. “Long-Term Cloud Forest Response to Climate Warming Revealed by Insect Speciation History.” Evolution. Wiley, 2021. https://doi.org/10.1111/evo.14111."},"date_published":"2021-02-01T00:00:00Z"},{"publication_identifier":{"eissn":["14209101"],"issn":["1010061X"]},"month":"02","project":[{"_id":"2662AADE-B435-11E9-9278-68D0E5697425","grant_number":"M02463","name":"Sex chromosomes and species barriers","call_identifier":"FWF"}],"quality_controlled":"1","isi":1,"oa":1,"external_id":{"isi":["000587769700001"],"pmid":["33107098"]},"main_file_link":[{"url":"https://doi.org/10.1111/jeb.13723","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1111/jeb.13723","publisher":"Wiley","department":[{"_id":"NiBa"}],"publication_status":"published","pmid":1,"year":"2021","acknowledgement":"This work was supported by the EU Marie Curie Career Integration grant (FP7‐PEOPLE‐2011‐CIG grant agreement PCIG10‐GA‐2011‐304164) attributed to CS. SA was supported by a PhD fellowship from the French Région PACA and the Plant Breeding division of INRA, in partnership with Gautier Semences. CF was supported by an Austrian Science Foundation FWF grant (Project M 2463‐B29). Authors thank Mathilde Causse and Beatriz Vicoso for their team leading. Thanks to the Italian Eggplant Genome Consortium, which includes the DISAFA, Plant Genetics and Breeding (University of Torino), the Biotechnology Department (University of Verona), the CREA‐ORL in Montanaso Lombardo (LO) and the ENEA in Rome for providing access to the eggplant genome reference. Thanks to CRB‐lég ( https://www6.paca.inra.fr/gafl_eng/Vegetables-GRC ) for managing and providing the genetic resources, to Marie‐Christine Daunay and Alain Palloix (INRA UR1052) for assistance in choosing the biological material used, to Muriel Latreille and Sylvain Santoni from the UMR AGAP (INRA Montpellier, France) for their help with RNAseq library preparation, to Jean‐Paul Bouchet and Jacques Lagnel (INRA UR1052) for their Bioinformatics assistance.","volume":34,"date_updated":"2023-08-04T11:19:26Z","date_created":"2020-12-06T23:01:16Z","related_material":{"record":[{"relation":"research_data","status":"public","id":"13065"}]},"author":[{"last_name":"Arnoux","first_name":"Stéphanie","full_name":"Arnoux, Stéphanie"},{"orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse","first_name":"Christelle","full_name":"Fraisse, Christelle"},{"full_name":"Sauvage, Christopher","last_name":"Sauvage","first_name":"Christopher"}],"scopus_import":"1","article_processing_charge":"No","day":"01","page":"270-283","article_type":"original","citation":{"apa":"Arnoux, S., Fraisse, C., & Sauvage, C. (2021). Genomic inference of complex domestication histories in three Solanaceae species. Journal of Evolutionary Biology. Wiley. https://doi.org/10.1111/jeb.13723","ieee":"S. Arnoux, C. Fraisse, and C. Sauvage, “Genomic inference of complex domestication histories in three Solanaceae species,” Journal of Evolutionary Biology, vol. 34, no. 2. Wiley, pp. 270–283, 2021.","ista":"Arnoux S, Fraisse C, Sauvage C. 2021. Genomic inference of complex domestication histories in three Solanaceae species. Journal of Evolutionary Biology. 34(2), 270–283.","ama":"Arnoux S, Fraisse C, Sauvage C. Genomic inference of complex domestication histories in three Solanaceae species. Journal of Evolutionary Biology. 2021;34(2):270-283. doi:10.1111/jeb.13723","chicago":"Arnoux, Stéphanie, Christelle Fraisse, and Christopher Sauvage. “Genomic Inference of Complex Domestication Histories in Three Solanaceae Species.” Journal of Evolutionary Biology. Wiley, 2021. https://doi.org/10.1111/jeb.13723.","short":"S. Arnoux, C. Fraisse, C. Sauvage, Journal of Evolutionary Biology 34 (2021) 270–283.","mla":"Arnoux, Stéphanie, et al. “Genomic Inference of Complex Domestication Histories in Three Solanaceae Species.” Journal of Evolutionary Biology, vol. 34, no. 2, Wiley, 2021, pp. 270–83, doi:10.1111/jeb.13723."},"publication":"Journal of Evolutionary Biology","date_published":"2021-02-01T00:00:00Z","type":"journal_article","issue":"2","abstract":[{"lang":"eng","text":"Domestication is a human‐induced selection process that imprints the genomes of domesticated populations over a short evolutionary time scale and that occurs in a given demographic context. Reconstructing historical gene flow, effective population size changes and their timing is therefore of fundamental interest to understand how plant demography and human selection jointly shape genomic divergence during domestication. Yet, the comparison under a single statistical framework of independent domestication histories across different crop species has been little evaluated so far. Thus, it is unclear whether domestication leads to convergent demographic changes that similarly affect crop genomes. To address this question, we used existing and new transcriptome data on three crop species of Solanaceae (eggplant, pepper and tomato), together with their close wild relatives. We fitted twelve demographic models of increasing complexity on the unfolded joint allele frequency spectrum for each wild/crop pair, and we found evidence for both shared and species‐specific demographic processes between species. A convergent history of domestication with gene flow was inferred for all three species, along with evidence of strong reduction in the effective population size during the cultivation stage of tomato and pepper. The absence of any reduction in size of the crop in eggplant stands out from the classical view of the domestication process; as does the existence of a “protracted period” of management before cultivation. Our results also suggest divergent management strategies of modern cultivars among species as their current demography substantially differs. Finally, the timing of domestication is species‐specific and supported by the few historical records available."}],"intvolume":" 34","title":"Genomic inference of complex domestication histories in three Solanaceae species","status":"public","_id":"8928","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version"},{"file_date_updated":"2021-02-09T09:04:02Z","publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Wiley","year":"2021","acknowledgement":"We would like to thank all the participants in the speciation symposium of the Marine Evolution Conference in Sweden for the interesting discussions and to all the contributors to this special\r\nissue. We thank Nicolas Bierne and Wolf Blanckenhorn (reviewer and editor, respectively) for valuable suggestions during the revision of the manuscript, and Roger K. Butlin and Anja M. Westram for very helpful comments on a previous draft. We would also like to thank Wolf Blanckenhorn and Nicola Cook, the Editor in Chief and the Managing Editor of the Journal of Evolutionary Biology, respectively, for the encouragement and support in putting together this special issue, and to all reviewers involved. RF was financed by the European Union's Horizon 2020 Research and Innovation Programme under the Marie Sklodowska-Curie Grant Agreement Number 706376 and is currently financed by the FEDER Funds through the Operational Competitiveness Factors Program COMPETE and by National Funds through the Foundation for Science and Technology (FCT) within the scope of the project ‘Hybrabbid' (PTDC/BIA-EVL/30628/2017-POCI-01-0145-FEDER-030628). KJ was funded by the Swedish\r\nResearch Council, VR. SS was supported by NERC and ERC funding awarded to Roger K. Butlin.","date_created":"2021-02-07T23:01:13Z","date_updated":"2023-08-07T13:42:08Z","volume":34,"author":[{"full_name":"Faria, Rui","last_name":"Faria","first_name":"Rui"},{"first_name":"Kerstin","last_name":"Johannesson","full_name":"Johannesson, Kerstin"},{"full_name":"Stankowski, Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","first_name":"Sean","last_name":"Stankowski"}],"month":"01","publication_identifier":{"issn":["1010061X"],"eissn":["14209101"]},"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":["000608367500001"]},"language":[{"iso":"eng"}],"doi":"10.1111/jeb.13756","type":"journal_article","abstract":[{"lang":"eng","text":"Marine environments are inhabited by a broad representation of the tree of life, yet our understanding of speciation in marine ecosystems is extremely limited compared with terrestrial and freshwater environments. Developing a more comprehensive picture of speciation in marine environments requires that we 'dive under the surface' by studying a wider range of taxa and ecosystems is necessary for a more comprehensive picture of speciation. Although studying marine evolutionary processes is often challenging, recent technological advances in different fields, from maritime engineering to genomics, are making it increasingly possible to study speciation of marine life forms across diverse ecosystems and taxa. Motivated by recent research in the field, including the 14 contributions in this issue, we highlight and discuss six axes of research that we think will deepen our understanding of speciation in the marine realm: (a) study a broader range of marine environments and organisms; (b) identify the reproductive barriers driving speciation between marine taxa; (c) understand the role of different genomic architectures underlying reproductive isolation; (d) infer the evolutionary history of divergence using model‐based approaches; (e) study patterns of hybridization and introgression between marine taxa; and (f) implement highly interdisciplinary, collaborative research programmes. In outlining these goals, we hope to inspire researchers to continue filling this critical knowledge gap surrounding the origins of marine biodiversity."}],"issue":"1","status":"public","ddc":["570"],"title":"Speciation in marine environments: Diving under the surface","intvolume":" 34","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9100","file":[{"file_id":"9108","relation":"main_file","date_created":"2021-02-09T09:04:02Z","date_updated":"2021-02-09T09:04:02Z","success":1,"checksum":"5755856a5368d4b4cdd6fad5ab27f4d1","file_name":"2021_JourEvolBiology_Faria.pdf","access_level":"open_access","creator":"dernst","file_size":561340,"content_type":"application/pdf"}],"oa_version":"Published Version","scopus_import":"1","day":"18","has_accepted_license":"1","article_processing_charge":"No","article_type":"original","page":"4-15","publication":"Journal of Evolutionary Biology","citation":{"ama":"Faria R, Johannesson K, Stankowski S. Speciation in marine environments: Diving under the surface. Journal of Evolutionary Biology. 2021;34(1):4-15. doi:10.1111/jeb.13756","ista":"Faria R, Johannesson K, Stankowski S. 2021. Speciation in marine environments: Diving under the surface. Journal of Evolutionary Biology. 34(1), 4–15.","ieee":"R. Faria, K. Johannesson, and S. Stankowski, “Speciation in marine environments: Diving under the surface,” Journal of Evolutionary Biology, vol. 34, no. 1. Wiley, pp. 4–15, 2021.","apa":"Faria, R., Johannesson, K., & Stankowski, S. (2021). Speciation in marine environments: Diving under the surface. Journal of Evolutionary Biology. Wiley. https://doi.org/10.1111/jeb.13756","mla":"Faria, Rui, et al. “Speciation in Marine Environments: Diving under the Surface.” Journal of Evolutionary Biology, vol. 34, no. 1, Wiley, 2021, pp. 4–15, doi:10.1111/jeb.13756.","short":"R. Faria, K. Johannesson, S. Stankowski, Journal of Evolutionary Biology 34 (2021) 4–15.","chicago":"Faria, Rui, Kerstin Johannesson, and Sean Stankowski. “Speciation in Marine Environments: Diving under the Surface.” Journal of Evolutionary Biology. Wiley, 2021. https://doi.org/10.1111/jeb.13756."},"date_published":"2021-01-18T00:00:00Z"},{"month":"02","publication_identifier":{"issn":["1943-2631"]},"quality_controlled":"1","isi":1,"project":[{"name":"Sex chromosomes and species barriers","call_identifier":"FWF","_id":"2662AADE-B435-11E9-9278-68D0E5697425","grant_number":"M02463"}],"main_file_link":[{"url":"https://doi.org/10.1093/genetics/iyaa025","open_access":"1"}],"oa":1,"external_id":{"isi":["000637218100005"]},"acknowledged_ssus":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"doi":"10.1093/genetics/iyaa025","article_number":"iyaa025","publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Genetics Society of America","acknowledgement":"The computations were performed with the IST Austria High-Performance Computing (HPC) Cluster and the Institut Français de Bioinformatique (IFB) Core Cluster. We are grateful to Nick Barton and Beatriz Vicoso for critical comments on the model and the manuscript. We also thank Brian Charlesworth, Stuart Baird, and an anonymous reviewer for insightful comments.\r\nC.F. was supported by an Austrian Science Foundation FWF grant (Project M 2463-B29).","year":"2021","date_updated":"2023-08-07T13:47:01Z","date_created":"2021-02-18T14:41:30Z","volume":217,"author":[{"full_name":"Fraisse, Christelle","first_name":"Christelle","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075"},{"full_name":"Sachdeva, Himani","id":"42377A0A-F248-11E8-B48F-1D18A9856A87","last_name":"Sachdeva","first_name":"Himani"}],"day":"01","article_processing_charge":"No","article_type":"original","publication":"Genetics","citation":{"mla":"Fraisse, Christelle, and Himani Sachdeva. “The Rates of Introgression and Barriers to Genetic Exchange between Hybridizing Species: Sex Chromosomes vs Autosomes.” Genetics, vol. 217, no. 2, iyaa025, Genetics Society of America, 2021, doi:10.1093/genetics/iyaa025.","short":"C. Fraisse, H. Sachdeva, Genetics 217 (2021).","chicago":"Fraisse, Christelle, and Himani Sachdeva. “The Rates of Introgression and Barriers to Genetic Exchange between Hybridizing Species: Sex Chromosomes vs Autosomes.” Genetics. Genetics Society of America, 2021. https://doi.org/10.1093/genetics/iyaa025.","ama":"Fraisse C, Sachdeva H. The rates of introgression and barriers to genetic exchange between hybridizing species: Sex chromosomes vs autosomes. Genetics. 2021;217(2). doi:10.1093/genetics/iyaa025","ista":"Fraisse C, Sachdeva H. 2021. The rates of introgression and barriers to genetic exchange between hybridizing species: Sex chromosomes vs autosomes. Genetics. 217(2), iyaa025.","ieee":"C. Fraisse and H. Sachdeva, “The rates of introgression and barriers to genetic exchange between hybridizing species: Sex chromosomes vs autosomes,” Genetics, vol. 217, no. 2. Genetics Society of America, 2021.","apa":"Fraisse, C., & Sachdeva, H. (2021). The rates of introgression and barriers to genetic exchange between hybridizing species: Sex chromosomes vs autosomes. Genetics. Genetics Society of America. https://doi.org/10.1093/genetics/iyaa025"},"date_published":"2021-02-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Interspecific crossing experiments have shown that sex chromosomes play a major role in reproductive isolation between many pairs of species. However, their ability to act as reproductive barriers, which hamper interspecific genetic exchange, has rarely been evaluated quantitatively compared to Autosomes. This genome-wide limitation of gene flow is essential for understanding the complete separation of species, and thus speciation. Here, we develop a mainland-island model of secondary contact between hybridizing species of an XY (or ZW) sexual system. We obtain theoretical predictions for the frequency of introgressed alleles, and the strength of the barrier to neutral gene flow for the two types of chromosomes carrying multiple interspecific barrier loci. Theoretical predictions are obtained for scenarios where introgressed alleles are rare. We show that the same analytical expressions apply for sex chromosomes and autosomes, but with different sex-averaged effective parameters. The specific features of sex chromosomes (hemizygosity and absence of recombination in the heterogametic sex) lead to reduced levels of introgression on the X (or Z) compared to autosomes. This effect can be enhanced by certain types of sex-biased forces, but it remains overall small (except when alleles causing incompatibilities are recessive). We discuss these predictions in the light of empirical data comprising model-based tests of introgression and cline surveys in various biological systems."}],"issue":"2","title":"The rates of introgression and barriers to genetic exchange between hybridizing species: Sex chromosomes vs autosomes","status":"public","intvolume":" 217","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9168","oa_version":"Published Version"},{"volume":21,"date_created":"2021-02-14T23:01:14Z","date_updated":"2023-08-07T13:45:18Z","author":[{"first_name":"Christelle","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle"},{"last_name":"Popovic","first_name":"Iva","full_name":"Popovic, Iva"},{"first_name":"Clément","last_name":"Mazoyer","full_name":"Mazoyer, Clément"},{"full_name":"Spataro, Bruno","first_name":"Bruno","last_name":"Spataro"},{"full_name":"Delmotte, Stéphane","first_name":"Stéphane","last_name":"Delmotte"},{"full_name":"Romiguier, Jonathan","last_name":"Romiguier","first_name":"Jonathan"},{"full_name":"Loire, Étienne","first_name":"Étienne","last_name":"Loire"},{"full_name":"Simon, Alexis","first_name":"Alexis","last_name":"Simon"},{"first_name":"Nicolas","last_name":"Galtier","full_name":"Galtier, Nicolas"},{"first_name":"Laurent","last_name":"Duret","full_name":"Duret, Laurent"},{"first_name":"Nicolas","last_name":"Bierne","full_name":"Bierne, Nicolas"},{"last_name":"Vekemans","first_name":"Xavier","full_name":"Vekemans, Xavier"},{"first_name":"Camille","last_name":"Roux","full_name":"Roux, Camille"}],"publisher":"Wiley","department":[{"_id":"NiBa"}],"publication_status":"published","year":"2021","publication_identifier":{"issn":["1755098X"],"eissn":["17550998"]},"month":"01","language":[{"iso":"eng"}],"doi":"10.1111/1755-0998.13323","isi":1,"quality_controlled":"1","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2020.06.15.151597v2","open_access":"1"}],"external_id":{"isi":["000614183100001"]},"oa":1,"abstract":[{"lang":"eng","text":"We present DILS, a deployable statistical analysis platform for conducting demographic inferences with linked selection from population genomic data using an Approximate Bayesian Computation framework. DILS takes as input single‐population or two‐population data sets (multilocus fasta sequences) and performs three types of analyses in a hierarchical manner, identifying: (a) the best demographic model to study the importance of gene flow and population size change on the genetic patterns of polymorphism and divergence, (b) the best genomic model to determine whether the effective size Ne and migration rate N, m are heterogeneously distributed along the genome (implying linked selection) and (c) loci in genomic regions most associated with barriers to gene flow. Also available via a Web interface, an objective of DILS is to facilitate collaborative research in speciation genomics. Here, we show the performance and limitations of DILS by using simulations and finally apply the method to published data on a divergence continuum composed by 28 pairs of Mytilus mussel populations/species."}],"type":"journal_article","oa_version":"Preprint","intvolume":" 21","status":"public","title":"DILS: Demographic inferences with linked selection by using ABC","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9119","article_processing_charge":"No","day":"15","scopus_import":"1","date_published":"2021-01-15T00:00:00Z","page":"2629-2644","article_type":"original","citation":{"chicago":"Fraisse, Christelle, Iva Popovic, Clément Mazoyer, Bruno Spataro, Stéphane Delmotte, Jonathan Romiguier, Étienne Loire, et al. “DILS: Demographic Inferences with Linked Selection by Using ABC.” Molecular Ecology Resources. Wiley, 2021. https://doi.org/10.1111/1755-0998.13323.","mla":"Fraisse, Christelle, et al. “DILS: Demographic Inferences with Linked Selection by Using ABC.” Molecular Ecology Resources, vol. 21, Wiley, 2021, pp. 2629–44, doi:10.1111/1755-0998.13323.","short":"C. Fraisse, I. Popovic, C. Mazoyer, B. Spataro, S. Delmotte, J. Romiguier, É. Loire, A. Simon, N. Galtier, L. Duret, N. Bierne, X. Vekemans, C. Roux, Molecular Ecology Resources 21 (2021) 2629–2644.","ista":"Fraisse C, Popovic I, Mazoyer C, Spataro B, Delmotte S, Romiguier J, Loire É, Simon A, Galtier N, Duret L, Bierne N, Vekemans X, Roux C. 2021. DILS: Demographic inferences with linked selection by using ABC. Molecular Ecology Resources. 21, 2629–2644.","ieee":"C. Fraisse et al., “DILS: Demographic inferences with linked selection by using ABC,” Molecular Ecology Resources, vol. 21. Wiley, pp. 2629–2644, 2021.","apa":"Fraisse, C., Popovic, I., Mazoyer, C., Spataro, B., Delmotte, S., Romiguier, J., … Roux, C. (2021). DILS: Demographic inferences with linked selection by using ABC. Molecular Ecology Resources. Wiley. https://doi.org/10.1111/1755-0998.13323","ama":"Fraisse C, Popovic I, Mazoyer C, et al. DILS: Demographic inferences with linked selection by using ABC. Molecular Ecology Resources. 2021;21:2629-2644. doi:10.1111/1755-0998.13323"},"publication":"Molecular Ecology Resources"},{"article_processing_charge":"No","has_accepted_license":"1","day":"21","scopus_import":"1","date_published":"2021-06-21T00:00:00Z","citation":{"chicago":"Meier, Joana I., Patricio A. Salazar, Marek Kučka, Robert William Davies, Andreea Dréau, Ismael Aldás, Olivia Box Power, et al. “Haplotype Tagging Reveals Parallel Formation of Hybrid Races in Two Butterfly Species.” PNAS. Proceedings of the National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2015005118.","mla":"Meier, Joana I., et al. “Haplotype Tagging Reveals Parallel Formation of Hybrid Races in Two Butterfly Species.” PNAS, vol. 118, no. 25, e2015005118, Proceedings of the National Academy of Sciences, 2021, doi:10.1073/pnas.2015005118.","short":"J.I. Meier, P.A. Salazar, M. Kučka, R.W. Davies, A. Dréau, I. Aldás, O.B. Power, N.J. Nadeau, J.R. Bridle, C. Rolian, N.H. Barton, W.O. McMillan, C.D. Jiggins, Y.F. Chan, PNAS 118 (2021).","ista":"Meier JI, Salazar PA, Kučka M, Davies RW, Dréau A, Aldás I, Power OB, Nadeau NJ, Bridle JR, Rolian C, Barton NH, McMillan WO, Jiggins CD, Chan YF. 2021. Haplotype tagging reveals parallel formation of hybrid races in two butterfly species. PNAS. 118(25), e2015005118.","apa":"Meier, J. I., Salazar, P. A., Kučka, M., Davies, R. W., Dréau, A., Aldás, I., … Chan, Y. F. (2021). Haplotype tagging reveals parallel formation of hybrid races in two butterfly species. PNAS. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2015005118","ieee":"J. I. Meier et al., “Haplotype tagging reveals parallel formation of hybrid races in two butterfly species,” PNAS, vol. 118, no. 25. Proceedings of the National Academy of Sciences, 2021.","ama":"Meier JI, Salazar PA, Kučka M, et al. Haplotype tagging reveals parallel formation of hybrid races in two butterfly species. PNAS. 2021;118(25). doi:10.1073/pnas.2015005118"},"publication":"PNAS","article_type":"original","issue":"25","abstract":[{"lang":"eng","text":"Genetic variation segregates as linked sets of variants, or haplotypes. Haplotypes and linkage are central to genetics and underpin virtually all genetic and selection analysis. And yet, genomic data often lack haplotype information, due to constraints in sequencing technologies. Here we present “haplotagging”, a simple, low-cost linked-read sequencing technique that allows sequencing of hundreds of individuals while retaining linkage information. We apply haplotagging to construct megabase-size haplotypes for over 600 individual butterflies (Heliconius erato and H. melpomene), which form overlapping hybrid zones across an elevational gradient in Ecuador. Haplotagging identifies loci controlling distinctive high- and lowland wing color patterns. Divergent haplotypes are found at the same major loci in both species, while chromosome rearrangements show no parallelism. Remarkably, in both species the geographic clines for the major wing pattern loci are displaced by 18 km, leading to the rise of a novel hybrid morph in the centre of the hybrid zone. We propose that shared warning signalling (Müllerian mimicry) may couple the cline shifts seen in both species, and facilitate the parallel co-emergence of a novel hybrid morph in both co-mimetic species. Our results show the power of efficient haplotyping methods when combined with large-scale sequencing data from natural populations."}],"type":"journal_article","oa_version":"Published Version","file":[{"date_created":"2022-03-08T08:18:16Z","date_updated":"2022-03-08T08:18:16Z","checksum":"cb30c6166b2132ee60d616b31a1a7c29","success":1,"relation":"main_file","file_id":"10835","file_size":20592929,"content_type":"application/pdf","creator":"dernst","file_name":"2021_PNAS_Meier.pdf","access_level":"open_access"}],"_id":"9375","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 118","ddc":["570"],"status":"public","title":"Haplotype tagging reveals parallel formation of hybrid races in two butterfly species","publication_identifier":{"eissn":["0027-8424"]},"month":"06","doi":"10.1073/pnas.2015005118","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"isi":["000671755600001"],"pmid":["34155138"]},"oa":1,"isi":1,"quality_controlled":"1","file_date_updated":"2022-03-08T08:18:16Z","article_number":"e2015005118","author":[{"full_name":"Meier, Joana I.","last_name":"Meier","first_name":"Joana I."},{"last_name":"Salazar","first_name":"Patricio A.","full_name":"Salazar, Patricio A."},{"first_name":"Marek","last_name":"Kučka","full_name":"Kučka, Marek"},{"last_name":"Davies","first_name":"Robert William","full_name":"Davies, Robert William"},{"full_name":"Dréau, Andreea","first_name":"Andreea","last_name":"Dréau"},{"last_name":"Aldás","first_name":"Ismael","full_name":"Aldás, Ismael"},{"first_name":"Olivia Box","last_name":"Power","full_name":"Power, Olivia Box"},{"full_name":"Nadeau, Nicola J.","first_name":"Nicola J.","last_name":"Nadeau"},{"full_name":"Bridle, Jon R.","first_name":"Jon R.","last_name":"Bridle"},{"full_name":"Rolian, Campbell","last_name":"Rolian","first_name":"Campbell"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H"},{"full_name":"McMillan, W. Owen","first_name":"W. Owen","last_name":"McMillan"},{"last_name":"Jiggins","first_name":"Chris D.","full_name":"Jiggins, Chris D."},{"last_name":"Chan","first_name":"Yingguang Frank","full_name":"Chan, Yingguang Frank"}],"volume":118,"date_created":"2021-05-07T17:10:21Z","date_updated":"2023-08-08T13:33:09Z","pmid":1,"acknowledgement":"We thank Felicity Jones for input into experimental design, helpful discussion and improving the manuscript. We thank the Rolian, Jiggins, Chan and Jones Labs members for support, insightful scientific discussion and improving the manuscript. We thank the Rolian lab members, the Animal Resource Centre staff at the University of Calgary, and Caroline Schmid and Ann-Katrin Geysel at the Friedrich Miescher Laboratory for animal husbandry. We thank Christa Lanz, Rebecca Schwab and Ilja Bezrukov for assistance with high-throughput sequencing and associated data processing; Andre Noll and the MPI Tübingen IT team for computational support. We thank Ben Haller and Richard Durbin for helpful discussions. We thank David M. Kingsley for thoughtful input that has greatly improved our manuscript. J.I.M. is supported by a Research Fellowship from St. John’s College, Cambridge. A.D. was supported by a European Research Council Consolidator Grant (No. 617279 “EvolRecombAdapt”, P/I Felicity Jones). C.R. is supported by Discovery Grant #4181932 from the Natural Sciences and Engineering Research Council of Canada and by the Faculty of Veterinary Medicine at the University of Calgary. C.D.J. is supported by a BBSRC grant BB/R007500 and a European Research Council Advanced Grant (No. 339873 “SpeciationGenetics”). M.K. and Y.F.C. are supported by the Max Planck Society and a European Research Council Starting Grant (No. 639096 “HybridMiX”).","year":"2021","department":[{"_id":"NiBa"}],"publisher":"Proceedings of the National Academy of Sciences","publication_status":"published"},{"month":"05","publication_identifier":{"eissn":["2056-3744"]},"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":["000647846200001"]},"isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Theoretical and empirical approaches to understanding Parallel Adaptation","grant_number":"797747","_id":"265B41B8-B435-11E9-9278-68D0E5697425"}],"doi":"10.1002/evl3.227","language":[{"iso":"eng"}],"file_date_updated":"2021-10-15T08:26:02Z","ec_funded":1,"acknowledgement":"We are very grateful to Irena Senčić for technical assistance and to Michelle Kortyna and Sean Holland at the Center for Anchored Phylogenomics for assistance with data collection. RKB was funded by the Natural Environment Research Council and by the European Research Council. KJ was funded by the Swedish Research Councils VR and Formas (Linnaeus Grant: 217‐2008‐1719). JL was funded by a studentship from the Leverhulme Centre for Advanced Biological Modelling. AMW was funded by the European Union's Horizon 2020 research and innovation program under Marie Skłodowska‐Curie Grant agreement no. 797747. RF was funded by the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska‐Curie Grant agreement No. 706376 and by FEDER Funds through the Operational Competitiveness Factors Program—COMPETE and by National Funds through FCT—Foundation for Science and Technology within the scope of the project “Hybrabbid” (PTDC/BIA‐EVL/30628/2017‐ POCI‐01‐0145‐FEDER‐030628). We are grateful to other members of the Littorina research group for helpful discussions. We thank Claire Mérot and an anonymous referee for insightful comments on an earlier version. ","year":"2021","publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Wiley","author":[{"last_name":"Koch","first_name":"Eva L.","full_name":"Koch, Eva L."},{"last_name":"Morales","first_name":"Hernán E.","full_name":"Morales, Hernán E."},{"first_name":"Jenny","last_name":"Larsson","full_name":"Larsson, Jenny"},{"last_name":"Westram","first_name":"Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","full_name":"Westram, Anja M"},{"full_name":"Faria, Rui","last_name":"Faria","first_name":"Rui"},{"full_name":"Lemmon, Alan R.","first_name":"Alan R.","last_name":"Lemmon"},{"full_name":"Lemmon, E. Moriarty","first_name":"E. Moriarty","last_name":"Lemmon"},{"last_name":"Johannesson","first_name":"Kerstin","full_name":"Johannesson, Kerstin"},{"full_name":"Butlin, Roger K.","last_name":"Butlin","first_name":"Roger K."}],"related_material":{"record":[{"id":"12987","status":"public","relation":"research_data"}]},"date_updated":"2023-08-08T13:34:08Z","date_created":"2021-05-16T22:01:47Z","volume":5,"scopus_import":"1","day":"07","has_accepted_license":"1","article_processing_charge":"No","publication":"Evolution Letters","citation":{"chicago":"Koch, Eva L., Hernán E. Morales, Jenny Larsson, Anja M Westram, Rui Faria, Alan R. Lemmon, E. Moriarty Lemmon, Kerstin Johannesson, and Roger K. Butlin. “Genetic Variation for Adaptive Traits Is Associated with Polymorphic Inversions in Littorina Saxatilis.” Evolution Letters. Wiley, 2021. https://doi.org/10.1002/evl3.227.","mla":"Koch, Eva L., et al. “Genetic Variation for Adaptive Traits Is Associated with Polymorphic Inversions in Littorina Saxatilis.” Evolution Letters, vol. 5, no. 3, Wiley, 2021, pp. 196–213, doi:10.1002/evl3.227.","short":"E.L. Koch, H.E. Morales, J. Larsson, A.M. Westram, R. Faria, A.R. Lemmon, E.M. Lemmon, K. Johannesson, R.K. Butlin, Evolution Letters 5 (2021) 196–213.","ista":"Koch EL, Morales HE, Larsson J, Westram AM, Faria R, Lemmon AR, Lemmon EM, Johannesson K, Butlin RK. 2021. Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis. Evolution Letters. 5(3), 196–213.","ieee":"E. L. Koch et al., “Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis,” Evolution Letters, vol. 5, no. 3. Wiley, pp. 196–213, 2021.","apa":"Koch, E. L., Morales, H. E., Larsson, J., Westram, A. M., Faria, R., Lemmon, A. R., … Butlin, R. K. (2021). Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis. Evolution Letters. Wiley. https://doi.org/10.1002/evl3.227","ama":"Koch EL, Morales HE, Larsson J, et al. Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis. Evolution Letters. 2021;5(3):196-213. doi:10.1002/evl3.227"},"article_type":"original","page":"196-213","date_published":"2021-05-07T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Chromosomal inversions have long been recognized for their role in local adaptation. By suppressing recombination in heterozygous individuals, they can maintain coadapted gene complexes and protect them from homogenizing effects of gene flow. However, to fully understand their importance for local adaptation we need to know their influence on phenotypes under divergent selection. For this, the marine snail Littorina saxatilis provides an ideal study system. Divergent ecotypes adapted to wave action and crab predation occur in close proximity on intertidal shores with gene flow between them. Here, we used F2 individuals obtained from crosses between the ecotypes to test for associations between genomic regions and traits distinguishing the Crab‐/Wave‐adapted ecotypes including size, shape, shell thickness, and behavior. We show that most of these traits are influenced by two previously detected inversion regions that are divergent between ecotypes. We thus gain a better understanding of one important underlying mechanism responsible for the rapid and repeated formation of ecotypes: divergent selection acting on inversions. We also found that some inversions contributed to more than one trait suggesting that they may contain several loci involved in adaptation, consistent with the hypothesis that suppression of recombination within inversions facilitates differentiation in the presence of gene flow."}],"issue":"3","_id":"9394","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis","ddc":["570"],"status":"public","intvolume":" 5","oa_version":"Published Version","file":[{"file_size":3021108,"content_type":"application/pdf","creator":"cchlebak","access_level":"open_access","file_name":"2021_EvolutionLetters_Koch.pdf","checksum":"023b1608e311f0fda30593ba3d0a4e0b","success":1,"date_updated":"2021-10-15T08:26:02Z","date_created":"2021-10-15T08:26:02Z","relation":"main_file","file_id":"10142"}]},{"date_published":"2021-05-10T00:00:00Z","page":"R428-R429","article_type":"original","citation":{"chicago":"Stankowski, Sean, and Mark Ravinet. “Quantifying the Use of Species Concepts.” Current Biology. Cell Press, 2021. https://doi.org/10.1016/j.cub.2021.03.060.","mla":"Stankowski, Sean, and Mark Ravinet. “Quantifying the Use of Species Concepts.” Current Biology, vol. 31, no. 9, Cell Press, 2021, pp. R428–29, doi:10.1016/j.cub.2021.03.060.","short":"S. Stankowski, M. Ravinet, Current Biology 31 (2021) R428–R429.","ista":"Stankowski S, Ravinet M. 2021. Quantifying the use of species concepts. Current Biology. 31(9), R428–R429.","ieee":"S. Stankowski and M. Ravinet, “Quantifying the use of species concepts,” Current Biology, vol. 31, no. 9. Cell Press, pp. R428–R429, 2021.","apa":"Stankowski, S., & Ravinet, M. (2021). Quantifying the use of species concepts. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2021.03.060","ama":"Stankowski S, Ravinet M. Quantifying the use of species concepts. Current Biology. 2021;31(9):R428-R429. doi:10.1016/j.cub.2021.03.060"},"publication":"Current Biology","article_processing_charge":"No","day":"10","scopus_import":"1","oa_version":"Published Version","intvolume":" 31","title":"Quantifying the use of species concepts","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9392","issue":"9","abstract":[{"lang":"eng","text":"Humans conceptualize the diversity of life by classifying individuals into types we call ‘species’1. The species we recognize influence political and financial decisions and guide our understanding of how units of diversity evolve and interact. Although the idea of species may seem intuitive, a debate about the best way to define them has raged even before Darwin2. So much energy has been devoted to the so-called ‘species problem’ that no amount of discourse will ever likely solve it2,3. Dozens of species concepts are currently recognized3, but we lack a concrete understanding of how much researchers actually disagree and the factors that cause them to think differently1,2. To address this, we used a survey to quantify the species problem for the first time. The results indicate that the disagreement is extensive: two randomly chosen respondents will most likely disagree on the nature of species. The probability of disagreement is not predicted by researcher experience or broad study system, but tended to be lower among researchers with similar focus, training and who study the same organism. Should we see this diversity of perspectives as a problem? We argue that we should not."}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1016/j.cub.2021.03.060","isi":1,"quality_controlled":"1","external_id":{"pmid":["33974865"],"isi":["000654741200004"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cub.2021.03.060"}],"oa":1,"publication_identifier":{"issn":["09609822"],"eissn":["18790445"]},"month":"05","volume":31,"date_updated":"2023-08-08T13:34:38Z","date_created":"2021-05-16T22:01:46Z","author":[{"full_name":"Stankowski, Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","last_name":"Stankowski","first_name":"Sean"},{"full_name":"Ravinet, Mark","last_name":"Ravinet","first_name":"Mark"}],"department":[{"_id":"NiBa"}],"publisher":"Cell Press","publication_status":"published","pmid":1,"acknowledgement":"We thank Christopher Cooney, Martin Garlovsky, Anja M. Westram, Carina Baskett, Stefanie Belohlavy, Michal Hledik, Arka Pal, Nicholas H. Barton, Roger K. Butlin and members of the University of Sheffield Speciation Journal Club for feedback on draft survey questions and/or comments on a draft manuscript. Three anonymous reviewers gave thoughtful feedback that improved the manuscript. We thank Ahmad Nadeem, who was paid to build the Shiny app. We are especially grateful to everyone who took part in the survey. Ethical approval for the survey was obtained through the University of Sheffield Ethics Review Procedure (Application 029768). S.S. was supported by a NERC grant awarded to Roger K. Butlin.","year":"2021"},{"tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"citation":{"ista":"Koch E, Morales HE, Larsson J, Westram AM, Faria R, Lemmon AR, Lemmon EM, Johannesson K, Butlin RK. 2021. Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis, Dryad, 10.5061/DRYAD.ZGMSBCCB4.","ieee":"E. Koch et al., “Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis.” Dryad, 2021.","apa":"Koch, E., Morales, H. E., Larsson, J., Westram, A. M., Faria, R., Lemmon, A. R., … Butlin, R. K. (2021). Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis. Dryad. https://doi.org/10.5061/DRYAD.ZGMSBCCB4","ama":"Koch E, Morales HE, Larsson J, et al. Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis. 2021. doi:10.5061/DRYAD.ZGMSBCCB4","chicago":"Koch, Eva, Hernán E. Morales, Jenny Larsson, Anja M Westram, Rui Faria, Alan R. Lemmon, E. Moriarty Lemmon, Kerstin Johannesson, and Roger K. Butlin. “Data from: Genetic Variation for Adaptive Traits Is Associated with Polymorphic Inversions in Littorina Saxatilis.” Dryad, 2021. https://doi.org/10.5061/DRYAD.ZGMSBCCB4.","mla":"Koch, Eva, et al. Data from: Genetic Variation for Adaptive Traits Is Associated with Polymorphic Inversions in Littorina Saxatilis. Dryad, 2021, doi:10.5061/DRYAD.ZGMSBCCB4.","short":"E. Koch, H.E. Morales, J. Larsson, A.M. Westram, R. Faria, A.R. Lemmon, E.M. Lemmon, K. Johannesson, R.K. Butlin, (2021)."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.zgmsbccb4"}],"oa":1,"date_published":"2021-04-10T00:00:00Z","doi":"10.5061/DRYAD.ZGMSBCCB4","has_accepted_license":"1","article_processing_charge":"No","day":"10","month":"04","year":"2021","_id":"12987","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Dryad","department":[{"_id":"NiBa"}],"title":"Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis","status":"public","ddc":["570"],"related_material":{"record":[{"id":"9394","relation":"used_in_publication","status":"public"}]},"author":[{"last_name":"Koch","first_name":"Eva","full_name":"Koch, Eva"},{"full_name":"Morales, Hernán E.","last_name":"Morales","first_name":"Hernán E."},{"first_name":"Jenny","last_name":"Larsson","full_name":"Larsson, Jenny"},{"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":"Rui","last_name":"Faria","full_name":"Faria, Rui"},{"last_name":"Lemmon","first_name":"Alan R.","full_name":"Lemmon, Alan R."},{"first_name":"E. Moriarty","last_name":"Lemmon","full_name":"Lemmon, E. Moriarty"},{"last_name":"Johannesson","first_name":"Kerstin","full_name":"Johannesson, Kerstin"},{"first_name":"Roger K.","last_name":"Butlin","full_name":"Butlin, Roger K."}],"oa_version":"Published Version","date_updated":"2023-08-08T13:34:07Z","date_created":"2023-05-16T12:34:09Z","type":"research_data_reference","abstract":[{"text":"Chromosomal inversion polymorphisms, segments of chromosomes that are flipped in orientation and occur in reversed order in some individuals, have long been recognized to play an important role in local adaptation. They can reduce recombination in heterozygous individuals and thus help to maintain sets of locally adapted alleles. In a wide range of organisms, populations adapted to different habitats differ in frequency of inversion arrangements. However, getting a full understanding of the importance of inversions for adaptation requires confirmation of their influence on traits under divergent selection. Here, we studied a marine snail, Littorina saxatilis, that has evolved ecotypes adapted to wave exposure or crab predation. These two types occur in close proximity on different parts of the shore. Gene flow between them exists in contact zones. However, they exhibit strong phenotypic divergence in several traits under habitat-specific selection, including size, shape and behaviour. We used crosses between these ecotypes to identify genomic regions that explain variation in these traits by using QTL analysis and variance partitioning across linkage groups. We could show that previously detected inversion regions contribute to adaptive divergence. Some inversions influenced multiple traits suggesting that they contain sets of locally adaptive alleles. Our study also identified regions without known inversions that are important for phenotypic divergence. Thus, we provide a more complete overview of the importance of inversions in relation to the remaining genome.","lang":"eng"}]},{"scopus_import":"1","day":"12","has_accepted_license":"1","article_processing_charge":"No","publication":"Biology letters","citation":{"short":"M. Lagator, H. Uecker, P. Neve, Biology Letters 17 (2021).","mla":"Lagator, Mato, et al. “Adaptation at Different Points along Antibiotic Concentration Gradients.” Biology Letters, vol. 17, no. 5, 20200913, Royal Society of London, 2021, doi:10.1098/rsbl.2020.0913.","chicago":"Lagator, Mato, Hildegard Uecker, and Paul Neve. “Adaptation at Different Points along Antibiotic Concentration Gradients.” Biology Letters. Royal Society of London, 2021. https://doi.org/10.1098/rsbl.2020.0913.","ama":"Lagator M, Uecker H, Neve P. Adaptation at different points along antibiotic concentration gradients. Biology letters. 2021;17(5). doi:10.1098/rsbl.2020.0913","ieee":"M. Lagator, H. Uecker, and P. Neve, “Adaptation at different points along antibiotic concentration gradients,” Biology letters, vol. 17, no. 5. Royal Society of London, 2021.","apa":"Lagator, M., Uecker, H., & Neve, P. (2021). Adaptation at different points along antibiotic concentration gradients. Biology Letters. Royal Society of London. https://doi.org/10.1098/rsbl.2020.0913","ista":"Lagator M, Uecker H, Neve P. 2021. Adaptation at different points along antibiotic concentration gradients. Biology letters. 17(5), 20200913."},"date_published":"2021-05-12T00:00:00Z","type":"journal_article","abstract":[{"text":"Antibiotic concentrations vary dramatically in the body and the environment. Hence, understanding the dynamics of resistance evolution along antibiotic concentration gradients is critical for predicting and slowing the emergence and spread of resistance. While it has been shown that increasing the concentration of an antibiotic slows resistance evolution, how adaptation to one antibiotic concentration correlates with fitness at other points along the gradient has not received much attention. Here, we selected populations of Escherichia coli at several points along a concentration gradient for three different antibiotics, asking how rapidly resistance evolved and whether populations became specialized to the antibiotic concentration they were selected on. Populations selected at higher concentrations evolved resistance more slowly but exhibited equal or higher fitness across the whole gradient. Populations selected at lower concentrations evolved resistance rapidly, but overall fitness in the presence of antibiotics was lower. However, these populations readily adapted to higher concentrations upon subsequent selection. Our results indicate that resistance management strategies must account not only for the rates of resistance evolution but also for the fitness of evolved strains.","lang":"eng"}],"issue":"5","_id":"9410","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"Adaptation at different points along antibiotic concentration gradients","ddc":["570"],"intvolume":" 17","file":[{"file_name":"2021_BiologyLetters_Lagator.pdf","access_level":"open_access","content_type":"application/pdf","file_size":726759,"creator":"kschuh","relation":"main_file","file_id":"9425","date_created":"2021-05-25T14:09:03Z","date_updated":"2021-05-25T14:09:03Z","checksum":"9c13c1f5af7609c97c741f11d293188a","success":1}],"oa_version":"Published Version","month":"05","publication_identifier":{"eissn":["1744957X"]},"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":["000651501400001"],"pmid":[" 33975485"]},"isi":1,"quality_controlled":"1","project":[{"name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"doi":"10.1098/rsbl.2020.0913","language":[{"iso":"eng"}],"article_number":"20200913","file_date_updated":"2021-05-25T14:09:03Z","ec_funded":1,"acknowledgement":"We would like to thank Martin Ackermann, Camilo Barbosa, Nick Barton, Jonathan Bollback, Sebastian Bonhoeffer, Nick Colegrave, Calin Guet, Alex Hall, Sally Otto, Tiago Paixao, Srdjan Sarikas, Hinrich Schulenburg, Marjon de Vos and Michael Whitlock for insightful support.","year":"2021","pmid":1,"publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Royal Society of London","author":[{"id":"345D25EC-F248-11E8-B48F-1D18A9856A87","last_name":"Lagator","first_name":"Mato","full_name":"Lagator, Mato"},{"id":"2DB8F68A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9435-2813","first_name":"Hildegard","last_name":"Uecker","full_name":"Uecker, Hildegard"},{"first_name":"Paul","last_name":"Neve","full_name":"Neve, Paul"}],"date_created":"2021-05-23T22:01:43Z","date_updated":"2023-08-08T13:44:35Z","volume":17},{"volume":30,"date_updated":"2023-08-08T13:59:18Z","date_created":"2021-06-06T22:01:31Z","author":[{"last_name":"Berdan","first_name":"Emma L.","full_name":"Berdan, Emma L."},{"last_name":"Blanckaert","first_name":"Alexandre","full_name":"Blanckaert, Alexandre"},{"first_name":"Tanja","last_name":"Slotte","full_name":"Slotte, Tanja"},{"full_name":"Suh, Alexander","last_name":"Suh","first_name":"Alexander"},{"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":"Fragata, Inês","last_name":"Fragata","first_name":"Inês"}],"department":[{"_id":"NiBa"}],"publisher":"Wiley","publication_status":"published","acknowledgement":"We thank the editor, two helpful reviewers, Roger Butlin, Kerstin Johannesson, Valentina Peona, Rike Stelkens, Julie Blommaert, Nick Barton, and João Alpedrinha for helpful comments that improved the manuscript. The authors acknowledge funding from the Swedish Research Council Formas (2017-01597 to AS), the Swedish Research Council Vetenskapsrådet (2016-05139 to AS, 2019-04452 to TS) and from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 757451 to TS). ELB was funded by a Carl Tryggers grant awarded to Tanja Slotte. Anja M. Westram was funded by the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 797747. Inês Fragata was funded by a Junior Researcher contract from FCT (CEECIND/02616/2018).","year":"2021","ec_funded":1,"file_date_updated":"2021-06-11T15:34:53Z","language":[{"iso":"eng"}],"doi":"10.1111/mec.15936","project":[{"_id":"265B41B8-B435-11E9-9278-68D0E5697425","grant_number":"797747","name":"Theoretical and empirical approaches to understanding Parallel Adaptation","call_identifier":"H2020"}],"isi":1,"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"external_id":{"isi":["000652056400001"]},"publication_identifier":{"issn":["09621083"],"eissn":["1365294X"]},"month":"06","oa_version":"Published Version","file":[{"creator":"kschuh","content_type":"application/pdf","file_size":1031978,"file_name":"2021_MolecularEcology_Berdan.pdf","access_level":"open_access","date_updated":"2021-06-11T15:34:53Z","date_created":"2021-06-11T15:34:53Z","success":1,"checksum":"e6f4731365bde2614b333040a08265d8","file_id":"9545","relation":"main_file"}],"intvolume":" 30","status":"public","title":"Unboxing mutations: Connecting mutation types with evolutionary consequences","ddc":["570"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9470","issue":"12","abstract":[{"text":"A key step in understanding the genetic basis of different evolutionary outcomes (e.g., adaptation) is to determine the roles played by different mutation types (e.g., SNPs, translocations and inversions). To do this we must simultaneously consider different mutation types in an evolutionary framework. Here, we propose a research framework that directly utilizes the most important characteristics of mutations, their population genetic effects, to determine their relative evolutionary significance in a given scenario. We review known population genetic effects of different mutation types and show how these may be connected to different evolutionary outcomes. We provide examples of how to implement this framework and pinpoint areas where more data, theory and synthesis are needed. Linking experimental and theoretical approaches to examine different mutation types simultaneously is a critical step towards understanding their evolutionary significance.","lang":"eng"}],"type":"journal_article","date_published":"2021-06-01T00:00:00Z","page":"2710-2723","citation":{"mla":"Berdan, Emma L., et al. “Unboxing Mutations: Connecting Mutation Types with Evolutionary Consequences.” Molecular Ecology, vol. 30, no. 12, Wiley, 2021, pp. 2710–23, doi:10.1111/mec.15936.","short":"E.L. Berdan, A. Blanckaert, T. Slotte, A. Suh, A.M. Westram, I. Fragata, Molecular Ecology 30 (2021) 2710–2723.","chicago":"Berdan, Emma L., Alexandre Blanckaert, Tanja Slotte, Alexander Suh, Anja M Westram, and Inês Fragata. “Unboxing Mutations: Connecting Mutation Types with Evolutionary Consequences.” Molecular Ecology. Wiley, 2021. https://doi.org/10.1111/mec.15936.","ama":"Berdan EL, Blanckaert A, Slotte T, Suh A, Westram AM, Fragata I. Unboxing mutations: Connecting mutation types with evolutionary consequences. Molecular Ecology. 2021;30(12):2710-2723. doi:10.1111/mec.15936","ista":"Berdan EL, Blanckaert A, Slotte T, Suh A, Westram AM, Fragata I. 2021. Unboxing mutations: Connecting mutation types with evolutionary consequences. Molecular Ecology. 30(12), 2710–2723.","apa":"Berdan, E. L., Blanckaert, A., Slotte, T., Suh, A., Westram, A. M., & Fragata, I. (2021). Unboxing mutations: Connecting mutation types with evolutionary consequences. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.15936","ieee":"E. L. Berdan, A. Blanckaert, T. Slotte, A. Suh, A. M. Westram, and I. Fragata, “Unboxing mutations: Connecting mutation types with evolutionary consequences,” Molecular Ecology, vol. 30, no. 12. Wiley, pp. 2710–2723, 2021."},"publication":"Molecular Ecology","has_accepted_license":"1","article_processing_charge":"No","day":"01","scopus_import":"1"},{"oa_version":"Published Version","file":[{"checksum":"ae4df60eb62f4491278588548d0c1f93","success":1,"date_updated":"2021-08-09T11:52:14Z","date_created":"2021-08-09T11:52:14Z","relation":"main_file","file_id":"9835","content_type":"application/pdf","file_size":773921,"creator":"asandaue","access_level":"open_access","file_name":"2021_PLoSONE_Hledík.pdf"}],"title":"Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program","ddc":["610"],"status":"public","intvolume":" 16","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9816","abstract":[{"text":"Aims: Mass antigen testing programs have been challenged because of an alleged insufficient specificity, leading to a large number of false positives. The objective of this study is to derive a lower bound of the specificity of the SD Biosensor Standard Q Ag-Test in large scale practical use.\r\nMethods: Based on county data from the nationwide tests for SARS-CoV-2 in Slovakia between 31.10.–1.11. 2020 we calculate a lower confidence bound for the specificity. As positive test results were not systematically verified by PCR tests, we base the lower bound on a worst case assumption, assuming all positives to be false positives.\r\nResults: 3,625,332 persons from 79 counties were tested. The lowest positivity rate was observed in the county of Rožňava where 100 out of 34307 (0.29%) tests were positive. This implies a test specificity of at least 99.6% (97.5% one-sided lower confidence bound, adjusted for multiplicity).\r\nConclusion: The obtained lower bound suggests a higher specificity compared to earlier studies in spite of the underlying worst case assumption and the application in a mass testing setting. The actual specificity is expected to exceed 99.6% if the prevalence in the respective regions was non-negligible at the time of testing. To our knowledge, this estimate constitutes the first bound obtained from large scale practical use of an antigen test.","lang":"eng"}],"issue":"7","type":"journal_article","date_published":"2021-07-29T00:00:00Z","article_type":"original","publication":"PLoS ONE","citation":{"ista":"Hledik M, Polechova J, Beiglböck M, Herdina AN, Strassl R, Posch M. 2021. Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program. PLoS ONE. 16(7), e0255267.","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.","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","ama":"Hledik M, Polechova J, Beiglböck M, Herdina AN, Strassl R, Posch M. Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program. PLoS ONE. 2021;16(7). doi:10.1371/journal.pone.0255267","chicago":"Hledik, Michal, Jitka Polechova, Mathias Beiglböck, Anna Nele Herdina, Robert Strassl, and Martin Posch. “Analysis of the Specificity of a COVID-19 Antigen Test in the Slovak Mass Testing Program.” PLoS ONE. Public Library of Science, 2021. https://doi.org/10.1371/journal.pone.0255267.","mla":"Hledik, Michal, et al. “Analysis of the Specificity of a COVID-19 Antigen Test in the Slovak Mass Testing Program.” PLoS ONE, vol. 16, no. 7, e0255267, Public Library of Science, 2021, doi:10.1371/journal.pone.0255267.","short":"M. Hledik, J. Polechova, M. Beiglböck, A.N. Herdina, R. Strassl, M. Posch, PLoS ONE 16 (2021)."},"day":"29","article_processing_charge":"Yes","has_accepted_license":"1","scopus_import":"1","date_created":"2021-08-08T22:01:26Z","date_updated":"2023-08-10T14:26:32Z","volume":16,"author":[{"first_name":"Michal","last_name":"Hledik","id":"4171253A-F248-11E8-B48F-1D18A9856A87","full_name":"Hledik, Michal"},{"id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0951-3112","first_name":"Jitka","last_name":"Polechova","full_name":"Polechova, Jitka"},{"full_name":"Beiglböck, Mathias","last_name":"Beiglböck","first_name":"Mathias"},{"full_name":"Herdina, Anna Nele","first_name":"Anna Nele","last_name":"Herdina"},{"full_name":"Strassl, Robert","last_name":"Strassl","first_name":"Robert"},{"full_name":"Posch, Martin","last_name":"Posch","first_name":"Martin"}],"publication_status":"published","publisher":"Public Library of Science","department":[{"_id":"NiBa"}],"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.","pmid":1,"file_date_updated":"2021-08-09T11:52:14Z","article_number":"e0255267","language":[{"iso":"eng"}],"doi":"10.1371/journal.pone.0255267","isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000685248200095"],"pmid":["34324553"]},"month":"07","publication_identifier":{"eissn":["1932-6203"]}},{"date_updated":"2023-09-05T15:44:06Z","date_created":"2021-03-20T08:22:10Z","volume":75,"author":[{"last_name":"Szep","first_name":"Eniko","id":"485BB5A4-F248-11E8-B48F-1D18A9856A87","full_name":"Szep, Eniko"},{"first_name":"Himani","last_name":"Sachdeva","id":"42377A0A-F248-11E8-B48F-1D18A9856A87","full_name":"Sachdeva, Himani"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H"}],"related_material":{"record":[{"status":"public","relation":"research_data","id":"13062"}]},"publication_status":"published","publisher":"Wiley","department":[{"_id":"NiBa"}],"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.","file_date_updated":"2021-08-11T13:39:19Z","language":[{"iso":"eng"}],"doi":"10.1111/evo.14210","isi":1,"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"isi":["000636966300001"]},"month":"05","publication_identifier":{"issn":["0014-3820"],"eissn":["1558-5646"]},"file":[{"file_name":"2021_Evolution_Szep.pdf","access_level":"open_access","content_type":"application/pdf","file_size":734102,"creator":"kschuh","relation":"main_file","file_id":"9886","date_created":"2021-08-11T13:39:19Z","date_updated":"2021-08-11T13:39:19Z","checksum":"b90fb5767d623602046fed03725e16ca","success":1}],"oa_version":"Published Version","status":"public","ddc":["570"],"title":"Polygenic local adaptation in metapopulations: A stochastic eco‐evolutionary model","intvolume":" 75","_id":"9252","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","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."}],"issue":"5","type":"journal_article","date_published":"2021-05-01T00:00:00Z","article_type":"original","page":"1030-1045","publication":"Evolution","citation":{"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","ista":"Szep E, Sachdeva H, Barton NH. 2021. Polygenic local adaptation in metapopulations: A stochastic eco‐evolutionary model. Evolution. 75(5), 1030–1045.","ieee":"E. Szep, H. Sachdeva, and N. H. Barton, “Polygenic local adaptation in metapopulations: A stochastic eco‐evolutionary model,” Evolution, vol. 75, no. 5. Wiley, pp. 1030–1045, 2021.","apa":"Szep, E., Sachdeva, H., & Barton, N. H. (2021). Polygenic local adaptation in metapopulations: A stochastic eco‐evolutionary model. Evolution. Wiley. https://doi.org/10.1111/evo.14210","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.","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."},"day":"01","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics","General Agricultural and Biological Sciences"],"scopus_import":"1"},{"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"main_file_link":[{"open_access":"1","url":"https://onlinelibrary.wiley.com/doi/10.1111/evo.14235"}],"external_id":{"isi":["000647224000001"]},"isi":1,"quality_controlled":"1","doi":"10.1111/evo.14235","language":[{"iso":"eng"}],"month":"04","publication_identifier":{"eissn":["1558-5646"],"issn":["0014-3820"]},"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","department":[{"_id":"NiBa"}],"publisher":"Wiley","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."},{"full_name":"Bank, Claudia","first_name":"Claudia","last_name":"Bank"},{"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":"Samuel M.","last_name":"Flaxman","full_name":"Flaxman, Samuel M."},{"first_name":"Tatiana","last_name":"Giraud","full_name":"Giraud, Tatiana"},{"first_name":"Robin","last_name":"Hopkins","full_name":"Hopkins, Robin"},{"full_name":"Larson, Erica L.","first_name":"Erica L.","last_name":"Larson"},{"full_name":"Maan, Martine E.","last_name":"Maan","first_name":"Martine E."},{"full_name":"Meier, Joana","first_name":"Joana","last_name":"Meier"},{"first_name":"Richard","last_name":"Merrill","full_name":"Merrill, Richard"},{"last_name":"Noor","first_name":"Mohamed A. F.","full_name":"Noor, Mohamed A. F."},{"full_name":"Ortiz‐Barrientos, Daniel","last_name":"Ortiz‐Barrientos","first_name":"Daniel"},{"full_name":"Qvarnström, Anna","last_name":"Qvarnström","first_name":"Anna"}],"date_updated":"2023-09-05T15:44:33Z","date_created":"2021-05-06T04:34:47Z","volume":75,"publication":"Evolution","citation":{"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.","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."},"article_type":"original","page":"978-988","date_published":"2021-04-19T00:00:00Z","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics","General Agricultural and Biological Sciences"],"day":"19","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"9374","status":"public","title":"Homage to Felsenstein 1981, or why are there so few/many species?","intvolume":" 75","oa_version":"Published Version","type":"journal_article","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"},{"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","date_updated":"2023-09-05T15:44:05Z","date_created":"2023-05-23T16:17:02Z","oa_version":"Published Version","author":[{"full_name":"Szep, Eniko","id":"485BB5A4-F248-11E8-B48F-1D18A9856A87","first_name":"Eniko","last_name":"Szep"},{"full_name":"Sachdeva, Himani","id":"42377A0A-F248-11E8-B48F-1D18A9856A87","first_name":"Himani","last_name":"Sachdeva"},{"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":[{"id":"9252","status":"public","relation":"used_in_publication"}]},"ddc":["570"],"status":"public","title":"Supplementary code for: Polygenic local adaptation in metapopulations: A stochastic eco-evolutionary model","publisher":"Dryad","department":[{"_id":"NiBa"}],"_id":"13062","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2021","day":"02","month":"03","article_processing_charge":"No","date_published":"2021-03-02T00:00:00Z","doi":"10.5061/DRYAD.8GTHT76P1","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":{"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","ieee":"E. Szep, H. Sachdeva, and N. H. Barton, “Supplementary code for: Polygenic local adaptation in metapopulations: A stochastic eco-evolutionary model.” Dryad, 2021.","apa":"Szep, E., Sachdeva, H., & Barton, N. H. (2021). Supplementary code for: Polygenic local adaptation in metapopulations: A stochastic eco-evolutionary model. Dryad. https://doi.org/10.5061/DRYAD.8GTHT76P1","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"}]},{"status":"public","title":"Defining the speciation continuum","ddc":["570"],"intvolume":" 75","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9383","file":[{"date_created":"2022-03-25T12:02:04Z","date_updated":"2022-03-25T12:02:04Z","success":1,"checksum":"96f6ccf15d95a4e9f7c0b27eee570fa6","file_id":"10921","relation":"main_file","creator":"kschuh","file_size":719991,"content_type":"application/pdf","file_name":"2021_Evolution_Stankowski.pdf","access_level":"open_access"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"A primary roadblock to our understanding of speciation is that it usually occurs over a timeframe that is too long to study from start to finish. The idea of a speciation continuum provides something of a solution to this problem; rather than observing the entire process, we can simply reconstruct it from the multitude of speciation events that surround us. But what do we really mean when we talk about the speciation continuum, and can it really help us understand speciation? We explored these questions using a literature review and online survey of speciation researchers. Although most researchers were familiar with the concept and thought it was useful, our survey revealed extensive disagreement about what the speciation continuum actually tells us. This is due partly to the lack of a clear definition. Here, we provide an explicit definition that is compatible with the Biological Species Concept. That is, the speciation continuum is a continuum of reproductive isolation. After outlining the logic of the definition in light of alternatives, we explain why attempts to reconstruct the speciation process from present‐day populations will ultimately fail. We then outline how we think the speciation continuum concept can continue to act as a foundation for understanding the continuum of reproductive isolation that surrounds us.","lang":"eng"}],"issue":"6","article_type":"original","page":"1256-1273","publication":"Evolution","citation":{"mla":"Stankowski, Sean, and Mark Ravinet. “Defining the Speciation Continuum.” Evolution, vol. 75, no. 6, Oxford University Press, 2021, pp. 1256–73, doi:10.1111/evo.14215.","short":"S. Stankowski, M. Ravinet, Evolution 75 (2021) 1256–1273.","chicago":"Stankowski, Sean, and Mark Ravinet. “Defining the Speciation Continuum.” Evolution. Oxford University Press, 2021. https://doi.org/10.1111/evo.14215.","ama":"Stankowski S, Ravinet M. Defining the speciation continuum. Evolution. 2021;75(6):1256-1273. doi:10.1111/evo.14215","ista":"Stankowski S, Ravinet M. 2021. Defining the speciation continuum. Evolution. 75(6), 1256–1273.","apa":"Stankowski, S., & Ravinet, M. (2021). Defining the speciation continuum. Evolution. Oxford University Press. https://doi.org/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."},"date_published":"2021-03-22T00:00:00Z","scopus_import":"1","day":"22","article_processing_charge":"No","has_accepted_license":"1","publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Oxford University Press","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","date_updated":"2023-10-18T08:16:01Z","date_created":"2021-05-09T22:01:39Z","volume":75,"author":[{"full_name":"Stankowski, Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","first_name":"Sean","last_name":"Stankowski"},{"full_name":"Ravinet, Mark","last_name":"Ravinet","first_name":"Mark"}],"file_date_updated":"2022-03-25T12:02:04Z","isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"external_id":{"isi":["000647226400001"]},"language":[{"iso":"eng"}],"doi":"10.1111/evo.14215","month":"03","publication_identifier":{"eissn":["1558-5646"],"issn":["0014-3820"]}},{"author":[{"id":"43161670-5719-11EA-8025-FABC3DDC885E","first_name":"Sean","last_name":"Stankowski","full_name":"Stankowski, Sean"},{"first_name":"Daria","last_name":"Shipilina","id":"428A94B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1145-9226","full_name":"Shipilina, Daria"},{"orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","first_name":"Anja M","full_name":"Westram, Anja M"}],"oa_version":"None","volume":2,"date_created":"2024-02-14T12:05:50Z","date_updated":"2024-02-19T09:54:18Z","year":"2021","_id":"14984","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Wiley","department":[{"_id":"NiBa"}],"intvolume":" 2","title":"Hybrid Zones","status":"public","publication_status":"published","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","date_published":"2021-05-28T00:00:00Z","doi":"10.1002/9780470015902.a0029355","language":[{"iso":"eng"}],"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","ieee":"S. Stankowski, D. Shipilina, and A. M. Westram, “Hybrid Zones,” in Encyclopedia of Life Sciences, vol. 2, Wiley, 2021.","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","ista":"Stankowski S, Shipilina D, Westram AM. 2021.Hybrid Zones. In: Encyclopedia of Life Sciences. vol. 2.","short":"S. Stankowski, D. Shipilina, A.M. Westram, in:, Encyclopedia of Life Sciences, Wiley, 2021.","mla":"Stankowski, Sean, et al. “Hybrid Zones.” Encyclopedia of Life Sciences, vol. 2, Wiley, 2021, doi:10.1002/9780470015902.a0029355.","chicago":"Stankowski, Sean, Daria Shipilina, and Anja M Westram. “Hybrid Zones.” In Encyclopedia of Life Sciences, Vol. 2. ELS. Wiley, 2021. https://doi.org/10.1002/9780470015902.a0029355."},"publication":"Encyclopedia of Life Sciences","quality_controlled":"1","article_processing_charge":"No","publication_identifier":{"eisbn":["9780470015902"],"isbn":["9780470016176"]},"day":"28","month":"05","series_title":"eLS"},{"file_date_updated":"2021-02-24T17:45:13Z","abstract":[{"lang":"eng","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."}],"type":"research_data","author":[{"full_name":"Surendranadh, Parvathy","first_name":"Parvathy","last_name":"Surendranadh","id":"455235B8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Arathoon, Louise S","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1771-714X","first_name":"Louise S","last_name":"Arathoon"},{"first_name":"Carina","last_name":"Baskett","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7354-8574","full_name":"Baskett, Carina"},{"full_name":"Field, David","last_name":"Field","first_name":"David","orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Pickup","first_name":"Melinda","orcid":"0000-0001-6118-0541","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","full_name":"Pickup, Melinda"},{"last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"}],"contributor":[{"first_name":"Parvathy","last_name":"Surendranadh","contributor_type":"project_member","id":"455235B8-F248-11E8-B48F-1D18A9856A87"},{"id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","last_name":"Arathoon","contributor_type":"project_member","first_name":"Louise S"},{"id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","first_name":"Carina","last_name":"Baskett","contributor_type":"project_member"},{"contributor_type":"project_member","last_name":"Field","first_name":"David","orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-6118-0541","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","last_name":"Pickup","contributor_type":"project_member","first_name":"Melinda"},{"first_name":"Nicholas H","contributor_type":"project_leader","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"11411"},{"id":"11321","status":"public","relation":"later_version"},{"relation":"earlier_version","status":"public","id":"8254"}]},"date_updated":"2024-02-21T12:41:09Z","date_created":"2021-02-24T17:49:21Z","file":[{"checksum":"f85537815809a8a4b7da9d01163f88c0","success":1,"date_created":"2021-02-24T17:45:13Z","date_updated":"2021-02-24T17:45:13Z","relation":"main_file","file_id":"9193","file_size":5934452,"content_type":"application/x-zip-compressed","creator":"larathoo","access_level":"open_access","file_name":"Data_Code.zip"}],"oa_version":"Published Version","_id":"9192","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2021","status":"public","ddc":["576"],"title":"Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"publisher":"Institute of Science and Technology Austria","day":"26","month":"02","article_processing_charge":"No","has_accepted_license":"1","doi":"10.15479/AT:ISTA:9192","date_published":"2021-02-26T00:00:00Z","citation":{"chicago":"Surendranadh, Parvathy, Louise S Arathoon, Carina Baskett, David Field, Melinda Pickup, and Nicholas H Barton. “Effects of Fine-Scale Population Structure on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus.” Institute of Science and Technology Austria, 2021. https://doi.org/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.","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.","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"},"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},{"intvolume":" 17","ddc":["570"],"title":"A developmentally descriptive method for quantifying shape in gastropod shells","status":"public","_id":"7651","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"date_updated":"2020-07-14T12:48:01Z","date_created":"2020-04-14T12:31:16Z","checksum":"4eb102304402f5c56432516b84df86d6","relation":"main_file","file_id":"7660","file_size":1556190,"content_type":"application/pdf","creator":"dernst","file_name":"2020_JournRoyalSociety_Larsson.pdf","access_level":"open_access"}],"oa_version":"Published Version","type":"journal_article","issue":"163","abstract":[{"lang":"eng","text":"The growth of snail shells can be described by simple mathematical rules. Variation in a few parameters can explain much of the diversity of shell shapes seen in nature. However, empirical studies of gastropod shell shape variation typically use geometric morphometric approaches, which do not capture this growth pattern. We have developed a way to infer a set of developmentally descriptive shape parameters based on three-dimensional logarithmic helicospiral growth and using landmarks from two-dimensional shell images as input. We demonstrate the utility of this approach, and compare it to the geometric morphometric approach, using a large set of Littorina saxatilis shells in which locally adapted populations differ in shape. Our method can be modified easily to make it applicable to a wide range of shell forms, which would allow for investigations of the similarities and differences between and within many different species of gastropods."}],"article_type":"original","citation":{"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.","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."},"publication":"Journal of The Royal Society Interface","date_published":"2020-02-01T00:00:00Z","scopus_import":1,"has_accepted_license":"1","article_processing_charge":"No","day":"01","department":[{"_id":"NiBa"}],"publisher":"The Royal Society","publication_status":"published","year":"2020","volume":17,"date_created":"2020-04-08T15:19:17Z","date_updated":"2021-01-12T08:14:41Z","author":[{"full_name":"Larsson, J.","first_name":"J.","last_name":"Larsson"},{"first_name":"Anja M","last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M"},{"last_name":"Bengmark","first_name":"S.","full_name":"Bengmark, S."},{"last_name":"Lundh","first_name":"T.","full_name":"Lundh, T."},{"full_name":"Butlin, R. K.","last_name":"Butlin","first_name":"R. K."}],"article_number":"20190721","file_date_updated":"2020-07-14T12:48:01Z","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1098/rsif.2019.0721","publication_identifier":{"eissn":["1742-5662"],"issn":["1742-5689"]},"month":"02"},{"abstract":[{"lang":"eng","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."}],"type":"book_chapter","author":[{"full_name":"Westram, Anja M","last_name":"Westram","first_name":"Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Rui","last_name":"Faria","full_name":"Faria, Rui"},{"full_name":"Butlin, Roger","first_name":"Roger","last_name":"Butlin"},{"full_name":"Johannesson, Kerstin","last_name":"Johannesson","first_name":"Kerstin"}],"date_created":"2021-02-15T12:39:04Z","date_updated":"2021-02-15T13:18:16Z","oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9123","year":"2020","publication_status":"published","status":"public","title":"Inversions and Evolution","publisher":"Wiley","department":[{"_id":"NiBa"}],"month":"05","day":"16","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":{"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.","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.","ama":"Westram AM, Faria R, Butlin R, Johannesson K. Inversions and Evolution. In: 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. ."},"quality_controlled":"1"},{"month":"09","day":"22","article_processing_charge":"No","doi":"10.5061/DRYAD.R4XGXD29N","date_published":"2020-09-22T00:00:00Z","oa":1,"tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"main_file_link":[{"url":"https://doi.org/10.5061/dryad.r4xgxd29n","open_access":"1"}],"citation":{"chicago":"Simon, Alexis, Christelle Fraisse, Tahani El Ayari, Cathy Liautard-Haag, Petr Strelkov, John Welch, and Nicolas Bierne. “How Do Species Barriers Decay? Concordance and Local Introgression in Mosaic Hybrid Zones of Mussels.” Dryad, 2020. https://doi.org/10.5061/DRYAD.R4XGXD29N.","short":"A. Simon, C. Fraisse, T. El Ayari, C. Liautard-Haag, P. Strelkov, J. Welch, N. Bierne, (2020).","mla":"Simon, Alexis, et al. How Do Species Barriers Decay? Concordance and Local Introgression in Mosaic Hybrid Zones of Mussels. Dryad, 2020, doi:10.5061/DRYAD.R4XGXD29N.","ieee":"A. Simon et al., “How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels.” Dryad, 2020.","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","ista":"Simon A, Fraisse C, El Ayari T, Liautard-Haag C, Strelkov P, Welch J, Bierne N. 2020. How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels, Dryad, 10.5061/DRYAD.R4XGXD29N.","ama":"Simon A, Fraisse C, El Ayari T, et al. How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels. 2020. doi:10.5061/DRYAD.R4XGXD29N"},"abstract":[{"lang":"eng","text":"The Mytilus complex of marine mussel species forms a mosaic of hybrid zones, found across temperate regions of the globe. This allows us to study \"replicated\" instances of secondary contact between closely-related species. Previous work on this complex has shown that local introgression is both widespread and highly heterogeneous, and has identified SNPs that are outliers of differentiation between lineages. Here, we developed an ancestry-informative panel of such SNPs. We then compared their frequencies in newly-sampled populations, including samples from within the hybrid zones, and parental populations at different distances from the contact. Results show that close to the hybrid zones, some outlier loci are near to fixation for the heterospecific allele, suggesting enhanced local introgression, or the local sweep of a shared ancestral allele. Conversely, genomic cline analyses, treating local parental populations as the reference, reveal a globally high concordance among loci, albeit with a few signals of asymmetric introgression. Enhanced local introgression at specific loci is consistent with the early transfer of adaptive variants after contact, possibly including asymmetric bi-stable variants (Dobzhansky-Muller incompatibilities), or haplotypes loaded with fewer deleterious mutations. Having escaped one barrier, however, these variants can be trapped or delayed at the next barrier, confining the introgression locally. These results shed light on the decay of species barriers during phases of contact."}],"type":"research_data_reference","author":[{"first_name":"Alexis","last_name":"Simon","full_name":"Simon, Alexis"},{"first_name":"Christelle","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle"},{"full_name":"El Ayari, Tahani","first_name":"Tahani","last_name":"El Ayari"},{"last_name":"Liautard-Haag","first_name":"Cathy","full_name":"Liautard-Haag, Cathy"},{"first_name":"Petr","last_name":"Strelkov","full_name":"Strelkov, Petr"},{"first_name":"John","last_name":"Welch","full_name":"Welch, John"},{"last_name":"Bierne","first_name":"Nicolas","full_name":"Bierne, Nicolas"}],"related_material":{"record":[{"id":"8708","relation":"used_in_publication","status":"public"}]},"date_created":"2023-05-23T16:48:27Z","date_updated":"2023-08-04T11:04:11Z","oa_version":"Published Version","_id":"13073","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2020","title":"How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels","status":"public","ddc":["570"],"department":[{"_id":"NiBa"}],"publisher":"Dryad"}]