[{"external_id":{"isi":["000647226400001"]},"_id":"9383","publication_status":"published","author":[{"first_name":"Sean","full_name":"Stankowski, Sean","last_name":"Stankowski","id":"43161670-5719-11EA-8025-FABC3DDC885E"},{"last_name":"Ravinet","first_name":"Mark","full_name":"Ravinet, Mark"}],"publisher":"Oxford University Press","day":"22","doi":"10.1111/evo.14215","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"}],"article_processing_charge":"No","ddc":["570"],"has_accepted_license":"1","date_updated":"2023-10-18T08:16:01Z","month":"03","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.","article_type":"original","oa":1,"oa_version":"Published Version","file_date_updated":"2022-03-25T12:02:04Z","date_created":"2021-05-09T22:01:39Z","tmp":{"short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png"},"quality_controlled":"1","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Stankowski, Sean, and Mark Ravinet. “Defining the Speciation Continuum.” <i>Evolution</i>. Oxford University Press, 2021. <a href=\"https://doi.org/10.1111/evo.14215\">https://doi.org/10.1111/evo.14215</a>.","apa":"Stankowski, S., &#38; Ravinet, M. (2021). Defining the speciation continuum. <i>Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1111/evo.14215\">https://doi.org/10.1111/evo.14215</a>","ieee":"S. Stankowski and M. Ravinet, “Defining the speciation continuum,” <i>Evolution</i>, vol. 75, no. 6. Oxford University Press, pp. 1256–1273, 2021.","mla":"Stankowski, Sean, and Mark Ravinet. “Defining the Speciation Continuum.” <i>Evolution</i>, vol. 75, no. 6, Oxford University Press, 2021, pp. 1256–73, doi:<a href=\"https://doi.org/10.1111/evo.14215\">10.1111/evo.14215</a>.","ama":"Stankowski S, Ravinet M. Defining the speciation continuum. <i>Evolution</i>. 2021;75(6):1256-1273. doi:<a href=\"https://doi.org/10.1111/evo.14215\">10.1111/evo.14215</a>","ista":"Stankowski S, Ravinet M. 2021. Defining the speciation continuum. Evolution. 75(6), 1256–1273.","short":"S. Stankowski, M. Ravinet, Evolution 75 (2021) 1256–1273."},"status":"public","volume":75,"year":"2021","issue":"6","type":"journal_article","file":[{"date_updated":"2022-03-25T12:02:04Z","date_created":"2022-03-25T12:02:04Z","content_type":"application/pdf","file_size":719991,"relation":"main_file","checksum":"96f6ccf15d95a4e9f7c0b27eee570fa6","file_name":"2021_Evolution_Stankowski.pdf","creator":"kschuh","file_id":"10921","access_level":"open_access","success":1}],"language":[{"iso":"eng"}],"publication":"Evolution","title":"Defining the speciation continuum","intvolume":"        75","page":"1256-1273","date_published":"2021-03-22T00:00:00Z","license":"https://creativecommons.org/licenses/by-nc/4.0/","isi":1,"publication_identifier":{"eissn":["1558-5646"],"issn":["0014-3820"]},"department":[{"_id":"NiBa"}]},{"ddc":["570"],"day":"10","_id":"9392","external_id":{"isi":["000654741200004"],"pmid":["33974865"]},"publisher":"Cell Press","author":[{"first_name":"Sean","full_name":"Stankowski, Sean","last_name":"Stankowski","id":"43161670-5719-11EA-8025-FABC3DDC885E"},{"last_name":"Ravinet","full_name":"Ravinet, Mark","first_name":"Mark"}],"publication_status":"published","article_processing_charge":"No","abstract":[{"text":"Humans conceptualize the diversity of life by classifying individuals into types we call ‘species’1. The species we recognize influence political and financial decisions and guide our understanding of how units of diversity evolve and interact. Although the idea of species may seem intuitive, a debate about the best way to define them has raged even before Darwin2. So much energy has been devoted to the so-called ‘species problem’ that no amount of discourse will ever likely solve it2,3. Dozens of species concepts are currently recognized3, but we lack a concrete understanding of how much researchers actually disagree and the factors that cause them to think differently1,2. To address this, we used a survey to quantify the species problem for the first time. The results indicate that the disagreement is extensive: two randomly chosen respondents will most likely disagree on the nature of species. The probability of disagreement is not predicted by researcher experience or broad study system, but tended to be lower among researchers with similar focus, training and who study the same organism. Should we see this diversity of perspectives as a problem? We argue that we should not.","lang":"eng"}],"doi":"10.1016/j.cub.2021.03.060","article_type":"original","oa":1,"oa_version":"Published Version","month":"05","date_updated":"2026-06-18T19:49:12Z","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.","main_file_link":[{"url":"https://doi.org/10.1016/j.cub.2021.03.060","open_access":"1"}],"pmid":1,"issue":"9","year":"2021","type":"journal_article","title":"Quantifying the use of species concepts","corr_author":"1","publication":"Current Biology","language":[{"iso":"eng"}],"quality_controlled":"1","scopus_import":"1","date_created":"2021-05-16T22:01:46Z","volume":31,"status":"public","citation":{"mla":"Stankowski, Sean, and Mark Ravinet. “Quantifying the Use of Species Concepts.” <i>Current Biology</i>, vol. 31, no. 9, Cell Press, 2021, pp. R428–29, doi:<a href=\"https://doi.org/10.1016/j.cub.2021.03.060\">10.1016/j.cub.2021.03.060</a>.","ama":"Stankowski S, Ravinet M. Quantifying the use of species concepts. <i>Current Biology</i>. 2021;31(9):R428-R429. doi:<a href=\"https://doi.org/10.1016/j.cub.2021.03.060\">10.1016/j.cub.2021.03.060</a>","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.","chicago":"Stankowski, Sean, and Mark Ravinet. “Quantifying the Use of Species Concepts.” <i>Current Biology</i>. Cell Press, 2021. <a href=\"https://doi.org/10.1016/j.cub.2021.03.060\">https://doi.org/10.1016/j.cub.2021.03.060</a>.","apa":"Stankowski, S., &#38; Ravinet, M. (2021). Quantifying the use of species concepts. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2021.03.060\">https://doi.org/10.1016/j.cub.2021.03.060</a>","ieee":"S. Stankowski and M. Ravinet, “Quantifying the use of species concepts,” <i>Current Biology</i>, vol. 31, no. 9. Cell Press, pp. R428–R429, 2021."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"NiBa"}],"publication_identifier":{"issn":["0960-9822"],"eissn":["1879-0445"]},"isi":1,"intvolume":"        31","date_published":"2021-05-10T00:00:00Z","page":"R428-R429"},{"doi":"10.1002/evl3.227","article_processing_charge":"No","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."}],"_id":"9394","author":[{"full_name":"Koch, Eva L.","first_name":"Eva L.","last_name":"Koch"},{"last_name":"Morales","first_name":"Hernán E.","full_name":"Morales, Hernán E."},{"full_name":"Larsson, Jenny","first_name":"Jenny","last_name":"Larsson"},{"last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","first_name":"Anja M"},{"first_name":"Rui","full_name":"Faria, Rui","last_name":"Faria"},{"last_name":"Lemmon","full_name":"Lemmon, Alan R.","first_name":"Alan R."},{"last_name":"Lemmon","first_name":"E. Moriarty","full_name":"Lemmon, E. Moriarty"},{"first_name":"Kerstin","full_name":"Johannesson, Kerstin","last_name":"Johannesson"},{"last_name":"Butlin","full_name":"Butlin, Roger K.","first_name":"Roger K."}],"publication_status":"published","publisher":"Wiley","external_id":{"isi":["000647846200001"]},"project":[{"call_identifier":"H2020","grant_number":"797747","name":"Theoretical and empirical approaches to understanding Parallel Adaptation","_id":"265B41B8-B435-11E9-9278-68D0E5697425"}],"day":"07","ec_funded":1,"ddc":["570"],"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. ","has_accepted_license":"1","date_updated":"2026-04-07T14:01:29Z","month":"05","file_date_updated":"2021-10-15T08:26:02Z","oa_version":"Published Version","oa":1,"article_type":"original","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.","mla":"Koch, Eva L., et al. “Genetic Variation for Adaptive Traits Is Associated with Polymorphic Inversions in Littorina Saxatilis.” <i>Evolution Letters</i>, vol. 5, no. 3, Wiley, 2021, pp. 196–213, doi:<a href=\"https://doi.org/10.1002/evl3.227\">10.1002/evl3.227</a>.","ama":"Koch EL, Morales HE, Larsson J, et al. Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis. <i>Evolution Letters</i>. 2021;5(3):196-213. doi:<a href=\"https://doi.org/10.1002/evl3.227\">10.1002/evl3.227</a>","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. <i>Evolution Letters</i>. Wiley. <a href=\"https://doi.org/10.1002/evl3.227\">https://doi.org/10.1002/evl3.227</a>","ieee":"E. L. Koch <i>et al.</i>, “Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis,” <i>Evolution Letters</i>, vol. 5, no. 3. Wiley, pp. 196–213, 2021.","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.” <i>Evolution Letters</i>. Wiley, 2021. <a href=\"https://doi.org/10.1002/evl3.227\">https://doi.org/10.1002/evl3.227</a>."},"status":"public","volume":5,"date_created":"2021-05-16T22:01:47Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"quality_controlled":"1","scopus_import":"1","related_material":{"record":[{"id":"12987","status":"public","relation":"research_data"}]},"file":[{"success":1,"file_id":"10142","access_level":"open_access","creator":"cchlebak","checksum":"023b1608e311f0fda30593ba3d0a4e0b","file_name":"2021_EvolutionLetters_Koch.pdf","relation":"main_file","file_size":3021108,"content_type":"application/pdf","date_updated":"2021-10-15T08:26:02Z","date_created":"2021-10-15T08:26:02Z"}],"language":[{"iso":"eng"}],"publication":"Evolution Letters","title":"Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis","issue":"3","type":"journal_article","year":"2021","page":"196-213","date_published":"2021-05-07T00:00:00Z","intvolume":"         5","isi":1,"department":[{"_id":"NiBa"}],"publication_identifier":{"eissn":["2056-3744"]}},{"quality_controlled":"1","scopus_import":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_created":"2021-05-23T22:01:43Z","volume":17,"status":"public","citation":{"ama":"Lagator M, Uecker H, Neve P. Adaptation at different points along antibiotic concentration gradients. <i>Biology letters</i>. 2021;17(5). doi:<a href=\"https://doi.org/10.1098/rsbl.2020.0913\">10.1098/rsbl.2020.0913</a>","mla":"Lagator, Mato, et al. “Adaptation at Different Points along Antibiotic Concentration Gradients.” <i>Biology Letters</i>, vol. 17, no. 5, 20200913, Royal Society of London, 2021, doi:<a href=\"https://doi.org/10.1098/rsbl.2020.0913\">10.1098/rsbl.2020.0913</a>.","ista":"Lagator M, Uecker H, Neve P. 2021. Adaptation at different points along antibiotic concentration gradients. Biology letters. 17(5), 20200913.","short":"M. Lagator, H. Uecker, P. Neve, Biology Letters 17 (2021).","chicago":"Lagator, Mato, Hildegard Uecker, and Paul Neve. “Adaptation at Different Points along Antibiotic Concentration Gradients.” <i>Biology Letters</i>. Royal Society of London, 2021. <a href=\"https://doi.org/10.1098/rsbl.2020.0913\">https://doi.org/10.1098/rsbl.2020.0913</a>.","ieee":"M. Lagator, H. Uecker, and P. Neve, “Adaptation at different points along antibiotic concentration gradients,” <i>Biology letters</i>, vol. 17, no. 5. Royal Society of London, 2021.","apa":"Lagator, M., Uecker, H., &#38; Neve, P. (2021). Adaptation at different points along antibiotic concentration gradients. <i>Biology Letters</i>. Royal Society of London. <a href=\"https://doi.org/10.1098/rsbl.2020.0913\">https://doi.org/10.1098/rsbl.2020.0913</a>"},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","pmid":1,"type":"journal_article","issue":"5","year":"2021","title":"Adaptation at different points along antibiotic concentration gradients","publication":"Biology letters","corr_author":"1","language":[{"iso":"eng"}],"file":[{"access_level":"open_access","file_id":"9425","success":1,"creator":"kschuh","relation":"main_file","file_size":726759,"checksum":"9c13c1f5af7609c97c741f11d293188a","file_name":"2021_BiologyLetters_Lagator.pdf","date_updated":"2021-05-25T14:09:03Z","date_created":"2021-05-25T14:09:03Z","content_type":"application/pdf"}],"intvolume":"        17","date_published":"2021-05-12T00:00:00Z","article_number":"20200913","publication_identifier":{"eissn":["1744-957X"]},"department":[{"_id":"NiBa"}],"isi":1,"day":"12","project":[{"grant_number":"250152","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation"}],"_id":"9410","publication_status":"published","author":[{"last_name":"Lagator","id":"345D25EC-F248-11E8-B48F-1D18A9856A87","first_name":"Mato","full_name":"Lagator, Mato"},{"id":"2DB8F68A-F248-11E8-B48F-1D18A9856A87","last_name":"Uecker","full_name":"Uecker, Hildegard","orcid":"0000-0001-9435-2813","first_name":"Hildegard"},{"full_name":"Neve, Paul","first_name":"Paul","last_name":"Neve"}],"publisher":"Royal Society of London","external_id":{"isi":["000651501400001"],"pmid":[" 33975485"]},"article_processing_charge":"No","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"}],"doi":"10.1098/rsbl.2020.0913","ddc":["570"],"ec_funded":1,"month":"05","date_updated":"2026-04-02T14:02:44Z","has_accepted_license":"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.","oa":1,"file_date_updated":"2021-05-25T14:09:03Z","oa_version":"Published Version"},{"ec_funded":1,"ddc":["570"],"abstract":[{"lang":"eng","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."}],"article_processing_charge":"No","doi":"10.1111/mec.15936","day":"01","project":[{"call_identifier":"H2020","grant_number":"797747","_id":"265B41B8-B435-11E9-9278-68D0E5697425","name":"Theoretical and empirical approaches to understanding Parallel Adaptation"}],"_id":"9470","publication_status":"published","publisher":"Wiley","external_id":{"isi":["000652056400001"]},"author":[{"first_name":"Emma L.","full_name":"Berdan, Emma L.","last_name":"Berdan"},{"last_name":"Blanckaert","full_name":"Blanckaert, Alexandre","first_name":"Alexandre"},{"first_name":"Tanja","full_name":"Slotte, Tanja","last_name":"Slotte"},{"last_name":"Suh","first_name":"Alexander","full_name":"Suh, Alexander"},{"last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","first_name":"Anja M"},{"full_name":"Fragata, Inês","first_name":"Inês","last_name":"Fragata"}],"file_date_updated":"2021-06-11T15:34:53Z","oa_version":"Published Version","oa":1,"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).","month":"06","date_updated":"2026-04-16T08:19:26Z","has_accepted_license":"1","title":"Unboxing mutations: Connecting mutation types with evolutionary consequences","publication":"Molecular Ecology","language":[{"iso":"eng"}],"file":[{"creator":"kschuh","file_id":"9545","access_level":"open_access","success":1,"date_updated":"2021-06-11T15:34:53Z","date_created":"2021-06-11T15:34:53Z","content_type":"application/pdf","relation":"main_file","file_size":1031978,"checksum":"e6f4731365bde2614b333040a08265d8","file_name":"2021_MolecularEcology_Berdan.pdf"}],"year":"2021","type":"journal_article","issue":"12","volume":30,"status":"public","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"ama":"Berdan EL, Blanckaert A, Slotte T, Suh A, Westram AM, Fragata I. Unboxing mutations: Connecting mutation types with evolutionary consequences. <i>Molecular Ecology</i>. 2021;30(12):2710-2723. doi:<a href=\"https://doi.org/10.1111/mec.15936\">10.1111/mec.15936</a>","mla":"Berdan, Emma L., et al. “Unboxing Mutations: Connecting Mutation Types with Evolutionary Consequences.” <i>Molecular Ecology</i>, vol. 30, no. 12, Wiley, 2021, pp. 2710–23, doi:<a href=\"https://doi.org/10.1111/mec.15936\">10.1111/mec.15936</a>.","short":"E.L. Berdan, A. Blanckaert, T. Slotte, A. Suh, A.M. Westram, I. Fragata, Molecular Ecology 30 (2021) 2710–2723.","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.","chicago":"Berdan, Emma L., Alexandre Blanckaert, Tanja Slotte, Alexander Suh, Anja M Westram, and Inês Fragata. “Unboxing Mutations: Connecting Mutation Types with Evolutionary Consequences.” <i>Molecular Ecology</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/mec.15936\">https://doi.org/10.1111/mec.15936</a>.","ieee":"E. L. Berdan, A. Blanckaert, T. Slotte, A. Suh, A. M. Westram, and I. Fragata, “Unboxing mutations: Connecting mutation types with evolutionary consequences,” <i>Molecular Ecology</i>, vol. 30, no. 12. Wiley, pp. 2710–2723, 2021.","apa":"Berdan, E. L., Blanckaert, A., Slotte, T., Suh, A., Westram, A. M., &#38; Fragata, I. (2021). Unboxing mutations: Connecting mutation types with evolutionary consequences. <i>Molecular Ecology</i>. Wiley. <a href=\"https://doi.org/10.1111/mec.15936\">https://doi.org/10.1111/mec.15936</a>"},"quality_controlled":"1","scopus_import":"1","tmp":{"short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png"},"date_created":"2021-06-06T22:01:31Z","department":[{"_id":"NiBa"}],"publication_identifier":{"issn":["0962-1083"],"eissn":["1365-294X"]},"isi":1,"date_published":"2021-06-01T00:00:00Z","page":"2710-2723","intvolume":"        30"},{"title":"Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program","publication":"PLoS ONE","language":[{"iso":"eng"}],"file":[{"creator":"asandaue","success":1,"access_level":"open_access","file_id":"9835","content_type":"application/pdf","date_updated":"2021-08-09T11:52:14Z","date_created":"2021-08-09T11:52:14Z","checksum":"ae4df60eb62f4491278588548d0c1f93","file_name":"2021_PLoSONE_Hledík.pdf","relation":"main_file","file_size":773921}],"pmid":1,"type":"journal_article","issue":"7","year":"2021","volume":16,"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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,” <i>PLoS ONE</i>, vol. 16, no. 7. Public Library of Science, 2021.","apa":"Hledik, M., Polechova, J., Beiglböck, M., Herdina, A. N., Strassl, R., &#38; Posch, M. (2021). Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program. <i>PLoS ONE</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0255267\">https://doi.org/10.1371/journal.pone.0255267</a>","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.” <i>PLoS ONE</i>. Public Library of Science, 2021. <a href=\"https://doi.org/10.1371/journal.pone.0255267\">https://doi.org/10.1371/journal.pone.0255267</a>.","short":"M. Hledik, J. Polechova, M. Beiglböck, A.N. Herdina, R. Strassl, M. Posch, PLoS ONE 16 (2021).","ista":"Hledik M, Polechova J, Beiglböck M, Herdina AN, Strassl R, Posch M. 2021. Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program. PLoS ONE. 16(7), e0255267.","ama":"Hledik M, Polechova J, Beiglböck M, Herdina AN, Strassl R, Posch M. Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program. <i>PLoS ONE</i>. 2021;16(7). doi:<a href=\"https://doi.org/10.1371/journal.pone.0255267\">10.1371/journal.pone.0255267</a>","mla":"Hledik, Michal, et al. “Analysis of the Specificity of a COVID-19 Antigen Test in the Slovak Mass Testing Program.” <i>PLoS ONE</i>, vol. 16, no. 7, e0255267, Public Library of Science, 2021, doi:<a href=\"https://doi.org/10.1371/journal.pone.0255267\">10.1371/journal.pone.0255267</a>."},"scopus_import":"1","quality_controlled":"1","date_created":"2021-08-08T22:01:26Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication_identifier":{"eissn":["1932-6203"]},"department":[{"_id":"NiBa"}],"isi":1,"article_number":"e0255267","date_published":"2021-07-29T00:00:00Z","intvolume":"        16","ddc":["610"],"article_processing_charge":"Yes","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"}],"doi":"10.1371/journal.pone.0255267","day":"29","_id":"9816","publication_status":"published","author":[{"id":"4171253A-F248-11E8-B48F-1D18A9856A87","last_name":"Hledik","first_name":"Michal","full_name":"Hledik, Michal"},{"id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","last_name":"Polechova","full_name":"Polechova, Jitka","orcid":"0000-0003-0951-3112","first_name":"Jitka"},{"first_name":"Mathias","full_name":"Beiglböck, Mathias","last_name":"Beiglböck"},{"last_name":"Herdina","first_name":"Anna Nele","full_name":"Herdina, Anna Nele"},{"full_name":"Strassl, Robert","first_name":"Robert","last_name":"Strassl"},{"full_name":"Posch, Martin","first_name":"Martin","last_name":"Posch"}],"publisher":"Public Library of Science","external_id":{"isi":["000685248200095"],"pmid":["34324553"]},"file_date_updated":"2021-08-09T11:52:14Z","oa_version":"Published Version","oa":1,"article_type":"original","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.","month":"07","date_updated":"2023-08-10T14:26:32Z","has_accepted_license":"1"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"S. Arnoux, C. Fraisse, C. Sauvage, (2020).","ista":"Arnoux S, Fraisse C, Sauvage C. 2020. VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species, Dryad, <a href=\"https://doi.org/10.5061/DRYAD.Q2BVQ83HD\">10.5061/DRYAD.Q2BVQ83HD</a>.","ama":"Arnoux S, Fraisse C, Sauvage C. VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species. 2020. doi:<a href=\"https://doi.org/10.5061/DRYAD.Q2BVQ83HD\">10.5061/DRYAD.Q2BVQ83HD</a>","mla":"Arnoux, Stephanie, et al. <i>VCF Files of Synonymous SNPs Related to: Genomic Inference of Complex Domestication Histories in Three Solanaceae Species</i>. Dryad, 2020, doi:<a href=\"https://doi.org/10.5061/DRYAD.Q2BVQ83HD\">10.5061/DRYAD.Q2BVQ83HD</a>.","ieee":"S. Arnoux, C. Fraisse, and C. Sauvage, “VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species.” Dryad, 2020.","apa":"Arnoux, S., Fraisse, C., &#38; Sauvage, C. (2020). VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species. Dryad. <a href=\"https://doi.org/10.5061/DRYAD.Q2BVQ83HD\">https://doi.org/10.5061/DRYAD.Q2BVQ83HD</a>","chicago":"Arnoux, Stephanie, Christelle Fraisse, and Christopher Sauvage. “VCF Files of Synonymous SNPs Related to: Genomic Inference of Complex Domestication Histories in Three Solanaceae Species.” Dryad, 2020. <a href=\"https://doi.org/10.5061/DRYAD.Q2BVQ83HD\">https://doi.org/10.5061/DRYAD.Q2BVQ83HD</a>."},"article_processing_charge":"No","abstract":[{"text":"Domestication is a human-induced selection process that imprints the genomes of domesticated populations over a short evolutionary time scale, and that occurs in a given demographic context. Reconstructing historical gene flow, effective population size changes and their timing is therefore of fundamental interest to understand how plant demography and human selection jointly shape genomic divergence during domestication. Yet, the comparison under a single statistical framework of independent domestication histories across different crop species has been little evaluated so far. Thus, it is unclear whether domestication leads to convergent demographic changes that similarly affect crop genomes. To address this question, we used existing and new transcriptome data on three crop species of Solanaceae (eggplant, pepper and tomato), together with their close wild relatives. We fitted twelve demographic models of increasing complexity on the unfolded joint allele frequency spectrum for each wild/crop pair, and we found evidence for both shared and species-specific demographic processes between species. A convergent history of domestication with gene-flow was inferred for all three species, along with evidence of strong reduction in the effective population size during the cultivation stage of tomato and pepper. The absence of any reduction in size of the crop in eggplant stands out from the classical view of the domestication process; as does the existence of a “protracted period” of management before cultivation. Our results also suggest divergent management strategies of modern cultivars among species as their current demography substantially differs. Finally, the timing of domestication is species-specific and supported by the few historical records available.","lang":"eng"}],"status":"public","doi":"10.5061/DRYAD.Q2BVQ83HD","_id":"13065","tmp":{"legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","short":"CC0 (1.0)","name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png"},"date_created":"2023-05-23T16:30:20Z","author":[{"full_name":"Arnoux, Stephanie","first_name":"Stephanie","last_name":"Arnoux"},{"orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle","first_name":"Christelle","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sauvage, Christopher","first_name":"Christopher","last_name":"Sauvage"}],"publisher":"Dryad","day":"19","related_material":{"link":[{"relation":"software","url":"https://github.com/starnoux/arnoux_et_al_2019"}],"record":[{"relation":"used_in_publication","id":"8928","status":"public"}]},"title":"VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species","ddc":["570"],"type":"research_data_reference","year":"2020","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.q2bvq83hd"}],"date_published":"2020-10-19T00:00:00Z","date_updated":"2026-06-18T19:37:16Z","month":"10","oa_version":"Published Version","license":"https://creativecommons.org/publicdomain/zero/1.0/","oa":1,"department":[{"_id":"NiBa"}]},{"article_processing_charge":"No","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."}],"status":"public","doi":"10.5061/DRYAD.R4XGXD29N","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Simon, Alexis, et al. <i>How Do Species Barriers Decay? Concordance and Local Introgression in Mosaic Hybrid Zones of Mussels</i>. Dryad, 2020, doi:<a href=\"https://doi.org/10.5061/DRYAD.R4XGXD29N\">10.5061/DRYAD.R4XGXD29N</a>.","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:<a href=\"https://doi.org/10.5061/DRYAD.R4XGXD29N\">10.5061/DRYAD.R4XGXD29N</a>","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, <a href=\"https://doi.org/10.5061/DRYAD.R4XGXD29N\">10.5061/DRYAD.R4XGXD29N</a>.","short":"A. Simon, C. Fraisse, T. El Ayari, C. Liautard-Haag, P. Strelkov, J. Welch, N. Bierne, (2020).","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. <a href=\"https://doi.org/10.5061/DRYAD.R4XGXD29N\">https://doi.org/10.5061/DRYAD.R4XGXD29N</a>.","apa":"Simon, A., Fraisse, C., El Ayari, T., Liautard-Haag, C., Strelkov, P., Welch, J., &#38; Bierne, N. (2020). How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels. Dryad. <a href=\"https://doi.org/10.5061/DRYAD.R4XGXD29N\">https://doi.org/10.5061/DRYAD.R4XGXD29N</a>","ieee":"A. Simon <i>et al.</i>, “How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels.” Dryad, 2020."},"day":"22","related_material":{"record":[{"id":"8708","status":"public","relation":"used_in_publication"}]},"_id":"13073","tmp":{"legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","short":"CC0 (1.0)","name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png"},"publisher":"Dryad","date_created":"2023-05-23T16:48:27Z","author":[{"full_name":"Simon, Alexis","first_name":"Alexis","last_name":"Simon"},{"last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle","orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle"},{"last_name":"El Ayari","full_name":"El Ayari, Tahani","first_name":"Tahani"},{"full_name":"Liautard-Haag, Cathy","first_name":"Cathy","last_name":"Liautard-Haag"},{"first_name":"Petr","full_name":"Strelkov, Petr","last_name":"Strelkov"},{"full_name":"Welch, John","first_name":"John","last_name":"Welch"},{"full_name":"Bierne, Nicolas","first_name":"Nicolas","last_name":"Bierne"}],"title":"How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels","type":"research_data_reference","year":"2020","ddc":["570"],"date_published":"2020-09-22T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.r4xgxd29n"}],"month":"09","date_updated":"2025-07-10T12:01:22Z","oa_version":"Published Version","oa":1,"department":[{"_id":"NiBa"}]},{"citation":{"ista":"Larsson J, Westram AM, Bengmark S, Lundh T, Butlin RK. 2020. A developmentally descriptive method for quantifying shape in gastropod shells. Journal of The Royal Society Interface. 17(163), 20190721.","short":"J. Larsson, A.M. Westram, S. Bengmark, T. Lundh, R.K. Butlin, Journal of The Royal Society Interface 17 (2020).","ama":"Larsson J, Westram AM, Bengmark S, Lundh T, Butlin RK. A developmentally descriptive method for quantifying shape in gastropod shells. <i>Journal of The Royal Society Interface</i>. 2020;17(163). doi:<a href=\"https://doi.org/10.1098/rsif.2019.0721\">10.1098/rsif.2019.0721</a>","mla":"Larsson, J., et al. “A Developmentally Descriptive Method for Quantifying Shape in Gastropod Shells.” <i>Journal of The Royal Society Interface</i>, vol. 17, no. 163, 20190721, The Royal Society, 2020, doi:<a href=\"https://doi.org/10.1098/rsif.2019.0721\">10.1098/rsif.2019.0721</a>.","ieee":"J. Larsson, A. M. Westram, S. Bengmark, T. Lundh, and R. K. Butlin, “A developmentally descriptive method for quantifying shape in gastropod shells,” <i>Journal of The Royal Society Interface</i>, vol. 17, no. 163. The Royal Society, 2020.","apa":"Larsson, J., Westram, A. M., Bengmark, S., Lundh, T., &#38; Butlin, R. K. (2020). A developmentally descriptive method for quantifying shape in gastropod shells. <i>Journal of The Royal Society Interface</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rsif.2019.0721\">https://doi.org/10.1098/rsif.2019.0721</a>","chicago":"Larsson, J., Anja M Westram, S. Bengmark, T. Lundh, and R. K. Butlin. “A Developmentally Descriptive Method for Quantifying Shape in Gastropod Shells.” <i>Journal of The Royal Society Interface</i>. The Royal Society, 2020. <a href=\"https://doi.org/10.1098/rsif.2019.0721\">https://doi.org/10.1098/rsif.2019.0721</a>."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","volume":17,"date_created":"2020-04-08T15:19:17Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"scopus_import":1,"quality_controlled":"1","file":[{"content_type":"application/pdf","date_created":"2020-04-14T12:31:16Z","date_updated":"2020-07-14T12:48:01Z","file_name":"2020_JournRoyalSociety_Larsson.pdf","checksum":"4eb102304402f5c56432516b84df86d6","relation":"main_file","file_size":1556190,"creator":"dernst","access_level":"open_access","file_id":"7660"}],"language":[{"iso":"eng"}],"publication":"Journal of The Royal Society Interface","title":"A developmentally descriptive method for quantifying shape in gastropod shells","type":"journal_article","year":"2020","issue":"163","article_number":"20190721","date_published":"2020-02-01T00:00:00Z","intvolume":"        17","publication_identifier":{"eissn":["1742-5662"],"issn":["1742-5689"]},"department":[{"_id":"NiBa"}],"doi":"10.1098/rsif.2019.0721","article_processing_charge":"No","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."}],"_id":"7651","publication_status":"published","publisher":"The Royal Society","author":[{"last_name":"Larsson","full_name":"Larsson, J.","first_name":"J."},{"full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram"},{"full_name":"Bengmark, S.","first_name":"S.","last_name":"Bengmark"},{"last_name":"Lundh","full_name":"Lundh, T.","first_name":"T."},{"last_name":"Butlin","first_name":"R. K.","full_name":"Butlin, R. K."}],"day":"01","ddc":["570"],"has_accepted_license":"1","date_updated":"2021-01-12T08:14:41Z","month":"02","oa_version":"Published Version","file_date_updated":"2020-07-14T12:48:01Z","article_type":"original","oa":1},{"acknowledgement":"We are very grateful to I. Sencic, L. Brettell, A.‐L. Liabot, J. Galindo, M. Ravinet, and A. Butlin for their help with field sampling and mating experiments. This work was funded by the Natural Environment Research Council, European Research Council and Swedish Research Council VR and we are also very grateful for the support of the Linnaeus Centre for Marine Evolutionary Biology at the University of Gothenburg. The simulations were performed on resources at Chalmers Centre for Computational Science and Engineering (C3SE) provided by the Swedish National Infrastructure for Computing (SNIC). AMW was funded by the European Union's Horizon 2020 research and innovation program under Marie Skłodowska‐Curie grant agreement no. 797747.","month":"07","has_accepted_license":"1","date_updated":"2025-07-10T11:54:58Z","oa_version":"Published Version","file_date_updated":"2020-11-25T10:49:48Z","oa":1,"article_type":"original","doi":"10.1111/evo.14027","abstract":[{"lang":"eng","text":"When divergent populations are connected by gene flow, the establishment of complete reproductive isolation usually requires the joint action of multiple barrier effects. One example where multiple barrier effects are coupled consists of a single trait that is under divergent natural selection and also mediates assortative mating. Such multiple‐effect traits can strongly reduce gene flow. However, there are few cases where patterns of assortative mating have been described quantitatively and their impact on gene flow has been determined. Two ecotypes of the coastal marine snail, Littorina saxatilis , occur in North Atlantic rocky‐shore habitats dominated by either crab predation or wave action. There is evidence for divergent natural selection acting on size, and size‐assortative mating has previously been documented. Here, we analyze the mating pattern in L. saxatilis with respect to size in intensively sampled transects across boundaries between the habitats. We show that the mating pattern is mostly conserved between ecotypes and that it generates both assortment and directional sexual selection for small male size. Using simulations, we show that the mating pattern can contribute to reproductive isolation between ecotypes but the barrier to gene flow is likely strengthened more by sexual selection than by assortment."}],"article_processing_charge":"No","project":[{"_id":"265B41B8-B435-11E9-9278-68D0E5697425","name":"Theoretical and empirical approaches to understanding Parallel Adaptation","grant_number":"797747","call_identifier":"H2020"}],"day":"01","_id":"7995","external_id":{"isi":["000539780800001"]},"publication_status":"published","publisher":"Wiley","author":[{"last_name":"Perini","first_name":"Samuel","full_name":"Perini, Samuel"},{"last_name":"Rafajlović","full_name":"Rafajlović, Marina","first_name":"Marina"},{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","first_name":"Anja M","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969"},{"first_name":"Kerstin","full_name":"Johannesson, Kerstin","last_name":"Johannesson"},{"last_name":"Butlin","first_name":"Roger K.","full_name":"Butlin, Roger K."}],"ec_funded":1,"ddc":["570"],"date_published":"2020-07-01T00:00:00Z","page":"1482-1497","intvolume":"        74","isi":1,"publication_identifier":{"issn":["0014-3820"],"eissn":["1558-5646"]},"department":[{"_id":"NiBa"}],"status":"public","volume":74,"citation":{"short":"S. Perini, M. Rafajlović, A.M. Westram, K. Johannesson, R.K. Butlin, Evolution 74 (2020) 1482–1497.","ista":"Perini S, Rafajlović M, Westram AM, Johannesson K, Butlin RK. 2020. Assortative mating, sexual selection, and their consequences for gene flow in Littorina. Evolution. 74(7), 1482–1497.","mla":"Perini, Samuel, et al. “Assortative Mating, Sexual Selection, and Their Consequences for Gene Flow in Littorina.” <i>Evolution</i>, vol. 74, no. 7, Wiley, 2020, pp. 1482–97, doi:<a href=\"https://doi.org/10.1111/evo.14027\">10.1111/evo.14027</a>.","ama":"Perini S, Rafajlović M, Westram AM, Johannesson K, Butlin RK. Assortative mating, sexual selection, and their consequences for gene flow in Littorina. <i>Evolution</i>. 2020;74(7):1482-1497. doi:<a href=\"https://doi.org/10.1111/evo.14027\">10.1111/evo.14027</a>","apa":"Perini, S., Rafajlović, M., Westram, A. M., Johannesson, K., &#38; Butlin, R. K. (2020). Assortative mating, sexual selection, and their consequences for gene flow in Littorina. <i>Evolution</i>. Wiley. <a href=\"https://doi.org/10.1111/evo.14027\">https://doi.org/10.1111/evo.14027</a>","ieee":"S. Perini, M. Rafajlović, A. M. Westram, K. Johannesson, and R. K. Butlin, “Assortative mating, sexual selection, and their consequences for gene flow in Littorina,” <i>Evolution</i>, vol. 74, no. 7. Wiley, pp. 1482–1497, 2020.","chicago":"Perini, Samuel, Marina Rafajlović, Anja M Westram, Kerstin Johannesson, and Roger K. Butlin. “Assortative Mating, Sexual Selection, and Their Consequences for Gene Flow in Littorina.” <i>Evolution</i>. Wiley, 2020. <a href=\"https://doi.org/10.1111/evo.14027\">https://doi.org/10.1111/evo.14027</a>."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","quality_controlled":"1","related_material":{"record":[{"status":"public","id":"8809","relation":"research_data"}]},"date_created":"2020-06-22T09:14:21Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication":"Evolution","title":"Assortative mating, sexual selection, and their consequences for gene flow in Littorina","file":[{"file_size":1080810,"relation":"main_file","checksum":"56235bf1e2a9e25f96196bb13b6b754d","file_name":"2020_Evolution_Perini.pdf","date_updated":"2020-11-25T10:49:48Z","date_created":"2020-11-25T10:49:48Z","content_type":"application/pdf","access_level":"open_access","file_id":"8808","success":1,"creator":"dernst"}],"language":[{"iso":"eng"}],"type":"journal_article","year":"2020","issue":"7"},{"quality_controlled":"1","scopus_import":"1","date_created":"2020-07-13T03:41:39Z","volume":375,"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"N.H. Barton, Philosophical Transactions of the Royal Society. Series B: Biological Sciences 375 (2020).","ista":"Barton NH. 2020. On the completion of speciation. Philosophical Transactions of the Royal Society. Series B: Biological Sciences. 375(1806), 20190530.","mla":"Barton, Nicholas H. “On the Completion of Speciation.” <i>Philosophical Transactions of the Royal Society. Series B: Biological Sciences</i>, vol. 375, no. 1806, 20190530, The Royal Society, 2020, doi:<a href=\"https://doi.org/10.1098/rstb.2019.0530\">10.1098/rstb.2019.0530</a>.","ama":"Barton NH. On the completion of speciation. <i>Philosophical Transactions of the Royal Society Series B: Biological Sciences</i>. 2020;375(1806). doi:<a href=\"https://doi.org/10.1098/rstb.2019.0530\">10.1098/rstb.2019.0530</a>","apa":"Barton, N. H. (2020). On the completion of speciation. <i>Philosophical Transactions of the Royal Society. Series B: Biological Sciences</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rstb.2019.0530\">https://doi.org/10.1098/rstb.2019.0530</a>","ieee":"N. H. Barton, “On the completion of speciation,” <i>Philosophical Transactions of the Royal Society. Series B: Biological Sciences</i>, vol. 375, no. 1806. The Royal Society, 2020.","chicago":"Barton, Nicholas H. “On the Completion of Speciation.” <i>Philosophical Transactions of the Royal Society. Series B: Biological Sciences</i>. The Royal Society, 2020. <a href=\"https://doi.org/10.1098/rstb.2019.0530\">https://doi.org/10.1098/rstb.2019.0530</a>."},"pmid":1,"year":"2020","issue":"1806","type":"journal_article","title":"On the completion of speciation","publication":"Philosophical Transactions of the Royal Society. Series B: Biological Sciences","language":[{"iso":"eng"}],"intvolume":"       375","date_published":"2020-07-12T00:00:00Z","article_number":"20190530","department":[{"_id":"NiBa"}],"publication_identifier":{"issn":["0962-8436"],"eissn":["1471-2970"]},"isi":1,"OA_place":"repository","day":"12","publisher":"The Royal Society","_id":"8112","external_id":{"pmid":["32654647"],"isi":["000552662100002"]},"author":[{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","article_processing_charge":"No","doi":"10.1098/rstb.2019.0530","month":"07","date_updated":"2025-06-25T07:45:22Z","main_file_link":[{"open_access":"1","url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC7423282/"}],"OA_type":"green","article_type":"letter_note","oa":1,"oa_version":"Submitted Version"},{"acknowledgement":"Funding was provided by the Natural Environment Research Council (NERC) and the European Research Council. We thank Rui Faria, Nicola Nadeau, Martin Garlovsky and Hernan Morales for advice and/or useful discussion during the project. Richard Turney, Graciela Sotelo, Jenny Larson, Stéphane Loisel and Meghan Wharton participated in the collection and processing of samples. Mark Dunning helped with the development of bioinformatic pipelines. The analysis of genomic data was conducted on the University of Sheffield High-performance computer, ShARC. Jeffrey Feder and an anonymous reviewer provided comments that improved the manuscript.","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1098/rstb.2019.0545"}],"month":"07","date_updated":"2026-06-18T19:30:29Z","oa_version":"Published Version","oa":1,"article_type":"original","abstract":[{"text":"The evolution of strong reproductive isolation (RI) is fundamental to the origins and maintenance of biological diversity, especially in situations where geographical distributions of taxa broadly overlap. But what is the history behind strong barriers currently acting in sympatry? Using whole-genome sequencing and single nucleotide polymorphism genotyping, we inferred (i) the evolutionary relationships, (ii) the strength of RI, and (iii) the demographic history of divergence between two broadly sympatric taxa of intertidal snail. Despite being cryptic, based on external morphology, Littorina arcana and Littorina saxatilis differ in their mode of female reproduction (egg-laying versus brooding), which may generate a strong post-zygotic barrier. We show that egg-laying and brooding snails are closely related, but genetically distinct. Genotyping of 3092 snails from three locations failed to recover any recent hybrid or backcrossed individuals, confirming that RI is strong. There was, however, evidence for a very low level of asymmetrical introgression, suggesting that isolation remains incomplete. The presence of strong, asymmetrical RI was further supported by demographic analysis of these populations. Although the taxa are currently broadly sympatric, demographic modelling suggests that they initially diverged during a short period of geographical separation involving very low gene flow. Our study suggests that some geographical separation may kick-start the evolution of strong RI, facilitating subsequent coexistence of taxa in sympatry. The strength of RI needed to achieve sympatry and the subsequent effect of sympatry on RI remain open questions.","lang":"eng"}],"article_processing_charge":"No","doi":"10.1098/rstb.2019.0545","day":"12","publisher":"The Royal Society","_id":"8167","external_id":{"pmid":["32654639"],"isi":["000552662100014"]},"author":[{"last_name":"Stankowski","id":"43161670-5719-11EA-8025-FABC3DDC885E","first_name":"Sean","full_name":"Stankowski, Sean"},{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","first_name":"Anja M"},{"first_name":"Zuzanna B.","full_name":"Zagrodzka, Zuzanna B.","last_name":"Zagrodzka"},{"last_name":"Eyres","first_name":"Isobel","full_name":"Eyres, Isobel"},{"last_name":"Broquet","first_name":"Thomas","full_name":"Broquet, Thomas"},{"full_name":"Johannesson, Kerstin","first_name":"Kerstin","last_name":"Johannesson"},{"last_name":"Butlin","full_name":"Butlin, Roger K.","first_name":"Roger K."}],"publication_status":"published","ddc":["570"],"date_published":"2020-07-12T00:00:00Z","article_number":"20190545","intvolume":"       375","department":[{"_id":"NiBa"}],"publication_identifier":{"eissn":["1471-2970"]},"isi":1,"volume":375,"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Stankowski S, Westram AM, Zagrodzka ZB, et al. The evolution of strong reproductive isolation between sympatric intertidal snails. <i>Philosophical Transactions of the Royal Society Series B: Biological Sciences</i>. 2020;375(1806). doi:<a href=\"https://doi.org/10.1098/rstb.2019.0545\">10.1098/rstb.2019.0545</a>","mla":"Stankowski, Sean, et al. “The Evolution of Strong Reproductive Isolation between Sympatric Intertidal Snails.” <i>Philosophical Transactions of the Royal Society. Series B: Biological Sciences</i>, vol. 375, no. 1806, 20190545, The Royal Society, 2020, doi:<a href=\"https://doi.org/10.1098/rstb.2019.0545\">10.1098/rstb.2019.0545</a>.","ista":"Stankowski S, Westram AM, Zagrodzka ZB, Eyres I, Broquet T, Johannesson K, Butlin RK. 2020. The evolution of strong reproductive isolation between sympatric intertidal snails. Philosophical Transactions of the Royal Society. Series B: Biological Sciences. 375(1806), 20190545.","short":"S. Stankowski, A.M. Westram, Z.B. Zagrodzka, I. Eyres, T. Broquet, K. Johannesson, R.K. Butlin, Philosophical Transactions of the Royal Society. Series B: Biological Sciences 375 (2020).","chicago":"Stankowski, Sean, Anja M Westram, Zuzanna B. Zagrodzka, Isobel Eyres, Thomas Broquet, Kerstin Johannesson, and Roger K. Butlin. “The Evolution of Strong Reproductive Isolation between Sympatric Intertidal Snails.” <i>Philosophical Transactions of the Royal Society. Series B: Biological Sciences</i>. The Royal Society, 2020. <a href=\"https://doi.org/10.1098/rstb.2019.0545\">https://doi.org/10.1098/rstb.2019.0545</a>.","ieee":"S. Stankowski <i>et al.</i>, “The evolution of strong reproductive isolation between sympatric intertidal snails,” <i>Philosophical Transactions of the Royal Society. Series B: Biological Sciences</i>, vol. 375, no. 1806. The Royal Society, 2020.","apa":"Stankowski, S., Westram, A. M., Zagrodzka, Z. B., Eyres, I., Broquet, T., Johannesson, K., &#38; Butlin, R. K. (2020). The evolution of strong reproductive isolation between sympatric intertidal snails. <i>Philosophical Transactions of the Royal Society. Series B: Biological Sciences</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rstb.2019.0545\">https://doi.org/10.1098/rstb.2019.0545</a>"},"scopus_import":"1","quality_controlled":"1","date_created":"2020-07-26T22:01:01Z","title":"The evolution of strong reproductive isolation between sympatric intertidal snails","publication":"Philosophical Transactions of the Royal Society. Series B: Biological Sciences","language":[{"iso":"eng"}],"pmid":1,"issue":"1806","year":"2020","type":"journal_article"},{"ddc":["570"],"ec_funded":1,"_id":"8168","publisher":"The Royal Society","publication_status":"published","external_id":{"pmid":["32654637"],"isi":["000552662100001"]},"author":[{"full_name":"Kulmuni, Jonna","first_name":"Jonna","last_name":"Kulmuni"},{"last_name":"Butlin","first_name":"Roger K.","full_name":"Butlin, Roger K."},{"full_name":"Lucek, Kay","first_name":"Kay","last_name":"Lucek"},{"last_name":"Savolainen","first_name":"Vincent","full_name":"Savolainen, Vincent"},{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","first_name":"Anja M"}],"day":"12","project":[{"grant_number":"797747","call_identifier":"H2020","_id":"265B41B8-B435-11E9-9278-68D0E5697425","name":"Theoretical and empirical approaches to understanding Parallel Adaptation"}],"abstract":[{"text":"Speciation, that is, the evolution of reproductive barriers eventually leading to complete isolation, is a crucial process generating biodiversity. Recent work has contributed much to our understanding of how reproductive barriers begin to evolve, and how they are maintained in the face of gene flow. However, little is known about the transition from partial to strong reproductive isolation (RI) and the completion of speciation. We argue that the evolution of strong RI is likely to involve different processes, or new interactions among processes, compared with the evolution of the first reproductive barriers. Transition to strong RI may be brought about by changing external conditions, for example, following secondary contact. However, the increasing levels of RI themselves create opportunities for new barriers to evolve and, and interaction or coupling among barriers. These changing processes may depend on genomic architecture and leave detectable signals in the genome. We outline outstanding questions and suggest more theoretical and empirical work, considering both patterns and processes associated with strong RI, is needed to understand how speciation is completed.","lang":"eng"}],"article_processing_charge":"No","doi":"10.1098/rstb.2019.0528","oa":1,"article_type":"original","oa_version":"Published Version","date_updated":"2026-06-18T19:30:51Z","month":"07","main_file_link":[{"url":"https://doi.org/10.1098/rstb.2019.0528","open_access":"1"}],"type":"journal_article","issue":"1806","year":"2020","pmid":1,"language":[{"iso":"eng"}],"title":"Towards the completion of speciation: The evolution of reproductive isolation beyond the first barriers","publication":"Philosophical Transactions of the Royal Society. Series B: Biological sciences","date_created":"2020-07-26T22:01:01Z","scopus_import":"1","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Kulmuni J, Butlin RK, Lucek K, Savolainen V, Westram AM. Towards the completion of speciation: The evolution of reproductive isolation beyond the first barriers. <i>Philosophical Transactions of the Royal Society Series B: Biological sciences</i>. 2020;375(1806). doi:<a href=\"https://doi.org/10.1098/rstb.2019.0528\">10.1098/rstb.2019.0528</a>","mla":"Kulmuni, Jonna, et al. “Towards the Completion of Speciation: The Evolution of Reproductive Isolation beyond the First Barriers.” <i>Philosophical Transactions of the Royal Society. Series B: Biological Sciences</i>, vol. 375, no. 1806, 20190528, The Royal Society, 2020, doi:<a href=\"https://doi.org/10.1098/rstb.2019.0528\">10.1098/rstb.2019.0528</a>.","short":"J. Kulmuni, R.K. Butlin, K. Lucek, V. Savolainen, A.M. Westram, Philosophical Transactions of the Royal Society. Series B: Biological Sciences 375 (2020).","ista":"Kulmuni J, Butlin RK, Lucek K, Savolainen V, Westram AM. 2020. Towards the completion of speciation: The evolution of reproductive isolation beyond the first barriers. Philosophical Transactions of the Royal Society. Series B: Biological sciences. 375(1806), 20190528.","chicago":"Kulmuni, Jonna, Roger K. Butlin, Kay Lucek, Vincent Savolainen, and Anja M Westram. “Towards the Completion of Speciation: The Evolution of Reproductive Isolation beyond the First Barriers.” <i>Philosophical Transactions of the Royal Society. Series B: Biological Sciences</i>. The Royal Society, 2020. <a href=\"https://doi.org/10.1098/rstb.2019.0528\">https://doi.org/10.1098/rstb.2019.0528</a>.","ieee":"J. Kulmuni, R. K. Butlin, K. Lucek, V. Savolainen, and A. M. Westram, “Towards the completion of speciation: The evolution of reproductive isolation beyond the first barriers,” <i>Philosophical Transactions of the Royal Society. Series B: Biological sciences</i>, vol. 375, no. 1806. The Royal Society, 2020.","apa":"Kulmuni, J., Butlin, R. K., Lucek, K., Savolainen, V., &#38; Westram, A. M. (2020). Towards the completion of speciation: The evolution of reproductive isolation beyond the first barriers. <i>Philosophical Transactions of the Royal Society. Series B: Biological Sciences</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rstb.2019.0528\">https://doi.org/10.1098/rstb.2019.0528</a>"},"volume":375,"status":"public","publication_identifier":{"issn":["0962-8436"],"eissn":["1471-2970"]},"department":[{"_id":"NiBa"}],"isi":1,"intvolume":"       375","date_published":"2020-07-12T00:00:00Z","article_number":"20190528"},{"_id":"8169","publisher":"The Royal Society","author":[{"last_name":"Shang","first_name":"Huiying","full_name":"Shang, Huiying"},{"last_name":"Hess","full_name":"Hess, Jaqueline","first_name":"Jaqueline"},{"orcid":"0000-0001-6118-0541","full_name":"Pickup, Melinda","first_name":"Melinda","last_name":"Pickup","id":"2C78037E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478","full_name":"Field, David","first_name":"David"},{"first_name":"Pär K.","full_name":"Ingvarsson, Pär K.","last_name":"Ingvarsson"},{"full_name":"Liu, Jianquan","first_name":"Jianquan","last_name":"Liu"},{"first_name":"Christian","full_name":"Lexer, Christian","last_name":"Lexer"}],"publication_status":"published","external_id":{"pmid":["32654641"],"isi":["000552662100013"]},"day":"12","abstract":[{"text":"Many recent studies have addressed the mechanisms operating during the early stages of speciation, but surprisingly few studies have tested theoretical predictions on the evolution of strong reproductive isolation (RI). To help address this gap, we first undertook a quantitative review of the hybrid zone literature for flowering plants in relation to reproductive barriers. Then, using Populus as an exemplary model group, we analysed genome-wide variation for phylogenetic tree topologies in both early- and late-stage speciation taxa to determine how these patterns may be related to the genomic architecture of RI. Our plant literature survey revealed variation in barrier complexity and an association between barrier number and introgressive gene flow. Focusing on Populus, our genome-wide analysis of tree topologies in speciating poplar taxa points to unusually complex genomic architectures of RI, consistent with earlier genome-wide association studies. These architectures appear to facilitate the ‘escape’ of introgressed genome segments from polygenic barriers even with strong RI, thus affecting their relationships with recombination rates. Placed within the context of the broader literature, our data illustrate how phylogenomic approaches hold great promise for addressing the evolution and temporary breakdown of RI during late stages of speciation.","lang":"eng"}],"article_processing_charge":"No","doi":"10.1098/rstb.2019.0544","date_updated":"2026-04-03T09:31:37Z","month":"07","OA_type":"closed access","acknowledgement":"This work was supported by a fellowship from the China Scholarship Council (CSC) to H.S., Swiss National Science Foundation (SNF) grant no. 31003A_149306 to C.L., doctoral programme grant W1225-B20 to a faculty team including C.L., and the University of Vienna. We thank members of J.L.’s lab for collecting samples, Michael Barfuss and Elfi Grasserbauer for help in the laboratory, the Next Generation Sequencing Platform of the University of Berne for sequencing, the Vienna Scientific Cluster (VSC) for access to computational resources, and Claus Vogel and members of the PopGen Vienna graduate school for helpful discussions.","article_type":"original","oa_version":"None","date_created":"2020-07-26T22:01:02Z","scopus_import":"1","quality_controlled":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"chicago":"Shang, Huiying, Jaqueline Hess, Melinda Pickup, David Field, Pär K. Ingvarsson, Jianquan Liu, and Christian Lexer. “Evolution of Strong Reproductive Isolation in Plants: Broad-Scale Patterns and Lessons from a Perennial Model Group.” <i>Philosophical Transactions of the Royal Society. Series B: Biological Sciences</i>. The Royal Society, 2020. <a href=\"https://doi.org/10.1098/rstb.2019.0544\">https://doi.org/10.1098/rstb.2019.0544</a>.","apa":"Shang, H., Hess, J., Pickup, M., Field, D., Ingvarsson, P. K., Liu, J., &#38; Lexer, C. (2020). Evolution of strong reproductive isolation in plants: Broad-scale patterns and lessons from a perennial model group. <i>Philosophical Transactions of the Royal Society. Series B: Biological Sciences</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rstb.2019.0544\">https://doi.org/10.1098/rstb.2019.0544</a>","ieee":"H. Shang <i>et al.</i>, “Evolution of strong reproductive isolation in plants: Broad-scale patterns and lessons from a perennial model group,” <i>Philosophical Transactions of the Royal Society. Series B: Biological Sciences</i>, vol. 375, no. 1806. The Royal Society, 2020.","mla":"Shang, Huiying, et al. “Evolution of Strong Reproductive Isolation in Plants: Broad-Scale Patterns and Lessons from a Perennial Model Group.” <i>Philosophical Transactions of the Royal Society. Series B: Biological Sciences</i>, vol. 375, no. 1806, 20190544, The Royal Society, 2020, doi:<a href=\"https://doi.org/10.1098/rstb.2019.0544\">10.1098/rstb.2019.0544</a>.","ama":"Shang H, Hess J, Pickup M, et al. Evolution of strong reproductive isolation in plants: Broad-scale patterns and lessons from a perennial model group. <i>Philosophical Transactions of the Royal Society Series B: Biological Sciences</i>. 2020;375(1806). doi:<a href=\"https://doi.org/10.1098/rstb.2019.0544\">10.1098/rstb.2019.0544</a>","short":"H. Shang, J. Hess, M. Pickup, D. Field, P.K. Ingvarsson, J. Liu, C. Lexer, Philosophical Transactions of the Royal Society. Series B: Biological Sciences 375 (2020).","ista":"Shang H, Hess J, Pickup M, Field D, Ingvarsson PK, Liu J, Lexer C. 2020. Evolution of strong reproductive isolation in plants: Broad-scale patterns and lessons from a perennial model group. Philosophical Transactions of the Royal Society. Series B: Biological Sciences. 375(1806), 20190544."},"volume":375,"status":"public","type":"journal_article","issue":"1806","year":"2020","pmid":1,"language":[{"iso":"eng"}],"title":"Evolution of strong reproductive isolation in plants: Broad-scale patterns and lessons from a perennial model group","publication":"Philosophical Transactions of the Royal Society. Series B: Biological Sciences","intvolume":"       375","date_published":"2020-07-12T00:00:00Z","article_number":"20190544","publication_identifier":{"eissn":["1471-2970"]},"department":[{"_id":"NiBa"}],"isi":1},{"contributor":[{"last_name":"Arathoon","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","contributor_type":"data_collector","first_name":"Louise S"},{"contributor_type":"project_member","first_name":"Parvathy","id":"455235B8-F248-11E8-B48F-1D18A9856A87","last_name":"Surendranadh"},{"first_name":"Nicholas H","contributor_type":"project_member","orcid":"0000-0002-8548-5240","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David","contributor_type":"project_member","orcid":"0000-0002-4014-8478"},{"contributor_type":"project_member","first_name":"Melinda","orcid":"0000-0001-6118-0541","last_name":"Pickup","id":"2C78037E-F248-11E8-B48F-1D18A9856A87"},{"id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","last_name":"Baskett","contributor_type":"project_member","first_name":"Carina"}],"oa_version":"Published Version","file_date_updated":"2020-08-18T08:03:23Z","department":[{"_id":"NiBa"}],"oa":1,"date_published":"2020-08-18T00:00:00Z","month":"08","date_updated":"2024-10-09T21:02:14Z","has_accepted_license":"1","title":"Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus)","corr_author":"1","file":[{"file_name":"Data_Rcode_MathematicaNB.zip","checksum":"4f1382ed4384751b6013398c11557bf6","file_size":5778420,"relation":"main_file","content_type":"application/x-zip-compressed","date_created":"2020-08-18T08:03:23Z","date_updated":"2020-08-18T08:03:23Z","success":1,"access_level":"open_access","file_id":"8280","creator":"dernst"}],"type":"research_data","year":"2020","ddc":["576"],"article_processing_charge":"No","abstract":[{"text":"Here are the research data underlying the publication \"Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus)\". Further information are summed up in the README document.\r\nThe files for this record have been updated and are now found in the linked DOI https://doi.org/10.15479/AT:ISTA:9192.","lang":"eng"}],"status":"public","doi":"10.15479/AT:ISTA:8254","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"L.S. Arathoon, (2020).","ista":"Arathoon LS. 2020. Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus), Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:8254\">10.15479/AT:ISTA:8254</a>.","ama":"Arathoon LS. Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus). 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8254\">10.15479/AT:ISTA:8254</a>","mla":"Arathoon, Louise S. <i>Estimating Inbreeding and Its Effects in a Long-Term Study of Snapdragons (Antirrhinum Majus)</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8254\">10.15479/AT:ISTA:8254</a>.","ieee":"L. S. Arathoon, “Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus).” Institute of Science and Technology Austria, 2020.","apa":"Arathoon, L. S. (2020). Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus). Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8254\">https://doi.org/10.15479/AT:ISTA:8254</a>","chicago":"Arathoon, Louise S. “Estimating Inbreeding and Its Effects in a Long-Term Study of Snapdragons (Antirrhinum Majus).” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8254\">https://doi.org/10.15479/AT:ISTA:8254</a>."},"day":"18","related_material":{"record":[{"relation":"later_version","status":"public","id":"9192"},{"id":"11321","status":"public","relation":"later_version"}]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"last_name":"Arathoon","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","first_name":"Louise S","orcid":"0000-0003-1771-714X","full_name":"Arathoon, Louise S"}],"_id":"8254","publisher":"Institute of Science and Technology Austria","date_created":"2020-08-12T12:49:23Z"},{"file_date_updated":"2020-09-28T07:25:37Z","oa_version":"Published Version","oa":1,"has_accepted_license":"1","date_updated":"2026-04-08T07:21:44Z","month":"09","ddc":["570"],"doi":"10.15479/AT:ISTA:8574","article_processing_charge":"No","abstract":[{"lang":"eng","text":"This thesis concerns itself with the interactions of evolutionary and ecological forces and the consequences on genetic diversity and the ultimate survival of populations. It is important to understand what signals processes \r\nleave on the genome and what we can infer from such data, which is usually abundant but noisy. Furthermore, understanding how and when populations adapt or go extinct is important for practical purposes,  such as the genetic management of populations, as well as for theoretical questions, since local adaptation can be the first step toward speciation. \r\nIn Chapter 2, we introduce the method of maximum entropy to approximate the demographic changes of a population in a simple setting, namely the logistic growth model with immigration. We show that this method is not only a powerful \r\ntool in physics but can be gainfully applied in an ecological framework. We investigate how well it approximates the real \r\nbehavior of the system, and find that is does so, even in unexpected situations. Finally, we illustrate how it can model changing environments.\r\nIn Chapter 3, we analyze the co-evolution of allele frequencies and population sizes in an infinite island model.\r\nWe give conditions under which polygenic adaptation to a rare habitat is possible. The model we use is based on the diffusion approximation, considers eco-evolutionary feedback mechanisms (hard selection), and treats both \r\ndrift and environmental fluctuations explicitly. We also look at limiting scenarios, for which we derive analytical expressions. \r\nIn Chapter 4, we present a coalescent based simulation tool to obtain patterns of diversity in a spatially explicit subdivided population, in which the demographic history of each subpopulation can be specified. We compare \r\nthe results to existing predictions, and explore the relative importance of time and space under a variety of spatial arrangements and demographic histories, such as expansion and extinction. \r\nIn the last chapter, we give a brief outlook to further research. "}],"publisher":"Institute of Science and Technology Austria","_id":"8574","author":[{"first_name":"Eniko","full_name":"Szep, Eniko","id":"485BB5A4-F248-11E8-B48F-1D18A9856A87","last_name":"Szep"}],"publication_status":"published","day":"20","OA_place":"publisher","supervisor":[{"last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H"}],"publication_identifier":{"eissn":["2663-337X"]},"department":[{"_id":"NiBa"}],"page":"158","alternative_title":["ISTA Thesis"],"date_published":"2020-09-20T00:00:00Z","file":[{"access_level":"open_access","file_id":"8575","success":1,"creator":"dernst","relation":"main_file","file_size":6354833,"checksum":"20e71f015fbbd78fea708893ad634ed0","file_name":"thesis_EnikoSzep_final.pdf","date_updated":"2020-09-28T07:25:35Z","date_created":"2020-09-28T07:25:35Z","content_type":"application/pdf"},{"file_id":"8576","access_level":"closed","creator":"dernst","file_size":23020401,"relation":"source_file","file_name":"thesisFiles_EnikoSzep.zip","checksum":"a8de2c14a1bb4e53c857787efbb289e1","date_created":"2020-09-28T07:25:37Z","date_updated":"2020-09-28T07:25:37Z","content_type":"application/x-zip-compressed"}],"language":[{"iso":"eng"}],"corr_author":"1","title":"Local adaptation in metapopulations","type":"dissertation","year":"2020","citation":{"chicago":"Szep, Eniko. “Local Adaptation in Metapopulations.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8574\">https://doi.org/10.15479/AT:ISTA:8574</a>.","ieee":"E. Szep, “Local adaptation in metapopulations,” Institute of Science and Technology Austria, 2020.","apa":"Szep, E. (2020). <i>Local adaptation in metapopulations</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8574\">https://doi.org/10.15479/AT:ISTA:8574</a>","ama":"Szep E. Local adaptation in metapopulations. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8574\">10.15479/AT:ISTA:8574</a>","mla":"Szep, Eniko. <i>Local Adaptation in Metapopulations</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8574\">10.15479/AT:ISTA:8574</a>.","ista":"Szep E. 2020. Local adaptation in metapopulations. Institute of Science and Technology Austria.","short":"E. Szep, Local Adaptation in Metapopulations, Institute of Science and Technology Austria, 2020."},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","status":"public","date_created":"2020-09-28T07:33:38Z","degree_awarded":"PhD"},{"citation":{"ista":"Perini S, Rafajlovic M, Westram AM, Johannesson K, Butlin R. 2020. Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina, Dryad, <a href=\"https://doi.org/10.5061/dryad.qrfj6q5cn\">10.5061/dryad.qrfj6q5cn</a>.","short":"S. Perini, M. Rafajlovic, A.M. Westram, K. Johannesson, R. Butlin, (2020).","mla":"Perini, Samuel, et al. <i>Data from: Assortative Mating, Sexual Selection and Their Consequences for Gene Flow in Littorina</i>. Dryad, 2020, doi:<a href=\"https://doi.org/10.5061/dryad.qrfj6q5cn\">10.5061/dryad.qrfj6q5cn</a>.","ama":"Perini S, Rafajlovic M, Westram AM, Johannesson K, Butlin R. Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina. 2020. doi:<a href=\"https://doi.org/10.5061/dryad.qrfj6q5cn\">10.5061/dryad.qrfj6q5cn</a>","apa":"Perini, S., Rafajlovic, M., Westram, A. M., Johannesson, K., &#38; Butlin, R. (2020). Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina. Dryad. <a href=\"https://doi.org/10.5061/dryad.qrfj6q5cn\">https://doi.org/10.5061/dryad.qrfj6q5cn</a>","ieee":"S. Perini, M. Rafajlovic, A. M. Westram, K. Johannesson, and R. Butlin, “Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina.” Dryad, 2020.","chicago":"Perini, Samuel, Marina Rafajlovic, Anja M Westram, Kerstin Johannesson, and Roger Butlin. “Data from: Assortative Mating, Sexual Selection and Their Consequences for Gene Flow in Littorina.” Dryad, 2020. <a href=\"https://doi.org/10.5061/dryad.qrfj6q5cn\">https://doi.org/10.5061/dryad.qrfj6q5cn</a>."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","doi":"10.5061/dryad.qrfj6q5cn","status":"public","article_processing_charge":"No","abstract":[{"text":"When divergent populations are connected by gene flow, the establishment of complete reproductive isolation usually requires the joint action of multiple barrier effects. One example where multiple barrier effects are coupled consists of a single trait that is under divergent natural selection and also mediates assortative mating. Such multiple-effect traits can strongly reduce gene flow. However, there are few cases where patterns of assortative mating have been described quantitatively and their impact on gene flow has been determined. Two ecotypes of the coastal marine snail, Littorina saxatilis, occur in North Atlantic rocky-shore habitats dominated by either crab predation or wave action. There is evidence for divergent natural selection acting on size, and size-assortative mating has previously been documented. Here, we analyze the mating pattern in L. saxatilis with respect to size in intensively-sampled transects across boundaries between the habitats. We show that the mating pattern is mostly conserved between ecotypes and that it generates both assortment and directional sexual selection for small male size. Using simulations, we show that the mating pattern can contribute to reproductive isolation between ecotypes but the barrier to gene flow is likely strengthened more by sexual selection than by assortment.","lang":"eng"}],"_id":"8809","tmp":{"legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","short":"CC0 (1.0)","name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png"},"publisher":"Dryad","date_created":"2020-11-25T11:07:25Z","author":[{"last_name":"Perini","first_name":"Samuel","full_name":"Perini, Samuel"},{"last_name":"Rafajlovic","first_name":"Marina","full_name":"Rafajlovic, Marina"},{"last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","first_name":"Anja M"},{"full_name":"Johannesson, Kerstin","first_name":"Kerstin","last_name":"Johannesson"},{"last_name":"Butlin","full_name":"Butlin, Roger","first_name":"Roger"}],"related_material":{"record":[{"id":"7995","status":"public","relation":"used_in_publication"}]},"day":"01","title":"Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina","year":"2020","type":"research_data_reference","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.qrfj6q5cn"}],"date_published":"2020-07-01T00:00:00Z","has_accepted_license":"1","date_updated":"2025-07-10T11:54:59Z","month":"07","oa_version":"Published Version","oa":1,"department":[{"_id":"NiBa"}]},{"year":"2020","type":"book_chapter","language":[{"iso":"eng"}],"title":"Inversions and Evolution","publication":"eLS","author":[{"first_name":"Anja M","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Rui","full_name":"Faria, Rui","last_name":"Faria"},{"first_name":"Roger","full_name":"Butlin, Roger","last_name":"Butlin"},{"last_name":"Johannesson","first_name":"Kerstin","full_name":"Johannesson, Kerstin"}],"_id":"9123","date_created":"2021-02-15T12:39:04Z","publisher":"Wiley","publication_status":"published","day":"16","quality_controlled":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"mla":"Westram, Anja M., et al. “Inversions and Evolution.” <i>ELS</i>, Wiley, 2020, doi:<a href=\"https://doi.org/10.1002/9780470015902.a0029007\">10.1002/9780470015902.a0029007</a>.","ama":"Westram AM, Faria R, Butlin R, Johannesson K. Inversions and Evolution. In: <i>ELS</i>. Wiley; 2020. doi:<a href=\"https://doi.org/10.1002/9780470015902.a0029007\">10.1002/9780470015902.a0029007</a>","short":"A.M. Westram, R. Faria, R. Butlin, K. Johannesson, in:, ELS, Wiley, 2020.","ista":"Westram AM, Faria R, Butlin R, Johannesson K. 2020.Inversions and Evolution. In: eLS. .","chicago":"Westram, Anja M, Rui Faria, Roger Butlin, and Kerstin Johannesson. “Inversions and Evolution.” In <i>ELS</i>. Wiley, 2020. <a href=\"https://doi.org/10.1002/9780470015902.a0029007\">https://doi.org/10.1002/9780470015902.a0029007</a>.","apa":"Westram, A. M., Faria, R., Butlin, R., &#38; Johannesson, K. (2020). Inversions and Evolution. In <i>eLS</i>. Wiley. <a href=\"https://doi.org/10.1002/9780470015902.a0029007\">https://doi.org/10.1002/9780470015902.a0029007</a>","ieee":"A. M. Westram, R. Faria, R. Butlin, and K. Johannesson, “Inversions and Evolution,” in <i>eLS</i>, Wiley, 2020."},"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."}],"article_processing_charge":"No","doi":"10.1002/9780470015902.a0029007","status":"public","department":[{"_id":"NiBa"}],"publication_identifier":{"eissn":["9780470015902"],"isbn":["9780470016176"]},"oa_version":"None","date_updated":"2026-04-16T10:25:26Z","month":"05","date_published":"2020-05-16T00:00:00Z"},{"year":"2020","type":"research_data_reference","title":"Simulation code for Fig S2 from the distribution of epistasis on simple fitness landscapes","related_material":{"record":[{"relation":"used_in_publication","id":"6467","status":"public"}]},"day":"15","date_created":"2021-08-06T11:18:15Z","_id":"9798","publisher":"Royal Society of London","author":[{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse","full_name":"Fraisse, Christelle","orcid":"0000-0001-8441-5075","first_name":"Christelle"},{"last_name":"Welch","first_name":"John J.","full_name":"Welch, John J."}],"status":"public","doi":"10.6084/m9.figshare.7957472.v1","article_processing_charge":"No","abstract":[{"text":"Fitness interactions between mutations can influence a population’s evolution in many different ways. While epistatic effects are difficult to measure precisely, important information is captured by the mean and variance of log fitnesses for individuals carrying different numbers of mutations. We derive predictions for these quantities from a class of simple fitness landscapes, based on models of optimizing selection on quantitative traits. We also explore extensions to the models, including modular pleiotropy, variable effect sizes, mutational bias and maladaptation of the wild type. We illustrate our approach by reanalysing a large dataset of mutant effects in a yeast snoRNA. Though characterized by some large epistatic effects, these data give a good overall fit to the non-epistatic null model, suggesting that epistasis might have limited influence on the evolutionary dynamics in this system. We also show how the amount of epistasis depends on both the underlying fitness landscape and the distribution of mutations, and so is expected to vary in consistent ways between new mutations, standing variation and fixed mutations.","lang":"eng"}],"user_id":"0043cee0-e5fc-11ee-9736-f83bc23afbf0","citation":{"ieee":"C. Fraisse and J. J. Welch, “Simulation code for Fig S2 from the distribution of epistasis on simple fitness landscapes.” Royal Society of London, 2020.","apa":"Fraisse, C., &#38; Welch, J. J. (2020). Simulation code for Fig S2 from the distribution of epistasis on simple fitness landscapes. Royal Society of London. <a href=\"https://doi.org/10.6084/m9.figshare.7957472.v1\">https://doi.org/10.6084/m9.figshare.7957472.v1</a>","chicago":"Fraisse, Christelle, and John J. Welch. “Simulation Code for Fig S2 from the Distribution of Epistasis on Simple Fitness Landscapes.” Royal Society of London, 2020. <a href=\"https://doi.org/10.6084/m9.figshare.7957472.v1\">https://doi.org/10.6084/m9.figshare.7957472.v1</a>.","ista":"Fraisse C, Welch JJ. 2020. Simulation code for Fig S2 from the distribution of epistasis on simple fitness landscapes, Royal Society of London, <a href=\"https://doi.org/10.6084/m9.figshare.7957472.v1\">10.6084/m9.figshare.7957472.v1</a>.","short":"C. Fraisse, J.J. Welch, (2020).","ama":"Fraisse C, Welch JJ. Simulation code for Fig S2 from the distribution of epistasis on simple fitness landscapes. 2020. doi:<a href=\"https://doi.org/10.6084/m9.figshare.7957472.v1\">10.6084/m9.figshare.7957472.v1</a>","mla":"Fraisse, Christelle, and John J. Welch. <i>Simulation Code for Fig S2 from the Distribution of Epistasis on Simple Fitness Landscapes</i>. Royal Society of London, 2020, doi:<a href=\"https://doi.org/10.6084/m9.figshare.7957472.v1\">10.6084/m9.figshare.7957472.v1</a>."},"oa":1,"department":[{"_id":"BeVi"},{"_id":"NiBa"}],"OA_place":"publisher","oa_version":"Published Version","month":"10","date_updated":"2026-06-18T19:05:02Z","date_published":"2020-10-15T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.7957472.v1"}],"OA_type":"hybrid"},{"title":"Simulation code for Fig S1 from the distribution of epistasis on simple fitness landscapes","year":"2020","type":"research_data_reference","abstract":[{"lang":"eng","text":"Fitness interactions between mutations can influence a population’s evolution in many different ways. While epistatic effects are difficult to measure precisely, important information is captured by the mean and variance of log fitnesses for individuals carrying different numbers of mutations. We derive predictions for these quantities from a class of simple fitness landscapes, based on models of optimizing selection on quantitative traits. We also explore extensions to the models, including modular pleiotropy, variable effect sizes, mutational bias and maladaptation of the wild type. We illustrate our approach by reanalysing a large dataset of mutant effects in a yeast snoRNA. Though characterized by some large epistatic effects, these data give a good overall fit to the non-epistatic null model, suggesting that epistasis might have limited influence on the evolutionary dynamics in this system. We also show how the amount of epistasis depends on both the underlying fitness landscape and the distribution of mutations, and so is expected to vary in consistent ways between new mutations, standing variation and fixed mutations."}],"article_processing_charge":"No","doi":"10.6084/m9.figshare.7957469.v1","status":"public","citation":{"short":"C. Fraisse, J.J. Welch, (2020).","ista":"Fraisse C, Welch JJ. 2020. Simulation code for Fig S1 from the distribution of epistasis on simple fitness landscapes, Royal Society of London, <a href=\"https://doi.org/10.6084/m9.figshare.7957469.v1\">10.6084/m9.figshare.7957469.v1</a>.","ama":"Fraisse C, Welch JJ. Simulation code for Fig S1 from the distribution of epistasis on simple fitness landscapes. 2020. doi:<a href=\"https://doi.org/10.6084/m9.figshare.7957469.v1\">10.6084/m9.figshare.7957469.v1</a>","mla":"Fraisse, Christelle, and John J. Welch. <i>Simulation Code for Fig S1 from the Distribution of Epistasis on Simple Fitness Landscapes</i>. Royal Society of London, 2020, doi:<a href=\"https://doi.org/10.6084/m9.figshare.7957469.v1\">10.6084/m9.figshare.7957469.v1</a>.","ieee":"C. Fraisse and J. J. Welch, “Simulation code for Fig S1 from the distribution of epistasis on simple fitness landscapes.” Royal Society of London, 2020.","apa":"Fraisse, C., &#38; Welch, J. J. (2020). Simulation code for Fig S1 from the distribution of epistasis on simple fitness landscapes. Royal Society of London. <a href=\"https://doi.org/10.6084/m9.figshare.7957469.v1\">https://doi.org/10.6084/m9.figshare.7957469.v1</a>","chicago":"Fraisse, Christelle, and John J. Welch. “Simulation Code for Fig S1 from the Distribution of Epistasis on Simple Fitness Landscapes.” Royal Society of London, 2020. <a href=\"https://doi.org/10.6084/m9.figshare.7957469.v1\">https://doi.org/10.6084/m9.figshare.7957469.v1</a>."},"user_id":"0043cee0-e5fc-11ee-9736-f83bc23afbf0","day":"15","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"6467"}]},"publisher":"Royal Society of London","_id":"9799","date_created":"2021-08-06T11:26:57Z","author":[{"last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle","first_name":"Christelle"},{"first_name":"John J.","full_name":"Welch, John J.","last_name":"Welch"}],"OA_place":"publisher","oa_version":"Published Version","oa":1,"department":[{"_id":"BeVi"},{"_id":"NiBa"}],"date_published":"2020-10-15T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.7957469.v1"}],"OA_type":"hybrid","month":"10","date_updated":"2026-06-18T19:05:02Z"}]