[{"publisher":"Dryad","year":"2021","author":[{"first_name":"Eva","full_name":"Koch, Eva","last_name":"Koch"},{"first_name":"Hernán E.","last_name":"Morales","full_name":"Morales, Hernán E."},{"last_name":"Larsson","full_name":"Larsson, Jenny","first_name":"Jenny"},{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","last_name":"Westram"},{"first_name":"Rui","full_name":"Faria, Rui","last_name":"Faria"},{"first_name":"Alan R.","last_name":"Lemmon","full_name":"Lemmon, Alan R."},{"first_name":"E. Moriarty","last_name":"Lemmon","full_name":"Lemmon, E. Moriarty"},{"full_name":"Johannesson, Kerstin","last_name":"Johannesson","first_name":"Kerstin"},{"first_name":"Roger K.","full_name":"Butlin, Roger K.","last_name":"Butlin"}],"type":"research_data_reference","OA_place":"publisher","status":"public","fulldoi":"https://doi.org/10.5061/DRYAD.ZGMSBCCB4","citation":{"ista":"Koch E, Morales HE, Larsson J, Westram AM, Faria R, Lemmon AR, Lemmon EM, Johannesson K, Butlin RK. 2021. Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis, Dryad, <a href=\"https://doi.org/10.5061/DRYAD.ZGMSBCCB4\">10.5061/DRYAD.ZGMSBCCB4</a>.","ieee":"E. Koch <i>et al.</i>, “Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis.” Dryad, 2021.","chicago":"Koch, Eva, Hernán E. Morales, Jenny Larsson, Anja M Westram, Rui Faria, Alan R. Lemmon, E. Moriarty Lemmon, Kerstin Johannesson, and Roger K. Butlin. “Data from: Genetic Variation for Adaptive Traits Is Associated with Polymorphic Inversions in Littorina Saxatilis.” Dryad, 2021. <a href=\"https://doi.org/10.5061/DRYAD.ZGMSBCCB4\">https://doi.org/10.5061/DRYAD.ZGMSBCCB4</a>.","ama":"Koch E, Morales HE, Larsson J, et al. Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis. 2021. doi:<a href=\"https://doi.org/10.5061/DRYAD.ZGMSBCCB4\">10.5061/DRYAD.ZGMSBCCB4</a>","apa":"Koch, E., Morales, H. E., Larsson, J., Westram, A. M., Faria, R., Lemmon, A. R., … Butlin, R. K. (2021). Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis. Dryad. <a href=\"https://doi.org/10.5061/DRYAD.ZGMSBCCB4\">https://doi.org/10.5061/DRYAD.ZGMSBCCB4</a>","mla":"Koch, Eva, et al. <i>Data from: Genetic Variation for Adaptive Traits Is Associated with Polymorphic Inversions in Littorina Saxatilis</i>. Dryad, 2021, doi:<a href=\"https://doi.org/10.5061/DRYAD.ZGMSBCCB4\">10.5061/DRYAD.ZGMSBCCB4</a>.","short":"E. Koch, H.E. Morales, J. Larsson, A.M. Westram, R. Faria, A.R. Lemmon, E.M. Lemmon, K. Johannesson, R.K. Butlin, (2021)."},"article_processing_charge":"No","oa_version":"Published Version","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_created":"2023-05-16T12:34:09Z","related_material":{"record":[{"relation":"used_in_publication","id":"9394","status":"public"}]},"_id":"12987","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.zgmsbccb4"}],"ddc":["570"],"doi":"10.5061/DRYAD.ZGMSBCCB4","month":"04","has_accepted_license":"1","date_updated":"2026-04-07T14:01:30Z","department":[{"_id":"NiBa"}],"date_published":"2021-04-10T00:00:00Z","oa":1,"tmp":{"name":"Creative Commons Public Domain Dedication (CC0 1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","short":"CC0 (1.0)","image":"/images/cc_0.png"},"day":"10","abstract":[{"lang":"eng","text":"Chromosomal inversion polymorphisms, segments of chromosomes that are flipped in orientation and occur in reversed order in some individuals, have long been recognized to play an important role in local adaptation. They can reduce recombination in heterozygous individuals and thus help to maintain sets of locally adapted alleles. In a wide range of organisms, populations adapted to different habitats differ in frequency of inversion arrangements. However, getting a full understanding of the importance of inversions for adaptation requires confirmation of their influence on traits under divergent selection. Here, we studied a marine snail, Littorina saxatilis, that has evolved ecotypes adapted to wave exposure or crab predation. These two types occur in close proximity on different parts of the shore. Gene flow between them exists in contact zones. However, they exhibit strong phenotypic divergence in several traits under habitat-specific selection, including size, shape and behaviour. We used crosses between these ecotypes to identify genomic regions that explain variation in these traits by using QTL analysis and variance partitioning across linkage groups. We could show that previously detected inversion regions contribute to adaptive divergence. Some inversions influenced multiple traits suggesting that they contain sets of locally adaptive alleles. Our study also identified regions without known inversions that are important for phenotypic divergence. Thus, we provide a more complete overview of the importance of inversions in relation to the remaining genome."}],"title":"Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis"},{"ddc":["570"],"month":"03","doi":"10.5061/DRYAD.8GTHT76P1","date_updated":"2025-06-12T06:35:39Z","date_published":"2021-03-02T00:00:00Z","department":[{"_id":"NiBa"}],"oa":1,"day":"02","tmp":{"name":"Creative Commons Public Domain Dedication (CC0 1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","short":"CC0 (1.0)","image":"/images/cc_0.png"},"abstract":[{"text":"This paper analyzes the conditions for local adaptation in a metapopulation with infinitely many islands under a model of hard selection, where population size depends on local fitness. Each island belongs to one of two distinct ecological niches or habitats. Fitness is influenced by an additive trait which is under habitat-dependent directional selection. Our analysis is based on the diffusion approximation and  accounts for both genetic drift and demographic stochasticity. By neglecting linkage disequilibria, it yields the joint distribution of allele frequencies and population size on each island. We find that under hard selection, the conditions for local adaptation in a rare habitat are more restrictive for more polygenic traits: even moderate migration load per locus at very many loci is sufficient for population sizes to decline. This further reduces the efficacy of selection at individual loci due to increased drift and because smaller populations are more prone to swamping due to migration, causing a positive feedback between increasing maladaptation and declining population sizes. Our analysis also highlights the importance of demographic stochasticity, which  exacerbates the decline in numbers of maladapted populations, leading to population collapse in the rare habitat at significantly lower migration than predicted by deterministic arguments.","lang":"eng"}],"title":"Supplementary code for: Polygenic local adaptation in metapopulations: A stochastic eco-evolutionary model","publisher":"Dryad","year":"2021","corr_author":"1","author":[{"full_name":"Szep, Eniko","last_name":"Szep","id":"485BB5A4-F248-11E8-B48F-1D18A9856A87","first_name":"Eniko"},{"first_name":"Himani","id":"42377A0A-F248-11E8-B48F-1D18A9856A87","last_name":"Sachdeva","full_name":"Sachdeva, Himani"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton"}],"type":"research_data_reference","status":"public","fulldoi":"https://doi.org/10.5061/DRYAD.8GTHT76P1","citation":{"chicago":"Szep, Eniko, Himani Sachdeva, and Nicholas H Barton. “Supplementary Code for: Polygenic Local Adaptation in Metapopulations: A Stochastic Eco-Evolutionary Model.” Dryad, 2021. <a href=\"https://doi.org/10.5061/DRYAD.8GTHT76P1\">https://doi.org/10.5061/DRYAD.8GTHT76P1</a>.","ama":"Szep E, Sachdeva H, Barton NH. Supplementary code for: Polygenic local adaptation in metapopulations: A stochastic eco-evolutionary model. 2021. doi:<a href=\"https://doi.org/10.5061/DRYAD.8GTHT76P1\">10.5061/DRYAD.8GTHT76P1</a>","ista":"Szep E, Sachdeva H, Barton NH. 2021. Supplementary code for: Polygenic local adaptation in metapopulations: A stochastic eco-evolutionary model, Dryad, <a href=\"https://doi.org/10.5061/DRYAD.8GTHT76P1\">10.5061/DRYAD.8GTHT76P1</a>.","ieee":"E. Szep, H. Sachdeva, and N. H. Barton, “Supplementary code for: Polygenic local adaptation in metapopulations: A stochastic eco-evolutionary model.” Dryad, 2021.","short":"E. Szep, H. Sachdeva, N.H. Barton, (2021).","mla":"Szep, Eniko, et al. <i>Supplementary Code for: Polygenic Local Adaptation in Metapopulations: A Stochastic Eco-Evolutionary Model</i>. Dryad, 2021, doi:<a href=\"https://doi.org/10.5061/DRYAD.8GTHT76P1\">10.5061/DRYAD.8GTHT76P1</a>.","apa":"Szep, E., Sachdeva, H., &#38; Barton, N. H. (2021). Supplementary code for: Polygenic local adaptation in metapopulations: A stochastic eco-evolutionary model. Dryad. <a href=\"https://doi.org/10.5061/DRYAD.8GTHT76P1\">https://doi.org/10.5061/DRYAD.8GTHT76P1</a>"},"oa_version":"Published Version","article_processing_charge":"No","date_created":"2023-05-23T16:17:02Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"status":"public","id":"9252","relation":"used_in_publication"}]},"main_file_link":[{"url":"https://doi.org/10.5061/dryad.8gtht76p1","open_access":"1"}],"_id":"13062"},{"fulldoi":"https://doi.org/10.1002/9780470015902.a0029355","status":"public","article_processing_charge":"No","citation":{"short":"S. Stankowski, D. Shipilina, A.M. Westram, in:, Encyclopedia of Life Sciences, Wiley, 2021.","mla":"Stankowski, Sean, et al. “Hybrid Zones.” <i>Encyclopedia of Life Sciences</i>, vol. 2, Wiley, 2021, doi:<a href=\"https://doi.org/10.1002/9780470015902.a0029355\">10.1002/9780470015902.a0029355</a>.","apa":"Stankowski, S., Shipilina, D., &#38; Westram, A. M. (2021). Hybrid Zones. In <i>Encyclopedia of Life Sciences</i> (Vol. 2). Wiley. <a href=\"https://doi.org/10.1002/9780470015902.a0029355\">https://doi.org/10.1002/9780470015902.a0029355</a>","ama":"Stankowski S, Shipilina D, Westram AM. Hybrid Zones. In: <i>Encyclopedia of Life Sciences</i>. Vol 2. eLS. Wiley; 2021. doi:<a href=\"https://doi.org/10.1002/9780470015902.a0029355\">10.1002/9780470015902.a0029355</a>","chicago":"Stankowski, Sean, Daria Shipilina, and Anja M Westram. “Hybrid Zones.” In <i>Encyclopedia of Life Sciences</i>, Vol. 2. ELS. Wiley, 2021. <a href=\"https://doi.org/10.1002/9780470015902.a0029355\">https://doi.org/10.1002/9780470015902.a0029355</a>.","ista":"Stankowski S, Shipilina D, Westram AM. 2021.Hybrid Zones. In: Encyclopedia of Life Sciences. vol. 2.","ieee":"S. Stankowski, D. Shipilina, and A. M. Westram, “Hybrid Zones,” in <i>Encyclopedia of Life Sciences</i>, vol. 2, Wiley, 2021."},"oa_version":"None","language":[{"iso":"eng"}],"date_created":"2024-02-14T12:05:50Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14984","volume":2,"year":"2021","corr_author":"1","publisher":"Wiley","author":[{"last_name":"Stankowski","full_name":"Stankowski, Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","first_name":"Sean"},{"id":"428A94B0-F248-11E8-B48F-1D18A9856A87","first_name":"Daria","last_name":"Shipilina","full_name":"Shipilina, Daria","orcid":"0000-0002-1145-9226"},{"orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","last_name":"Westram","first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87"}],"type":"book_chapter","publication_identifier":{"eisbn":["9780470015902"],"isbn":["9780470016176"]},"publication":"Encyclopedia of Life Sciences","intvolume":"         2","abstract":[{"lang":"eng","text":"Hybrid zones are narrow geographic regions where different populations, races or interbreeding species meet and mate, producing mixed ‘hybrid’ offspring. They are relatively common and can be found in a diverse range of organisms and environments. The study of hybrid zones has played an important role in our understanding of the origin of species, with hybrid zones having been described as ‘natural laboratories’. This is because they allow us to study,in situ, the conditions and evolutionary forces that enable divergent taxa to remain distinct despite some ongoing gene exchange between them."}],"series_title":"eLS","publication_status":"published","title":"Hybrid Zones","month":"05","doi":"10.1002/9780470015902.a0029355","date_updated":"2024-10-09T21:08:11Z","department":[{"_id":"NiBa"}],"date_published":"2021-05-28T00:00:00Z","quality_controlled":"1","day":"28"},{"publication":"PLoS Computational Biology","publication_identifier":{"issn":["1553-734X"],"eissn":["1553-7358"]},"article_number":"e1009661","external_id":{"pmid":["34851948"],"arxiv":["2102.03669"]},"publication_status":"published","title":"Dynamic maximum entropy provides accurate approximation of structured population dynamics","has_accepted_license":"1","doi":"10.1371/journal.pcbi.1009661","ddc":["570"],"arxiv":1,"department":[{"_id":"NiBa"},{"_id":"GaTk"}],"scopus_import":"1","citation":{"ista":"Bodova K, Szep E, Barton NH. 2021. Dynamic maximum entropy provides accurate approximation of structured population dynamics. PLoS Computational Biology. 17(12), e1009661.","ieee":"K. Bodova, E. Szep, and N. H. Barton, “Dynamic maximum entropy provides accurate approximation of structured population dynamics,” <i>PLoS Computational Biology</i>, vol. 17, no. 12. Public Library of Science, 2021.","chicago":"Bodova, Katarina, Eniko Szep, and Nicholas H Barton. “Dynamic Maximum Entropy Provides Accurate Approximation of Structured Population Dynamics.” <i>PLoS Computational Biology</i>. Public Library of Science, 2021. <a href=\"https://doi.org/10.1371/journal.pcbi.1009661\">https://doi.org/10.1371/journal.pcbi.1009661</a>.","ama":"Bodova K, Szep E, Barton NH. Dynamic maximum entropy provides accurate approximation of structured population dynamics. <i>PLoS Computational Biology</i>. 2021;17(12). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1009661\">10.1371/journal.pcbi.1009661</a>","short":"K. Bodova, E. Szep, N.H. Barton, PLoS Computational Biology 17 (2021).","apa":"Bodova, K., Szep, E., &#38; Barton, N. H. (2021). Dynamic maximum entropy provides accurate approximation of structured population dynamics. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1009661\">https://doi.org/10.1371/journal.pcbi.1009661</a>","mla":"Bodova, Katarina, et al. “Dynamic Maximum Entropy Provides Accurate Approximation of Structured Population Dynamics.” <i>PLoS Computational Biology</i>, vol. 17, no. 12, e1009661, Public Library of Science, 2021, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1009661\">10.1371/journal.pcbi.1009661</a>."},"oa_version":"Published Version","fulldoi":"https://doi.org/10.1371/journal.pcbi.1009661","file":[{"creator":"dernst","relation":"main_file","file_id":"11383","content_type":"application/pdf","file_size":2299486,"checksum":"dcd185d4f7e0acee25edf1d6537f447e","date_updated":"2022-05-16T08:53:11Z","file_name":"2021_PLOsComBio_Bodova.pdf","date_created":"2022-05-16T08:53:11Z","success":1,"access_level":"open_access"}],"volume":17,"language":[{"iso":"eng"}],"year":"2021","acknowledged_ssus":[{"_id":"ScienComp"}],"publisher":"Public Library of Science","pmid":1,"acknowledgement":"Computational resources for the study were provided by the Institute of Science and Technology, Austria.\r\nKB received funding from the Scientific Grant Agency of the Slovak Republic under the Grants Nos. 1/0755/19 and 1/0521/20.","intvolume":"        17","file_date_updated":"2022-05-16T08:53:11Z","abstract":[{"lang":"eng","text":"Realistic models of biological processes typically involve interacting components on multiple scales, driven by changing environment and inherent stochasticity. Such models are often analytically and numerically intractable. We revisit a dynamic maximum entropy method that combines a static maximum entropy with a quasi-stationary approximation. This allows us to reduce stochastic non-equilibrium dynamics expressed by the Fokker-Planck equation to a simpler low-dimensional deterministic dynamics, without the need to track microscopic details. Although the method has been previously applied to a few (rather complicated) applications in population genetics, our main goal here is to explain and to better understand how the method works. We demonstrate the usefulness of the method for two widely studied stochastic problems, highlighting its accuracy in capturing important macroscopic quantities even in rapidly changing non-stationary conditions. For the Ornstein-Uhlenbeck process, the method recovers the exact dynamics whilst for a stochastic island model with migration from other habitats, the approximation retains high macroscopic accuracy under a wide range of scenarios in a dynamic environment."}],"date_updated":"2024-10-09T21:01:16Z","month":"12","day":"01","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","oa":1,"date_published":"2021-12-01T00:00:00Z","article_processing_charge":"No","status":"public","_id":"10535","date_created":"2021-12-12T23:01:27Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Katarína","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","last_name":"Bod'ová","full_name":"Bod'ová, Katarína","orcid":"0000-0002-7214-0171"},{"id":"485BB5A4-F248-11E8-B48F-1D18A9856A87","first_name":"Eniko","full_name":"Szep, Eniko","last_name":"Szep"},{"last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"article_type":"original","corr_author":"1","issue":"12","type":"journal_article"},{"volume":34,"main_file_link":[{"url":"https://doi.org/10.1101/818559","open_access":"1"}],"language":[{"iso":"eng"}],"oa_version":"Preprint","citation":{"mla":"Simon, Alexis, et al. “How Do Species Barriers Decay? Concordance and Local Introgression in Mosaic Hybrid Zones of Mussels.” <i>Journal of Evolutionary Biology</i>, vol. 34, no. 1, Wiley, 2021, pp. 208–23, doi:<a href=\"https://doi.org/10.1111/jeb.13709\">10.1111/jeb.13709</a>.","apa":"Simon, A., Fraisse, C., El Ayari, T., Liautard‐Haag, C., Strelkov, P., Welch, J. J., &#38; Bierne, N. (2021). How do species barriers decay? Concordance and local introgression in mosaic hybrid zones of mussels. <i>Journal of Evolutionary Biology</i>. Wiley. <a href=\"https://doi.org/10.1111/jeb.13709\">https://doi.org/10.1111/jeb.13709</a>","short":"A. Simon, C. Fraisse, T. El Ayari, C. Liautard‐Haag, P. Strelkov, J.J. Welch, N. Bierne, Journal of Evolutionary Biology 34 (2021) 208–223.","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. <i>Journal of Evolutionary Biology</i>. 2021;34(1):208-223. doi:<a href=\"https://doi.org/10.1111/jeb.13709\">10.1111/jeb.13709</a>","chicago":"Simon, Alexis, Christelle Fraisse, Tahani El Ayari, Cathy Liautard‐Haag, Petr Strelkov, John J Welch, and Nicolas Bierne. “How Do Species Barriers Decay? Concordance and Local Introgression in Mosaic Hybrid Zones of Mussels.” <i>Journal of Evolutionary Biology</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/jeb.13709\">https://doi.org/10.1111/jeb.13709</a>.","ista":"Simon A, Fraisse C, El Ayari T, Liautard‐Haag C, Strelkov P, Welch JJ, Bierne N. 2021. How do species barriers decay? Concordance and local introgression in mosaic hybrid zones of mussels. Journal of Evolutionary Biology. 34(1), 208–223.","ieee":"A. Simon <i>et al.</i>, “How do species barriers decay? Concordance and local introgression in mosaic hybrid zones of mussels,” <i>Journal of Evolutionary Biology</i>, vol. 34, no. 1. Wiley, pp. 208–223, 2021."},"scopus_import":"1","fulldoi":"https://doi.org/10.1111/jeb.13709","pmid":1,"publisher":"Wiley","year":"2021","external_id":{"pmid":["33045123"],"isi":["000579599700001"]},"title":"How do species barriers decay? Concordance and local introgression in mosaic hybrid zones of mussels","publication_status":"published","publication_identifier":{"issn":["1010-061X"],"eissn":["1420-9101"]},"publication":"Journal of Evolutionary Biology","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"doi":"10.1111/jeb.13709","related_material":{"record":[{"relation":"research_data","id":"13073","status":"public"}]},"_id":"8708","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2020-10-25T23:01:20Z","article_processing_charge":"No","status":"public","issue":"1","type":"journal_article","isi":1,"author":[{"full_name":"Simon, Alexis","last_name":"Simon","first_name":"Alexis"},{"orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle"},{"last_name":"El Ayari","full_name":"El Ayari, Tahani","first_name":"Tahani"},{"first_name":"Cathy","last_name":"Liautard‐Haag","full_name":"Liautard‐Haag, Cathy"},{"first_name":"Petr","full_name":"Strelkov, Petr","last_name":"Strelkov"},{"full_name":"Welch, John J","last_name":"Welch","first_name":"John J"},{"last_name":"Bierne","full_name":"Bierne, Nicolas","first_name":"Nicolas"}],"article_type":"original","page":"208-223","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."}],"acknowledgement":"Data used in this work were partly produced through the genotyping and sequencing facilities of ISEM and LabEx CeMEB, an ANR ‘Investissements d'avenir’ program (ANR‐10‐LABX‐04‐01) This project benefited from the Montpellier Bioinformatics Biodiversity platform supported by the LabEx CeMEB. We thank Norah Saarman, Grant Pogson, Célia Gosset and Pierre‐Alexandre Gagnaire for providing samples. This work was funded by a Languedoc‐Roussillon ‘Chercheur(se)s d'Avenir’ grant (Connect7 project). P. Strelkov was supported by the Russian Science Foundation project 19‐74‐20024. This is article 2020‐240 of Institut des Sciences de l'Evolution de Montpellier.","intvolume":"        34","oa":1,"quality_controlled":"1","day":"01","date_published":"2021-01-01T00:00:00Z","date_updated":"2025-07-10T12:01:23Z","month":"01"},{"publication":"Evolution","publication_identifier":{"eissn":["1558-5646"],"issn":["0014-3820"]},"external_id":{"pmid":["33078844"],"isi":["000583190600001"]},"publication_status":"published","title":"Long-term cloud forest response to climate warming revealed by insect speciation history","doi":"10.1111/evo.14111","department":[{"_id":"NiBa"}],"oa_version":"Submitted Version","citation":{"apa":"Salces-Castellano, A., Stankowski, S., Arribas, P., Patino, J., Karger, D. N., Butlin, R., &#38; Emerson, B. C. (2021). Long-term cloud forest response to climate warming revealed by insect speciation history. <i>Evolution</i>. Wiley. <a href=\"https://doi.org/10.1111/evo.14111\">https://doi.org/10.1111/evo.14111</a>","mla":"Salces-Castellano, Antonia, et al. “Long-Term Cloud Forest Response to Climate Warming Revealed by Insect Speciation History.” <i>Evolution</i>, vol. 75, no. 2, Wiley, 2021, pp. 231–44, doi:<a href=\"https://doi.org/10.1111/evo.14111\">10.1111/evo.14111</a>.","short":"A. Salces-Castellano, S. Stankowski, P. Arribas, J. Patino, D.N. Karger, R. Butlin, B.C. Emerson, Evolution 75 (2021) 231–244.","ieee":"A. Salces-Castellano <i>et al.</i>, “Long-term cloud forest response to climate warming revealed by insect speciation history,” <i>Evolution</i>, vol. 75, no. 2. Wiley, pp. 231–244, 2021.","ista":"Salces-Castellano A, Stankowski S, Arribas P, Patino J, Karger DN, Butlin R, Emerson BC. 2021. Long-term cloud forest response to climate warming revealed by insect speciation history. Evolution. 75(2), 231–244.","chicago":"Salces-Castellano, Antonia, Sean Stankowski, Paula Arribas, Jairo Patino, Dirk N.  Karger, Roger Butlin, and Brent C. Emerson. “Long-Term Cloud Forest Response to Climate Warming Revealed by Insect Speciation History.” <i>Evolution</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/evo.14111\">https://doi.org/10.1111/evo.14111</a>.","ama":"Salces-Castellano A, Stankowski S, Arribas P, et al. Long-term cloud forest response to climate warming revealed by insect speciation history. <i>Evolution</i>. 2021;75(2):231-244. doi:<a href=\"https://doi.org/10.1111/evo.14111\">10.1111/evo.14111</a>"},"scopus_import":"1","fulldoi":"https://doi.org/10.1111/evo.14111","main_file_link":[{"open_access":"1","url":"http://hdl.handle.net/10261/223937"}],"volume":75,"language":[{"iso":"eng"}],"year":"2021","publisher":"Wiley","pmid":1,"intvolume":"        75","acknowledgement":"This work was financed by the Spanish Agencia Estatal de Investigación (CGL2017‐85718‐P), awarded to BCE, and co‐financed by FEDER. It was also supported by the Spanish Ministerio de Ciencia, Innovación y Universidades (EQC2018‐004418‐P), awarded to BCE. AS‐C was funded by the Spanish Ministerio de Ciencia, Innovación y Universidades through an FPU PhD fellowship (FPU014/02948). The authors thank Instituto Tecnológico y de Energías Renovables (ITER), S.A for providing access to the Teide High‐Performance Computing facility (Teide‐HPC). Fieldwork was supported by collecting permit AFF 107/17 (sigma number 2017‐00572) kindly provided by the Cabildo of Tenerife. The authors wish to thank the following for field work and sample sorting and identification: A. J. Pérez‐Delgado, H. López, and C. Andújar. We also thank V. García‐Olivares for assistance with laboratory and bioinformatic work.","abstract":[{"lang":"eng","text":"Montane cloud forests are areas of high endemism, and are one of the more vulnerable terrestrial ecosystems to climate change. Thus, understanding how they both contribute to the generation of biodiversity, and will respond to ongoing climate change, are important and related challenges. The widely accepted model for montane cloud forest dynamics involves upslope forcing of their range limits with global climate warming. However, limited climate data provides some support for an alternative model, where range limits are forced downslope with climate warming. Testing between these two models is challenging, due to the inherent limitations of climate and pollen records. We overcome this with an alternative source of historical information, testing between competing model predictions using genomic data and demographic analyses for a species of beetle tightly associated to an oceanic island cloud forest. Results unequivocally support the alternative model: populations that were isolated at higher elevation peaks during the Last Glacial Maximum are now in contact and hybridizing at lower elevations. Our results suggest that genomic data are a rich source of information to further understand how montane cloud forest biodiversity originates, and how it is likely to be impacted by ongoing climate change."}],"date_updated":"2023-08-04T11:09:49Z","month":"02","quality_controlled":"1","day":"01","oa":1,"date_published":"2021-02-01T00:00:00Z","article_processing_charge":"No","status":"public","_id":"8743","related_material":{"link":[{"url":"https://doi.org/10.1111/evo.14225","relation":"erratum"}]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_created":"2020-11-08T23:01:26Z","author":[{"first_name":"Antonia","last_name":"Salces-Castellano","full_name":"Salces-Castellano, Antonia"},{"first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean","last_name":"Stankowski"},{"full_name":"Arribas, Paula","last_name":"Arribas","first_name":"Paula"},{"first_name":"Jairo","last_name":"Patino","full_name":"Patino, Jairo"},{"last_name":"Karger","full_name":"Karger, Dirk N. ","first_name":"Dirk N. "},{"first_name":"Roger","last_name":"Butlin","full_name":"Butlin, Roger"},{"first_name":"Brent C.","full_name":"Emerson, Brent C.","last_name":"Emerson"}],"page":"231-244","article_type":"original","type":"journal_article","issue":"2","isi":1},{"language":[{"iso":"eng"}],"volume":34,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/jeb.13723"}],"fulldoi":"https://doi.org/10.1111/jeb.13723","project":[{"name":"Sex chromosomes and species barriers","call_identifier":"FWF","_id":"2662AADE-B435-11E9-9278-68D0E5697425","grant_number":"M02463"}],"oa_version":"Published Version","citation":{"ieee":"S. Arnoux, C. Fraisse, and C. Sauvage, “Genomic inference of complex domestication histories in three Solanaceae species,” <i>Journal of Evolutionary Biology</i>, vol. 34, no. 2. Wiley, pp. 270–283, 2021.","ista":"Arnoux S, Fraisse C, Sauvage C. 2021. Genomic inference of complex domestication histories in three Solanaceae species. Journal of Evolutionary Biology. 34(2), 270–283.","chicago":"Arnoux, Stéphanie, Christelle Fraisse, and Christopher Sauvage. “Genomic Inference of Complex Domestication Histories in Three Solanaceae Species.” <i>Journal of Evolutionary Biology</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/jeb.13723\">https://doi.org/10.1111/jeb.13723</a>.","ama":"Arnoux S, Fraisse C, Sauvage C. Genomic inference of complex domestication histories in three Solanaceae species. <i>Journal of Evolutionary Biology</i>. 2021;34(2):270-283. doi:<a href=\"https://doi.org/10.1111/jeb.13723\">10.1111/jeb.13723</a>","short":"S. Arnoux, C. Fraisse, C. Sauvage, Journal of Evolutionary Biology 34 (2021) 270–283.","apa":"Arnoux, S., Fraisse, C., &#38; Sauvage, C. (2021). Genomic inference of complex domestication histories in three Solanaceae species. <i>Journal of Evolutionary Biology</i>. Wiley. <a href=\"https://doi.org/10.1111/jeb.13723\">https://doi.org/10.1111/jeb.13723</a>","mla":"Arnoux, Stéphanie, et al. “Genomic Inference of Complex Domestication Histories in Three Solanaceae Species.” <i>Journal of Evolutionary Biology</i>, vol. 34, no. 2, Wiley, 2021, pp. 270–83, doi:<a href=\"https://doi.org/10.1111/jeb.13723\">10.1111/jeb.13723</a>."},"scopus_import":"1","pmid":1,"publisher":"Wiley","year":"2021","title":"Genomic inference of complex domestication histories in three Solanaceae species","publication_status":"published","external_id":{"pmid":["33107098"],"isi":["000587769700001"]},"publication_identifier":{"issn":["1010-061X"],"eissn":["1420-9101"]},"publication":"Journal of Evolutionary Biology","department":[{"_id":"NiBa"}],"ddc":["570"],"doi":"10.1111/jeb.13723","date_created":"2020-12-06T23:01:16Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"relation":"research_data","id":"13065","status":"public"}]},"_id":"8928","status":"public","article_processing_charge":"No","type":"journal_article","isi":1,"issue":"2","article_type":"original","page":"270-283","author":[{"first_name":"Stéphanie","last_name":"Arnoux","full_name":"Arnoux, Stéphanie"},{"full_name":"Fraisse, Christelle","orcid":"0000-0001-8441-5075","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle"},{"first_name":"Christopher","full_name":"Sauvage, Christopher","last_name":"Sauvage"}],"abstract":[{"lang":"eng","text":"Domestication is a human‐induced selection process that imprints the genomes of domesticated populations over a short evolutionary time scale and that occurs in a given demographic context. Reconstructing historical gene flow, effective population size changes and their timing is therefore of fundamental interest to understand how plant demography and human selection jointly shape genomic divergence during domestication. Yet, the comparison under a single statistical framework of independent domestication histories across different crop species has been little evaluated so far. Thus, it is unclear whether domestication leads to convergent demographic changes that similarly affect crop genomes. To address this question, we used existing and new transcriptome data on three crop species of Solanaceae (eggplant, pepper and tomato), together with their close wild relatives. We fitted twelve demographic models of increasing complexity on the unfolded joint allele frequency spectrum for each wild/crop pair, and we found evidence for both shared and species‐specific demographic processes between species. A convergent history of domestication with gene flow was inferred for all three species, along with evidence of strong reduction in the effective population size during the cultivation stage of tomato and pepper. The absence of any reduction in size of the crop in eggplant stands out from the classical view of the domestication process; as does the existence of a “protracted period” of management before cultivation. Our results also suggest divergent management strategies of modern cultivars among species as their current demography substantially differs. Finally, the timing of domestication is species‐specific and supported by the few historical records available."}],"acknowledgement":"This work was supported by the EU Marie Curie Career Integration grant (FP7‐PEOPLE‐2011‐CIG grant agreement PCIG10‐GA‐2011‐304164) attributed to CS. SA was supported by a PhD fellowship from the French Région PACA and the Plant Breeding division of INRA, in partnership with Gautier Semences. CF was supported by an Austrian Science Foundation FWF grant (Project M 2463‐B29). Authors thank Mathilde Causse and Beatriz Vicoso for their team leading. Thanks to the Italian Eggplant Genome Consortium, which includes the DISAFA, Plant Genetics and Breeding (University of Torino), the Biotechnology Department (University of Verona), the CREA‐ORL in Montanaso Lombardo (LO) and the ENEA in Rome for providing access to the eggplant genome reference. Thanks to CRB‐lég ( https://www6.paca.inra.fr/gafl_eng/Vegetables-GRC ) for managing and providing the genetic resources, to Marie‐Christine Daunay and Alain Palloix (INRA UR1052) for assistance in choosing the biological material used, to Muriel Latreille and Sylvain Santoni from the UMR AGAP (INRA Montpellier, France) for their help with RNAseq library preparation, to Jean‐Paul Bouchet and Jacques Lagnel (INRA UR1052) for their Bioinformatics assistance.","intvolume":"        34","date_published":"2021-02-01T00:00:00Z","oa":1,"day":"01","quality_controlled":"1","month":"02","date_updated":"2026-06-18T19:37:17Z"},{"department":[{"_id":"NiBa"}],"ddc":["570"],"doi":"10.1111/jeb.13756","has_accepted_license":"1","title":"Speciation in marine environments: Diving under the surface","publication_status":"published","external_id":{"isi":["000608367500001"]},"publication":"Journal of Evolutionary Biology","publication_identifier":{"eissn":["1420-9101"],"issn":["1010-061X"]},"publisher":"Wiley","year":"2021","language":[{"iso":"eng"}],"volume":34,"file":[{"success":1,"date_created":"2021-02-09T09:04:02Z","access_level":"open_access","content_type":"application/pdf","file_id":"9108","relation":"main_file","creator":"dernst","date_updated":"2021-02-09T09:04:02Z","file_name":"2021_JourEvolBiology_Faria.pdf","file_size":561340,"checksum":"5755856a5368d4b4cdd6fad5ab27f4d1"}],"fulldoi":"https://doi.org/10.1111/jeb.13756","citation":{"ama":"Faria R, Johannesson K, Stankowski S. Speciation in marine environments: Diving under the surface. <i>Journal of Evolutionary Biology</i>. 2021;34(1):4-15. doi:<a href=\"https://doi.org/10.1111/jeb.13756\">10.1111/jeb.13756</a>","chicago":"Faria, Rui, Kerstin Johannesson, and Sean Stankowski. “Speciation in Marine Environments: Diving under the Surface.” <i>Journal of Evolutionary Biology</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/jeb.13756\">https://doi.org/10.1111/jeb.13756</a>.","ieee":"R. Faria, K. Johannesson, and S. Stankowski, “Speciation in marine environments: Diving under the surface,” <i>Journal of Evolutionary Biology</i>, vol. 34, no. 1. Wiley, pp. 4–15, 2021.","ista":"Faria R, Johannesson K, Stankowski S. 2021. Speciation in marine environments: Diving under the surface. Journal of Evolutionary Biology. 34(1), 4–15.","mla":"Faria, Rui, et al. “Speciation in Marine Environments: Diving under the Surface.” <i>Journal of Evolutionary Biology</i>, vol. 34, no. 1, Wiley, 2021, pp. 4–15, doi:<a href=\"https://doi.org/10.1111/jeb.13756\">10.1111/jeb.13756</a>.","apa":"Faria, R., Johannesson, K., &#38; Stankowski, S. (2021). Speciation in marine environments: Diving under the surface. <i>Journal of Evolutionary Biology</i>. Wiley. <a href=\"https://doi.org/10.1111/jeb.13756\">https://doi.org/10.1111/jeb.13756</a>","short":"R. Faria, K. Johannesson, S. Stankowski, Journal of Evolutionary Biology 34 (2021) 4–15."},"scopus_import":"1","oa_version":"Published Version","date_published":"2021-01-18T00:00:00Z","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","day":"18","month":"01","date_updated":"2025-07-10T12:01:37Z","file_date_updated":"2021-02-09T09:04:02Z","abstract":[{"text":"Marine environments are inhabited by a broad representation of the tree of life, yet our understanding of speciation in marine ecosystems is extremely limited compared with terrestrial and freshwater environments. Developing a more comprehensive picture of speciation in marine environments requires that we 'dive under the surface' by studying a wider range of taxa and ecosystems is necessary for a more comprehensive picture of speciation. Although studying marine evolutionary processes is often challenging, recent technological advances in different fields, from maritime engineering to genomics, are making it increasingly possible to study speciation of marine life forms across diverse ecosystems and taxa. Motivated by recent research in the field, including the 14 contributions in this issue, we highlight and discuss six axes of research that we think will deepen our understanding of speciation in the marine realm: (a) study a broader range of marine environments and organisms; (b) identify the reproductive barriers driving speciation between marine taxa; (c) understand the role of different genomic architectures underlying reproductive isolation; (d) infer the evolutionary history of divergence using model‐based approaches; (e) study patterns of hybridization and introgression between marine taxa; and (f) implement highly interdisciplinary, collaborative research programmes. In outlining these goals, we hope to inspire researchers to continue filling this critical knowledge gap surrounding the origins of marine biodiversity.","lang":"eng"}],"acknowledgement":"We would like to thank all the participants in the speciation symposium of the Marine Evolution Conference in Sweden for the interesting discussions and to all the contributors to this special\r\nissue. We thank Nicolas Bierne and Wolf Blanckenhorn (reviewer and editor, respectively) for valuable suggestions during the revision of the manuscript, and Roger K. Butlin and Anja M. Westram for very helpful comments on a previous draft. We would also like to thank Wolf Blanckenhorn and Nicola Cook, the Editor in Chief and the Managing Editor of the Journal of Evolutionary Biology, respectively, for the encouragement and support in putting together this special issue, and to all reviewers involved. RF was financed by the European Union's Horizon 2020 Research and Innovation Programme under the Marie Sklodowska-Curie Grant Agreement Number 706376 and is currently financed by the FEDER Funds through the Operational Competitiveness Factors Program COMPETE and by National Funds through the Foundation for Science and Technology (FCT) within the scope of the project ‘Hybrabbid' (PTDC/BIA-EVL/30628/2017-POCI-01-0145-FEDER-030628). KJ was funded by the Swedish\r\nResearch Council, VR. SS was supported by NERC and ERC funding awarded to Roger K. Butlin.","intvolume":"        34","type":"journal_article","isi":1,"issue":"1","page":"4-15","article_type":"original","author":[{"first_name":"Rui","full_name":"Faria, Rui","last_name":"Faria"},{"first_name":"Kerstin","full_name":"Johannesson, Kerstin","last_name":"Johannesson"},{"id":"43161670-5719-11EA-8025-FABC3DDC885E","first_name":"Sean","full_name":"Stankowski, Sean","last_name":"Stankowski"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2021-02-07T23:01:13Z","_id":"9100","status":"public","article_processing_charge":"No"},{"article_processing_charge":"No","status":"public","_id":"9119","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2021-02-14T23:01:14Z","author":[{"orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle"},{"first_name":"Iva","full_name":"Popovic, Iva","last_name":"Popovic"},{"full_name":"Mazoyer, Clément","last_name":"Mazoyer","first_name":"Clément"},{"first_name":"Bruno","full_name":"Spataro, Bruno","last_name":"Spataro"},{"last_name":"Delmotte","full_name":"Delmotte, Stéphane","first_name":"Stéphane"},{"first_name":"Jonathan","last_name":"Romiguier","full_name":"Romiguier, Jonathan"},{"last_name":"Loire","full_name":"Loire, Étienne","first_name":"Étienne"},{"first_name":"Alexis","last_name":"Simon","full_name":"Simon, Alexis"},{"full_name":"Galtier, Nicolas","last_name":"Galtier","first_name":"Nicolas"},{"full_name":"Duret, Laurent","last_name":"Duret","first_name":"Laurent"},{"last_name":"Bierne","full_name":"Bierne, Nicolas","first_name":"Nicolas"},{"first_name":"Xavier","full_name":"Vekemans, Xavier","last_name":"Vekemans"},{"first_name":"Camille","last_name":"Roux","full_name":"Roux, Camille"}],"page":"2629-2644","article_type":"original","corr_author":"1","isi":1,"type":"journal_article","intvolume":"        21","abstract":[{"text":"We present DILS, a deployable statistical analysis platform for conducting demographic inferences with linked selection from population genomic data using an Approximate Bayesian Computation framework. DILS takes as input single‐population or two‐population data sets (multilocus fasta sequences) and performs three types of analyses in a hierarchical manner, identifying: (a) the best demographic model to study the importance of gene flow and population size change on the genetic patterns of polymorphism and divergence, (b) the best genomic model to determine whether the effective size Ne and migration rate N, m are heterogeneously distributed along the genome (implying linked selection) and (c) loci in genomic regions most associated with barriers to gene flow. Also available via a Web interface, an objective of DILS is to facilitate collaborative research in speciation genomics. Here, we show the performance and limitations of DILS by using simulations and finally apply the method to published data on a divergence continuum composed by 28 pairs of Mytilus mussel populations/species.","lang":"eng"}],"date_updated":"2025-06-12T06:34:23Z","month":"01","quality_controlled":"1","day":"15","oa":1,"date_published":"2021-01-15T00:00:00Z","citation":{"mla":"Fraisse, Christelle, et al. “DILS: Demographic Inferences with Linked Selection by Using ABC.” <i>Molecular Ecology Resources</i>, vol. 21, Wiley, 2021, pp. 2629–44, doi:<a href=\"https://doi.org/10.1111/1755-0998.13323\">10.1111/1755-0998.13323</a>.","apa":"Fraisse, C., Popovic, I., Mazoyer, C., Spataro, B., Delmotte, S., Romiguier, J., … Roux, C. (2021). DILS: Demographic inferences with linked selection by using ABC. <i>Molecular Ecology Resources</i>. Wiley. <a href=\"https://doi.org/10.1111/1755-0998.13323\">https://doi.org/10.1111/1755-0998.13323</a>","short":"C. Fraisse, I. Popovic, C. Mazoyer, B. Spataro, S. Delmotte, J. Romiguier, É. Loire, A. Simon, N. Galtier, L. Duret, N. Bierne, X. Vekemans, C. Roux, Molecular Ecology Resources 21 (2021) 2629–2644.","ama":"Fraisse C, Popovic I, Mazoyer C, et al. DILS: Demographic inferences with linked selection by using ABC. <i>Molecular Ecology Resources</i>. 2021;21:2629-2644. doi:<a href=\"https://doi.org/10.1111/1755-0998.13323\">10.1111/1755-0998.13323</a>","chicago":"Fraisse, Christelle, Iva Popovic, Clément Mazoyer, Bruno Spataro, Stéphane Delmotte, Jonathan Romiguier, Étienne Loire, et al. “DILS: Demographic Inferences with Linked Selection by Using ABC.” <i>Molecular Ecology Resources</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/1755-0998.13323\">https://doi.org/10.1111/1755-0998.13323</a>.","ista":"Fraisse C, Popovic I, Mazoyer C, Spataro B, Delmotte S, Romiguier J, Loire É, Simon A, Galtier N, Duret L, Bierne N, Vekemans X, Roux C. 2021. DILS: Demographic inferences with linked selection by using ABC. Molecular Ecology Resources. 21, 2629–2644.","ieee":"C. Fraisse <i>et al.</i>, “DILS: Demographic inferences with linked selection by using ABC,” <i>Molecular Ecology Resources</i>, vol. 21. Wiley, pp. 2629–2644, 2021."},"scopus_import":"1","oa_version":"Preprint","fulldoi":"https://doi.org/10.1111/1755-0998.13323","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2020.06.15.151597v2"}],"volume":21,"language":[{"iso":"eng"}],"year":"2021","publisher":"Wiley","pmid":1,"publication":"Molecular Ecology Resources","publication_identifier":{"issn":["1755-098X"],"eissn":["1755-0998"]},"external_id":{"pmid":["33448666"],"isi":["000614183100001"]},"publication_status":"published","title":"DILS: Demographic inferences with linked selection by using ABC","doi":"10.1111/1755-0998.13323","department":[{"_id":"NiBa"}]},{"type":"research_data","publisher":"Institute of Science and Technology Austria","year":"2021","author":[{"full_name":"Surendranadh, Parvathy","orcid":"0000-0001-6395-386X","last_name":"Surendranadh","first_name":"Parvathy","id":"455235B8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Arathoon","orcid":"0000-0003-1771-714X","full_name":"Arathoon, Louise S","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","first_name":"Louise S"},{"first_name":"Carina","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","last_name":"Baskett","full_name":"Baskett, Carina","orcid":"0000-0002-7354-8574"},{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David","last_name":"Field","full_name":"Field, David","orcid":"0000-0002-4014-8478"},{"id":"2C78037E-F248-11E8-B48F-1D18A9856A87","first_name":"Melinda","last_name":"Pickup","orcid":"0000-0001-6118-0541","full_name":"Pickup, Melinda"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton"}],"date_created":"2021-02-24T17:49:21Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"status":"public","id":"8254","relation":"earlier_version"},{"status":"public","relation":"later_version","id":"11321"},{"relation":"used_in_publication","id":"11411","status":"public"}]},"_id":"9192","file":[{"date_created":"2021-02-24T17:45:13Z","success":1,"access_level":"open_access","creator":"larathoo","relation":"main_file","content_type":"application/x-zip-compressed","file_id":"9193","file_name":"Data_Code.zip","date_updated":"2021-02-24T17:45:13Z","checksum":"f85537815809a8a4b7da9d01163f88c0","file_size":5934452}],"status":"public","fulldoi":"https://doi.org/10.15479/AT:ISTA:9192","contributor":[{"first_name":"Parvathy","id":"455235B8-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member","last_name":"Surendranadh"},{"last_name":"Arathoon","first_name":"Louise S","contributor_type":"project_member","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87"},{"contributor_type":"project_member","id":"3B4A7CE2-F248-11E8-B48F-1D18A9856A87","first_name":"Carina","last_name":"Baskett"},{"last_name":"Field","orcid":"0000-0002-4014-8478","contributor_type":"project_member","id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David"},{"last_name":"Pickup","orcid":"0000-0001-6118-0541","first_name":"Melinda","contributor_type":"project_member","id":"2C78037E-F248-11E8-B48F-1D18A9856A87"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_leader","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton"}],"citation":{"ieee":"P. Surendranadh, L. S. Arathoon, C. Baskett, D. Field, M. Pickup, and N. H. Barton, “Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus.” Institute of Science and Technology Austria, 2021.","ista":"Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. 2021. Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:9192\">10.15479/AT:ISTA:9192</a>.","ama":"Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. 2021. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:9192\">10.15479/AT:ISTA:9192</a>","chicago":"Surendranadh, Parvathy, Louise S Arathoon, Carina Baskett, David Field, Melinda Pickup, and Nicholas H Barton. “Effects of Fine-Scale Population Structure on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/AT:ISTA:9192\">https://doi.org/10.15479/AT:ISTA:9192</a>.","apa":"Surendranadh, P., Arathoon, L. S., Baskett, C., Field, D., Pickup, M., &#38; Barton, N. H. (2021). Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:9192\">https://doi.org/10.15479/AT:ISTA:9192</a>","mla":"Surendranadh, Parvathy, et al. <i>Effects of Fine-Scale Population Structure on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:9192\">10.15479/AT:ISTA:9192</a>.","short":"P. Surendranadh, L.S. Arathoon, C. Baskett, D. Field, M. Pickup, N.H. Barton, (2021)."},"oa_version":"Published Version","article_processing_charge":"No","date_published":"2021-02-26T00:00:00Z","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"day":"26","ddc":["576"],"month":"02","doi":"10.15479/AT:ISTA:9192","has_accepted_license":"1","date_updated":"2025-04-15T08:20:40Z","title":"Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus","file_date_updated":"2021-02-24T17:45:13Z","abstract":[{"lang":"eng","text":"Here are the research data underlying the publication \" Effects of fine-scale population structure on inbreeding in a long-term study of snapdragons (Antirrhinum majus).\" Further information are summed up in the README document."}]},{"volume":75,"language":[{"iso":"eng"}],"scopus_import":"1","oa_version":"Published Version","citation":{"chicago":"Szep, Eniko, Himani Sachdeva, and Nicholas H Barton. “Polygenic Local Adaptation in Metapopulations: A Stochastic Eco‐evolutionary Model.” <i>Evolution</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/evo.14210\">https://doi.org/10.1111/evo.14210</a>.","ama":"Szep E, Sachdeva H, Barton NH. Polygenic local adaptation in metapopulations: A stochastic eco‐evolutionary model. <i>Evolution</i>. 2021;75(5):1030-1045. doi:<a href=\"https://doi.org/10.1111/evo.14210\">10.1111/evo.14210</a>","ieee":"E. Szep, H. Sachdeva, and N. H. Barton, “Polygenic local adaptation in metapopulations: A stochastic eco‐evolutionary model,” <i>Evolution</i>, vol. 75, no. 5. Wiley, pp. 1030–1045, 2021.","ista":"Szep E, Sachdeva H, Barton NH. 2021. Polygenic local adaptation in metapopulations: A stochastic eco‐evolutionary model. Evolution. 75(5), 1030–1045.","short":"E. Szep, H. Sachdeva, N.H. Barton, Evolution 75 (2021) 1030–1045.","mla":"Szep, Eniko, et al. “Polygenic Local Adaptation in Metapopulations: A Stochastic Eco‐evolutionary Model.” <i>Evolution</i>, vol. 75, no. 5, Wiley, 2021, pp. 1030–45, doi:<a href=\"https://doi.org/10.1111/evo.14210\">10.1111/evo.14210</a>.","apa":"Szep, E., Sachdeva, H., &#38; Barton, N. H. (2021). Polygenic local adaptation in metapopulations: A stochastic eco‐evolutionary model. <i>Evolution</i>. Wiley. <a href=\"https://doi.org/10.1111/evo.14210\">https://doi.org/10.1111/evo.14210</a>"},"file":[{"file_size":734102,"checksum":"b90fb5767d623602046fed03725e16ca","date_updated":"2021-08-11T13:39:19Z","file_name":"2021_Evolution_Szep.pdf","creator":"kschuh","relation":"main_file","content_type":"application/pdf","file_id":"9886","access_level":"open_access","date_created":"2021-08-11T13:39:19Z","success":1}],"fulldoi":"https://doi.org/10.1111/evo.14210","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics","General Agricultural and Biological Sciences"],"pmid":1,"publisher":"Wiley","year":"2021","external_id":{"pmid":["33742441"],"isi":["000636966300001"]},"title":"Polygenic local adaptation in metapopulations: A stochastic eco‐evolutionary model","publication_status":"published","publication_identifier":{"issn":["0014-3820"],"eissn":["1558-5646"]},"publication":"Evolution","department":[{"_id":"NiBa"}],"has_accepted_license":"1","ddc":["570"],"doi":"10.1111/evo.14210","related_material":{"record":[{"relation":"research_data","id":"13062","status":"public"}]},"_id":"9252","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2021-03-20T08:22:10Z","article_processing_charge":"Yes (via OA deal)","status":"public","issue":"5","isi":1,"type":"journal_article","author":[{"id":"485BB5A4-F248-11E8-B48F-1D18A9856A87","first_name":"Eniko","full_name":"Szep, Eniko","last_name":"Szep"},{"first_name":"Himani","id":"42377A0A-F248-11E8-B48F-1D18A9856A87","last_name":"Sachdeva","full_name":"Sachdeva, Himani"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton"}],"page":"1030-1045","corr_author":"1","article_type":"original","abstract":[{"lang":"eng","text":"This paper analyses the conditions for local adaptation in a metapopulation with infinitely many islands under a model of hard selection, where population size depends on local fitness. Each island belongs to one of two distinct ecological niches or habitats. Fitness is influenced by an additive trait which is under habitat‐dependent directional selection. Our analysis is based on the diffusion approximation and accounts for both genetic drift and demographic stochasticity. By neglecting linkage disequilibria, it yields the joint distribution of allele frequencies and population size on each island. We find that under hard selection, the conditions for local adaptation in a rare habitat are more restrictive for more polygenic traits: even moderate migration load per locus at very many loci is sufficient for population sizes to decline. This further reduces the efficacy of selection at individual loci due to increased drift and because smaller populations are more prone to swamping due to migration, causing a positive feedback between increasing maladaptation and declining population sizes. Our analysis also highlights the importance of demographic stochasticity, which exacerbates the decline in numbers of maladapted populations, leading to population collapse in the rare habitat at significantly lower migration than predicted by deterministic arguments."}],"file_date_updated":"2021-08-11T13:39:19Z","intvolume":"        75","acknowledgement":"We thank the reviewers for their helpful comments, and also our colleagues, for illuminating discussions over the long gestation of this paper.","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"day":"01","quality_controlled":"1","date_published":"2021-05-01T00:00:00Z","date_updated":"2025-06-12T06:35:39Z","month":"05"},{"year":"2021","publisher":"Wiley","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics","General Agricultural and Biological Sciences"],"scopus_import":"1","citation":{"ama":"Butlin RK, Servedio MR, Smadja CM, et al. Homage to Felsenstein 1981, or why are there so few/many species? <i>Evolution</i>. 2021;75(5):978-988. doi:<a href=\"https://doi.org/10.1111/evo.14235\">10.1111/evo.14235</a>","chicago":"Butlin, Roger K., Maria R. Servedio, Carole M. Smadja, Claudia Bank, Nicholas H Barton, Samuel M. Flaxman, Tatiana Giraud, et al. “Homage to Felsenstein 1981, or Why Are There so Few/Many Species?” <i>Evolution</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/evo.14235\">https://doi.org/10.1111/evo.14235</a>.","ista":"Butlin RK, Servedio MR, Smadja CM, Bank C, Barton NH, Flaxman SM, Giraud T, Hopkins R, Larson EL, Maan ME, Meier J, Merrill R, Noor MAF, Ortiz‐Barrientos D, Qvarnström A. 2021. Homage to Felsenstein 1981, or why are there so few/many species? Evolution. 75(5), 978–988.","ieee":"R. K. Butlin <i>et al.</i>, “Homage to Felsenstein 1981, or why are there so few/many species?,” <i>Evolution</i>, vol. 75, no. 5. Wiley, pp. 978–988, 2021.","short":"R.K. Butlin, M.R. Servedio, C.M. Smadja, C. Bank, N.H. Barton, S.M. Flaxman, T. Giraud, R. Hopkins, E.L. Larson, M.E. Maan, J. Meier, R. Merrill, M.A.F. Noor, D. Ortiz‐Barrientos, A. Qvarnström, Evolution 75 (2021) 978–988.","mla":"Butlin, Roger K., et al. “Homage to Felsenstein 1981, or Why Are There so Few/Many Species?” <i>Evolution</i>, vol. 75, no. 5, Wiley, 2021, pp. 978–88, doi:<a href=\"https://doi.org/10.1111/evo.14235\">10.1111/evo.14235</a>.","apa":"Butlin, R. K., Servedio, M. R., Smadja, C. M., Bank, C., Barton, N. H., Flaxman, S. M., … Qvarnström, A. (2021). Homage to Felsenstein 1981, or why are there so few/many species? <i>Evolution</i>. Wiley. <a href=\"https://doi.org/10.1111/evo.14235\">https://doi.org/10.1111/evo.14235</a>"},"oa_version":"Published Version","fulldoi":"https://doi.org/10.1111/evo.14235","main_file_link":[{"open_access":"1","url":"https://onlinelibrary.wiley.com/doi/10.1111/evo.14235"}],"volume":75,"language":[{"iso":"eng"}],"doi":"10.1111/evo.14235","ddc":["570"],"department":[{"_id":"NiBa"}],"publication":"Evolution","publication_identifier":{"eissn":["1558-5646"],"issn":["0014-3820"]},"external_id":{"isi":["000647224000001"]},"publication_status":"published","title":"Homage to Felsenstein 1981, or why are there so few/many species?","author":[{"first_name":"Roger K.","last_name":"Butlin","full_name":"Butlin, Roger K."},{"first_name":"Maria R.","last_name":"Servedio","full_name":"Servedio, Maria R."},{"last_name":"Smadja","full_name":"Smadja, Carole M.","first_name":"Carole M."},{"first_name":"Claudia","last_name":"Bank","full_name":"Bank, Claudia"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"last_name":"Flaxman","full_name":"Flaxman, Samuel M.","first_name":"Samuel M."},{"first_name":"Tatiana","full_name":"Giraud, Tatiana","last_name":"Giraud"},{"first_name":"Robin","last_name":"Hopkins","full_name":"Hopkins, Robin"},{"last_name":"Larson","full_name":"Larson, Erica L.","first_name":"Erica L."},{"first_name":"Martine E.","full_name":"Maan, Martine E.","last_name":"Maan"},{"full_name":"Meier, Joana","last_name":"Meier","first_name":"Joana"},{"last_name":"Merrill","full_name":"Merrill, Richard","first_name":"Richard"},{"last_name":"Noor","full_name":"Noor, Mohamed A. F.","first_name":"Mohamed A. F."},{"last_name":"Ortiz‐Barrientos","full_name":"Ortiz‐Barrientos, Daniel","first_name":"Daniel"},{"first_name":"Anna","full_name":"Qvarnström, Anna","last_name":"Qvarnström"}],"page":"978-988","article_type":"original","type":"journal_article","isi":1,"issue":"5","article_processing_charge":"No","status":"public","_id":"9374","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2021-05-06T04:34:47Z","date_updated":"2026-06-18T19:48:42Z","month":"04","day":"19","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","oa":1,"date_published":"2021-04-19T00:00:00Z","intvolume":"        75","acknowledgement":"RKB was funded by the Natural Environment Research Council (NE/P012272/1 & NE/P001610/1), the European Research Council (693030 BARRIERS), and the Swedish Research Council (VR) (2018‐03695). MRS was funded by the National Science Foundation (Grant No. DEB1939290).","abstract":[{"lang":"eng","text":"If there are no constraints on the process of speciation, then the number of species might be expected to match the number of available niches and this number might be indefinitely large. One possible constraint is the opportunity for allopatric divergence. In 1981, Felsenstein used a simple and elegant model to ask if there might also be genetic constraints. He showed that progress towards speciation could be described by the build‐up of linkage disequilibrium among divergently selected loci and between these loci and those contributing to other forms of reproductive isolation. Therefore, speciation is opposed by recombination, because it tends to break down linkage disequilibria. Felsenstein then introduced a crucial distinction between “two‐allele” models, which are subject to this effect, and “one‐allele” models, which are free from the recombination constraint. These fundamentally important insights have been the foundation for both empirical and theoretical studies of speciation ever since."}]},{"publisher":"National Academy of Sciences","year":"2021","pmid":1,"citation":{"short":"J.I. Meier, P.A. Salazar, M. Kučka, R.W. Davies, A. Dréau, I. Aldás, O.B. Power, N.J. Nadeau, J.R. Bridle, C. Rolian, N.H. Barton, W.O. McMillan, C.D. Jiggins, Y.F. Chan, Proceedings of the National Academy of Sciences of the United States of America 118 (2021).","mla":"Meier, Joana I., et al. “Haplotype Tagging Reveals Parallel Formation of Hybrid Races in Two Butterfly Species.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 118, no. 25, e2015005118, National Academy of Sciences, 2021, doi:<a href=\"https://doi.org/10.1073/pnas.2015005118\">10.1073/pnas.2015005118</a>.","apa":"Meier, J. I., Salazar, P. A., Kučka, M., Davies, R. W., Dréau, A., Aldás, I., … Chan, Y. F. (2021). Haplotype tagging reveals parallel formation of hybrid races in two butterfly species. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2015005118\">https://doi.org/10.1073/pnas.2015005118</a>","chicago":"Meier, Joana I., Patricio A. Salazar, Marek Kučka, Robert William Davies, Andreea Dréau, Ismael Aldás, Olivia Box Power, et al. “Haplotype Tagging Reveals Parallel Formation of Hybrid Races in Two Butterfly Species.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2021. <a href=\"https://doi.org/10.1073/pnas.2015005118\">https://doi.org/10.1073/pnas.2015005118</a>.","ama":"Meier JI, Salazar PA, Kučka M, et al. Haplotype tagging reveals parallel formation of hybrid races in two butterfly species. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2021;118(25). doi:<a href=\"https://doi.org/10.1073/pnas.2015005118\">10.1073/pnas.2015005118</a>","ieee":"J. I. Meier <i>et al.</i>, “Haplotype tagging reveals parallel formation of hybrid races in two butterfly species,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 118, no. 25. National Academy of Sciences, 2021.","ista":"Meier JI, Salazar PA, Kučka M, Davies RW, Dréau A, Aldás I, Power OB, Nadeau NJ, Bridle JR, Rolian C, Barton NH, McMillan WO, Jiggins CD, Chan YF. 2021. Haplotype tagging reveals parallel formation of hybrid races in two butterfly species. Proceedings of the National Academy of Sciences of the United States of America. 118(25), e2015005118."},"oa_version":"Published Version","scopus_import":"1","file":[{"content_type":"application/pdf","file_id":"10835","relation":"main_file","creator":"dernst","file_size":20592929,"checksum":"cb30c6166b2132ee60d616b31a1a7c29","date_updated":"2022-03-08T08:18:16Z","file_name":"2021_PNAS_Meier.pdf","success":1,"date_created":"2022-03-08T08:18:16Z","access_level":"open_access"}],"fulldoi":"https://doi.org/10.1073/pnas.2015005118","volume":118,"language":[{"iso":"eng"}],"has_accepted_license":"1","ddc":["570"],"doi":"10.1073/pnas.2015005118","department":[{"_id":"NiBa"}],"article_number":"e2015005118","publication_identifier":{"eissn":["0027-8424"]},"publication":"Proceedings of the National Academy of Sciences of the United States of America","external_id":{"pmid":["34155138"],"isi":["000671755600001"]},"title":"Haplotype tagging reveals parallel formation of hybrid races in two butterfly species","publication_status":"published","author":[{"first_name":"Joana I.","last_name":"Meier","full_name":"Meier, Joana I."},{"first_name":"Patricio A.","full_name":"Salazar, Patricio A.","last_name":"Salazar"},{"first_name":"Marek","last_name":"Kučka","full_name":"Kučka, Marek"},{"full_name":"Davies, Robert William","last_name":"Davies","first_name":"Robert William"},{"full_name":"Dréau, Andreea","last_name":"Dréau","first_name":"Andreea"},{"full_name":"Aldás, Ismael","last_name":"Aldás","first_name":"Ismael"},{"last_name":"Power","full_name":"Power, Olivia Box","first_name":"Olivia Box"},{"last_name":"Nadeau","full_name":"Nadeau, Nicola J.","first_name":"Nicola J."},{"full_name":"Bridle, Jon R.","last_name":"Bridle","first_name":"Jon R."},{"full_name":"Rolian, Campbell","last_name":"Rolian","first_name":"Campbell"},{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"full_name":"McMillan, W. Owen","last_name":"McMillan","first_name":"W. Owen"},{"first_name":"Chris D.","full_name":"Jiggins, Chris D.","last_name":"Jiggins"},{"first_name":"Yingguang Frank","full_name":"Chan, Yingguang Frank","last_name":"Chan"}],"article_type":"original","type":"journal_article","issue":"25","isi":1,"article_processing_charge":"No","status":"public","_id":"9375","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2021-05-07T17:10:21Z","date_updated":"2025-05-14T10:58:04Z","month":"06","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"quality_controlled":"1","day":"21","date_published":"2021-06-21T00:00:00Z","abstract":[{"lang":"eng","text":"Genetic variation segregates as linked sets of variants, or haplotypes. Haplotypes and linkage are central to genetics and underpin virtually all genetic and selection analysis. And yet, genomic data often lack haplotype information, due to constraints in sequencing technologies. Here we present “haplotagging”, a simple, low-cost linked-read sequencing technique that allows sequencing of hundreds of individuals while retaining linkage information. We apply haplotagging to construct megabase-size haplotypes for over 600 individual butterflies (Heliconius erato and H. melpomene), which form overlapping hybrid zones across an elevational gradient in Ecuador. Haplotagging identifies loci controlling distinctive high- and lowland wing color patterns. Divergent haplotypes are found at the same major loci in both species, while chromosome rearrangements show no parallelism. Remarkably, in both species the geographic clines for the major wing pattern loci are displaced by 18 km, leading to the rise of a novel hybrid morph in the centre of the hybrid zone. We propose that shared warning signalling (Müllerian mimicry) may couple the cline shifts seen in both species, and facilitate the parallel co-emergence of a novel hybrid morph in both co-mimetic species. Our results show the power of efficient haplotyping methods when combined with large-scale sequencing data from natural populations."}],"file_date_updated":"2022-03-08T08:18:16Z","intvolume":"       118","acknowledgement":"We thank Felicity Jones for input into experimental design, helpful discussion and improving the manuscript. We thank the Rolian, Jiggins, Chan and Jones Labs members for support, insightful scientific discussion and improving the manuscript. We thank the Rolian lab members, the Animal Resource Centre staff at the University of Calgary, and Caroline Schmid and Ann-Katrin Geysel at the Friedrich Miescher Laboratory for animal husbandry. We thank Christa Lanz, Rebecca Schwab and Ilja Bezrukov for assistance with high-throughput sequencing and associated data processing; Andre Noll and the MPI Tübingen IT team for computational support. We thank Ben Haller and Richard Durbin for helpful discussions. We thank David M. Kingsley for thoughtful input that has greatly improved our manuscript. J.I.M. is supported by a Research Fellowship from St. John’s College, Cambridge. A.D. was supported by a European Research Council Consolidator Grant (No. 617279 “EvolRecombAdapt”, P/I Felicity Jones). C.R. is supported by Discovery Grant #4181932 from the Natural Sciences and Engineering Research Council of Canada and by the Faculty of Veterinary Medicine at the University of Calgary. C.D.J. is supported by a BBSRC grant BB/R007500 and a European Research Council Advanced Grant (No. 339873 “SpeciationGenetics”). M.K. and Y.F.C. are supported by the Max Planck Society and a European Research Council Starting Grant (No. 639096 “HybridMiX”)."},{"status":"public","article_processing_charge":"No","date_created":"2021-05-09T22:01:39Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9383","page":"1256-1273","article_type":"original","author":[{"first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","last_name":"Stankowski","full_name":"Stankowski, Sean"},{"first_name":"Mark","full_name":"Ravinet, Mark","last_name":"Ravinet"}],"type":"journal_article","issue":"6","isi":1,"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.","intvolume":"        75","abstract":[{"lang":"eng","text":"A primary roadblock to our understanding of speciation is that it usually occurs over a timeframe that is too long to study from start to finish. The idea of a speciation continuum provides something of a solution to this problem; rather than observing the entire process, we can simply reconstruct it from the multitude of speciation events that surround us. But what do we really mean when we talk about the speciation continuum, and can it really help us understand speciation? We explored these questions using a literature review and online survey of speciation researchers. Although most researchers were familiar with the concept and thought it was useful, our survey revealed extensive disagreement about what the speciation continuum actually tells us. This is due partly to the lack of a clear definition. Here, we provide an explicit definition that is compatible with the Biological Species Concept. That is, the speciation continuum is a continuum of reproductive isolation. After outlining the logic of the definition in light of alternatives, we explain why attempts to reconstruct the speciation process from present‐day populations will ultimately fail. We then outline how we think the speciation continuum concept can continue to act as a foundation for understanding the continuum of reproductive isolation that surrounds us."}],"file_date_updated":"2022-03-25T12:02:04Z","month":"03","date_updated":"2023-10-18T08:16:01Z","date_published":"2021-03-22T00:00:00Z","quality_controlled":"1","tmp":{"short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"day":"22","oa":1,"fulldoi":"https://doi.org/10.1111/evo.14215","file":[{"date_created":"2022-03-25T12:02:04Z","success":1,"access_level":"open_access","relation":"main_file","creator":"kschuh","file_id":"10921","content_type":"application/pdf","checksum":"96f6ccf15d95a4e9f7c0b27eee570fa6","file_size":719991,"file_name":"2021_Evolution_Stankowski.pdf","date_updated":"2022-03-25T12:02:04Z"}],"oa_version":"Published Version","citation":{"ista":"Stankowski S, Ravinet M. 2021. Defining the speciation continuum. Evolution. 75(6), 1256–1273.","ieee":"S. Stankowski and M. Ravinet, “Defining the speciation continuum,” <i>Evolution</i>, vol. 75, no. 6. Oxford University Press, pp. 1256–1273, 2021.","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>.","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>","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>","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>.","short":"S. Stankowski, M. Ravinet, Evolution 75 (2021) 1256–1273."},"scopus_import":"1","language":[{"iso":"eng"}],"volume":75,"year":"2021","publisher":"Oxford University Press","publication":"Evolution","publication_identifier":{"issn":["0014-3820"],"eissn":["1558-5646"]},"publication_status":"published","title":"Defining the speciation continuum","external_id":{"isi":["000647226400001"]},"doi":"10.1111/evo.14215","ddc":["570"],"has_accepted_license":"1","department":[{"_id":"NiBa"}]},{"oa":1,"day":"10","quality_controlled":"1","date_published":"2021-05-10T00:00:00Z","date_updated":"2026-06-18T19:49:12Z","month":"05","abstract":[{"lang":"eng","text":"Humans conceptualize the diversity of life by classifying individuals into types we call ‘species’1. The species we recognize influence political and financial decisions and guide our understanding of how units of diversity evolve and interact. Although the idea of species may seem intuitive, a debate about the best way to define them has raged even before Darwin2. So much energy has been devoted to the so-called ‘species problem’ that no amount of discourse will ever likely solve it2,3. Dozens of species concepts are currently recognized3, but we lack a concrete understanding of how much researchers actually disagree and the factors that cause them to think differently1,2. To address this, we used a survey to quantify the species problem for the first time. The results indicate that the disagreement is extensive: two randomly chosen respondents will most likely disagree on the nature of species. The probability of disagreement is not predicted by researcher experience or broad study system, but tended to be lower among researchers with similar focus, training and who study the same organism. Should we see this diversity of perspectives as a problem? We argue that we should not."}],"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.","intvolume":"        31","type":"journal_article","isi":1,"issue":"9","author":[{"last_name":"Stankowski","full_name":"Stankowski, Sean","first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E"},{"first_name":"Mark","full_name":"Ravinet, Mark","last_name":"Ravinet"}],"page":"R428-R429","article_type":"original","corr_author":"1","_id":"9392","date_created":"2021-05-16T22:01:46Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","status":"public","department":[{"_id":"NiBa"}],"ddc":["570"],"doi":"10.1016/j.cub.2021.03.060","external_id":{"isi":["000654741200004"],"pmid":["33974865"]},"title":"Quantifying the use of species concepts","publication_status":"published","publication":"Current Biology","publication_identifier":{"issn":["0960-9822"],"eissn":["1879-0445"]},"pmid":1,"publisher":"Cell Press","year":"2021","volume":31,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cub.2021.03.060"}],"language":[{"iso":"eng"}],"oa_version":"Published Version","scopus_import":"1","citation":{"short":"S. Stankowski, M. Ravinet, Current Biology 31 (2021) R428–R429.","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>","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>.","ista":"Stankowski S, Ravinet M. 2021. Quantifying the use of species concepts. Current Biology. 31(9), R428–R429.","ieee":"S. Stankowski and M. Ravinet, “Quantifying the use of species concepts,” <i>Current Biology</i>, vol. 31, no. 9. Cell Press, pp. R428–R429, 2021.","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>.","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>"},"fulldoi":"https://doi.org/10.1016/j.cub.2021.03.060"},{"article_type":"original","page":"196-213","author":[{"first_name":"Eva L.","full_name":"Koch, Eva L.","last_name":"Koch"},{"first_name":"Hernán E.","full_name":"Morales, Hernán E.","last_name":"Morales"},{"full_name":"Larsson, Jenny","last_name":"Larsson","first_name":"Jenny"},{"full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","last_name":"Westram","first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Rui","last_name":"Faria","full_name":"Faria, Rui"},{"first_name":"Alan R.","last_name":"Lemmon","full_name":"Lemmon, Alan R."},{"first_name":"E. Moriarty","full_name":"Lemmon, E. Moriarty","last_name":"Lemmon"},{"first_name":"Kerstin","full_name":"Johannesson, Kerstin","last_name":"Johannesson"},{"first_name":"Roger K.","last_name":"Butlin","full_name":"Butlin, Roger K."}],"issue":"3","type":"journal_article","isi":1,"status":"public","article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_created":"2021-05-16T22:01:47Z","related_material":{"record":[{"relation":"research_data","id":"12987","status":"public"}]},"_id":"9394","month":"05","date_updated":"2026-04-07T14:01:29Z","date_published":"2021-05-07T00:00:00Z","oa":1,"day":"07","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","file_date_updated":"2021-10-15T08:26:02Z","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."}],"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. ","intvolume":"         5","publisher":"Wiley","year":"2021","file":[{"date_updated":"2021-10-15T08:26:02Z","file_name":"2021_EvolutionLetters_Koch.pdf","checksum":"023b1608e311f0fda30593ba3d0a4e0b","file_size":3021108,"creator":"cchlebak","relation":"main_file","content_type":"application/pdf","file_id":"10142","access_level":"open_access","date_created":"2021-10-15T08:26:02Z","success":1}],"fulldoi":"https://doi.org/10.1002/evl3.227","project":[{"_id":"265B41B8-B435-11E9-9278-68D0E5697425","grant_number":"797747","name":"Theoretical and empirical approaches to understanding Parallel Adaptation","call_identifier":"H2020"}],"citation":{"ista":"Koch EL, Morales HE, Larsson J, Westram AM, Faria R, Lemmon AR, Lemmon EM, Johannesson K, Butlin RK. 2021. Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis. Evolution Letters. 5(3), 196–213.","ieee":"E. L. Koch <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.","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>","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>.","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>","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>.","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."},"scopus_import":"1","oa_version":"Published Version","language":[{"iso":"eng"}],"volume":5,"ddc":["570"],"doi":"10.1002/evl3.227","has_accepted_license":"1","department":[{"_id":"NiBa"}],"ec_funded":1,"publication":"Evolution Letters","publication_identifier":{"eissn":["2056-3744"]},"title":"Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis","publication_status":"published","external_id":{"isi":["000647846200001"]}},{"ec_funded":1,"department":[{"_id":"NiBa"}],"has_accepted_license":"1","ddc":["570"],"doi":"10.1098/rsbl.2020.0913","external_id":{"isi":["000651501400001"],"pmid":[" 33975485"]},"title":"Adaptation at different points along antibiotic concentration gradients","publication_status":"published","article_number":"20200913","publication":"Biology letters","publication_identifier":{"eissn":["1744-957X"]},"pmid":1,"publisher":"Royal Society of London","year":"2021","volume":17,"language":[{"iso":"eng"}],"scopus_import":"1","oa_version":"Published Version","citation":{"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.","ista":"Lagator M, Uecker H, Neve P. 2021. Adaptation at different points along antibiotic concentration gradients. Biology letters. 17(5), 20200913.","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>","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>.","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>","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>.","short":"M. Lagator, H. Uecker, P. Neve, Biology Letters 17 (2021)."},"file":[{"relation":"main_file","creator":"kschuh","file_id":"9425","content_type":"application/pdf","file_name":"2021_BiologyLetters_Lagator.pdf","date_updated":"2021-05-25T14:09:03Z","checksum":"9c13c1f5af7609c97c741f11d293188a","file_size":726759,"date_created":"2021-05-25T14:09:03Z","success":1,"access_level":"open_access"}],"project":[{"name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152"}],"fulldoi":"https://doi.org/10.1098/rsbl.2020.0913","oa":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"day":"12","date_published":"2021-05-12T00:00:00Z","date_updated":"2026-04-02T14:02:44Z","month":"05","file_date_updated":"2021-05-25T14:09:03Z","abstract":[{"lang":"eng","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."}],"intvolume":"        17","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.","issue":"5","isi":1,"type":"journal_article","author":[{"full_name":"Lagator, Mato","last_name":"Lagator","id":"345D25EC-F248-11E8-B48F-1D18A9856A87","first_name":"Mato"},{"orcid":"0000-0001-9435-2813","full_name":"Uecker, Hildegard","last_name":"Uecker","id":"2DB8F68A-F248-11E8-B48F-1D18A9856A87","first_name":"Hildegard"},{"first_name":"Paul","last_name":"Neve","full_name":"Neve, Paul"}],"corr_author":"1","_id":"9410","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_created":"2021-05-23T22:01:43Z","article_processing_charge":"No","status":"public"},{"publisher":"Wiley","year":"2021","language":[{"iso":"eng"}],"volume":30,"file":[{"content_type":"application/pdf","file_id":"9545","relation":"main_file","creator":"kschuh","file_size":1031978,"checksum":"e6f4731365bde2614b333040a08265d8","file_name":"2021_MolecularEcology_Berdan.pdf","date_updated":"2021-06-11T15:34:53Z","success":1,"date_created":"2021-06-11T15:34:53Z","access_level":"open_access"}],"fulldoi":"https://doi.org/10.1111/mec.15936","project":[{"_id":"265B41B8-B435-11E9-9278-68D0E5697425","grant_number":"797747","name":"Theoretical and empirical approaches to understanding Parallel Adaptation","call_identifier":"H2020"}],"scopus_import":"1","oa_version":"Published Version","citation":{"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>","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.","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.","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>","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>."},"department":[{"_id":"NiBa"}],"ec_funded":1,"ddc":["570"],"doi":"10.1111/mec.15936","has_accepted_license":"1","title":"Unboxing mutations: Connecting mutation types with evolutionary consequences","publication_status":"published","external_id":{"isi":["000652056400001"]},"publication":"Molecular Ecology","publication_identifier":{"eissn":["1365-294X"],"issn":["0962-1083"]},"type":"journal_article","issue":"12","isi":1,"page":"2710-2723","author":[{"first_name":"Emma L.","last_name":"Berdan","full_name":"Berdan, Emma L."},{"first_name":"Alexandre","full_name":"Blanckaert, Alexandre","last_name":"Blanckaert"},{"last_name":"Slotte","full_name":"Slotte, Tanja","first_name":"Tanja"},{"last_name":"Suh","full_name":"Suh, Alexander","first_name":"Alexander"},{"last_name":"Westram","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M"},{"first_name":"Inês","full_name":"Fragata, Inês","last_name":"Fragata"}],"date_created":"2021-06-06T22:01:31Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","_id":"9470","status":"public","article_processing_charge":"No","date_published":"2021-06-01T00:00:00Z","oa":1,"quality_controlled":"1","tmp":{"short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"day":"01","month":"06","date_updated":"2026-04-16T08:19:26Z","abstract":[{"text":"A key step in understanding the genetic basis of different evolutionary outcomes (e.g., adaptation) is to determine the roles played by different mutation types (e.g., SNPs, translocations and inversions). To do this we must simultaneously consider different mutation types in an evolutionary framework. Here, we propose a research framework that directly utilizes the most important characteristics of mutations, their population genetic effects, to determine their relative evolutionary significance in a given scenario. We review known population genetic effects of different mutation types and show how these may be connected to different evolutionary outcomes. We provide examples of how to implement this framework and pinpoint areas where more data, theory and synthesis are needed. Linking experimental and theoretical approaches to examine different mutation types simultaneously is a critical step towards understanding their evolutionary significance.","lang":"eng"}],"file_date_updated":"2021-06-11T15:34:53Z","intvolume":"        30","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)."},{"has_accepted_license":"1","doi":"10.1371/journal.pone.0255267","ddc":["610"],"department":[{"_id":"NiBa"}],"publication_identifier":{"eissn":["1932-6203"]},"publication":"PLoS ONE","article_number":"e0255267","external_id":{"isi":["000685248200095"],"pmid":["34324553"]},"publication_status":"published","title":"Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program","year":"2021","publisher":"Public Library of Science","pmid":1,"oa_version":"Published Version","citation":{"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>","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>.","ista":"Hledik M, Polechova J, Beiglböck M, Herdina AN, Strassl R, Posch M. 2021. Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program. PLoS ONE. 16(7), e0255267.","ieee":"M. Hledik, J. Polechova, M. Beiglböck, A. N. Herdina, R. Strassl, and M. Posch, “Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program,” <i>PLoS ONE</i>, vol. 16, no. 7. Public Library of Science, 2021.","short":"M. Hledik, J. Polechova, M. Beiglböck, A.N. Herdina, R. Strassl, M. Posch, PLoS ONE 16 (2021).","mla":"Hledik, Michal, et al. “Analysis of the Specificity of a COVID-19 Antigen Test in the Slovak Mass Testing Program.” <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>.","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>"},"scopus_import":"1","fulldoi":"https://doi.org/10.1371/journal.pone.0255267","file":[{"date_created":"2021-08-09T11:52:14Z","success":1,"access_level":"open_access","creator":"asandaue","relation":"main_file","file_id":"9835","content_type":"application/pdf","date_updated":"2021-08-09T11:52:14Z","file_name":"2021_PLoSONE_Hledík.pdf","checksum":"ae4df60eb62f4491278588548d0c1f93","file_size":773921}],"volume":16,"language":[{"iso":"eng"}],"date_updated":"2023-08-10T14:26:32Z","month":"07","day":"29","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","oa":1,"date_published":"2021-07-29T00:00:00Z","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.","intvolume":"        16","file_date_updated":"2021-08-09T11:52:14Z","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"}],"author":[{"full_name":"Hledik, Michal","last_name":"Hledik","first_name":"Michal","id":"4171253A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jitka","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","last_name":"Polechova","full_name":"Polechova, Jitka","orcid":"0000-0003-0951-3112"},{"full_name":"Beiglböck, Mathias","last_name":"Beiglböck","first_name":"Mathias"},{"last_name":"Herdina","full_name":"Herdina, Anna Nele","first_name":"Anna Nele"},{"last_name":"Strassl","full_name":"Strassl, Robert","first_name":"Robert"},{"full_name":"Posch, Martin","last_name":"Posch","first_name":"Martin"}],"article_type":"original","issue":"7","isi":1,"type":"journal_article","article_processing_charge":"Yes","status":"public","_id":"9816","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_created":"2021-08-08T22:01:26Z"},{"OA_place":"publisher","pmid":1,"acknowledged_ssus":[{"_id":"ScienComp"}],"year":"2021","publisher":"Genetics Society of America","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/genetics/iyaa025"}],"volume":217,"fulldoi":"https://doi.org/10.1093/genetics/iyaa025","project":[{"name":"Sex chromosomes and species barriers","call_identifier":"FWF","_id":"2662AADE-B435-11E9-9278-68D0E5697425","grant_number":"M02463"}],"citation":{"mla":"Fraisse, Christelle, and Himani Sachdeva. “The Rates of Introgression and Barriers to Genetic Exchange between Hybridizing Species: Sex Chromosomes vs Autosomes.” <i>Genetics</i>, vol. 217, no. 2, iyaa025, Genetics Society of America, 2021, doi:<a href=\"https://doi.org/10.1093/genetics/iyaa025\">10.1093/genetics/iyaa025</a>.","apa":"Fraisse, C., &#38; Sachdeva, H. (2021). The rates of introgression and barriers to genetic exchange between hybridizing species: Sex chromosomes vs autosomes. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1093/genetics/iyaa025\">https://doi.org/10.1093/genetics/iyaa025</a>","short":"C. Fraisse, H. Sachdeva, Genetics 217 (2021).","chicago":"Fraisse, Christelle, and Himani Sachdeva. “The Rates of Introgression and Barriers to Genetic Exchange between Hybridizing Species: Sex Chromosomes vs Autosomes.” <i>Genetics</i>. Genetics Society of America, 2021. <a href=\"https://doi.org/10.1093/genetics/iyaa025\">https://doi.org/10.1093/genetics/iyaa025</a>.","ama":"Fraisse C, Sachdeva H. The rates of introgression and barriers to genetic exchange between hybridizing species: Sex chromosomes vs autosomes. <i>Genetics</i>. 2021;217(2). doi:<a href=\"https://doi.org/10.1093/genetics/iyaa025\">10.1093/genetics/iyaa025</a>","ista":"Fraisse C, Sachdeva H. 2021. The rates of introgression and barriers to genetic exchange between hybridizing species: Sex chromosomes vs autosomes. Genetics. 217(2), iyaa025.","ieee":"C. Fraisse and H. Sachdeva, “The rates of introgression and barriers to genetic exchange between hybridizing species: Sex chromosomes vs autosomes,” <i>Genetics</i>, vol. 217, no. 2. Genetics Society of America, 2021."},"scopus_import":"1","oa_version":"Published Version","department":[{"_id":"NiBa"}],"doi":"10.1093/genetics/iyaa025","ddc":["570"],"publication_status":"published","title":"The rates of introgression and barriers to genetic exchange between hybridizing species: Sex chromosomes vs autosomes","external_id":{"pmid":["33724409"],"isi":["000637218100005"]},"publication_identifier":{"issn":["1943-2631"]},"publication":"Genetics","article_number":"iyaa025","type":"journal_article","issue":"2","isi":1,"corr_author":"1","article_type":"original","author":[{"orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle"},{"full_name":"Sachdeva, Himani","last_name":"Sachdeva","first_name":"Himani","id":"42377A0A-F248-11E8-B48F-1D18A9856A87"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2021-02-18T14:41:30Z","_id":"9168","status":"public","article_processing_charge":"No","date_published":"2021-02-01T00:00:00Z","quality_controlled":"1","day":"01","oa":1,"month":"02","date_updated":"2026-07-28T12:39:03Z","OA_type":"free access","acknowledgement":"The computations were performed with the IST Austria High-Performance Computing (HPC) Cluster and the Institut Français de Bioinformatique (IFB) Core Cluster. We are grateful to Nick Barton and Beatriz Vicoso for critical comments on the model and the manuscript. We also thank Brian Charlesworth, Stuart Baird, and an anonymous reviewer for insightful comments.\r\nC.F. was supported by an Austrian Science Foundation FWF grant (Project M 2463-B29).","intvolume":"       217","abstract":[{"lang":"eng","text":"Interspecific crossing experiments have shown that sex chromosomes play a major role in reproductive isolation between many pairs of species. However, their ability to act as reproductive barriers, which hamper interspecific genetic exchange, has rarely been evaluated quantitatively compared to Autosomes. This genome-wide limitation of gene flow is essential for understanding the complete separation of species, and thus speciation. Here, we develop a mainland-island model of secondary contact between hybridizing species of an XY (or ZW) sexual system. We obtain theoretical predictions for the frequency of introgressed alleles, and the strength of the barrier to neutral gene flow for the two types of chromosomes carrying multiple interspecific barrier loci. Theoretical predictions are obtained for scenarios where introgressed alleles are rare. We show that the same analytical expressions apply for sex chromosomes and autosomes, but with different sex-averaged effective parameters. The specific features of sex chromosomes (hemizygosity and absence of recombination in the heterogametic sex) lead to reduced levels of introgression on the X (or Z) compared to autosomes. This effect can be enhanced by certain types of sex-biased forces, but it remains overall small (except when alleles causing incompatibilities are recessive). We discuss these predictions in the light of empirical data comprising model-based tests of introgression and cline surveys in various biological systems."}]}]