[{"publication_identifier":{"issn":["2056-3744"]},"publication":"Evolution Letters","ec_funded":1,"article_processing_charge":"Yes (via OA deal)","volume":7,"date_created":"2023-02-06T13:59:12Z","oa":1,"quality_controlled":"1","article_number":"qrac004","ddc":["570"],"article_type":"original","file_date_updated":"2023-08-16T11:43:33Z","publisher":"Oxford University Press","abstract":[{"text":"Differentiated X chromosomes are expected to have higher rates of adaptive divergence than autosomes, if new beneficial mutations are recessive (the “faster-X effect”), largely because these mutations are immediately exposed to selection in males. The evolution of X chromosomes after they stop recombining in males, but before they become hemizygous, has not been well explored theoretically. We use the diffusion approximation to infer substitution rates of beneficial and deleterious mutations under such a scenario. Our results show that selection is less efficient on diploid X loci than on autosomal and hemizygous X loci under a wide range of parameters. This “slower-X” effect is stronger for genes affecting primarily (or only) male fitness, and for sexually antagonistic genes. These unusual dynamics suggest that some of the peculiar features of X chromosomes, such as the differential accumulation of genes with sex-specific functions, may start arising earlier than previously appreciated.","lang":"eng"}],"status":"public","month":"02","author":[{"full_name":"Mrnjavac, Andrea","last_name":"Mrnjavac","id":"353FAC84-AE61-11E9-8BFC-00D3E5697425","first_name":"Andrea"},{"full_name":"Khudiakova, Kseniia","orcid":"0000-0002-6246-1465","id":"4E6DC800-AE37-11E9-AC72-31CAE5697425","last_name":"Khudiakova","first_name":"Kseniia"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","first_name":"Beatriz","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz"}],"publication_status":"published","citation":{"ista":"Mrnjavac A, Khudiakova K, Barton NH, Vicoso B. 2023. Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution. Evolution Letters. 7(1), qrac004.","chicago":"Mrnjavac, Andrea, Kseniia Khudiakova, Nicholas H Barton, and Beatriz Vicoso. “Slower-X: Reduced Efficiency of Selection in the Early Stages of X Chromosome Evolution.” <i>Evolution Letters</i>. Oxford University Press, 2023. <a href=\"https://doi.org/10.1093/evlett/qrac004\">https://doi.org/10.1093/evlett/qrac004</a>.","short":"A. Mrnjavac, K. Khudiakova, N.H. Barton, B. Vicoso, Evolution Letters 7 (2023).","mla":"Mrnjavac, Andrea, et al. “Slower-X: Reduced Efficiency of Selection in the Early Stages of X Chromosome Evolution.” <i>Evolution Letters</i>, vol. 7, no. 1, qrac004, Oxford University Press, 2023, doi:<a href=\"https://doi.org/10.1093/evlett/qrac004\">10.1093/evlett/qrac004</a>.","apa":"Mrnjavac, A., Khudiakova, K., Barton, N. H., &#38; Vicoso, B. (2023). Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution. <i>Evolution Letters</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/evlett/qrac004\">https://doi.org/10.1093/evlett/qrac004</a>","ieee":"A. Mrnjavac, K. Khudiakova, N. H. Barton, and B. Vicoso, “Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution,” <i>Evolution Letters</i>, vol. 7, no. 1. Oxford University Press, 2023.","ama":"Mrnjavac A, Khudiakova K, Barton NH, Vicoso B. Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution. <i>Evolution Letters</i>. 2023;7(1). doi:<a href=\"https://doi.org/10.1093/evlett/qrac004\">10.1093/evlett/qrac004</a>"},"project":[{"grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics","_id":"256E75B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"715257","_id":"250BDE62-B435-11E9-9278-68D0E5697425","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","call_identifier":"H2020"}],"corr_author":"1","title":"Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution","_id":"12521","intvolume":"         7","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"type":"journal_article","oa_version":"Published Version","has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"scopus_import":"1","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"18531"}]},"isi":1,"issue":"1","language":[{"iso":"eng"}],"acknowledgement":"We thank the Vicoso and Barton groups and ISTA Scientific Computing Unit. We also thank two anonymous reviewers for their valuable comments. This work was supported by the European Research Council under the European Union’s Horizon 2020 research and innovation program (grant agreements no. 715257 and no. 716117).","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"external_id":{"pmid":["37065438"],"isi":["001021692200001"]},"file":[{"creator":"dernst","date_created":"2023-08-16T11:43:33Z","access_level":"open_access","file_id":"14068","success":1,"date_updated":"2023-08-16T11:43:33Z","relation":"main_file","file_size":2592189,"file_name":"2023_EvLetters_Mrnjavac.pdf","checksum":"a240a041cb9b9b7c8ba93a4706674a3f","content_type":"application/pdf"}],"date_published":"2023-02-01T00:00:00Z","date_updated":"2026-07-25T22:30:19Z","doi":"10.1093/evlett/qrac004","day":"01","year":"2023","pmid":1},{"title":"The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome","publication_status":"published","citation":{"mla":"Lasne, Clementine, et al. “The Scorpionfly (Panorpa Cognata) Genome Highlights Conserved and Derived Features of the Peculiar Dipteran X Chromosome.” <i>Molecular Biology and Evolution</i>, vol. 40, no. 12, msad245, Oxford University Press, 2023, doi:<a href=\"https://doi.org/10.1093/molbev/msad245\">10.1093/molbev/msad245</a>.","ista":"Lasne C, Elkrewi MN, Toups MA, Layana Franco LA, Macon A, Vicoso B. 2023. The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome. Molecular Biology and Evolution. 40(12), msad245.","short":"C. Lasne, M.N. Elkrewi, M.A. Toups, L.A. Layana Franco, A. Macon, B. Vicoso, Molecular Biology and Evolution 40 (2023).","chicago":"Lasne, Clementine, Marwan N Elkrewi, Melissa A Toups, Lorena Alexandra Layana Franco, Ariana Macon, and Beatriz Vicoso. “The Scorpionfly (Panorpa Cognata) Genome Highlights Conserved and Derived Features of the Peculiar Dipteran X Chromosome.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2023. <a href=\"https://doi.org/10.1093/molbev/msad245\">https://doi.org/10.1093/molbev/msad245</a>.","apa":"Lasne, C., Elkrewi, M. N., Toups, M. A., Layana Franco, L. A., Macon, A., &#38; Vicoso, B. (2023). The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msad245\">https://doi.org/10.1093/molbev/msad245</a>","ieee":"C. Lasne, M. N. Elkrewi, M. A. Toups, L. A. Layana Franco, A. Macon, and B. Vicoso, “The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome,” <i>Molecular Biology and Evolution</i>, vol. 40, no. 12. Oxford University Press, 2023.","ama":"Lasne C, Elkrewi MN, Toups MA, Layana Franco LA, Macon A, Vicoso B. The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome. <i>Molecular Biology and Evolution</i>. 2023;40(12). doi:<a href=\"https://doi.org/10.1093/molbev/msad245\">10.1093/molbev/msad245</a>"},"author":[{"last_name":"Lasne","id":"02225f57-50d2-11eb-9ed8-8c92b9a34237","first_name":"Clementine","full_name":"Lasne, Clementine","orcid":"0000-0002-1197-8616"},{"id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","last_name":"Elkrewi","first_name":"Marwan N","full_name":"Elkrewi, Marwan N","orcid":"0000-0002-5328-7231"},{"full_name":"Toups, Melissa A","orcid":"0000-0002-9752-7380","last_name":"Toups","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","first_name":"Melissa A"},{"orcid":"0000-0002-1253-6297","full_name":"Layana Franco, Lorena Alexandra","first_name":"Lorena Alexandra","last_name":"Layana Franco","id":"02814589-eb8f-11eb-b029-a70074f3f18f"},{"last_name":"Macon","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","first_name":"Ariana","full_name":"Macon, Ariana"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","first_name":"Beatriz","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz"}],"corr_author":"1","project":[{"name":"The highjacking of meiosis for asexual reproduction","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","grant_number":"F8810"},{"name":"Mechanisms and Evolution of Reproductive Plasticity","_id":"ebb230e0-77a9-11ec-83b8-87a37e0241d3","grant_number":"ESP39 49461"}],"department":[{"_id":"BeVi"}],"intvolume":"        40","_id":"14613","oa_version":"Published Version","type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","has_accepted_license":"1","keyword":["Genetics","Molecular Biology","Ecology","Evolution","Behavior and Systematics"],"scopus_import":"1","related_material":{"link":[{"url":"https://ista.ac.at/en/news/on-the-hunt/","relation":"press_release","description":"News on ISTA webpage"}],"record":[{"status":"public","id":"14614","relation":"research_data"},{"id":"19386","relation":"dissertation_contains","status":"public"}]},"acknowledged_ssus":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"acknowledgement":"We thank the Vicoso lab for their assistance with specimen collection, and Tim Connallon for valuable comments and suggestions on earlier versions of the manuscript. Computational resources and support were provided by the Scientific Computing unit at the ISTA. This research was supported by grants from the Austrian Science Foundation to C.L.\r\n(FWF ESP 39), and to B.V. (FWF SFB F88-10).","isi":1,"issue":"12","date_published":"2023-12-01T00:00:00Z","date_updated":"2026-07-25T22:31:04Z","external_id":{"pmid":["37988296"],"isi":["001122489000003"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"date_updated":"2024-01-02T11:39:38Z","relation":"main_file","file_size":8623505,"file_name":"2023_MolecularBioEvo_Lasne.pdf","checksum":"47c1c72fb499f26ea52d216b242208c8","content_type":"application/pdf","creator":"dernst","date_created":"2024-01-02T11:39:38Z","access_level":"open_access","file_id":"14727","success":1}],"day":"01","year":"2023","pmid":1,"doi":"10.1093/molbev/msad245","publication_identifier":{"eissn":["1537-1719"],"issn":["0737-4038"]},"publication":"Molecular Biology and Evolution","date_created":"2023-11-27T16:14:37Z","oa":1,"quality_controlled":"1","article_processing_charge":"Yes","volume":40,"file_date_updated":"2024-01-02T11:39:38Z","article_type":"original","publisher":"Oxford University Press","ddc":["570"],"article_number":"msad245","month":"12","abstract":[{"lang":"eng","text":"Many insects carry an ancient X chromosome - the Drosophila Muller element F - that likely predates their origin. Interestingly, the X has undergone turnover in multiple fly species (Diptera) after being conserved for more than 450 MY. The long evolutionary distance between Diptera and other sequenced insect clades makes it difficult to infer what could have contributed to this sudden increase in rate of turnover. Here, we produce the first genome and transcriptome of a long overlooked sister-order to Diptera: Mecoptera. We compare the scorpionfly Panorpa cognata X-chromosome gene content, expression, and structure, to that of several dipteran species as well as more distantly-related insect orders (Orthoptera and Blattodea). We find high conservation of gene content between the mecopteran X and the dipteran Muller F element, as well as several shared biological features, such as the presence of dosage compensation and a low amount of genetic diversity, consistent with a low recombination rate. However, the two homologous X chromosomes differ strikingly in their size and number of genes they carry. Our results therefore support a common ancestry of the mecopteran and ancestral dipteran X chromosomes, and suggest that Muller element F shrank in size and gene content after the split of Diptera and Mecoptera, which may have contributed to its turnover in dipteran insects."}],"status":"public"},{"type":"journal_article","oa_version":"Submitted Version","_id":"10926","intvolume":"        88","department":[{"_id":"BeVi"}],"author":[{"full_name":"Perini, Samuel","last_name":"Perini","first_name":"Samuel"},{"first_name":"Rogerk","last_name":"Butlin","full_name":"Butlin, Rogerk"},{"first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969"},{"first_name":"Kerstin","last_name":"Johannesson","full_name":"Johannesson, Kerstin"}],"citation":{"mla":"Perini, Samuel, et al. “Very Short Mountings Are Enough for Sperm Transfer in Littorina Saxatilis.” <i>Journal of Molluscan Studies</i>, vol. 88, no. 1, eyab049, Oxford University Press, 2022, doi:<a href=\"https://doi.org/10.1093/mollus/eyab049\">10.1093/mollus/eyab049</a>.","ista":"Perini S, Butlin R, Westram AM, Johannesson K. 2022. Very short mountings are enough for sperm transfer in Littorina saxatilis. Journal of Molluscan Studies. 88(1), eyab049.","chicago":"Perini, Samuel, Rogerk Butlin, Anja M Westram, and Kerstin Johannesson. “Very Short Mountings Are Enough for Sperm Transfer in Littorina Saxatilis.” <i>Journal of Molluscan Studies</i>. Oxford University Press, 2022. <a href=\"https://doi.org/10.1093/mollus/eyab049\">https://doi.org/10.1093/mollus/eyab049</a>.","short":"S. Perini, R. Butlin, A.M. Westram, K. Johannesson, Journal of Molluscan Studies 88 (2022).","apa":"Perini, S., Butlin, R., Westram, A. M., &#38; Johannesson, K. (2022). Very short mountings are enough for sperm transfer in Littorina saxatilis. <i>Journal of Molluscan Studies</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/mollus/eyab049\">https://doi.org/10.1093/mollus/eyab049</a>","ieee":"S. Perini, R. Butlin, A. M. Westram, and K. Johannesson, “Very short mountings are enough for sperm transfer in Littorina saxatilis,” <i>Journal of Molluscan Studies</i>, vol. 88, no. 1. Oxford University Press, 2022.","ama":"Perini S, Butlin R, Westram AM, Johannesson K. Very short mountings are enough for sperm transfer in Littorina saxatilis. <i>Journal of Molluscan Studies</i>. 2022;88(1). doi:<a href=\"https://doi.org/10.1093/mollus/eyab049\">10.1093/mollus/eyab049</a>"},"publication_status":"published","title":"Very short mountings are enough for sperm transfer in Littorina saxatilis","doi":"10.1093/mollus/eyab049","day":"01","year":"2022","external_id":{"isi":["000759081600002"]},"date_published":"2022-03-01T00:00:00Z","date_updated":"2025-05-14T11:05:28Z","issue":"1","isi":1,"main_file_link":[{"open_access":"1","url":"https://eprints.whiterose.ac.uk/187332/"}],"language":[{"iso":"eng"}],"scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Journal of Molluscan Studies","publication_identifier":{"eissn":["1464-3766"],"issn":["0260-1230"]},"status":"public","abstract":[{"text":"Conflict over reproduction between females and males exists because of anisogamy and promiscuity. Together they generate differences in fitness optima between the sexes and result in antagonistic coevolution of female and male reproductive traits. Mounting duration is likely to be a compromise between male and female interests whose outcome depends on the intensity of sexual selection. The timing of sperm transfer during mounting is critical. For example, mountings may be interrupted before sperm is transferred as a consequence of female or male choice, or they may be prolonged to function as mate guarding. In the highly promiscuous intertidal snail Littorina saxatilis, mountings vary substantially in duration, from less than a minute to more than an hour, and it has been assumed that mountings of a few minutes do not result in any sperm being transferred. Here, we examined the timing of sperm transfer, a reproductive trait that is likely affected by sexual conflict. We performed time-controlled mounting trials using L. saxatilis males and virgin females, aiming to examine indirectly when the transfer of sperm starts. We observed the relationship between mounting duration and the proportion of developing embryos out of all eggs and embryos in the brood pouch. Developing embryos were observed in similar proportions in all treatments (i.e. 1, 5 and 10 or more minutes at which mountings were artificially interrupted), suggesting that sperm transfer begins rapidly (within 1 min) in L. saxatilis and very short matings do not result in sperm shortage in the females. We discuss how the observed pattern can be influenced by predation risk, population density, and female status and receptivity.","lang":"eng"}],"month":"03","article_number":"eyab049","publisher":"Oxford University Press","article_type":"original","article_processing_charge":"No","volume":88,"quality_controlled":"1","date_created":"2022-03-27T22:01:46Z","oa":1},{"ec_funded":1,"publication":"Evolution","publication_identifier":{"issn":["0014-3820"],"eissn":["1558-5646"]},"article_type":"original","file_date_updated":"2022-08-05T06:19:28Z","publisher":"Wiley","ddc":["570"],"oa":1,"date_created":"2022-04-24T22:01:44Z","quality_controlled":"1","article_processing_charge":"No","volume":76,"month":"05","abstract":[{"text":"Hybridization is a common evolutionary process with multiple possible outcomes. In vertebrates, interspecific hybridization has repeatedly generated parthenogenetic hybrid species. However, it is unknown whether the generation of parthenogenetic hybrids is a rare outcome of frequent hybridization between sexual species within a genus or the typical outcome of rare hybridization events. Darevskia is a genus of rock lizards with both hybrid parthenogenetic and sexual species. Using capture sequencing, we estimate phylogenetic relationships and gene flow among the sexual species, to determine how introgressive hybridization relates to the origins of parthenogenetic hybrids. We find evidence for widespread hybridization with gene flow, both between recently diverged species and deep branches. Surprisingly, we find no signal of gene flow between parental species of the parthenogenetic hybrids, suggesting that the parental pairs were either reproductively or geographically isolated early in their divergence. The generation of parthenogenetic hybrids in Darevskia is, then, a rare outcome of the total occurrence of hybridization within the genus, but the typical outcome when specific species pairs hybridize. Our results question the conventional view that parthenogenetic lineages are generated by hybridization in a window of divergence. Instead, they suggest that some lineages possess specific properties that underpin successful parthenogenetic reproduction.","lang":"eng"}],"status":"public","page":"899-914","title":"Parthenogenesis in Darevskia lizards: A rare outcome of common hybridization, not a common outcome of rare hybridization","publication_status":"published","author":[{"full_name":"Freitas, Susana","first_name":"Susana","last_name":"Freitas"},{"full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram"},{"full_name":"Schwander, Tanja","last_name":"Schwander","first_name":"Tanja"},{"last_name":"Arakelyan","first_name":"Marine","full_name":"Arakelyan, Marine"},{"last_name":"Ilgaz","first_name":"Çetin","full_name":"Ilgaz, Çetin"},{"full_name":"Kumlutas, Yusuf","last_name":"Kumlutas","first_name":"Yusuf"},{"last_name":"Harris","first_name":"David James","full_name":"Harris, David James"},{"full_name":"Carretero, Miguel A.","last_name":"Carretero","first_name":"Miguel A."},{"first_name":"Roger K.","last_name":"Butlin","full_name":"Butlin, Roger K."}],"citation":{"ieee":"S. Freitas <i>et al.</i>, “Parthenogenesis in Darevskia lizards: A rare outcome of common hybridization, not a common outcome of rare hybridization,” <i>Evolution</i>, vol. 76, no. 5. Wiley, pp. 899–914, 2022.","apa":"Freitas, S., Westram, A. M., Schwander, T., Arakelyan, M., Ilgaz, Ç., Kumlutas, Y., … Butlin, R. K. (2022). Parthenogenesis in Darevskia lizards: A rare outcome of common hybridization, not a common outcome of rare hybridization. <i>Evolution</i>. Wiley. <a href=\"https://doi.org/10.1111/evo.14462\">https://doi.org/10.1111/evo.14462</a>","ama":"Freitas S, Westram AM, Schwander T, et al. Parthenogenesis in Darevskia lizards: A rare outcome of common hybridization, not a common outcome of rare hybridization. <i>Evolution</i>. 2022;76(5):899-914. doi:<a href=\"https://doi.org/10.1111/evo.14462\">10.1111/evo.14462</a>","mla":"Freitas, Susana, et al. “Parthenogenesis in Darevskia Lizards: A Rare Outcome of Common Hybridization, Not a Common Outcome of Rare Hybridization.” <i>Evolution</i>, vol. 76, no. 5, Wiley, 2022, pp. 899–914, doi:<a href=\"https://doi.org/10.1111/evo.14462\">10.1111/evo.14462</a>.","ista":"Freitas S, Westram AM, Schwander T, Arakelyan M, Ilgaz Ç, Kumlutas Y, Harris DJ, Carretero MA, Butlin RK. 2022. Parthenogenesis in Darevskia lizards: A rare outcome of common hybridization, not a common outcome of rare hybridization. Evolution. 76(5), 899–914.","short":"S. Freitas, A.M. Westram, T. Schwander, M. Arakelyan, Ç. Ilgaz, Y. Kumlutas, D.J. Harris, M.A. Carretero, R.K. Butlin, Evolution 76 (2022) 899–914.","chicago":"Freitas, Susana, Anja M Westram, Tanja Schwander, Marine Arakelyan, Çetin Ilgaz, Yusuf Kumlutas, David James Harris, Miguel A. Carretero, and Roger K. Butlin. “Parthenogenesis in Darevskia Lizards: A Rare Outcome of Common Hybridization, Not a Common Outcome of Rare Hybridization.” <i>Evolution</i>. Wiley, 2022. <a href=\"https://doi.org/10.1111/evo.14462\">https://doi.org/10.1111/evo.14462</a>."},"project":[{"call_identifier":"H2020","name":"Theoretical and empirical approaches to understanding Parallel Adaptation","_id":"265B41B8-B435-11E9-9278-68D0E5697425","grant_number":"797747"}],"oa_version":"Published Version","type":"journal_article","department":[{"_id":"NiBa"},{"_id":"BeVi"}],"intvolume":"        76","_id":"11334","language":[{"iso":"eng"}],"acknowledgement":"The authors thank A. van der Meijden and F. Ahmadzadeh for providing specimens and tissue samples, and A. Vardanyan, C. Corti, F. Jorge, and S. Drovetski for support during field work. The authors also thank S. Qiu for assistance with python scripting, S. Rocha for her support in BEAST analysis, and B. Wielstra for his comments on\r\na previous version of the manuscript. SF was funded by FCT grant SFRH/BD/81483/2011 (a PhD individual grant). AMW was funded by the European Union’s Horizon 2020 research and innovation programme under Marie Skłodowska-Curie grant agreement no. 797747. TS acknowledges funding from the Swiss National Science Foundation (grants\r\nPP00P3_170627 and 31003A_182495). The work was carried out under financial support of the projects “Preserving Armenian biodiversity: Joint Portuguese – Armenian program for training in modern conservation biology” of Gulbenkian Foundation (Portugal) and PTDC/BIABEC/101256/2008 of Fundação para a Ciência e a Tecnologia (FCT, Portugal).","isi":1,"issue":"5","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","has_accepted_license":"1","scopus_import":"1","year":"2022","day":"01","pmid":1,"doi":"10.1111/evo.14462","date_updated":"2025-04-14T07:48:21Z","date_published":"2022-05-01T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","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)"},"external_id":{"pmid":["35323995"],"isi":["000781632500001"]},"file":[{"relation":"main_file","date_updated":"2022-08-05T06:19:28Z","content_type":"application/pdf","checksum":"c27c025ae9afcf6c804d46a909775ee5","file_name":"2022_Evolution_Freitas.pdf","file_size":2855214,"access_level":"open_access","date_created":"2022-08-05T06:19:28Z","creator":"dernst","success":1,"file_id":"11729"}]},{"publication_identifier":{"issn":["0962-8436"],"eissn":["1471-2970"]},"publication":"Philosophical Transactions of the Royal Society B: Biological Sciences","status":"public","abstract":[{"lang":"eng","text":"Local adaptation leads to differences between populations within a species. In many systems, similar environmental contrasts occur repeatedly, sometimes driving parallel phenotypic evolution. Understanding the genomic basis of local adaptation and parallel evolution is a major goal of evolutionary genomics. It is now known that by preventing the break-up of favourable combinations of alleles across multiple loci, genetic architectures that reduce recombination, like chromosomal inversions, can make an important contribution to local adaptation. However, little is known about whether inversions also contribute disproportionately to parallel evolution. Our aim here is to highlight this knowledge gap, to showcase existing studies, and to illustrate the differences between genomic architectures with and without inversions using simple models. We predict that by generating stronger effective selection, inversions can sometimes speed up the parallel adaptive process or enable parallel adaptation where it would be impossible otherwise, but this is highly dependent on the spatial setting. We highlight that further empirical work is needed, in particular to cover a broader taxonomic range and to understand the relative importance of inversions compared to genomic regions without inversions."}],"month":"08","article_processing_charge":"Yes (via OA deal)","volume":377,"quality_controlled":"1","date_created":"2022-07-08T11:41:56Z","oa":1,"ddc":["570"],"article_number":"20210203","publisher":"Royal Society of London","article_type":"original","file_date_updated":"2023-02-02T08:20:29Z","_id":"11546","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"intvolume":"       377","type":"journal_article","oa_version":"Published Version","project":[{"name":"Snapdragon Speciation","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","grant_number":"P32166"}],"corr_author":"1","citation":{"ama":"Westram AM, Faria R, Johannesson K, Butlin R, Barton NH. Inversions and parallel evolution. <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>. 2022;377(1856). doi:<a href=\"https://doi.org/10.1098/rstb.2021.0203\">10.1098/rstb.2021.0203</a>","ieee":"A. M. Westram, R. Faria, K. Johannesson, R. Butlin, and N. H. Barton, “Inversions and parallel evolution,” <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>, vol. 377, no. 1856. Royal Society of London, 2022.","apa":"Westram, A. M., Faria, R., Johannesson, K., Butlin, R., &#38; Barton, N. H. (2022). Inversions and parallel evolution. <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>. Royal Society of London. <a href=\"https://doi.org/10.1098/rstb.2021.0203\">https://doi.org/10.1098/rstb.2021.0203</a>","mla":"Westram, Anja M., et al. “Inversions and Parallel Evolution.” <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>, vol. 377, no. 1856, 20210203, Royal Society of London, 2022, doi:<a href=\"https://doi.org/10.1098/rstb.2021.0203\">10.1098/rstb.2021.0203</a>.","short":"A.M. Westram, R. Faria, K. Johannesson, R. Butlin, N.H. Barton, Philosophical Transactions of the Royal Society B: Biological Sciences 377 (2022).","chicago":"Westram, Anja M, Rui Faria, Kerstin Johannesson, Roger Butlin, and Nicholas H Barton. “Inversions and Parallel Evolution.” <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>. Royal Society of London, 2022. <a href=\"https://doi.org/10.1098/rstb.2021.0203\">https://doi.org/10.1098/rstb.2021.0203</a>.","ista":"Westram AM, Faria R, Johannesson K, Butlin R, Barton NH. 2022. Inversions and parallel evolution. Philosophical Transactions of the Royal Society B: Biological Sciences. 377(1856), 20210203."},"publication_status":"published","author":[{"full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","first_name":"Anja M","last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Faria, Rui","last_name":"Faria","first_name":"Rui"},{"first_name":"Kerstin","last_name":"Johannesson","full_name":"Johannesson, Kerstin"},{"full_name":"Butlin, Roger","last_name":"Butlin","first_name":"Roger"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"title":"Inversions and parallel evolution","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"content_type":"application/pdf","file_name":"2022_PhilosophicalTransactionsB_Westram.pdf","checksum":"49f69428f3dcf5ce3ff281f7d199e9df","file_size":920304,"relation":"main_file","date_updated":"2023-02-02T08:20:29Z","success":1,"file_id":"12479","access_level":"open_access","date_created":"2023-02-02T08:20:29Z","creator":"dernst"}],"external_id":{"isi":["000812317300005"],"pmid":["35694747"]},"date_published":"2022-08-01T00:00:00Z","date_updated":"2025-06-12T06:10:18Z","doi":"10.1098/rstb.2021.0203","pmid":1,"year":"2022","day":"01","keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology"],"scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","issue":"1856","isi":1,"acknowledgement":"We thank the editor and two anonymous reviewers for their helpful and interesting comments on this manuscript.","language":[{"iso":"eng"}]},{"title":"Dioecy and chromosomal sex determination are maintained through allopolyploid speciation in the plant genus Mercurialis","project":[{"name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","_id":"250BDE62-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"715257"}],"corr_author":"1","author":[{"last_name":"Toups","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","first_name":"Melissa A","orcid":"0000-0002-9752-7380","full_name":"Toups, Melissa A"},{"full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","first_name":"Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"John R.","last_name":"Pannell","full_name":"Pannell, John R."}],"publication_status":"published","citation":{"mla":"Toups, Melissa A., et al. “Dioecy and Chromosomal Sex Determination Are Maintained through Allopolyploid Speciation in the Plant Genus Mercurialis.” <i>PLoS Genetics</i>, vol. 18, no. 7, e1010226, Public Library of Science, 2022, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1010226\">10.1371/journal.pgen.1010226</a>.","ista":"Toups MA, Vicoso B, Pannell JR. 2022. Dioecy and chromosomal sex determination are maintained through allopolyploid speciation in the plant genus Mercurialis. PLoS Genetics. 18(7), e1010226.","chicago":"Toups, Melissa A, Beatriz Vicoso, and John R. Pannell. “Dioecy and Chromosomal Sex Determination Are Maintained through Allopolyploid Speciation in the Plant Genus Mercurialis.” <i>PLoS Genetics</i>. Public Library of Science, 2022. <a href=\"https://doi.org/10.1371/journal.pgen.1010226\">https://doi.org/10.1371/journal.pgen.1010226</a>.","short":"M.A. Toups, B. Vicoso, J.R. Pannell, PLoS Genetics 18 (2022).","apa":"Toups, M. A., Vicoso, B., &#38; Pannell, J. R. (2022). Dioecy and chromosomal sex determination are maintained through allopolyploid speciation in the plant genus Mercurialis. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1010226\">https://doi.org/10.1371/journal.pgen.1010226</a>","ieee":"M. A. Toups, B. Vicoso, and J. R. Pannell, “Dioecy and chromosomal sex determination are maintained through allopolyploid speciation in the plant genus Mercurialis,” <i>PLoS Genetics</i>, vol. 18, no. 7. Public Library of Science, 2022.","ama":"Toups MA, Vicoso B, Pannell JR. Dioecy and chromosomal sex determination are maintained through allopolyploid speciation in the plant genus Mercurialis. <i>PLoS Genetics</i>. 2022;18(7). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1010226\">10.1371/journal.pgen.1010226</a>"},"oa_version":"Published Version","type":"journal_article","intvolume":"        18","department":[{"_id":"BeVi"}],"_id":"11703","acknowledgement":"JRP was supported by the Swiss National Science Foundation (https://www.snf.ch/en), Sinergia grant 26073998. BV was supported by the European Research Council (https://erc.europa.eu/) under the European Union’s Horizon 2020 research and innovation program, grant number 715257. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.\r\nPlants were grown in Lausanne by Aline Revel, and RNA extraction and library preparation were performed by Dessislava Savova Bianchi. All sequencing and the IsoSeq3 analysis were carried out by Center for Integrative Genomics at the University of Lausanne. All other computational analyses were performed on the server at IST Austria.","language":[{"iso":"eng"}],"issue":"7","isi":1,"scopus_import":"1","has_accepted_license":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","pmid":1,"year":"2022","day":"06","doi":"10.1371/journal.pgen.1010226","date_published":"2022-07-06T00:00:00Z","date_updated":"2025-04-14T07:41:20Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_size":1620272,"checksum":"aa4c137f82635e700856c359dccfaa0a","file_name":"2022_PLoSGenetics_Toups.pdf","content_type":"application/pdf","date_updated":"2022-08-01T07:49:25Z","relation":"main_file","file_id":"11708","success":1,"creator":"dernst","date_created":"2022-08-01T07:49:25Z","access_level":"open_access"}],"external_id":{"pmid":["35793353"],"isi":["000886643100006"]},"ec_funded":1,"publication":"PLoS Genetics","publication_identifier":{"eissn":["1553-7404"]},"publisher":"Public Library of Science","file_date_updated":"2022-08-01T07:49:25Z","article_type":"original","ddc":["570"],"article_number":"e1010226","quality_controlled":"1","date_created":"2022-07-31T22:01:48Z","oa":1,"article_processing_charge":"No","volume":18,"month":"07","status":"public","abstract":[{"text":"Polyploidization may precipitate dramatic changes to the genome, including chromosome rearrangements, gene loss, and changes in gene expression. In dioecious plants, the sex-determining mechanism may also be disrupted by polyploidization, with the potential evolution of hermaphroditism. However, while dioecy appears to have persisted through a ploidy transition in some species, it is unknown whether the newly formed polyploid maintained its sex-determining system uninterrupted, or whether dioecy re-evolved after a period of hermaphroditism. Here, we develop a bioinformatic pipeline using RNA-sequencing data from natural populations to demonstrate that the allopolyploid plant Mercurialis canariensis directly inherited its sex-determining region from one of its diploid progenitor species, M. annua, and likely remained dioecious through the transition. The sex-determining region of M. canariensis is smaller than that of its diploid progenitor, suggesting that the non-recombining region of M. annua expanded subsequent to the polyploid origin of M. canariensis. Homeologous pairs show partial sexual subfunctionalization. We discuss the possibility that gene duplicates created by polyploidization might contribute to resolving sexual antagonism.","lang":"eng"}]},{"contributor":[{"orcid":"0000-0002-5328-7231","first_name":"Marwan N","last_name":"Elkrewi","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425"},{"last_name":"Khauratovich","first_name":"Uladzislava"},{"first_name":"Melissa A","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","last_name":"Toups"},{"id":"57854184-AAE0-11E9-8D04-98D6E5697425","last_name":"Bett","first_name":"Vincent K"},{"first_name":"Andrea","id":"353FAC84-AE61-11E9-8BFC-00D3E5697425","last_name":"Mrnjavac"},{"first_name":"Ariana","last_name":"Macon","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-8441-5075","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle"},{"first_name":"Luca","last_name":"Sax"},{"id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","last_name":"Huylmans","first_name":"Ann K"},{"last_name":"Hontoria ","first_name":"Francisco"},{"orcid":"0000-0002-4579-8306","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz"}],"title":"Data from Elkrewi, Khauratovich, Toups et al. 2022, \"ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp\"","author":[{"full_name":"Elkrewi, Marwan N","orcid":"0000-0002-5328-7231","last_name":"Elkrewi","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","first_name":"Marwan N"}],"citation":{"ama":"Elkrewi MN. Data from Elkrewi, Khauratovich, Toups et al. 2022, “ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp.” 2022. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:11653\">10.15479/AT:ISTA:11653</a>","apa":"Elkrewi, M. N. (2022). Data from Elkrewi, Khauratovich, Toups et al. 2022, “ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:11653\">https://doi.org/10.15479/AT:ISTA:11653</a>","ieee":"M. N. Elkrewi, “Data from Elkrewi, Khauratovich, Toups et al. 2022, ‘ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp.’” Institute of Science and Technology Austria, 2022.","short":"M.N. Elkrewi, (2022).","chicago":"Elkrewi, Marwan N. “Data from Elkrewi, Khauratovich, Toups et Al. 2022, ‘ZW Sex-Chromosome Evolution and Contagious Parthenogenesis in Artemia Brine Shrimp.’” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/AT:ISTA:11653\">https://doi.org/10.15479/AT:ISTA:11653</a>.","ista":"Elkrewi MN. 2022. Data from Elkrewi, Khauratovich, Toups et al. 2022, ‘ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:11653\">10.15479/AT:ISTA:11653</a>.","mla":"Elkrewi, Marwan N. <i>Data from Elkrewi, Khauratovich, Toups et Al. 2022, “ZW Sex-Chromosome Evolution and Contagious Parthenogenesis in Artemia Brine Shrimp.”</i> Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:11653\">10.15479/AT:ISTA:11653</a>."},"corr_author":"1","oa_version":"Published Version","type":"research_data","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"_id":"11653","file_date_updated":"2022-08-08T22:30:04Z","publisher":"Institute of Science and Technology Austria","ddc":["570"],"date_created":"2022-07-26T11:01:47Z","has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"12248"}]},"article_processing_charge":"No","month":"08","day":"05","year":"2022","abstract":[{"text":"Eurasian brine shrimp (genus Artemia) have closely related sexual and asexual lineages of parthenogenetic females, which produce rare males at low frequencies. Although they are known to have ZW chromosomes, these are not well characterized, and it is unclear whether they are shared across the clade. Furthermore, the underlying genetic architecture of the transmission of asexuality, which can occur when rare males mate with closely related sexual females, is not well understood. We produced a chromosome-level assembly for the sexual Eurasian species A. sinica and characterized in detail the pair of sex chromosomes of this species. We combined this new assembly with short-read genomic data for the sexual species A. sp. Kazakhstan and several asexual lineages of A. parthenogenetica, allowing us to perform an in-depth characterization of sex-chromosome evolution across the genus. We identified a small differentiated region of the ZW pair that is shared by all sexual and asexual lineages, supporting the shared ancestry of the sex chromosomes. We also inferred that recombination suppression has spread to larger sections of the chromosome independently in the American and Eurasian lineages. Finally, we took advantage of a rare male, which we backcrossed to sexual females, to explore the genetic basis of asexuality. Our results suggest that parthenogenesis is likely partly controlled by a locus on the Z chromosome, highlighting the interplay between sex determination and asexuality.","lang":"eng"}],"doi":"10.15479/AT:ISTA:11653","status":"public","date_updated":"2025-04-15T08:34:17Z","date_published":"2022-08-05T00:00:00Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_id":"11655","description":"The folder contains the following datasets (fasta files, and text files):\nSup. Dataset 1: Genome assemblies: A. sinica male high quality assembly, A. sp. Kazakhstan\nmale draft assembly\nSup. Dataset 2: Male transcriptome assemblies for A. sinica and A. franciscana\nSup. Dataset 3: Male and female coverage for A. sinica, A. sp. Kazakhstan, A. urmiana, and\nA. parthenogenetica females and rare male.\nSup. Dataset 4: Artemia sinica Male:female FST per 1Kb window\nSup. Dataset 5: FASTA file with candidate W scaffolds\nSup. Dataset 6: Candidate W-derived transcripts and alignments\nSup. Dataset 7: Gene expression with genomic location\nSup. Dataset 8: VCF for asexual female and rare male\nSup. Dataset 9: FST between backcrossed asexual and control females (pooled analysis)\nSup. Dataset 10: VCF of backcrossed asexual and control females (individual analysis using\nA. sp. Kazakhstan as the reference), and inferred ancestry\nSup. Dataset 11: GO and DE annotations of all the Artemia sinica transcripts and their\nlocations in the Artemia sinica male genome.\n","date_created":"2022-07-26T12:37:52Z","creator":"melkrewi","title":"Supplementary Datasets","access_level":"open_access","file_size":2209382998,"content_type":"application/x-zip-compressed","checksum":"5f1d7c6d7ab5375ed2564521432bed0c","file_name":"Data.zip","embargo":"2022-08-07","date_updated":"2022-08-08T22:30:04Z","relation":"main_file"}]},{"status":"public","abstract":[{"lang":"eng","text":"Eurasian brine shrimp (genus Artemia) have closely related sexual and asexual lineages of parthenogenetic females, which produce rare males at low frequencies. Although they are known to have ZW chromosomes, these are not well characterized, and it is unclear whether they are shared across the clade. Furthermore, the underlying genetic architecture of the transmission of asexuality, which can occur when rare males mate with closely related sexual females, is not well understood. We produced a chromosome-level assembly for the sexual Eurasian species Artemia sinica and characterized in detail the pair of sex chromosomes of this species. We combined this new assembly with short-read genomic data for the sexual species Artemia sp. Kazakhstan and several asexual lineages of Artemia parthenogenetica, allowing us to perform an in-depth characterization of sex-chromosome evolution across the genus. We identified a small differentiated region of the ZW pair that is shared by all sexual and asexual lineages, supporting the shared ancestry of the sex chromosomes. We also inferred that recombination suppression has spread to larger sections of the chromosome independently in the American and Eurasian lineages. Finally, we took advantage of a rare male, which we backcrossed to sexual females, to explore the genetic basis of asexuality. Our results suggest that parthenogenesis is likely partly controlled by a locus on the Z chromosome, highlighting the interplay between sex determination and asexuality."}],"month":"10","article_number":"iyac123","ddc":["570"],"publisher":"Oxford University Press","article_type":"original","file_date_updated":"2023-01-30T08:59:58Z","volume":222,"article_processing_charge":"No","quality_controlled":"1","date_created":"2023-01-16T09:56:10Z","oa":1,"publication":"Genetics","ec_funded":1,"publication_identifier":{"issn":["1943-2631"]},"doi":"10.1093/genetics/iyac123","pmid":1,"day":"01","year":"2022","file":[{"file_name":"2022_Genetics_Elkrewi.pdf","checksum":"f79ff5383e882ea3f95f3da47a78029d","content_type":"application/pdf","file_size":1347136,"relation":"main_file","date_updated":"2023-01-30T08:59:58Z","success":1,"file_id":"12440","access_level":"open_access","creator":"dernst","date_created":"2023-01-30T08:59:58Z"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"external_id":{"pmid":["35977389"],"isi":["000850270300001"]},"date_updated":"2026-07-25T22:31:04Z","date_published":"2022-10-01T00:00:00Z","issue":"2","isi":1,"acknowledgement":"This work was supported by the European Research Council under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 715257) and by the Austrian Science Foundation (FWF SFB F88-10).\r\nWe thank the Vicoso group for comments on the manuscript and the ISTA Scientific computing team and the Vienna Biocenter Sequencing facility for technical support.","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"keyword":["Genetics"],"related_material":{"record":[{"status":"public","id":"11653","relation":"research_data"},{"id":"19386","relation":"dissertation_contains","status":"public"}]},"scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","has_accepted_license":"1","type":"journal_article","oa_version":"Published Version","_id":"12248","department":[{"_id":"BeVi"}],"intvolume":"       222","project":[{"call_identifier":"H2020","_id":"250BDE62-B435-11E9-9278-68D0E5697425","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","grant_number":"715257"},{"_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","name":"The highjacking of meiosis for asexual reproduction","grant_number":"F8810"}],"corr_author":"1","publication_status":"published","author":[{"id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","last_name":"Elkrewi","first_name":"Marwan N","orcid":"0000-0002-5328-7231","full_name":"Elkrewi, Marwan N"},{"last_name":"Khauratovich","id":"5eba06f4-97d8-11ed-9f8f-d826ebdd9434","first_name":"Uladzislava","full_name":"Khauratovich, Uladzislava"},{"id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","last_name":"Toups","first_name":"Melissa A","full_name":"Toups, Melissa A","orcid":"0000-0002-9752-7380"},{"first_name":"Vincent K","last_name":"Bett","id":"57854184-AAE0-11E9-8D04-98D6E5697425","full_name":"Bett, Vincent K"},{"full_name":"Mrnjavac, Andrea","first_name":"Andrea","last_name":"Mrnjavac","id":"353FAC84-AE61-11E9-8BFC-00D3E5697425"},{"last_name":"Macon","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","first_name":"Ariana","full_name":"Macon, Ariana"},{"last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle","orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle"},{"full_name":"Sax, Luca","last_name":"Sax","id":"701c5602-97d8-11ed-96b5-b52773c70189","first_name":"Luca"},{"full_name":"Huylmans, Ann K","orcid":"0000-0001-8871-4961","first_name":"Ann K","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","last_name":"Huylmans"},{"first_name":"Francisco","last_name":"Hontoria","full_name":"Hontoria, Francisco"},{"orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso"}],"citation":{"ama":"Elkrewi MN, Khauratovich U, Toups MA, et al. ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp. <i>Genetics</i>. 2022;222(2). doi:<a href=\"https://doi.org/10.1093/genetics/iyac123\">10.1093/genetics/iyac123</a>","apa":"Elkrewi, M. N., Khauratovich, U., Toups, M. A., Bett, V. K., Mrnjavac, A., Macon, A., … Vicoso, B. (2022). ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp. <i>Genetics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/genetics/iyac123\">https://doi.org/10.1093/genetics/iyac123</a>","ieee":"M. N. Elkrewi <i>et al.</i>, “ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp,” <i>Genetics</i>, vol. 222, no. 2. Oxford University Press, 2022.","mla":"Elkrewi, Marwan N., et al. “ZW Sex-Chromosome Evolution and Contagious Parthenogenesis in Artemia Brine Shrimp.” <i>Genetics</i>, vol. 222, no. 2, iyac123, Oxford University Press, 2022, doi:<a href=\"https://doi.org/10.1093/genetics/iyac123\">10.1093/genetics/iyac123</a>.","short":"M.N. Elkrewi, U. Khauratovich, M.A. Toups, V.K. Bett, A. Mrnjavac, A. Macon, C. Fraisse, L. Sax, A.K. Huylmans, F. Hontoria, B. Vicoso, Genetics 222 (2022).","chicago":"Elkrewi, Marwan N, Uladzislava Khauratovich, Melissa A Toups, Vincent K Bett, Andrea Mrnjavac, Ariana Macon, Christelle Fraisse, et al. “ZW Sex-Chromosome Evolution and Contagious Parthenogenesis in Artemia Brine Shrimp.” <i>Genetics</i>. Oxford University Press, 2022. <a href=\"https://doi.org/10.1093/genetics/iyac123\">https://doi.org/10.1093/genetics/iyac123</a>.","ista":"Elkrewi MN, Khauratovich U, Toups MA, Bett VK, Mrnjavac A, Macon A, Fraisse C, Sax L, Huylmans AK, Hontoria F, Vicoso B. 2022. ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp. Genetics. 222(2), iyac123."},"title":"ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp"},{"publication_identifier":{"eissn":["1471-2954"]},"publication":"Proceedings of the Royal Society B: Biological Sciences","ec_funded":1,"page":"20211985","status":"public","abstract":[{"text":"The t-haplotype of mice is a classical model for autosomal transmission distortion. A largely non-recombining variant of the proximal region of chromosome 17, it is transmitted to more than 90% of the progeny of heterozygous males through the disabling of sperm carrying a standard chromosome. While extensive genetic and functional work has shed light on individual genes involved in drive, much less is known about the evolution and function of the rest of its hundreds of genes. Here, we characterize the sequence and expression of dozens of t-specific transcripts and of their chromosome 17 homologues. Many genes showed reduced expression of the t-allele, but an equal number of genes showed increased expression of their t-copy, consistent with increased activity or a newly evolved function. Genes on the t-haplotype had a significantly higher non-synonymous substitution rate than their homologues on the standard chromosome, with several genes harbouring dN/dS ratios above 1. Finally, the t-haplotype has acquired at least two genes from other chromosomes, which show high and tissue-specific expression. These results provide a first overview of the gene content of this selfish element, and support a more dynamic evolutionary scenario than expected of a large genomic region with almost no recombination.","lang":"eng"}],"month":"02","article_processing_charge":"No","volume":289,"quality_controlled":"1","oa":1,"date_created":"2022-02-20T23:01:31Z","ddc":["570"],"publisher":"The Royal Society","file_date_updated":"2022-02-21T08:17:38Z","article_type":"original","_id":"10767","department":[{"_id":"BeVi"}],"intvolume":"       289","type":"journal_article","oa_version":"Published Version","project":[{"call_identifier":"H2020","_id":"250BDE62-B435-11E9-9278-68D0E5697425","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","grant_number":"715257"}],"corr_author":"1","publication_status":"published","author":[{"orcid":"0000-0002-8489-9281","full_name":"Kelemen, Réka K","id":"48D3F8DE-F248-11E8-B48F-1D18A9856A87","last_name":"Kelemen","first_name":"Réka K"},{"orcid":"0000-0002-5328-7231","full_name":"Elkrewi, Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","last_name":"Elkrewi","first_name":"Marwan N"},{"full_name":"Lindholm, Anna K.","last_name":"Lindholm","first_name":"Anna K."},{"last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306"}],"citation":{"ama":"Kelemen RK, Elkrewi MN, Lindholm AK, Vicoso B. Novel patterns of expression and recruitment of new genes on the t-haplotype, a mouse selfish chromosome. <i>Proceedings of the Royal Society B: Biological Sciences</i>. 2022;289(1968):20211985. doi:<a href=\"https://doi.org/10.1098/rspb.2021.1985\">10.1098/rspb.2021.1985</a>","ieee":"R. K. Kelemen, M. N. Elkrewi, A. K. Lindholm, and B. Vicoso, “Novel patterns of expression and recruitment of new genes on the t-haplotype, a mouse selfish chromosome,” <i>Proceedings of the Royal Society B: Biological Sciences</i>, vol. 289, no. 1968. The Royal Society, p. 20211985, 2022.","apa":"Kelemen, R. K., Elkrewi, M. N., Lindholm, A. K., &#38; Vicoso, B. (2022). Novel patterns of expression and recruitment of new genes on the t-haplotype, a mouse selfish chromosome. <i>Proceedings of the Royal Society B: Biological Sciences</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rspb.2021.1985\">https://doi.org/10.1098/rspb.2021.1985</a>","chicago":"Kelemen, Réka K, Marwan N Elkrewi, Anna K. Lindholm, and Beatriz Vicoso. “Novel Patterns of Expression and Recruitment of New Genes on the T-Haplotype, a Mouse Selfish Chromosome.” <i>Proceedings of the Royal Society B: Biological Sciences</i>. The Royal Society, 2022. <a href=\"https://doi.org/10.1098/rspb.2021.1985\">https://doi.org/10.1098/rspb.2021.1985</a>.","short":"R.K. Kelemen, M.N. Elkrewi, A.K. Lindholm, B. Vicoso, Proceedings of the Royal Society B: Biological Sciences 289 (2022) 20211985.","ista":"Kelemen RK, Elkrewi MN, Lindholm AK, Vicoso B. 2022. Novel patterns of expression and recruitment of new genes on the t-haplotype, a mouse selfish chromosome. Proceedings of the Royal Society B: Biological Sciences. 289(1968), 20211985.","mla":"Kelemen, Réka K., et al. “Novel Patterns of Expression and Recruitment of New Genes on the T-Haplotype, a Mouse Selfish Chromosome.” <i>Proceedings of the Royal Society B: Biological Sciences</i>, vol. 289, no. 1968, The Royal Society, 2022, p. 20211985, doi:<a href=\"https://doi.org/10.1098/rspb.2021.1985\">10.1098/rspb.2021.1985</a>."},"title":"Novel patterns of expression and recruitment of new genes on the t-haplotype, a mouse selfish chromosome","external_id":{"pmid":["35135349"],"isi":["000752812800012"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_id":"10779","success":1,"date_created":"2022-02-21T08:17:38Z","creator":"dernst","access_level":"open_access","file_size":2366976,"content_type":"application/pdf","file_name":"2022_ProceedingsRoyalSocB_Kelemen.pdf","checksum":"27042a3706ae52a919fed1ac114bf7bb","date_updated":"2022-02-21T08:17:38Z","relation":"main_file"}],"date_published":"2022-02-09T00:00:00Z","date_updated":"2026-07-25T22:31:04Z","doi":"10.1098/rspb.2021.1985","pmid":1,"year":"2022","day":"09","related_material":{"record":[{"id":"17119","relation":"dissertation_contains","status":"public"},{"status":"public","relation":"dissertation_contains","id":"19386"}]},"scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","issue":"1968","isi":1,"acknowledgement":"This project has received funding from the European Research Council under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 715257) and from the Swiss National Science Foundation (grant no. 310030_189145).\r\nWe thank Jari Garbely of the Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland, for conducting the PCR verification. Barbara\r\nKonig, Gabi Stichel and A.K.L. collected mouse tissue samples, from the field study led by R.K.K. ","language":[{"iso":"eng"}]},{"ddc":["570"],"article_type":"original","file_date_updated":"2022-03-08T11:31:30Z","publisher":"Wiley","volume":30,"article_processing_charge":"No","oa":1,"date_created":"2022-03-08T11:28:32Z","quality_controlled":"1","abstract":[{"text":"Combining hybrid zone analysis with genomic data is a promising approach to understanding the genomic basis of adaptive divergence. It allows for the identification of genomic regions underlying barriers to gene flow. It also provides insights into spatial patterns of allele frequency change, informing about the interplay between environmental factors, dispersal and selection. However, when only a single hybrid zone is analysed, it is difficult to separate patterns generated by selection from those resulting from chance. Therefore, it is beneficial to look for repeatable patterns across replicate hybrid zones in the same system. We applied this approach to the marine snail Littorina saxatilis, which contains two ecotypes, adapted to wave-exposed rocks vs. high-predation boulder fields. The existence of numerous hybrid zones between ecotypes offered the opportunity to test for the repeatability of genomic architectures and spatial patterns of divergence. We sampled and phenotyped snails from seven replicate hybrid zones on the Swedish west coast and genotyped them for thousands of single nucleotide polymorphisms. Shell shape and size showed parallel clines across all zones. Many genomic regions showing steep clines and/or high differentiation were shared among hybrid zones, consistent with a common evolutionary history and extensive gene flow between zones, and supporting the importance of these regions for divergence. In particular, we found that several large putative inversions contribute to divergence in all locations. Additionally, we found evidence for consistent displacement of clines from the boulder–rock transition. Our results demonstrate patterns of spatial variation that would not be accessible without continuous spatial sampling, a large genomic data set and replicate hybrid zones.","lang":"eng"}],"status":"public","month":"08","page":"3797-3814","publication":"Molecular Ecology","publication_identifier":{"issn":["0962-1083"],"eissn":["1365-294X"]},"isi":1,"issue":"15","language":[{"iso":"eng"}],"acknowledgement":"We thank everyone who helped with fieldwork, snail processing and DNA extractions, particularly Laura Brettell, Mårten Duvetorp, Juan Galindo, Anne-Lise Liabot, Mark Ravinet, Irena Senčić and Zuzanna Zagrodzka. We are also grateful to Edinburgh Genomics for library preparation and sequencing, to Stuart Baird and Mark Ravinet for helpful discussions, and to three anonymous reviewers for their constructive comments. This work was supported by the Natural Environment Research Council (NE/K014021/1), the European Research Council (AdG-693030-BARRIERS), Swedish Research Councils Formas and Vetenskapsrådet through a Linnaeus grant to the Centre for Marine Evolutionary Biology (217-2008-1719), the European Regional Development Fund (POCI-01-0145-FEDER-030628), and the Fundação para a iência e a Tecnologia,\r\nPortugal (PTDC/BIA-EVL/\r\n30628/2017). A.M.W. and R.F. were\r\nfunded by the European Union’s Horizon 2020 research and innovation\r\nprogramme under Marie Skłodowska-Curie\r\ngrant agreements\r\nno. 754411/797747 and no. 706376, respectively.","has_accepted_license":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","scopus_import":"1","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"doi":"10.1111/mec.15861","day":"01","year":"2021","pmid":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"external_id":{"pmid":["33638231"],"isi":["000669439700001"]},"file":[{"file_size":1726548,"checksum":"d5611f243ceb63a0e091d6662ebd9cda","file_name":"2021_MolecularEcology_Westram.pdf","content_type":"application/pdf","date_updated":"2022-03-08T11:31:30Z","relation":"main_file","file_id":"10839","success":1,"creator":"dernst","date_created":"2022-03-08T11:31:30Z","access_level":"open_access"}],"date_updated":"2024-10-09T21:01:47Z","date_published":"2021-08-01T00:00:00Z","citation":{"ama":"Westram AM, Faria R, Johannesson K, Butlin R. Using replicate hybrid zones to understand the genomic basis of adaptive divergence. <i>Molecular Ecology</i>. 2021;30(15):3797-3814. doi:<a href=\"https://doi.org/10.1111/mec.15861\">10.1111/mec.15861</a>","ieee":"A. M. Westram, R. Faria, K. Johannesson, and R. Butlin, “Using replicate hybrid zones to understand the genomic basis of adaptive divergence,” <i>Molecular Ecology</i>, vol. 30, no. 15. Wiley, pp. 3797–3814, 2021.","apa":"Westram, A. M., Faria, R., Johannesson, K., &#38; Butlin, R. (2021). Using replicate hybrid zones to understand the genomic basis of adaptive divergence. <i>Molecular Ecology</i>. Wiley. <a href=\"https://doi.org/10.1111/mec.15861\">https://doi.org/10.1111/mec.15861</a>","mla":"Westram, Anja M., et al. “Using Replicate Hybrid Zones to Understand the Genomic Basis of Adaptive Divergence.” <i>Molecular Ecology</i>, vol. 30, no. 15, Wiley, 2021, pp. 3797–814, doi:<a href=\"https://doi.org/10.1111/mec.15861\">10.1111/mec.15861</a>.","chicago":"Westram, Anja M, Rui Faria, Kerstin Johannesson, and Roger Butlin. “Using Replicate Hybrid Zones to Understand the Genomic Basis of Adaptive Divergence.” <i>Molecular Ecology</i>. Wiley, 2021. <a href=\"https://doi.org/10.1111/mec.15861\">https://doi.org/10.1111/mec.15861</a>.","short":"A.M. Westram, R. Faria, K. Johannesson, R. Butlin, Molecular Ecology 30 (2021) 3797–3814.","ista":"Westram AM, Faria R, Johannesson K, Butlin R. 2021. Using replicate hybrid zones to understand the genomic basis of adaptive divergence. Molecular Ecology. 30(15), 3797–3814."},"publication_status":"published","author":[{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","first_name":"Anja M","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969"},{"full_name":"Faria, Rui","last_name":"Faria","first_name":"Rui"},{"first_name":"Kerstin","last_name":"Johannesson","full_name":"Johannesson, Kerstin"},{"first_name":"Roger","last_name":"Butlin","full_name":"Butlin, Roger"}],"corr_author":"1","title":"Using replicate hybrid zones to understand the genomic basis of adaptive divergence","type":"journal_article","oa_version":"Published Version","_id":"10838","intvolume":"        30","department":[{"_id":"BeVi"}]},{"publication_identifier":{"eissn":["1471-2954"],"issn":["0962-8452"]},"publication":"Proceedings of the Royal Society B: Biological Sciences","ec_funded":1,"article_processing_charge":"Yes (via OA deal)","volume":288,"quality_controlled":"1","date_created":"2021-10-21T07:46:06Z","oa":1,"ddc":["595"],"article_number":"20211720","publisher":"The Royal Society","article_type":"original","file_date_updated":"2021-10-22T11:48:02Z","status":"public","abstract":[{"text":"While sexual reproduction is widespread among many taxa, asexual lineages have repeatedly evolved from sexual ancestors. Despite extensive research on the evolution of sex, it is still unclear whether this switch represents a major transition requiring major molecular reorganization, and how convergent the changes involved are. In this study, we investigated the phylogenetic relationship and patterns of gene expression of sexual and asexual lineages of Eurasian Artemia brine shrimp, to assess how gene expression patterns are affected by the transition to asexuality. We find only a few genes that are consistently associated with the evolution of asexuality, suggesting that this shift may not require an extensive overhauling of the meiotic machinery. While genes with sex-biased expression have high rates of expression divergence within Eurasian Artemia, neither female- nor male-biased genes appear to show unusual evolutionary patterns after sexuality is lost, contrary to theoretical expectations.","lang":"eng"}],"month":"09","project":[{"grant_number":"715257","_id":"250BDE62-B435-11E9-9278-68D0E5697425","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","call_identifier":"H2020"}],"citation":{"chicago":"Huylmans, Ann K, Ariana Macon, Francisco Hontoria, and Beatriz Vicoso. “Transitions to Asexuality and Evolution of Gene Expression in Artemia Brine Shrimp.” <i>Proceedings of the Royal Society B: Biological Sciences</i>. The Royal Society, 2021. <a href=\"https://doi.org/10.1098/rspb.2021.1720\">https://doi.org/10.1098/rspb.2021.1720</a>.","short":"A.K. Huylmans, A. Macon, F. Hontoria, B. Vicoso, Proceedings of the Royal Society B: Biological Sciences 288 (2021).","ista":"Huylmans AK, Macon A, Hontoria F, Vicoso B. 2021. Transitions to asexuality and evolution of gene expression in Artemia brine shrimp. Proceedings of the Royal Society B: Biological Sciences. 288(1959), 20211720.","mla":"Huylmans, Ann K., et al. “Transitions to Asexuality and Evolution of Gene Expression in Artemia Brine Shrimp.” <i>Proceedings of the Royal Society B: Biological Sciences</i>, vol. 288, no. 1959, 20211720, The Royal Society, 2021, doi:<a href=\"https://doi.org/10.1098/rspb.2021.1720\">10.1098/rspb.2021.1720</a>.","ama":"Huylmans AK, Macon A, Hontoria F, Vicoso B. Transitions to asexuality and evolution of gene expression in Artemia brine shrimp. <i>Proceedings of the Royal Society B: Biological Sciences</i>. 2021;288(1959). doi:<a href=\"https://doi.org/10.1098/rspb.2021.1720\">10.1098/rspb.2021.1720</a>","ieee":"A. K. Huylmans, A. Macon, F. Hontoria, and B. Vicoso, “Transitions to asexuality and evolution of gene expression in Artemia brine shrimp,” <i>Proceedings of the Royal Society B: Biological Sciences</i>, vol. 288, no. 1959. The Royal Society, 2021.","apa":"Huylmans, A. K., Macon, A., Hontoria, F., &#38; Vicoso, B. (2021). Transitions to asexuality and evolution of gene expression in Artemia brine shrimp. <i>Proceedings of the Royal Society B: Biological Sciences</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rspb.2021.1720\">https://doi.org/10.1098/rspb.2021.1720</a>"},"publication_status":"published","author":[{"first_name":"Ann K","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","last_name":"Huylmans","orcid":"0000-0001-8871-4961","full_name":"Huylmans, Ann K"},{"last_name":"Macon","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","first_name":"Ariana","full_name":"Macon, Ariana"},{"first_name":"Francisco","last_name":"Hontoria","full_name":"Hontoria, Francisco"},{"full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz"}],"title":"Transitions to asexuality and evolution of gene expression in Artemia brine shrimp","_id":"10166","department":[{"_id":"BeVi"}],"intvolume":"       288","type":"journal_article","oa_version":"Published Version","acknowledged_ssus":[{"_id":"ScienComp"}],"keyword":["asexual reproduction","parthenogenesis","sex-biased genes","sexual conflict","automixis","crustaceans"],"related_material":{"record":[{"id":"9949","relation":"research_data","status":"public"}],"link":[{"url":"https://doi.org/10.6084/m9.figshare.c.5615488.v1","relation":"supplementary_material"}]},"scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","has_accepted_license":"1","issue":"1959","isi":1,"acknowledgement":"We thank the Vicoso laboratory, Thomas Lenormand and Tanja Schwander for helpful discussions, the group of Gonzalo Gajardo, especially Cristian Gallardo-Escárate and Margarita Parraguez Donoso, for sequencing data and advice, and the IST Scientific Computing Group for their support. This work was supported by the European Research Council under the European Union's Horizon 2020 research and innovation program (grant agreement no. 715257).","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"external_id":{"pmid":["34547909"],"isi":["000697643700001"]},"file":[{"content_type":"application/pdf","checksum":"76e7f253b7040bca2ad76f82bd7c45c0","file_name":"2021_ProRoSocBBioSci_Huylmans.pdf","file_size":995806,"relation":"main_file","date_updated":"2021-10-22T11:48:02Z","success":1,"file_id":"10172","access_level":"open_access","date_created":"2021-10-22T11:48:02Z","creator":"cchlebak"}],"date_updated":"2025-04-14T07:41:20Z","date_published":"2021-09-22T00:00:00Z","doi":"10.1098/rspb.2021.1720","pmid":1,"year":"2021","day":"22"},{"article_type":"original","publisher":"Wiley","volume":34,"article_processing_charge":"No","oa":1,"date_created":"2020-10-25T23:01:20Z","quality_controlled":"1","abstract":[{"text":"The Mytilus complex of marine mussel species forms a mosaic of hybrid zones, found across temperate regions of the globe. This allows us to study ‘replicated’ instances of secondary contact between closely related species. Previous work on this complex has shown that local introgression is both widespread and highly heterogeneous, and has identified SNPs that are outliers of differentiation between lineages. Here, we developed an ancestry‐informative panel of such SNPs. We then compared their frequencies in newly sampled populations, including samples from within the hybrid zones, and parental populations at different distances from the contact. Results show that close to the hybrid zones, some outlier loci are near to fixation for the heterospecific allele, suggesting enhanced local introgression, or the local sweep of a shared ancestral allele. Conversely, genomic cline analyses, treating local parental populations as the reference, reveal a globally high concordance among loci, albeit with a few signals of asymmetric introgression. Enhanced local introgression at specific loci is consistent with the early transfer of adaptive variants after contact, possibly including asymmetric bi‐stable variants (Dobzhansky‐Muller incompatibilities), or haplotypes loaded with fewer deleterious mutations. Having escaped one barrier, however, these variants can be trapped or delayed at the next barrier, confining the introgression locally. These results shed light on the decay of species barriers during phases of contact.","lang":"eng"}],"status":"public","month":"01","page":"208-223","publication":"Journal of Evolutionary Biology","publication_identifier":{"eissn":["1420-9101"],"issn":["1010-061X"]},"isi":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/818559"}],"issue":"1","language":[{"iso":"eng"}],"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.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","related_material":{"record":[{"status":"public","relation":"research_data","id":"13073"}]},"doi":"10.1111/jeb.13709","year":"2021","day":"01","pmid":1,"external_id":{"isi":["000579599700001"],"pmid":["33045123"]},"date_updated":"2025-07-10T12:01:23Z","date_published":"2021-01-01T00:00:00Z","publication_status":"published","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>.","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>.","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.","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.","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>","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>","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."},"author":[{"full_name":"Simon, Alexis","first_name":"Alexis","last_name":"Simon"},{"first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse","full_name":"Fraisse, Christelle","orcid":"0000-0001-8441-5075"},{"first_name":"Tahani","last_name":"El Ayari","full_name":"El Ayari, Tahani"},{"last_name":"Liautard‐Haag","first_name":"Cathy","full_name":"Liautard‐Haag, Cathy"},{"full_name":"Strelkov, Petr","last_name":"Strelkov","first_name":"Petr"},{"full_name":"Welch, John J","first_name":"John J","last_name":"Welch"},{"full_name":"Bierne, Nicolas","last_name":"Bierne","first_name":"Nicolas"}],"title":"How do species barriers decay? Concordance and local introgression in mosaic hybrid zones of mussels","type":"journal_article","oa_version":"Preprint","_id":"8708","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"intvolume":"        34"},{"quality_controlled":"1","date_created":"2021-08-15T22:01:27Z","oa":1,"volume":12,"article_processing_charge":"Yes","publisher":"MDPI","article_type":"review","file_date_updated":"2021-08-16T09:49:35Z","article_number":"1136","ddc":["570"],"month":"08","status":"public","abstract":[{"lang":"eng","text":"About eight million animal species are estimated to live on Earth, and all except those belonging to one subphylum are invertebrates. Invertebrates are incredibly diverse in their morphologies, life histories, and in the range of the ecological niches that they occupy. A great variety of modes of reproduction and sex determination systems is also observed among them, and their mosaic-distribution across the phylogeny shows that transitions between them occur frequently and rapidly. Genetic conflict in its various forms is a long-standing theory to explain what drives those evolutionary transitions. Here, we review (1) the different modes of reproduction among invertebrate species, highlighting sexual reproduction as the probable ancestral state; (2) the paradoxical diversity of sex determination systems; (3) the different types of genetic conflicts that could drive the evolution of such different systems."}],"publication_identifier":{"eissn":["2073-4425"]},"ec_funded":1,"publication":"Genes","scopus_import":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","has_accepted_license":"1","language":[{"iso":"eng"}],"issue":"8","isi":1,"date_published":"2021-08-01T00:00:00Z","date_updated":"2026-04-02T14:05:14Z","file":[{"file_name":"2021_Genes_Picard.pdf","checksum":"744e60e56d290a96da3c91a9779f886f","content_type":"application/pdf","file_size":2297655,"relation":"main_file","date_updated":"2021-08-16T09:49:35Z","success":1,"file_id":"9926","access_level":"open_access","creator":"asandaue","date_created":"2021-08-16T09:49:35Z"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"external_id":{"pmid":["34440310"],"isi":["000690475900001"]},"pmid":1,"year":"2021","day":"01","doi":"10.3390/genes12081136","title":"Diversity of modes of reproduction and sex determination systems in invertebrates, and the putative contribution of genetic conflict","project":[{"grant_number":"715257","_id":"250BDE62-B435-11E9-9278-68D0E5697425","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","call_identifier":"H2020"}],"author":[{"orcid":"0000-0002-8101-2518","full_name":"Picard, Marion A L","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","last_name":"Picard","first_name":"Marion A L"},{"orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","first_name":"Beatriz"},{"full_name":"Bertrand, Stéphanie","first_name":"Stéphanie","last_name":"Bertrand"},{"full_name":"Escriva, Hector","last_name":"Escriva","first_name":"Hector"}],"publication_status":"published","citation":{"ieee":"M. A. L. Picard, B. Vicoso, S. Bertrand, and H. Escriva, “Diversity of modes of reproduction and sex determination systems in invertebrates, and the putative contribution of genetic conflict,” <i>Genes</i>, vol. 12, no. 8. MDPI, 2021.","apa":"Picard, M. A. L., Vicoso, B., Bertrand, S., &#38; Escriva, H. (2021). Diversity of modes of reproduction and sex determination systems in invertebrates, and the putative contribution of genetic conflict. <i>Genes</i>. MDPI. <a href=\"https://doi.org/10.3390/genes12081136\">https://doi.org/10.3390/genes12081136</a>","ama":"Picard MAL, Vicoso B, Bertrand S, Escriva H. Diversity of modes of reproduction and sex determination systems in invertebrates, and the putative contribution of genetic conflict. <i>Genes</i>. 2021;12(8). doi:<a href=\"https://doi.org/10.3390/genes12081136\">10.3390/genes12081136</a>","ista":"Picard MAL, Vicoso B, Bertrand S, Escriva H. 2021. Diversity of modes of reproduction and sex determination systems in invertebrates, and the putative contribution of genetic conflict. Genes. 12(8), 1136.","chicago":"Picard, Marion A L, Beatriz Vicoso, Stéphanie Bertrand, and Hector Escriva. “Diversity of Modes of Reproduction and Sex Determination Systems in Invertebrates, and the Putative Contribution of Genetic Conflict.” <i>Genes</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/genes12081136\">https://doi.org/10.3390/genes12081136</a>.","short":"M.A.L. Picard, B. Vicoso, S. Bertrand, H. Escriva, Genes 12 (2021).","mla":"Picard, Marion A. L., et al. “Diversity of Modes of Reproduction and Sex Determination Systems in Invertebrates, and the Putative Contribution of Genetic Conflict.” <i>Genes</i>, vol. 12, no. 8, 1136, MDPI, 2021, doi:<a href=\"https://doi.org/10.3390/genes12081136\">10.3390/genes12081136</a>."},"intvolume":"        12","department":[{"_id":"BeVi"}],"_id":"9908","oa_version":"Published Version","type":"journal_article"},{"title":"Data from Hyulmans et al 2021, \"Transitions to asexuality and evolution of gene expression in Artemia brine shrimp\"","citation":{"ista":"Vicoso B. 2021. Data from Hyulmans et al 2021, ‘Transitions to asexuality and evolution of gene expression in Artemia brine shrimp’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:9949\">10.15479/AT:ISTA:9949</a>.","short":"B. Vicoso, (2021).","chicago":"Vicoso, Beatriz. “Data from Hyulmans et Al 2021, ‘Transitions to Asexuality and Evolution of Gene Expression in Artemia Brine Shrimp.’” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/AT:ISTA:9949\">https://doi.org/10.15479/AT:ISTA:9949</a>.","mla":"Vicoso, Beatriz. <i>Data from Hyulmans et Al 2021, “Transitions to Asexuality and Evolution of Gene Expression in Artemia Brine Shrimp.”</i> Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:9949\">10.15479/AT:ISTA:9949</a>.","apa":"Vicoso, B. (2021). Data from Hyulmans et al 2021, “Transitions to asexuality and evolution of gene expression in Artemia brine shrimp.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:9949\">https://doi.org/10.15479/AT:ISTA:9949</a>","ieee":"B. Vicoso, “Data from Hyulmans et al 2021, ‘Transitions to asexuality and evolution of gene expression in Artemia brine shrimp.’” Institute of Science and Technology Austria, 2021.","ama":"Vicoso B. Data from Hyulmans et al 2021, “Transitions to asexuality and evolution of gene expression in Artemia brine shrimp.” 2021. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:9949\">10.15479/AT:ISTA:9949</a>"},"author":[{"full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","first_name":"Beatriz"}],"oa_version":"None","type":"research_data","department":[{"_id":"BeVi"}],"_id":"9949","publisher":"Institute of Science and Technology Austria","file_date_updated":"2021-08-21T13:43:59Z","related_material":{"record":[{"id":"10166","relation":"used_in_publication","status":"public"}]},"date_created":"2021-08-21T13:44:22Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"has_accepted_license":"1","article_processing_charge":"No","day":"24","month":"08","year":"2021","status":"public","doi":"10.15479/AT:ISTA:9949","date_published":"2021-08-24T00:00:00Z","date_updated":"2025-04-15T07:49:47Z","file":[{"checksum":"90461837eed66beac6fa302993cf0ca9","file_name":"Data.zip","content_type":"application/zip","file_size":139188306,"relation":"main_file","date_updated":"2021-08-21T13:43:59Z","success":1,"file_id":"9950","access_level":"open_access","creator":"bvicoso","date_created":"2021-08-21T13:43:59Z"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"}},{"scopus_import":"1","keyword":["sex chromosomes","evolutionary strata","W-linked gene","sex determining gene","schistosome parasites"],"related_material":{"record":[{"relation":"dissertation_contains","id":"19386","status":"public"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","acknowledged_ssus":[{"_id":"ScienComp"}],"acknowledgement":"The authors thank IT support at IST Austria for providing an optimal environment for bioinformatic analyses. This work was supported by an Austrian Science Foundation FWF grant (Project P28842) to B.V.","language":[{"iso":"eng"}],"issue":"12","isi":1,"date_updated":"2026-07-25T22:31:05Z","date_published":"2021-06-19T00:00:00Z","file":[{"file_id":"11352","success":1,"date_created":"2022-05-06T09:47:18Z","creator":"dernst","access_level":"open_access","file_size":1008594,"content_type":"application/pdf","file_name":"2021_MolecularBiolEvolution_Elkrewi.pdf","checksum":"1b096702fb356d9c0eb88e1b3fcff5f8","date_updated":"2022-05-06T09:47:18Z","relation":"main_file"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"external_id":{"pmid":["34146097"],"isi":["000741368600009"]},"pmid":1,"year":"2021","day":"19","doi":"10.1093/molbev/msab178","title":"Schistosome W-linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination","project":[{"call_identifier":"FWF","name":"Sex chromosome evolution under male- and female- heterogamety","_id":"250ED89C-B435-11E9-9278-68D0E5697425","grant_number":"P28842-B22"}],"corr_author":"1","author":[{"full_name":"Elkrewi, Marwan N","orcid":"0000-0002-5328-7231","first_name":"Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","last_name":"Elkrewi"},{"last_name":"Moldovan","id":"c8bb7f32-3315-11ec-b58b-e5950e6c14a0","first_name":"Mikhail A.","orcid":"0000-0002-8876-6494","full_name":"Moldovan, Mikhail A."},{"orcid":"0000-0002-8101-2518","full_name":"Picard, Marion A L","last_name":"Picard","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","first_name":"Marion A L"},{"first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306"}],"publication_status":"published","citation":{"mla":"Elkrewi, Marwan N., et al. “Schistosome W-Linked Genes Inform Temporal Dynamics of Sex Chromosome Evolution and Suggest Candidate for Sex Determination.” <i>Molecular Biology and Evolution</i>, vol. 138, no. 12, Oxford University Press, 2021, pp. 5345–58, doi:<a href=\"https://doi.org/10.1093/molbev/msab178\">10.1093/molbev/msab178</a>.","ista":"Elkrewi MN, Moldovan MA, Picard MAL, Vicoso B. 2021. Schistosome W-linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination. Molecular Biology and Evolution. 138(12), 5345–58.","chicago":"Elkrewi, Marwan N, Mikhail A. Moldovan, Marion A L Picard, and Beatriz Vicoso. “Schistosome W-Linked Genes Inform Temporal Dynamics of Sex Chromosome Evolution and Suggest Candidate for Sex Determination.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2021. <a href=\"https://doi.org/10.1093/molbev/msab178\">https://doi.org/10.1093/molbev/msab178</a>.","short":"M.N. Elkrewi, M.A. Moldovan, M.A.L. Picard, B. Vicoso, Molecular Biology and Evolution 138 (2021) 5345–58.","apa":"Elkrewi, M. N., Moldovan, M. A., Picard, M. A. L., &#38; Vicoso, B. (2021). Schistosome W-linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msab178\">https://doi.org/10.1093/molbev/msab178</a>","ieee":"M. N. Elkrewi, M. A. Moldovan, M. A. L. Picard, and B. Vicoso, “Schistosome W-linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination,” <i>Molecular Biology and Evolution</i>, vol. 138, no. 12. Oxford University Press, pp. 5345–58, 2021.","ama":"Elkrewi MN, Moldovan MA, Picard MAL, Vicoso B. Schistosome W-linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination. <i>Molecular Biology and Evolution</i>. 2021;138(12):5345-5358. doi:<a href=\"https://doi.org/10.1093/molbev/msab178\">10.1093/molbev/msab178</a>"},"department":[{"_id":"BeVi"}],"das_tickbox":"1","intvolume":"       138","_id":"10167","oa_version":"Published Version","type":"journal_article","quality_controlled":"1","date_created":"2021-10-21T07:49:12Z","oa":1,"article_processing_charge":"No","volume":138,"publisher":"Oxford University Press","article_type":"original","file_date_updated":"2022-05-06T09:47:18Z","ddc":["610"],"page":"5345-58","month":"06","status":"public","abstract":[{"text":"Schistosomes, the human parasites responsible for snail fever, are female-heterogametic. Different parts of their ZW sex chromosomes have stopped recombining in distinct lineages, creating “evolutionary strata” of various ages. Although the Z-chromosome is well characterized at the genomic and molecular level, the W-chromosome has remained largely unstudied from an evolutionary perspective, as only a few W-linked genes have been detected outside of the model species Schistosoma mansoni. Here, we characterize the gene content and evolution of the W-chromosomes of S. mansoni and of the divergent species S. japonicum. We use a combined RNA/DNA k-mer based pipeline to assemble around 100 candidate W-specific transcripts in each of the species. About half of them map to known protein coding genes, the majority homologous to S. mansoni Z-linked genes. We perform an extended analysis of the evolutionary strata present in the two species (including characterizing a previously undetected young stratum in S. japonicum) to infer patterns of sequence and expression evolution of W-linked genes at different time points after recombination was lost. W-linked genes show evidence of degeneration, including high rates of protein evolution and reduced expression. Most are found in young lineage-specific strata, with only a few high expression ancestral W-genes remaining, consistent with the progressive erosion of nonrecombining regions. Among these, the splicing factor u2af2 stands out as a promising candidate for primary sex determination, opening new avenues for understanding the molecular basis of the reproductive biology of this group.","lang":"eng"}],"publication_identifier":{"issn":["0737-4038"],"eissn":["1537-1719"]},"publication":"Molecular Biology and Evolution"},{"publication":"Molecular Ecology Resources","ec_funded":1,"publication_identifier":{"issn":["1755-098X"],"eissn":["1755-0998"]},"abstract":[{"text":"Sewall Wright developed FST for describing population differentiation and it has since been extended to many novel applications, including the detection of homomorphic sex chromosomes. However, there has been confusion regarding the expected estimate of FST for a fixed difference between the X‐ and Y‐chromosome when comparing males and females. Here, we attempt to resolve this confusion by contrasting two common FST estimators and explain why they yield different estimates when applied to the case of sex chromosomes. We show that this difference is true for many allele frequencies, but the situation characterized by fixed differences between the X‐ and Y‐chromosome is among the most extreme. To avoid additional confusion, we recommend that all authors using FST clearly state which estimator of FST their work uses.","lang":"eng"}],"status":"public","month":"11","page":"1517-1525","ddc":["570"],"file_date_updated":"2020-11-26T11:46:43Z","article_type":"original","publisher":"Wiley","article_processing_charge":"Yes (via OA deal)","volume":20,"date_created":"2020-07-07T08:56:16Z","oa":1,"quality_controlled":"1","type":"journal_article","oa_version":"Published Version","_id":"8099","intvolume":"        20","department":[{"_id":"BeVi"}],"citation":{"ama":"Gammerdinger WJ, Toups MA, Vicoso B. Disagreement in FST estimators: A case study from  sex chromosomes. <i>Molecular Ecology Resources</i>. 2020;20(6):1517-1525. doi:<a href=\"https://doi.org/10.1111/1755-0998.13210\">10.1111/1755-0998.13210</a>","apa":"Gammerdinger, W. J., Toups, M. A., &#38; Vicoso, B. (2020). Disagreement in FST estimators: A case study from  sex chromosomes. <i>Molecular Ecology Resources</i>. Wiley. <a href=\"https://doi.org/10.1111/1755-0998.13210\">https://doi.org/10.1111/1755-0998.13210</a>","ieee":"W. J. Gammerdinger, M. A. Toups, and B. Vicoso, “Disagreement in FST estimators: A case study from  sex chromosomes,” <i>Molecular Ecology Resources</i>, vol. 20, no. 6. Wiley, pp. 1517–1525, 2020.","mla":"Gammerdinger, William J., et al. “Disagreement in FST Estimators: A Case Study from  Sex Chromosomes.” <i>Molecular Ecology Resources</i>, vol. 20, no. 6, Wiley, 2020, pp. 1517–25, doi:<a href=\"https://doi.org/10.1111/1755-0998.13210\">10.1111/1755-0998.13210</a>.","chicago":"Gammerdinger, William J, Melissa A Toups, and Beatriz Vicoso. “Disagreement in FST Estimators: A Case Study from  Sex Chromosomes.” <i>Molecular Ecology Resources</i>. Wiley, 2020. <a href=\"https://doi.org/10.1111/1755-0998.13210\">https://doi.org/10.1111/1755-0998.13210</a>.","short":"W.J. Gammerdinger, M.A. Toups, B. Vicoso, Molecular Ecology Resources 20 (2020) 1517–1525.","ista":"Gammerdinger WJ, Toups MA, Vicoso B. 2020. Disagreement in FST estimators: A case study from  sex chromosomes. Molecular Ecology Resources. 20(6), 1517–1525."},"author":[{"full_name":"Gammerdinger, William J","orcid":"0000-0001-9638-1220","id":"3A7E01BC-F248-11E8-B48F-1D18A9856A87","last_name":"Gammerdinger","first_name":"William J"},{"orcid":"0000-0002-9752-7380","full_name":"Toups, Melissa A","first_name":"Melissa A","last_name":"Toups","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","first_name":"Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","corr_author":"1","project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"P28842-B22","call_identifier":"FWF","_id":"250ED89C-B435-11E9-9278-68D0E5697425","name":"Sex chromosome evolution under male- and female- heterogamety"}],"title":"Disagreement in FST estimators: A case study from  sex chromosomes","doi":"10.1111/1755-0998.13210","year":"2020","day":"01","pmid":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"relation":"main_file","date_updated":"2020-11-26T11:46:43Z","content_type":"application/pdf","file_name":"2020_MolecularEcologyRes_Gammerdinger.pdf","checksum":"3d87ebb8757dcd504f20c618b72e6575","file_size":820428,"access_level":"open_access","date_created":"2020-11-26T11:46:43Z","creator":"dernst","success":1,"file_id":"8814"}],"external_id":{"pmid":["32543001"],"isi":["000545451200001"]},"date_updated":"2025-04-15T08:18:38Z","date_published":"2020-11-01T00:00:00Z","isi":1,"issue":"6","language":[{"iso":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","has_accepted_license":"1","scopus_import":"1"},{"date_updated":"2026-06-18T19:05:02Z","date_published":"2020-10-15T00:00:00Z","month":"10","year":"2020","day":"15","abstract":[{"lang":"eng","text":"Fitness interactions between mutations can influence a population’s evolution in many different ways. While epistatic effects are difficult to measure precisely, important information is captured by the mean and variance of log fitnesses for individuals carrying different numbers of mutations. We derive predictions for these quantities from a class of simple fitness landscapes, based on models of optimizing selection on quantitative traits. We also explore extensions to the models, including modular pleiotropy, variable effect sizes, mutational bias and maladaptation of the wild type. We illustrate our approach by reanalysing a large dataset of mutant effects in a yeast snoRNA. Though characterized by some large epistatic effects, these data give a good overall fit to the non-epistatic null model, suggesting that epistasis might have limited influence on the evolutionary dynamics in this system. We also show how the amount of epistasis depends on both the underlying fitness landscape and the distribution of mutations, and so is expected to vary in consistent ways between new mutations, standing variation and fixed mutations."}],"doi":"10.6084/m9.figshare.7957472.v1","status":"public","user_id":"0043cee0-e5fc-11ee-9736-f83bc23afbf0","OA_type":"hybrid","oa":1,"date_created":"2021-08-06T11:18:15Z","related_material":{"record":[{"id":"6467","relation":"used_in_publication","status":"public"}]},"article_processing_charge":"No","publisher":"Royal Society of London","main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.7957472.v1","open_access":"1"}],"department":[{"_id":"BeVi"},{"_id":"NiBa"}],"_id":"9798","oa_version":"Published Version","type":"research_data_reference","title":"Simulation code for Fig S2 from the distribution of epistasis on simple fitness landscapes","author":[{"first_name":"Christelle","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","full_name":"Fraisse, Christelle","orcid":"0000-0001-8441-5075"},{"full_name":"Welch, John J.","last_name":"Welch","first_name":"John J."}],"citation":{"chicago":"Fraisse, Christelle, and John J. Welch. “Simulation Code for Fig S2 from the Distribution of Epistasis on Simple Fitness Landscapes.” Royal Society of London, 2020. <a href=\"https://doi.org/10.6084/m9.figshare.7957472.v1\">https://doi.org/10.6084/m9.figshare.7957472.v1</a>.","short":"C. Fraisse, J.J. Welch, (2020).","ista":"Fraisse C, Welch JJ. 2020. Simulation code for Fig S2 from the distribution of epistasis on simple fitness landscapes, Royal Society of London, <a href=\"https://doi.org/10.6084/m9.figshare.7957472.v1\">10.6084/m9.figshare.7957472.v1</a>.","mla":"Fraisse, Christelle, and John J. Welch. <i>Simulation Code for Fig S2 from the Distribution of Epistasis on Simple Fitness Landscapes</i>. Royal Society of London, 2020, doi:<a href=\"https://doi.org/10.6084/m9.figshare.7957472.v1\">10.6084/m9.figshare.7957472.v1</a>.","ama":"Fraisse C, Welch JJ. Simulation code for Fig S2 from the distribution of epistasis on simple fitness landscapes. 2020. doi:<a href=\"https://doi.org/10.6084/m9.figshare.7957472.v1\">10.6084/m9.figshare.7957472.v1</a>","ieee":"C. Fraisse and J. J. Welch, “Simulation code for Fig S2 from the distribution of epistasis on simple fitness landscapes.” Royal Society of London, 2020.","apa":"Fraisse, C., &#38; Welch, J. J. (2020). Simulation code for Fig S2 from the distribution of epistasis on simple fitness landscapes. Royal Society of London. <a href=\"https://doi.org/10.6084/m9.figshare.7957472.v1\">https://doi.org/10.6084/m9.figshare.7957472.v1</a>"},"OA_place":"publisher"},{"title":"Simulation code for Fig S1 from the distribution of epistasis on simple fitness landscapes","author":[{"first_name":"Christelle","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle"},{"last_name":"Welch","first_name":"John J.","full_name":"Welch, John J."}],"citation":{"short":"C. Fraisse, J.J. Welch, (2020).","chicago":"Fraisse, Christelle, and John J. Welch. “Simulation Code for Fig S1 from the Distribution of Epistasis on Simple Fitness Landscapes.” Royal Society of London, 2020. <a href=\"https://doi.org/10.6084/m9.figshare.7957469.v1\">https://doi.org/10.6084/m9.figshare.7957469.v1</a>.","ista":"Fraisse C, Welch JJ. 2020. Simulation code for Fig S1 from the distribution of epistasis on simple fitness landscapes, Royal Society of London, <a href=\"https://doi.org/10.6084/m9.figshare.7957469.v1\">10.6084/m9.figshare.7957469.v1</a>.","mla":"Fraisse, Christelle, and John J. Welch. <i>Simulation Code for Fig S1 from the Distribution of Epistasis on Simple Fitness Landscapes</i>. Royal Society of London, 2020, doi:<a href=\"https://doi.org/10.6084/m9.figshare.7957469.v1\">10.6084/m9.figshare.7957469.v1</a>.","ama":"Fraisse C, Welch JJ. Simulation code for Fig S1 from the distribution of epistasis on simple fitness landscapes. 2020. doi:<a href=\"https://doi.org/10.6084/m9.figshare.7957469.v1\">10.6084/m9.figshare.7957469.v1</a>","ieee":"C. Fraisse and J. J. Welch, “Simulation code for Fig S1 from the distribution of epistasis on simple fitness landscapes.” Royal Society of London, 2020.","apa":"Fraisse, C., &#38; Welch, J. J. (2020). Simulation code for Fig S1 from the distribution of epistasis on simple fitness landscapes. Royal Society of London. <a href=\"https://doi.org/10.6084/m9.figshare.7957469.v1\">https://doi.org/10.6084/m9.figshare.7957469.v1</a>"},"OA_place":"publisher","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"_id":"9799","oa_version":"Published Version","type":"research_data_reference","oa":1,"user_id":"0043cee0-e5fc-11ee-9736-f83bc23afbf0","OA_type":"hybrid","date_created":"2021-08-06T11:26:57Z","related_material":{"record":[{"relation":"used_in_publication","id":"6467","status":"public"}]},"article_processing_charge":"No","publisher":"Royal Society of London","main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.7957469.v1"}],"date_published":"2020-10-15T00:00:00Z","date_updated":"2026-06-18T19:05:02Z","day":"15","month":"10","year":"2020","abstract":[{"lang":"eng","text":"Fitness interactions between mutations can influence a population’s evolution in many different ways. While epistatic effects are difficult to measure precisely, important information is captured by the mean and variance of log fitnesses for individuals carrying different numbers of mutations. We derive predictions for these quantities from a class of simple fitness landscapes, based on models of optimizing selection on quantitative traits. We also explore extensions to the models, including modular pleiotropy, variable effect sizes, mutational bias and maladaptation of the wild type. We illustrate our approach by reanalysing a large dataset of mutant effects in a yeast snoRNA. Though characterized by some large epistatic effects, these data give a good overall fit to the non-epistatic null model, suggesting that epistasis might have limited influence on the evolutionary dynamics in this system. We also show how the amount of epistasis depends on both the underlying fitness landscape and the distribution of mutations, and so is expected to vary in consistent ways between new mutations, standing variation and fixed mutations."}],"doi":"10.6084/m9.figshare.7957469.v1","status":"public"},{"type":"research_data","oa_version":"Published Version","_id":"6060","department":[{"_id":"BeVi"}],"citation":{"short":"B. Vicoso, (2019).","chicago":"Vicoso, Beatriz. “Supplementary Data for ‘Sex-Biased Gene Expression and Dosage Compensation on the Artemia Franciscana Z-Chromosome’ (Huylman, Toups et Al., 2019). .” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:6060\">https://doi.org/10.15479/AT:ISTA:6060</a>.","ista":"Vicoso B. 2019. Supplementary data for ‘Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome’ (Huylman, Toups et al., 2019). , Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:6060\">10.15479/AT:ISTA:6060</a>.","mla":"Vicoso, Beatriz. <i>Supplementary Data for “Sex-Biased Gene Expression and Dosage Compensation on the Artemia Franciscana Z-Chromosome” (Huylman, Toups et Al., 2019). </i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6060\">10.15479/AT:ISTA:6060</a>.","ama":"Vicoso B. Supplementary data for “Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome” (Huylman, Toups et al., 2019). . 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6060\">10.15479/AT:ISTA:6060</a>","apa":"Vicoso, B. (2019). Supplementary data for “Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome” (Huylman, Toups et al., 2019). . Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6060\">https://doi.org/10.15479/AT:ISTA:6060</a>","ieee":"B. Vicoso, “Supplementary data for ‘Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome’ (Huylman, Toups et al., 2019). .” Institute of Science and Technology Austria, 2019."},"author":[{"last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306"}],"title":"Supplementary data for \"Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome\" (Huylman, Toups et al., 2019). ","status":"public","doi":"10.15479/AT:ISTA:6060","year":"2019","month":"02","day":"28","file":[{"date_updated":"2020-07-14T12:47:17Z","relation":"main_file","file_size":36646050,"file_name":"SupData.zip","checksum":"a338a622d728af0e3199cb07e6dd64d3","content_type":"application/zip","creator":"bvicoso","date_created":"2019-02-28T10:54:27Z","access_level":"open_access","file_id":"6061"}],"date_updated":"2025-04-15T07:49:47Z","date_published":"2019-02-28T00:00:00Z","publisher":"Institute of Science and Technology Austria","file_date_updated":"2020-07-14T12:47:17Z","article_processing_charge":"No","related_material":{"record":[{"relation":"research_paper","id":"6418","status":"public"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","date_created":"2019-02-28T10:55:15Z","oa":1},{"publication_identifier":{"eissn":["1537-1719"],"issn":["0737-4038"]},"publication":"Molecular biology and evolution","volume":36,"article_processing_charge":"No","oa":1,"date_created":"2019-03-10T22:59:19Z","quality_controlled":"1","publisher":"Oxford University Press","page":"500-515","abstract":[{"lang":"eng","text":"Pleiotropy is the well-established idea that a single mutation affects multiple phenotypes. If a mutation has opposite effects on fitness when expressed in different contexts, then genetic conflict arises. Pleiotropic conflict is expected to reduce the efficacy of selection by limiting the fixation of beneficial mutations through adaptation, and the removal of deleterious mutations through purifying selection. Although this has been widely discussed, in particular in the context of a putative “gender load,” it has yet to be systematically quantified. In this work, we empirically estimate to which extent different pleiotropic regimes impede the efficacy of selection in Drosophila melanogaster. We use whole-genome polymorphism data from a single African population and divergence data from D. simulans to estimate the fraction of adaptive fixations (α), the rate of adaptation (ωA), and the direction of selection (DoS). After controlling for confounding covariates, we find that the different pleiotropic regimes have a relatively small, but significant, effect on selection efficacy. Specifically, our results suggest that pleiotropic sexual antagonism may restrict the efficacy of selection, but that this conflict can be resolved by limiting the expression of genes to the sex where they are beneficial. Intermediate levels of pleiotropy across tissues and life stages can also lead to maladaptation in D. melanogaster, due to inefficient purifying selection combined with low frequency of mutations that confer a selective advantage. Thus, our study highlights the need to consider the efficacy of selection in the context of antagonistic pleiotropy, and of genetic conflict in general."}],"status":"public","month":"03","author":[{"full_name":"Fraisse, Christelle","orcid":"0000-0001-8441-5075","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle"},{"first_name":"Gemma","last_name":"Puixeu Sala","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8330-1754","full_name":"Puixeu Sala, Gemma"},{"orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz"}],"citation":{"ama":"Fraisse C, Puixeu Sala G, Vicoso B. Pleiotropy modulates the efficacy of selection in drosophila melanogaster. <i>Molecular biology and evolution</i>. 2019;36(3):500-515. doi:<a href=\"https://doi.org/10.1093/molbev/msy246\">10.1093/molbev/msy246</a>","ieee":"C. Fraisse, G. Puixeu Sala, and B. Vicoso, “Pleiotropy modulates the efficacy of selection in drosophila melanogaster,” <i>Molecular biology and evolution</i>, vol. 36, no. 3. Oxford University Press, pp. 500–515, 2019.","apa":"Fraisse, C., Puixeu Sala, G., &#38; Vicoso, B. (2019). Pleiotropy modulates the efficacy of selection in drosophila melanogaster. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msy246\">https://doi.org/10.1093/molbev/msy246</a>","chicago":"Fraisse, Christelle, Gemma Puixeu Sala, and Beatriz Vicoso. “Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2019. <a href=\"https://doi.org/10.1093/molbev/msy246\">https://doi.org/10.1093/molbev/msy246</a>.","short":"C. Fraisse, G. Puixeu Sala, B. Vicoso, Molecular Biology and Evolution 36 (2019) 500–515.","ista":"Fraisse C, Puixeu Sala G, Vicoso B. 2019. Pleiotropy modulates the efficacy of selection in drosophila melanogaster. Molecular biology and evolution. 36(3), 500–515.","mla":"Fraisse, Christelle, et al. “Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.” <i>Molecular Biology and Evolution</i>, vol. 36, no. 3, Oxford University Press, 2019, pp. 500–15, doi:<a href=\"https://doi.org/10.1093/molbev/msy246\">10.1093/molbev/msy246</a>."},"publication_status":"published","project":[{"grant_number":"P28842-B22","call_identifier":"FWF","name":"Sex chromosome evolution under male- and female- heterogamety","_id":"250ED89C-B435-11E9-9278-68D0E5697425"}],"title":"Pleiotropy modulates the efficacy of selection in drosophila melanogaster","_id":"6089","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"intvolume":"        36","type":"journal_article","oa_version":"Submitted Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","related_material":{"record":[{"id":"5757","relation":"popular_science","status":"public"}]},"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30590559"}],"isi":1,"issue":"3","language":[{"iso":"eng"}],"external_id":{"pmid":["30590559"],"isi":["000462585100006"]},"date_published":"2019-03-01T00:00:00Z","date_updated":"2025-04-15T08:18:38Z","doi":"10.1093/molbev/msy246","day":"01","year":"2019","pmid":1}]