[{"_id":"20833","abstract":[{"text":"Sex-chromosome systems are highly variable across animals, but how they transition from one to another is not well understood. Diptera have undergone multiple sex-chromosome turnovers and expansions while maintaining their general chromosomal content, which makes them an ideal clade to study such transitions. We analysed more than 100 dipteran whole-genome assemblies and identified 4 new lineages that underwent sex-chromosome turnover (in addition to the 5 previously reported). We find the majority of turnovers happened in the group Schizophora, which tend to have fewer genes on the F element (the chromosome homologous to the ancestral insect X chromosome) than lower dipterans, a factor previously hypothesized to facilitate turnover. Most derived X chromosomes have higher GC content than autosomes, consistent with a high prevalence of male-achiasmy in Diptera. In addition, an excess of gene movement out of the X is detected for most of these new X chromosomes, and many of these moved genes have high testis expression in Drosophila, suggesting that out-of-X gene movement contributes to the long-term demasculinization of X chromosomes.","lang":"eng"}],"status":"public","date_updated":"2026-01-08T13:49:40Z","date_published":"2026-01-08T00:00:00Z","author":[{"id":"02814589-eb8f-11eb-b029-a70074f3f18f","last_name":"Layana Franco","full_name":"Layana Franco, Lorena Alexandra","orcid":"0000-0002-1253-6297","first_name":"Lorena Alexandra"},{"full_name":"Toups, Melissa A","last_name":"Toups","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9752-7380","first_name":"Melissa A"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz","last_name":"Vicoso","first_name":"Beatriz","orcid":"0000-0002-4579-8306"}],"file":[{"date_updated":"2025-12-17T10:09:25Z","creator":"llayanaf","success":1,"date_created":"2025-12-17T10:09:25Z","file_name":"README.txt","content_type":"text/plain","relation":"main_file","access_level":"open_access","file_id":"20834","file_size":1201,"checksum":"0b79be6229f2ad9ac117ef00fc4f5c0e"},{"file_name":"Supplementary_Datasets.zip","date_created":"2025-12-17T10:10:11Z","content_type":"application/zip","relation":"main_file","date_updated":"2025-12-17T10:10:11Z","success":1,"creator":"llayanaf","file_size":19052849,"checksum":"daf1c03149dd170b14e5c8e109ee3c77","access_level":"open_access","file_id":"20835"},{"checksum":"251e7aab01917c2ad2fbccf465492ea1","file_size":4575,"file_id":"20837","access_level":"open_access","relation":"main_file","content_type":"application/zip","file_name":"Perl_scripts.zip","date_created":"2025-12-17T10:12:05Z","creator":"llayanaf","success":1,"date_updated":"2025-12-17T10:12:05Z"},{"checksum":"3cabf143b8cd286eae48c598da2b03bd","file_size":572362,"file_id":"20959","access_level":"open_access","content_type":"application/zip","relation":"main_file","date_created":"2026-01-08T01:35:08Z","file_name":"Supplementary_Tables.zip","creator":"llayanaf","success":1,"date_updated":"2026-01-08T01:35:08Z"}],"month":"01","type":"research_data","oa_version":"None","keyword":["Schizophora","sex chromosomes","sex-chromosome turnover","Diptera","genomic features","out-of-X movement."],"has_accepted_license":"1","day":"8","publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","oa":1,"citation":{"short":"L.A. Layana Franco, M.A. Toups, B. Vicoso, (2026).","ieee":"L. A. Layana Franco, M. A. Toups, and B. Vicoso, “Research Data for ‘Causes and consequences of sex-chromosome turnovers in Diptera.’” Institute of Science and Technology Austria, 2026.","mla":"Layana Franco, Lorena Alexandra, et al. <i>Research Data for “Causes and Consequences of Sex-Chromosome Turnovers in Diptera.”</i> Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20833\">10.15479/AT-ISTA-20833</a>.","chicago":"Layana Franco, Lorena Alexandra, Melissa A Toups, and Beatriz Vicoso. “Research Data for ‘Causes and Consequences of Sex-Chromosome Turnovers in Diptera.’” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-20833\">https://doi.org/10.15479/AT-ISTA-20833</a>.","apa":"Layana Franco, L. A., Toups, M. A., &#38; Vicoso, B. (2026). Research Data for “Causes and consequences of sex-chromosome turnovers in Diptera.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20833\">https://doi.org/10.15479/AT-ISTA-20833</a>","ista":"Layana Franco LA, Toups MA, Vicoso B. 2026. Research Data for ‘Causes and consequences of sex-chromosome turnovers in Diptera’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT-ISTA-20833\">10.15479/AT-ISTA-20833</a>.","ama":"Layana Franco LA, Toups MA, Vicoso B. Research Data for “Causes and consequences of sex-chromosome turnovers in Diptera.” 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20833\">10.15479/AT-ISTA-20833</a>"},"date_created":"2025-12-17T10:10:57Z","doi":"10.15479/AT-ISTA-20833","year":"2026","corr_author":"1","file_date_updated":"2026-01-08T01:35:08Z","title":"Research Data for 'Causes and consequences of sex-chromosome turnovers in Diptera'","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"department":[{"_id":"BeVi"}],"user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d"},{"citation":{"ieee":"L. A. Layana Franco, M. A. Toups, and B. Vicoso, “Research Data for ‘Causes and consequences of sex-chromosome turnovers in Diptera.’” Institute of Science and Technology Austria, 2026.","short":"L.A. Layana Franco, M.A. Toups, B. Vicoso, (2026).","mla":"Layana Franco, Lorena Alexandra, et al. <i>Research Data for “Causes and Consequences of Sex-Chromosome Turnovers in Diptera.”</i> Institute of Science and Technology Austria, 2026, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-21116\">10.15479/AT-ISTA-21116</a>.","ama":"Layana Franco LA, Toups MA, Vicoso B. Research Data for “Causes and consequences of sex-chromosome turnovers in Diptera.” 2026. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-21116\">10.15479/AT-ISTA-21116</a>","ista":"Layana Franco LA, Toups MA, Vicoso B. 2026. Research Data for ‘Causes and consequences of sex-chromosome turnovers in Diptera’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT-ISTA-21116\">10.15479/AT-ISTA-21116</a>.","apa":"Layana Franco, L. A., Toups, M. A., &#38; Vicoso, B. (2026). Research Data for “Causes and consequences of sex-chromosome turnovers in Diptera.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-21116\">https://doi.org/10.15479/AT-ISTA-21116</a>","chicago":"Layana Franco, Lorena Alexandra, Melissa A Toups, and Beatriz Vicoso. “Research Data for ‘Causes and Consequences of Sex-Chromosome Turnovers in Diptera.’” Institute of Science and Technology Austria, 2026. <a href=\"https://doi.org/10.15479/AT-ISTA-21116\">https://doi.org/10.15479/AT-ISTA-21116</a>."},"oa":1,"corr_author":"1","doi":"10.15479/AT-ISTA-21116","date_created":"2026-01-30T11:04:14Z","year":"2026","department":[{"_id":"BeVi"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","file_date_updated":"2026-01-30T11:00:56Z","title":"Research Data for \"Causes and consequences of sex-chromosome turnovers in Diptera\"","abstract":[{"text":"Sex-chromosome systems are highly variable across animals, but how they transition from one to another is not well understood. Diptera have undergone multiple sex-chromosome turnovers and expansions while maintaining their general chromosomal content, which makes them an ideal clade to study such transitions. We analyzed more than 100 dipteran whole-genome assemblies and identified 4 new lineages that underwent sex-chromosome turnover (in addition to the 5 previously reported). We find that the majority of turnovers happened in the group Schizophora, which tend to have fewer genes on Muller element F (the chromosome homologous to the ancestral insect X chromosome) than lower dipterans, a factor previously hypothesized to facilitate turnover. Most derived X chromosomes have higher GC content than autosomes, consistent with a high prevalence of male achiasmy in Diptera. In addition, an excess of gene movement out of the X is detected for most of these new X chromosomes, and many of these moved genes have high testis expression in Drosophila, suggesting that out-of-X gene movement contributes to the long-term demasculinization of X chromosomes.","lang":"eng"}],"_id":"21116","status":"public","date_updated":"2026-02-12T12:58:00Z","author":[{"orcid":"0000-0002-1253-6297","first_name":"Lorena Alexandra","last_name":"Layana Franco","full_name":"Layana Franco, Lorena Alexandra","id":"02814589-eb8f-11eb-b029-a70074f3f18f"},{"orcid":"0000-0002-9752-7380","first_name":"Melissa A","last_name":"Toups","full_name":"Toups, Melissa A","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-4579-8306","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","full_name":"Vicoso, Beatriz"}],"file":[{"file_name":"README.txt","date_created":"2026-01-30T11:00:24Z","relation":"main_file","content_type":"text/plain","date_updated":"2026-01-30T11:00:24Z","creator":"llayanaf","success":1,"file_size":1201,"checksum":"0b79be6229f2ad9ac117ef00fc4f5c0e","access_level":"open_access","file_id":"21117"},{"date_created":"2026-01-30T11:00:36Z","file_name":"Supplementary_Tables.zip","content_type":"application/zip","relation":"main_file","date_updated":"2026-01-30T11:00:36Z","creator":"llayanaf","success":1,"checksum":"a3cda72e4177fa1e5d3f0f6a88f8a79b","file_size":572403,"access_level":"open_access","file_id":"21118"},{"file_id":"21119","access_level":"open_access","file_size":19054553,"checksum":"efb5b64698d6ca9e7b675204f6fc1c29","creator":"llayanaf","success":1,"date_updated":"2026-01-30T11:00:48Z","relation":"main_file","content_type":"application/zip","date_created":"2026-01-30T11:00:48Z","file_name":"Supplementary_Datasets.zip"},{"checksum":"254e050f648e9783ba8fe11adb3b49db","file_size":4575,"access_level":"open_access","file_id":"21120","file_name":"Perl_scripts.zip","date_created":"2026-01-30T11:00:56Z","relation":"main_file","content_type":"application/zip","date_updated":"2026-01-30T11:00:56Z","creator":"llayanaf","success":1}],"date_published":"2026-01-02T00:00:00Z","oa_version":"Published Version","has_accepted_license":"1","day":"2","keyword":["Schizophora","sex chromosomes","sex-chromosome turnover","Diptera","genomic features","out-of-X movement."],"month":"01","type":"research_data","article_processing_charge":"No","publisher":"Institute of Science and Technology Austria"},{"month":"01","scopus_import":"1","oa_version":"Published Version","has_accepted_license":"1","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"}],"PlanS_conform":"1","external_id":{"pmid":["41592777"]},"OA_place":"publisher","project":[{"_id":"90ef7108-16d5-11f0-9cad-e6e116913473","name":"Does genetic drift set a limit on the adaptive evolution of sex-biased expression?","grant_number":"ESP 6331524"}],"date_updated":"2026-02-16T09:27:33Z","date_published":"2026-01-28T00:00:00Z","ddc":["570"],"author":[{"full_name":"De Castro Barbosa Rodrigues Barata, Carolina","id":"20565186-803f-11ed-ab7e-96a4ff7694ef","last_name":"De Castro Barbosa Rodrigues Barata","orcid":"0000-0003-1945-2245","first_name":"Carolina"},{"first_name":"Beatriz","orcid":"0000-0002-4579-8306","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"department":[{"_id":"BeVi"}],"article_number":"20252471","publication_identifier":{"eissn":["1471-2954"]},"acknowledgement":"This work was partly funded by an Austrian Science Foundation FWF ESPRIT fellowship (10.55776/ESP6331524) to C.B. We would like to thank the Vicoso group for their invaluable input and discussions throughout this work. We thank Filip Ruzicka for his insightful comments on the manuscript. All computational resources were provided by the Scientific Computing Unit at ISTA. This research was also supported through resources provided by the Imaging & Optics Facility (IOF) at ISTA.","doi":"10.1098/rspb.2025.2471","type":"journal_article","volume":293,"day":"28","issue":"2063","publication":"Proceedings of the Royal Society B Biological Sciences","publisher":"Royal Society of London","OA_type":"hybrid","article_processing_charge":"Yes (via OA deal)","intvolume":"       293","_id":"21161","pmid":1,"abstract":[{"lang":"eng","text":"In many species, sex-biased expression is widespread and thought to contribute to sexual dimorphism. While bulk RNA-sequencing has been instrumental in identifying strongly sex-biased genes, it lacks resolution to assess variation across cell-types and tissue compartments. Using single-nucleus expression data from the Fly Cell Atlas, we investigate sex differences in adult Drosophila melanogaster. We find that differences in cell-type composition between the sexes are not a major source of sex-bias, as for the vast majority of genes, the degree of sex-bias is similar regardless of whether sex differences in cell-type composition are controlled for or not. Our analysis confirms a deficit of X-linked male-biased genes in the body’s somatic tissues that is widespread across cell-types. We also find the excess of X-linked female-biased genes to be associated with nervous system cells in the head but with epithelial cells in the body’s somatic tissues, showing that single-nucleus data crucially resolves sex-bias at the cell-type level. We investigate dosage compensation (DC) across 15 tissues and 17 cell-types. We observe that it varies throughout the body. Surprisingly, we observe a lack of DC in a cluster of main cells within the male accessory glands. This result highlights the importance of understanding context-dependent DC."}],"status":"public","publication_status":"published","file":[{"date_updated":"2026-02-16T09:26:02Z","success":1,"creator":"dernst","file_name":"2026_RoyalSocPubProceedingsB_Barata.pdf","date_created":"2026-02-16T09:26:02Z","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_id":"21226","file_size":2230841,"checksum":"d76afebca0a6f112df0146ae2d929f36"}],"file_date_updated":"2026-02-16T09:26:02Z","title":"Single-nucleus resolution of sex-biased expression and dosage compensation in Drosophila melanogaster","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"citation":{"short":"C. de Castro Barbosa Rodrigues Barata, B. Vicoso, Proceedings of the Royal Society B Biological Sciences 293 (2026).","ieee":"C. de Castro Barbosa Rodrigues Barata and B. Vicoso, “Single-nucleus resolution of sex-biased expression and dosage compensation in Drosophila melanogaster,” <i>Proceedings of the Royal Society B Biological Sciences</i>, vol. 293, no. 2063. Royal Society of London, 2026.","mla":"de Castro Barbosa Rodrigues Barata, Carolina, and Beatriz Vicoso. “Single-Nucleus Resolution of Sex-Biased Expression and Dosage Compensation in Drosophila Melanogaster.” <i>Proceedings of the Royal Society B Biological Sciences</i>, vol. 293, no. 2063, 20252471, Royal Society of London, 2026, doi:<a href=\"https://doi.org/10.1098/rspb.2025.2471\">10.1098/rspb.2025.2471</a>.","ama":"de Castro Barbosa Rodrigues Barata C, Vicoso B. Single-nucleus resolution of sex-biased expression and dosage compensation in Drosophila melanogaster. <i>Proceedings of the Royal Society B Biological Sciences</i>. 2026;293(2063). doi:<a href=\"https://doi.org/10.1098/rspb.2025.2471\">10.1098/rspb.2025.2471</a>","ista":"de Castro Barbosa Rodrigues Barata C, Vicoso B. 2026. Single-nucleus resolution of sex-biased expression and dosage compensation in Drosophila melanogaster. Proceedings of the Royal Society B Biological Sciences. 293(2063), 20252471.","apa":"de Castro Barbosa Rodrigues Barata, C., &#38; Vicoso, B. (2026). Single-nucleus resolution of sex-biased expression and dosage compensation in Drosophila melanogaster. <i>Proceedings of the Royal Society B Biological Sciences</i>. Royal Society of London. <a href=\"https://doi.org/10.1098/rspb.2025.2471\">https://doi.org/10.1098/rspb.2025.2471</a>","chicago":"Castro Barbosa Rodrigues Barata, Carolina de, and Beatriz Vicoso. “Single-Nucleus Resolution of Sex-Biased Expression and Dosage Compensation in Drosophila Melanogaster.” <i>Proceedings of the Royal Society B Biological Sciences</i>. Royal Society of London, 2026. <a href=\"https://doi.org/10.1098/rspb.2025.2471\">https://doi.org/10.1098/rspb.2025.2471</a>."},"date_created":"2026-02-08T23:02:49Z","year":"2026","corr_author":"1","quality_controlled":"1","article_type":"original"},{"doi":"10.1093/molbev/msag020","acknowledgement":"This review is a product of the SMBE satellite workshop and the SNSF Scientific Exchange on the Genomic Consequences of Meiotic Drive. We thank the Society for Molecular Biology and Evolution (satellite grant to A.M.L., A.K.L., R.L.U., D.C.P.), the Swiss National Science Foundation (Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung IZSEZ0_217501 to A.K.L.), and the National Science Foundation Division of Molecular and Cellular Biosciences (NSF MCB Conference grant 2312190 to R.L.U.) for their generous support of the workshop.\r\n\r\nWe also thank the following for their support of individual authors: National Science Foundation Division of Molecular and Cellular Biosciences (NSF MCB CAREER 2047052 to R.L.U.), Division of Environmental Biology (NSF DEB-2344468 to L.F., NSF DEB-1737824 to K.A.D.), National Institute of General Medical Sciences (NIH R35GM119515 to A.M.L., NIH R01GM148442 to D.C.P.), European Research Council (PGErepro to L.R.), Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP 2020/06188-5 to A.B.S.M.F.), Royal Society (DHF\\R1\\180120 to L.R.), Wissenschaftskolleg zu Berlin (support for D.C.P.), and Vetenskapsrådet (Swedish Research Council VR grant number 2021-0429 to A.A.V.).","publication_identifier":{"eissn":["1537-1719"]},"article_number":"msag020","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"department":[{"_id":"BeVi"}],"author":[{"first_name":"Daven C.","full_name":"Presgraves, Daven C.","last_name":"Presgraves"},{"full_name":"Dawe, R. Kelly","last_name":"Dawe","first_name":"R. Kelly"},{"first_name":"Kelly A.","full_name":"Dyer, Kelly A.","last_name":"Dyer"},{"full_name":"Fishman, Lila","last_name":"Fishman","first_name":"Lila"},{"full_name":"Bhide, Soumitra A.","last_name":"Bhide","first_name":"Soumitra A."},{"first_name":"Sasha L.","last_name":"Bradshaw","full_name":"Bradshaw, Sasha L."},{"full_name":"Brady, Meghan J.","last_name":"Brady","first_name":"Meghan J."},{"first_name":"Alejandro","full_name":"Burga, Alejandro","last_name":"Burga"},{"first_name":"Cécile","last_name":"Courret","full_name":"Courret, Cécile"},{"first_name":"Brandon L.","full_name":"Fagen, Brandon L.","last_name":"Fagen"},{"first_name":"Ana Beatriz Stein","last_name":"Machado Ferretti","full_name":"Machado Ferretti, Ana Beatriz Stein"},{"first_name":"Réka K","orcid":"0000-0002-8489-9281","full_name":"Kelemen, Réka K","id":"48D3F8DE-F248-11E8-B48F-1D18A9856A87","last_name":"Kelemen"},{"first_name":"Jun","full_name":"Kitano, Jun","last_name":"Kitano"},{"last_name":"Liu","full_name":"Liu, Yiran","first_name":"Yiran"},{"full_name":"Martí, Emiliano","last_name":"Martí","first_name":"Emiliano"},{"last_name":"Erlenbach","full_name":"Erlenbach, Theresa","first_name":"Theresa"},{"full_name":"Reinhardt, Josephine A.","last_name":"Reinhardt","first_name":"Josephine A."},{"full_name":"Ross, Laura","last_name":"Ross","first_name":"Laura"},{"first_name":"Jan Niklas","full_name":"Runge, Jan Niklas","last_name":"Runge"},{"first_name":"Callie M.","full_name":"Swanepoel, Callie M.","last_name":"Swanepoel"},{"full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","orcid":"0000-0002-4579-8306","first_name":"Beatriz"},{"first_name":"Aaron A.","last_name":"Vogan","full_name":"Vogan, Aaron A."},{"full_name":"Lindholm, Anna K.","last_name":"Lindholm","first_name":"Anna K."},{"first_name":"Amanda M.","full_name":"Larracuente, Amanda M.","last_name":"Larracuente"},{"first_name":"Robert L.","full_name":"Unckless, Robert L.","last_name":"Unckless"}],"ddc":["570"],"date_published":"2026-02-02T00:00:00Z","date_updated":"2026-03-09T10:33:04Z","OA_place":"publisher","external_id":{"pmid":["41589062"]},"PlanS_conform":"1","language":[{"iso":"eng"}],"has_accepted_license":"1","oa_version":"Published Version","scopus_import":"1","month":"02","article_type":"original","quality_controlled":"1","year":"2026","date_created":"2026-03-08T23:01:45Z","citation":{"mla":"Presgraves, Daven C., et al. “The Evolutionary Genomics of Meiotic Drive.” <i>Molecular Biology and Evolution</i>, vol. 43, no. 2, msag020, Oxford University Press, 2026, doi:<a href=\"https://doi.org/10.1093/molbev/msag020\">10.1093/molbev/msag020</a>.","short":"D.C. Presgraves, R.K. Dawe, K.A. Dyer, L. Fishman, S.A. Bhide, S.L. Bradshaw, M.J. Brady, A. Burga, C. Courret, B.L. Fagen, A.B.S. Machado Ferretti, R.K. Kelemen, J. Kitano, Y. Liu, E. Martí, T. Erlenbach, J.A. Reinhardt, L. Ross, J.N. Runge, C.M. Swanepoel, B. Vicoso, A.A. Vogan, A.K. Lindholm, A.M. Larracuente, R.L. Unckless, Molecular Biology and Evolution 43 (2026).","ieee":"D. C. Presgraves <i>et al.</i>, “The evolutionary genomics of meiotic drive,” <i>Molecular Biology and Evolution</i>, vol. 43, no. 2. Oxford University Press, 2026.","ista":"Presgraves DC, Dawe RK, Dyer KA, Fishman L, Bhide SA, Bradshaw SL, Brady MJ, Burga A, Courret C, Fagen BL, Machado Ferretti ABS, Kelemen RK, Kitano J, Liu Y, Martí E, Erlenbach T, Reinhardt JA, Ross L, Runge JN, Swanepoel CM, Vicoso B, Vogan AA, Lindholm AK, Larracuente AM, Unckless RL. 2026. The evolutionary genomics of meiotic drive. Molecular Biology and Evolution. 43(2), msag020.","ama":"Presgraves DC, Dawe RK, Dyer KA, et al. The evolutionary genomics of meiotic drive. <i>Molecular Biology and Evolution</i>. 2026;43(2). doi:<a href=\"https://doi.org/10.1093/molbev/msag020\">10.1093/molbev/msag020</a>","chicago":"Presgraves, Daven C., R. Kelly Dawe, Kelly A. Dyer, Lila Fishman, Soumitra A. Bhide, Sasha L. Bradshaw, Meghan J. Brady, et al. “The Evolutionary Genomics of Meiotic Drive.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2026. <a href=\"https://doi.org/10.1093/molbev/msag020\">https://doi.org/10.1093/molbev/msag020</a>.","apa":"Presgraves, D. C., Dawe, R. K., Dyer, K. A., Fishman, L., Bhide, S. A., Bradshaw, S. L., … Unckless, R. L. (2026). The evolutionary genomics of meiotic drive. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msag020\">https://doi.org/10.1093/molbev/msag020</a>"},"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"The evolutionary genomics of meiotic drive","file_date_updated":"2026-03-09T10:32:02Z","file":[{"access_level":"open_access","file_id":"21414","checksum":"406e7cca0f2536d3bb877032fc837f9b","file_size":4533829,"date_updated":"2026-03-09T10:32:02Z","success":1,"creator":"dernst","file_name":"2026_MolecularBioEvolution_Presgraves.pdf","date_created":"2026-03-09T10:32:02Z","relation":"main_file","content_type":"application/pdf"}],"publication_status":"published","status":"public","pmid":1,"_id":"21409","abstract":[{"lang":"eng","text":"Meiotic drivers are selfish genetic elements that gain transmission advantages by distorting equal, Mendelian segregation. For decades, biologists have considered meiotic drivers as interesting, albeit esoteric, case studies. It is now clear, however, that meiotic drive is more common and phylogenetically widespread than previously supposed. Indeed, intensive study of a few well-known cases has begun to reveal the evolutionary genomic consequences of meiotic drive. We argue here that many features of genome evolution, content, and organization that are seemingly inexplicable by organismal adaptation or nearly neutral processes are instead best accounted for by recurrent histories of meiotic drive. We review how meiotic drive can affect the evolution of sequences, gene copy numbers, genes with functions in meiosis and gametogenesis, signatures of “selection,” chromosome rearrangements, and karyotype evolution. We also explore the interactions of meiotic drive elements with other classes of selfish genetic elements, including satellite DNAs, transposable elements, and with the endogenous host genes involved in drive suppression. Finally, we argue that some aspects of drive-mediated genome evolution are now sufficiently well established that we might reverse the direction of discovery—rather than ask how drive affects genome evolution, we can use genome data to discover new putative drive elements."}],"intvolume":"        43","article_processing_charge":"Yes","OA_type":"gold","publisher":"Oxford University Press","issue":"2","publication":"Molecular Biology and Evolution","day":"02","volume":43,"type":"journal_article","DOAJ_listed":"1"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Causes and consequences of sex-chromosome turnovers in Diptera","citation":{"ieee":"L. A. Layana Franco, M. A. Toups, and B. Vicoso, “Causes and consequences of sex-chromosome turnovers in Diptera,” <i>Evolution Letters</i>. Oxford University Press, 2026.","short":"L.A. Layana Franco, M.A. Toups, B. Vicoso, Evolution Letters (2026).","mla":"Layana Franco, Lorena Alexandra, et al. “Causes and Consequences of Sex-Chromosome Turnovers in Diptera.” <i>Evolution Letters</i>, qrag003, Oxford University Press, 2026, doi:<a href=\"https://doi.org/10.1093/evlett/qrag003\">10.1093/evlett/qrag003</a>.","apa":"Layana Franco, L. A., Toups, M. A., &#38; Vicoso, B. (2026). Causes and consequences of sex-chromosome turnovers in Diptera. <i>Evolution Letters</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/evlett/qrag003\">https://doi.org/10.1093/evlett/qrag003</a>","chicago":"Layana Franco, Lorena Alexandra, Melissa A Toups, and Beatriz Vicoso. “Causes and Consequences of Sex-Chromosome Turnovers in Diptera.” <i>Evolution Letters</i>. Oxford University Press, 2026. <a href=\"https://doi.org/10.1093/evlett/qrag003\">https://doi.org/10.1093/evlett/qrag003</a>.","ama":"Layana Franco LA, Toups MA, Vicoso B. Causes and consequences of sex-chromosome turnovers in Diptera. <i>Evolution Letters</i>. 2026. doi:<a href=\"https://doi.org/10.1093/evlett/qrag003\">10.1093/evlett/qrag003</a>","ista":"Layana Franco LA, Toups MA, Vicoso B. 2026. Causes and consequences of sex-chromosome turnovers in Diptera. Evolution Letters., qrag003."},"oa":1,"quality_controlled":"1","corr_author":"1","article_type":"original","date_created":"2026-03-23T15:05:42Z","year":"2026","day":"12","type":"journal_article","DOAJ_listed":"1","OA_type":"gold","article_processing_charge":"Yes","publication":"Evolution Letters","publisher":"Oxford University Press","main_file_link":[{"url":"https://doi.org/10.1093/evlett/qrag003","open_access":"1"}],"abstract":[{"text":"Sex-chromosome systems are highly variable across animals, but how they transition from one to another is not well understood. Diptera have undergone multiple sex-chromosome turnovers and expansions while maintaining their general chromosomal content, which makes them an ideal clade to study such transitions. We analyzed more than 100 dipteran whole-genome assemblies and identified 4 new lineages that underwent sex-chromosome turnover (in addition to the 5 previously reported). We find that the majority of turnovers happened in the group Schizophora, which tend to have fewer genes on Muller element F (the chromosome homologous to the ancestral insect X chromosome) than lower dipterans, a factor previously hypothesized to facilitate turnover. Most derived X chromosomes have higher GC content than autosomes, consistent with a high prevalence of male achiasmy in Diptera. In addition, an excess of gene movement out of the X is detected for most of these new X chromosomes, and many of these moved genes have high testis expression in Drosophila, suggesting that out-of-X gene movement contributes to the long-term demasculinization of X chromosomes.","lang":"eng"}],"_id":"21486","status":"public","publication_status":"epub_ahead","department":[{"_id":"BeVi"},{"_id":"GradSch"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"article_number":"qrag003","acknowledgement":"This work was supported by a grant from the Austrian Science Fund (FWF, grant number PAT 8748323) to B.V. We thank the Vicoso group for their feedback on an early version of the manuscript. We are grateful to Kamil Jaron and Julia Gries for helpful discussions and for sharing their unpublished work. Computational resources and support were provided by the Scientific Computing Unit at ISTA.","publication_identifier":{"eissn":["2056-3744"]},"doi":"10.1093/evlett/qrag003","oa_version":"Published Version","has_accepted_license":"1","month":"03","language":[{"iso":"eng"}],"OA_place":"publisher","project":[{"name":"Sex chromosomes in evolution and development","_id":"8ed82125-16d5-11f0-9cad-fbcae312235b","grant_number":"PAT 8748323"}],"date_updated":"2026-03-24T07:14:08Z","author":[{"orcid":"0000-0002-1253-6297","first_name":"Lorena Alexandra","full_name":"Layana Franco, Lorena Alexandra","id":"02814589-eb8f-11eb-b029-a70074f3f18f","last_name":"Layana Franco"},{"full_name":"Toups, Melissa A","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","last_name":"Toups","orcid":"0000-0002-9752-7380","first_name":"Melissa A"},{"first_name":"Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz","last_name":"Vicoso"}],"date_published":"2026-03-12T00:00:00Z","ddc":["570"]},{"doi":"10.1016/j.tree.2025.06.010","acknowledgement":"I thank the Vicoso group for in-depth discussions of the original article highlighted here. This work was supported by an Austrian Research Fund (FWF) grant to B.V. (PAT 8748323).","publication_identifier":{"issn":["0169-5347"]},"department":[{"_id":"BeVi"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"isi":1,"author":[{"first_name":"Beatriz","orcid":"0000-0002-4579-8306","last_name":"Vicoso","full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"date_published":"2025-08-01T00:00:00Z","ddc":["570"],"OA_place":"publisher","date_updated":"2025-12-30T09:22:29Z","project":[{"name":"Sex chromosomes in evolution and development","_id":"8ed82125-16d5-11f0-9cad-fbcae312235b","grant_number":"PAT 8748323"}],"PlanS_conform":"1","external_id":{"isi":["001550437400006"]},"language":[{"iso":"eng"}],"scopus_import":"1","oa_version":"Published Version","has_accepted_license":"1","month":"08","quality_controlled":"1","corr_author":"1","article_type":"original","date_created":"2025-07-13T22:01:23Z","year":"2025","citation":{"short":"B. Vicoso, Trends in Ecology and Evolution 40 (2025) 728–730.","ieee":"B. Vicoso, “Sex chromosome evolution in action in fourspine sticklebacks,” <i>Trends in Ecology and Evolution</i>, vol. 40, no. 8. Elsevier, pp. 728–730, 2025.","mla":"Vicoso, Beatriz. “Sex Chromosome Evolution in Action in Fourspine Sticklebacks.” <i>Trends in Ecology and Evolution</i>, vol. 40, no. 8, Elsevier, 2025, pp. 728–30, doi:<a href=\"https://doi.org/10.1016/j.tree.2025.06.010\">10.1016/j.tree.2025.06.010</a>.","apa":"Vicoso, B. (2025). Sex chromosome evolution in action in fourspine sticklebacks. <i>Trends in Ecology and Evolution</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tree.2025.06.010\">https://doi.org/10.1016/j.tree.2025.06.010</a>","chicago":"Vicoso, Beatriz. “Sex Chromosome Evolution in Action in Fourspine Sticklebacks.” <i>Trends in Ecology and Evolution</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.tree.2025.06.010\">https://doi.org/10.1016/j.tree.2025.06.010</a>.","ama":"Vicoso B. Sex chromosome evolution in action in fourspine sticklebacks. <i>Trends in Ecology and Evolution</i>. 2025;40(8):728-730. doi:<a href=\"https://doi.org/10.1016/j.tree.2025.06.010\">10.1016/j.tree.2025.06.010</a>","ista":"Vicoso B. 2025. Sex chromosome evolution in action in fourspine sticklebacks. Trends in Ecology and Evolution. 40(8), 728–730."},"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2025-12-30T09:21:14Z","title":"Sex chromosome evolution in action in fourspine sticklebacks","publication_status":"published","file":[{"date_updated":"2025-12-30T09:21:14Z","success":1,"creator":"dernst","date_created":"2025-12-30T09:21:14Z","file_name":"2025_TrendsEcoloEvolution_Vicoso.pdf","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"20905","file_size":699156,"checksum":"0a7c6e8600c878dac7082681e4409b50"}],"intvolume":"        40","_id":"20009","abstract":[{"lang":"eng","text":"The suppression of recombination between young X and Y chromosomes is a crucial step in their evolution, but why it occurs is not known. The detailed characterization of the polymorphic sex chromosomes of the fourspine stickleback by Liu et al. promises to shed new light on this longstanding question."}],"status":"public","OA_type":"hybrid","article_processing_charge":"Yes (via OA deal)","publication":"Trends in Ecology and Evolution","issue":"8","publisher":"Elsevier","volume":40,"day":"01","page":"728-730","type":"journal_article"},{"date_updated":"2025-09-30T14:06:38Z","project":[{"grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020"}],"OA_place":"publisher","author":[{"first_name":"Tim","last_name":"Connallon","full_name":"Connallon, Tim"},{"first_name":"Peter","full_name":"Czuppon, Peter","last_name":"Czuppon"},{"full_name":"Olito, Colin","last_name":"Olito","first_name":"Colin"},{"last_name":"Goedert","full_name":"Goedert, Debora","first_name":"Debora"},{"first_name":"Hanna","last_name":"Kokko","full_name":"Kokko, Hanna"},{"first_name":"Angela","full_name":"Nava-Bolaños, Angela","last_name":"Nava-Bolaños"},{"full_name":"Nilén, Sofie","last_name":"Nilén","first_name":"Sofie"},{"first_name":"Erik I","last_name":"Svensson","full_name":"Svensson, Erik I"},{"first_name":"Martyna","full_name":"Zwoinska, Martyna","last_name":"Zwoinska"},{"first_name":"Ludovic","last_name":"Dutoit","full_name":"Dutoit, Ludovic"},{"first_name":"Filip","last_name":"Ruzicka","id":"347955dd-57b0-11ee-9095-c28bdd368f4b","full_name":"Ruzicka, Filip"}],"ddc":["570"],"date_published":"2025-07-01T00:00:00Z","has_accepted_license":"1","oa_version":"Published Version","month":"07","external_id":{"isi":["001477180800001"]},"PlanS_conform":"1","language":[{"iso":"eng"}],"acknowledgement":"Support for this research came from the European Society of Evolutionary Biology (ESEB) through a “Special Topics Network” grant. Further financial support came from the European Research Council (ERC-2023-STG916 #101117517, to C.O.), the Swedish Research Council (#2022-03603, to C.O.; #2020‑03123, to E.I.S.), the Research Council of Norway (Norges forskningsråd #302619, to D.G.), the Alexander von Humboldt Foundation and the GenEvo graduate school (to H.K.), the Foundation for Zoological Research and the Birgitta Sintring Foundation (#S2024-0007, to M.K.Z.), a postdoctoral fellowship from the Consejo Nacional de Humanidades, Ciencias y Tecnología (to A.N.B.), and a H2020 Marie Skłodowska-Curie COFUND Action fellowship (#101034413, to F.R.). We wish to express our deepest gratitude to Lotte de Vries for extensive discussion of the project, rederiving some of our results, and providing comments on an earlier version of the manuscript, and to the European Society of Evolutionary Biology (ESEB) for a “Special Topics Network” grant that supported workshops that initiated this collaboration and facilitated many new ideas and friendships. We also thank two anonymous reviewers for their thoughtful comments and suggestions that helped us to substantially improve upon the original version of the article.","publication_identifier":{"issn":["0014-3820"],"eissn":["1558-5646"]},"doi":"10.1093/evolut/qpaf061","department":[{"_id":"BeVi"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"isi":1,"status":"public","intvolume":"        79","_id":"20044","abstract":[{"text":"Genetic trade-offs—which occur when variants that are beneficial in some contexts of natural selection are harmful in others—can influence a wide range of evolutionary phenomena, from the maintenance of genetic variation to the evolution of aging and sex differences. An extensive body of evolutionary theory has focused on the consequences of such trade-offs, and recent analyses of Fisher’s geometric model have further quantified the expected proportion of new mutations that exhibit trade-offs. However, the theory remains silent regarding the prevalence of trade-offs among the variants that contribute to adaptation. Here, we extend Fisher’s geometric model to predict the prevalence of trade-offs among the adaptive mutations that become established or fixed in a population. We consider trade-offs between sexes, habitats, fitness components, and temporally fluctuating environments. In all 4 scenarios, trade-off alleles are consistently under-represented among established relative to new beneficial mutations—an effect that arises from the greater susceptibility of trade-off alleles to genetic drift. Adaptation during a population size decline exacerbates this deficit of trade-offs among established mutations, whereas population expansions dampen it. Consequently, threatened populations should primarily adapt using unconditionally beneficial alleles, while invasive populations are more prone to adaptation using variants that exhibit trade-offs.","lang":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","date_created":"2025-07-22T10:04:57Z","file_name":"2025_Evolution_Connallon.pdf","success":1,"creator":"dernst","date_updated":"2025-07-22T10:04:57Z","file_size":8150623,"checksum":"68c4c996d0e8c9ee3d4fb61bca75b31a","file_id":"20068","access_level":"open_access"}],"publication_status":"published","day":"01","page":"1243-1255","volume":79,"type":"journal_article","article_processing_charge":"Yes (in subscription journal)","OA_type":"hybrid","publisher":"Oxford University Press","issue":"7","publication":"Evolution","citation":{"apa":"Connallon, T., Czuppon, P., Olito, C., Goedert, D., Kokko, H., Nava-Bolaños, A., … Ruzicka, F. (2025). Predicting the prevalence of genetic trade-offs among adaptive substitutions. <i>Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/evolut/qpaf061\">https://doi.org/10.1093/evolut/qpaf061</a>","chicago":"Connallon, Tim, Peter Czuppon, Colin Olito, Debora Goedert, Hanna Kokko, Angela Nava-Bolaños, Sofie Nilén, et al. “Predicting the Prevalence of Genetic Trade-Offs among Adaptive Substitutions.” <i>Evolution</i>. Oxford University Press, 2025. <a href=\"https://doi.org/10.1093/evolut/qpaf061\">https://doi.org/10.1093/evolut/qpaf061</a>.","ama":"Connallon T, Czuppon P, Olito C, et al. Predicting the prevalence of genetic trade-offs among adaptive substitutions. <i>Evolution</i>. 2025;79(7):1243-1255. doi:<a href=\"https://doi.org/10.1093/evolut/qpaf061\">10.1093/evolut/qpaf061</a>","ista":"Connallon T, Czuppon P, Olito C, Goedert D, Kokko H, Nava-Bolaños A, Nilén S, Svensson EI, Zwoinska M, Dutoit L, Ruzicka F. 2025. Predicting the prevalence of genetic trade-offs among adaptive substitutions. Evolution. 79(7), 1243–1255.","short":"T. Connallon, P. Czuppon, C. Olito, D. Goedert, H. Kokko, A. Nava-Bolaños, S. Nilén, E.I. Svensson, M. Zwoinska, L. Dutoit, F. Ruzicka, Evolution 79 (2025) 1243–1255.","ieee":"T. Connallon <i>et al.</i>, “Predicting the prevalence of genetic trade-offs among adaptive substitutions,” <i>Evolution</i>, vol. 79, no. 7. Oxford University Press, pp. 1243–1255, 2025.","mla":"Connallon, Tim, et al. “Predicting the Prevalence of Genetic Trade-Offs among Adaptive Substitutions.” <i>Evolution</i>, vol. 79, no. 7, Oxford University Press, 2025, pp. 1243–55, doi:<a href=\"https://doi.org/10.1093/evolut/qpaf061\">10.1093/evolut/qpaf061</a>."},"oa":1,"article_type":"original","quality_controlled":"1","year":"2025","date_created":"2025-07-21T07:57:28Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ec_funded":1,"title":"Predicting the prevalence of genetic trade-offs among adaptive substitutions","file_date_updated":"2025-07-22T10:04:57Z"},{"doi":"10.1016/j.cois.2025.101411","acknowledgement":"This work was supported by an Austrian Research Fund (FWF) grant to B.V. (PAT 8748323) and by the Louisiana Board of Regents Research Competitiveness Subprogram (LEQSF(2025-28)-RD-A-20) to MAT.","publication_identifier":{"issn":["2214-5745"],"eissn":["2214-5753"]},"article_number":"101411","department":[{"_id":"BeVi"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"isi":1,"author":[{"orcid":"0000-0002-9752-7380","first_name":"Melissa A","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","last_name":"Toups","full_name":"Toups, Melissa A"},{"orcid":"0000-0002-4579-8306","first_name":"Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz"}],"date_published":"2025-12-01T00:00:00Z","ddc":["570"],"OA_place":"publisher","date_updated":"2025-12-30T13:14:38Z","project":[{"name":"Sex chromosomes in evolution and development","_id":"8ed82125-16d5-11f0-9cad-fbcae312235b","grant_number":"PAT 8748323"}],"PlanS_conform":"1","external_id":{"isi":["001582424100001"]},"language":[{"iso":"eng"}],"scopus_import":"1","oa_version":"Published Version","has_accepted_license":"1","month":"12","quality_controlled":"1","corr_author":"1","article_type":"review","date_created":"2025-08-17T22:01:35Z","year":"2025","citation":{"ista":"Toups MA, Vicoso B. 2025. Insect sex chromosome evolution: Conservation, turnover, and mechanisms of dosage compensation. Current Opinion in Insect Science. 72, 101411.","ama":"Toups MA, Vicoso B. Insect sex chromosome evolution: Conservation, turnover, and mechanisms of dosage compensation. <i>Current Opinion in Insect Science</i>. 2025;72. doi:<a href=\"https://doi.org/10.1016/j.cois.2025.101411\">10.1016/j.cois.2025.101411</a>","chicago":"Toups, Melissa A, and Beatriz Vicoso. “Insect Sex Chromosome Evolution: Conservation, Turnover, and Mechanisms of Dosage Compensation.” <i>Current Opinion in Insect Science</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.cois.2025.101411\">https://doi.org/10.1016/j.cois.2025.101411</a>.","apa":"Toups, M. A., &#38; Vicoso, B. (2025). Insect sex chromosome evolution: Conservation, turnover, and mechanisms of dosage compensation. <i>Current Opinion in Insect Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cois.2025.101411\">https://doi.org/10.1016/j.cois.2025.101411</a>","mla":"Toups, Melissa A., and Beatriz Vicoso. “Insect Sex Chromosome Evolution: Conservation, Turnover, and Mechanisms of Dosage Compensation.” <i>Current Opinion in Insect Science</i>, vol. 72, 101411, Elsevier, 2025, doi:<a href=\"https://doi.org/10.1016/j.cois.2025.101411\">10.1016/j.cois.2025.101411</a>.","ieee":"M. A. Toups and B. Vicoso, “Insect sex chromosome evolution: Conservation, turnover, and mechanisms of dosage compensation,” <i>Current Opinion in Insect Science</i>, vol. 72. Elsevier, 2025.","short":"M.A. Toups, B. Vicoso, Current Opinion in Insect Science 72 (2025)."},"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2025-12-30T13:14:20Z","title":"Insect sex chromosome evolution: Conservation, turnover, and mechanisms of dosage compensation","publication_status":"published","file":[{"date_updated":"2025-12-30T13:14:20Z","success":1,"creator":"dernst","date_created":"2025-12-30T13:14:20Z","file_name":"2025_CurrOpinionInsectScience_Toups.pdf","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_id":"20917","file_size":897079,"checksum":"262640abc34277686b56eb60102976f6"}],"_id":"20182","abstract":[{"lang":"eng","text":"Sex chromosomes have evolved many times throughout the tree of life, and understanding what has shaped their unusual morphological, sequence, and regulatory features has been a long-standing goal. Most early insights into insect sex chromosome biology came from a few model species, such as the fruit fly Drosophila melanogaster, which limited broad-scale evolutionary inferences. More recently, extensive comparative genomics studies have uncovered several unexpected patterns, which we highlight in this review. First, we describe the conservation of the ancestral X chromosome over 450 million years but also its recurrent turnover (i.e. its reversal to an autosome when a new X chromosome arose) in at least one order. We then summarize classical and more recent findings on how insects modulate the expression of X-linked genes following the degradation of the Y chromosome and how the diverse mechanisms of dosage compensation identified may elucidate important principles of sex chromosome regulatory evolution."}],"intvolume":"        72","status":"public","OA_type":"hybrid","article_processing_charge":"Yes (via OA deal)","publication":"Current Opinion in Insect Science","publisher":"Elsevier","volume":72,"day":"01","type":"journal_article"},{"PlanS_conform":"1","external_id":{"pmid":["40713898"],"isi":["001547617100001"]},"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"oa_version":"Published Version","scopus_import":"1","has_accepted_license":"1","month":"08","author":[{"first_name":"Andrea","full_name":"Mrnjavac, Andrea","last_name":"Mrnjavac","id":"353FAC84-AE61-11E9-8BFC-00D3E5697425"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","first_name":"Beatriz"},{"first_name":"Tim","full_name":"Connallon, Tim","last_name":"Connallon"}],"date_published":"2025-08-01T00:00:00Z","ddc":["570"],"OA_place":"publisher","date_updated":"2025-09-30T14:25:57Z","article_number":"msaf177","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"isi":1,"department":[{"_id":"BeVi"}],"doi":"10.1093/molbev/msaf177","acknowledgement":"We thank Filip Ruzicka, Colin Olito, Akane Uesugi, Melissa Toups, Daniel Jeffries, the Associate Editor, and anonymous reviewers, for comments and suggestions on earlier versions of the paper. We are particularly grateful to Deborah Charlesworth and Brian Charlesworth for extensive comments on two different drafts of the manuscript. We also thank Aneil Agrawal and Thomas Lenormand for email correspondence about the data on dominance and ways to interpret it. Technical support was provided by ISTA Scientific Computing Unit.","publication_identifier":{"issn":["0737-4038"],"eissn":["1537-1719"]},"OA_type":"gold","article_processing_charge":"Yes","issue":"8","publication":"Molecular Biology and Evolution","publisher":"Oxford University Press","volume":42,"day":"01","DOAJ_listed":"1","type":"journal_article","publication_status":"published","file":[{"file_size":1239841,"checksum":"f40abffa56cb1e9ff65800f2a7d7b39a","file_id":"20274","access_level":"open_access","content_type":"application/pdf","relation":"main_file","date_created":"2025-09-02T07:47:32Z","file_name":"2025_MolecularBioEvolution_Mrnjavac.pdf","creator":"dernst","success":1,"date_updated":"2025-09-02T07:47:32Z"}],"abstract":[{"text":"The first influential hypothesis for sex chromosome evolution was proposed in 1914 by H. J. Muller, who argued that once recombination was suppressed between the X and Y chromosomes, Y-linked genes become “sheltered” from selection, leading to accumulation of recessive loss-of-function (LOF) mutations and decay of Y-linked genes. The hypothesis fell out of favor in the 1970s because early mathematical models failed to support it and data on the dominance of lethal mutations were viewed as incompatible with the hypothesis. We reevaluate the main arguments against Muller's hypothesis and find that they do not conclusively exclude a role for sheltering in sex chromosome evolution. By relaxing restrictive assumptions of earlier models, we show that sheltering promotes fixation of LOF mutations with sexually dimorphic fitness effects, resulting in decay of X-linked genes that are exclusively expressed by males and Y-linked genes that are primarily, though not necessarily exclusively, expressed by females. We further show that drift and other processes contributing to Y degeneration (i.e. selective interference and regulatory evolution) expand conditions of Y-linked gene loss by sheltering. The actual contribution of sheltering to sex chromosome evolution hinges upon the distribution of dominance and sex-specific fitness effects of LOF mutations, which we discuss.","lang":"eng"}],"_id":"20223","pmid":1,"intvolume":"        42","status":"public","related_material":{"link":[{"relation":"software","url":"https://git.ista.ac.at/bvicoso/xydegenerate"}]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","file_date_updated":"2025-09-02T07:47:32Z","title":"An extension of Muller's sheltering hypothesis for the evolution of sex chromosome gene content","quality_controlled":"1","article_type":"original","date_created":"2025-08-24T22:01:31Z","year":"2025","citation":{"ista":"Mrnjavac A, Vicoso B, Connallon T. 2025. An extension of Muller’s sheltering hypothesis for the evolution of sex chromosome gene content. Molecular Biology and Evolution. 42(8), msaf177.","ama":"Mrnjavac A, Vicoso B, Connallon T. An extension of Muller’s sheltering hypothesis for the evolution of sex chromosome gene content. <i>Molecular Biology and Evolution</i>. 2025;42(8). doi:<a href=\"https://doi.org/10.1093/molbev/msaf177\">10.1093/molbev/msaf177</a>","chicago":"Mrnjavac, Andrea, Beatriz Vicoso, and Tim Connallon. “An Extension of Muller’s Sheltering Hypothesis for the Evolution of Sex Chromosome Gene Content.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2025. <a href=\"https://doi.org/10.1093/molbev/msaf177\">https://doi.org/10.1093/molbev/msaf177</a>.","apa":"Mrnjavac, A., Vicoso, B., &#38; Connallon, T. (2025). An extension of Muller’s sheltering hypothesis for the evolution of sex chromosome gene content. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msaf177\">https://doi.org/10.1093/molbev/msaf177</a>","ieee":"A. Mrnjavac, B. Vicoso, and T. Connallon, “An extension of Muller’s sheltering hypothesis for the evolution of sex chromosome gene content,” <i>Molecular Biology and Evolution</i>, vol. 42, no. 8. Oxford University Press, 2025.","mla":"Mrnjavac, Andrea, et al. “An Extension of Muller’s Sheltering Hypothesis for the Evolution of Sex Chromosome Gene Content.” <i>Molecular Biology and Evolution</i>, vol. 42, no. 8, msaf177, Oxford University Press, 2025, doi:<a href=\"https://doi.org/10.1093/molbev/msaf177\">10.1093/molbev/msaf177</a>.","short":"A. Mrnjavac, B. Vicoso, T. Connallon, Molecular Biology and Evolution 42 (2025)."},"oa":1},{"volume":231,"day":"01","type":"journal_article","OA_type":"hybrid","article_processing_charge":"Yes (via OA deal)","publication":"Genetics","issue":"3","publisher":"Oxford University Press","_id":"20330","intvolume":"       231","abstract":[{"lang":"eng","text":"The evolution of sexual dimorphism (the difference in average trait values between females and males, SD), is often thought to be constrained by shared genetic architecture between the sexes. Indeed, it is commonly expected that SD should negatively correlate with the intersex correlation (the genetic correlation between effects of segregating variants in females and males, r fm), either because (1) traits with ancestrally low r fm are less constrained in their ability to respond to sex-specific selection and thus evolve to be more dimorphic, or because (2) sex-specific selection, driving sexual dimorphism evolution, also acts to reduce r fm. Despite the intuitive appeal and prominence of these ideas, their generality and the conditions in which they hold remain unclear. Here, we develop models incorporating sex-specific stabilizing selection, mutation and genetic drift to examine the relationship between r fm and SD. We show that the two commonly-discussed mechanisms with the potential to generate a negative correlation between SD and r fm could just as easily generate a positive association, since the standard line of reasoning hinges on a hidden assumption that sex-specific adaptation more frequently favors increased dimorphism than reduced dimorphism. Our results provide, to our knowledge, the first mechanistic framework for understanding the conditions under which a correlation between r fm and SD may arise and offer a compelling explanation for inconsistent empirical evidence. We also make the intriguing observation that—even when selection between the two sexes is identical—drift generates nonzero SD. We quantify this effect and discuss its significance."}],"status":"public","publication_status":"published","file":[{"access_level":"open_access","file_id":"20946","checksum":"bbb73bbf8617812d4d8db4af92be9538","file_size":1550562,"date_updated":"2026-01-05T13:03:18Z","success":1,"creator":"dernst","file_name":"2025_Genetics_Puixeu.pdf","date_created":"2026-01-05T13:03:18Z","relation":"main_file","content_type":"application/pdf"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2026-01-05T13:03:18Z","ec_funded":1,"title":"The relationship between sexual dimorphism and intersex correlation: Do models support intuition?","citation":{"ieee":"G. Puixeu Sala and L. Hayward, “The relationship between sexual dimorphism and intersex correlation: Do models support intuition?,” <i>Genetics</i>, vol. 231, no. 3. Oxford University Press, 2025.","mla":"Puixeu Sala, Gemma, and Laura Hayward. “The Relationship between Sexual Dimorphism and Intersex Correlation: Do Models Support Intuition?” <i>Genetics</i>, vol. 231, no. 3, iyaf175, Oxford University Press, 2025, doi:<a href=\"https://doi.org/10.1093/genetics/iyaf175\">10.1093/genetics/iyaf175</a>.","short":"G. Puixeu Sala, L. Hayward, Genetics 231 (2025).","chicago":"Puixeu Sala, Gemma, and Laura Hayward. “The Relationship between Sexual Dimorphism and Intersex Correlation: Do Models Support Intuition?” <i>Genetics</i>. Oxford University Press, 2025. <a href=\"https://doi.org/10.1093/genetics/iyaf175\">https://doi.org/10.1093/genetics/iyaf175</a>.","apa":"Puixeu Sala, G., &#38; Hayward, L. (2025). The relationship between sexual dimorphism and intersex correlation: Do models support intuition? <i>Genetics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/genetics/iyaf175\">https://doi.org/10.1093/genetics/iyaf175</a>","ista":"Puixeu Sala G, Hayward L. 2025. The relationship between sexual dimorphism and intersex correlation: Do models support intuition? Genetics. 231(3), iyaf175.","ama":"Puixeu Sala G, Hayward L. The relationship between sexual dimorphism and intersex correlation: Do models support intuition? <i>Genetics</i>. 2025;231(3). doi:<a href=\"https://doi.org/10.1093/genetics/iyaf175\">10.1093/genetics/iyaf175</a>"},"oa":1,"quality_controlled":"1","corr_author":"1","article_type":"original","date_created":"2025-09-10T05:48:04Z","year":"2025","scopus_import":"1","oa_version":"Published Version","has_accepted_license":"1","month":"11","PlanS_conform":"1","external_id":{"isi":["001598595000001"]},"language":[{"iso":"eng"}],"OA_place":"publisher","project":[{"grant_number":"25817","name":"Sexual conflict: resolution, constraints and biomedical implications","_id":"9B9DFC9E-BA93-11EA-9121-9846C619BF3A"},{"grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","name":"Understanding the evolution of continuous genomes","grant_number":"101055327"}],"date_updated":"2026-01-05T13:04:07Z","author":[{"orcid":"0000-0001-8330-1754","first_name":"Gemma","full_name":"Puixeu Sala, Gemma","last_name":"Puixeu Sala","id":"33AB266C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hayward, Laura","id":"fc885ee5-24bf-11eb-ad7b-bcc5104c0c1b","last_name":"Hayward","first_name":"Laura"}],"date_published":"2025-11-01T00:00:00Z","ddc":["570"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"department":[{"_id":"BeVi"},{"_id":"NiBa"}],"isi":1,"article_number":"iyaf175","acknowledgement":"We thank Tim Connallon for useful discussions and correspondence, Himani Sachdeva and Nick Barton for comments on the manuscript and the Scientific Computing unit at ISTA for technical support. GP is the recipient of a DOC Fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology Austria (DOC 25817) and received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant (agreement no. 665385). LH received funding from the European Research Council, under the HaplotypeStructure Grant (grant no. 101055327) to Nick Barton.","publication_identifier":{"issn":["1943-2631"]},"doi":"10.1093/genetics/iyaf175"},{"type":"journal_article","day":"01","page":"101-113","volume":141,"publisher":"Springer Nature","issue":"11","publication":"Matrix Biology","article_processing_charge":"Yes (in subscription journal)","OA_type":"hybrid","status":"public","_id":"20404","intvolume":"       141","pmid":1,"abstract":[{"text":"Collagens are fundamental components of extracellular matrices, requiring precise intracellular post-translational modifications for proper function. Among the modifications, prolyl 4-hydroxylation is critical to stabilise the collagen triple helix. In humans, this reaction is mediated by collagen prolyl 4-hydroxylases (P4Hs). While humans possess three genes encoding these enzymes (P4H⍺s), Drosophila melanogaster harbour at least 26 candidates for collagen P4H⍺s despite its simple genome, and it is poorly understood which of them are actually working on collagen in the fly. In this study, we addressed this question by carrying out thorough bioinformatic and biochemical analyses. We demonstrate that among the 26 potential collagen P4H⍺s, PH4⍺EFB shares the highest homology with vertebrate collagen P4H⍺s. Furthermore, while collagen P4Hs and their substrates must exist in the same cells, our transcriptomic analyses at the tissue and single cell levels showed a global co-expression of PH4⍺EFB but not the other P4H⍺-related genes with the collagen IV genes. Moreover, expression of PH4⍺EFB during embryogenesis was found to precede that of collagen IV, presumably enabling efficient collagen modification by PH4⍺EFB. Finally, biochemical assays confirm that PH4⍺EFB binds collagen, supporting its direct role in collagen IV modification. Collectively, we identify PH4⍺EFB as the primary and potentially constitutive prolyl 4-hydroxylase responsible for collagen IV biosynthesis in Drosophila. Our findings highlight the remarkably simple nature of Drosophila collagen IV biosynthesis, which may serve as a blueprint for defining the minimal requirements for collagen engineering.","lang":"eng"}],"file":[{"file_name":"2025_MatrixBiology_Ishikawa.pdf","date_created":"2026-01-05T13:09:01Z","relation":"main_file","content_type":"application/pdf","date_updated":"2026-01-05T13:09:01Z","success":1,"creator":"dernst","checksum":"764257db41865d19daec1935788f72d7","file_size":5844254,"access_level":"open_access","file_id":"20948"}],"publication_status":"published","title":"Evidence for the major role of PH4⍺EFB in the prolyl 4-hydroxylation of Drosophila collagen IV","file_date_updated":"2026-01-05T13:09:01Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"citation":{"ista":"Ishikawa Y, Toups MA, Elkrewi MN, Zajac AL, Horne-Badovinac S, Matsubayashi Y. 2025. Evidence for the major role of PH4⍺EFB in the prolyl 4-hydroxylation of Drosophila collagen IV. Matrix Biology. 141(11), 101–113.","ama":"Ishikawa Y, Toups MA, Elkrewi MN, Zajac AL, Horne-Badovinac S, Matsubayashi Y. Evidence for the major role of PH4⍺EFB in the prolyl 4-hydroxylation of Drosophila collagen IV. <i>Matrix Biology</i>. 2025;141(11):101-113. doi:<a href=\"https://doi.org/10.1016/j.matbio.2025.09.002\">10.1016/j.matbio.2025.09.002</a>","chicago":"Ishikawa, Yoshihiro, Melissa A Toups, Marwan N Elkrewi, Allison L. Zajac, Sally Horne-Badovinac, and Yutaka Matsubayashi. “Evidence for the Major Role of PH4⍺EFB in the Prolyl 4-Hydroxylation of Drosophila Collagen IV.” <i>Matrix Biology</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1016/j.matbio.2025.09.002\">https://doi.org/10.1016/j.matbio.2025.09.002</a>.","apa":"Ishikawa, Y., Toups, M. A., Elkrewi, M. N., Zajac, A. L., Horne-Badovinac, S., &#38; Matsubayashi, Y. (2025). Evidence for the major role of PH4⍺EFB in the prolyl 4-hydroxylation of Drosophila collagen IV. <i>Matrix Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1016/j.matbio.2025.09.002\">https://doi.org/10.1016/j.matbio.2025.09.002</a>","mla":"Ishikawa, Yoshihiro, et al. “Evidence for the Major Role of PH4⍺EFB in the Prolyl 4-Hydroxylation of Drosophila Collagen IV.” <i>Matrix Biology</i>, vol. 141, no. 11, Springer Nature, 2025, pp. 101–13, doi:<a href=\"https://doi.org/10.1016/j.matbio.2025.09.002\">10.1016/j.matbio.2025.09.002</a>.","short":"Y. Ishikawa, M.A. Toups, M.N. Elkrewi, A.L. Zajac, S. Horne-Badovinac, Y. Matsubayashi, Matrix Biology 141 (2025) 101–113.","ieee":"Y. Ishikawa, M. A. Toups, M. N. Elkrewi, A. L. Zajac, S. Horne-Badovinac, and Y. Matsubayashi, “Evidence for the major role of PH4⍺EFB in the prolyl 4-hydroxylation of Drosophila collagen IV,” <i>Matrix Biology</i>, vol. 141, no. 11. Springer Nature, pp. 101–113, 2025."},"year":"2025","date_created":"2025-09-28T22:01:26Z","article_type":"original","quality_controlled":"1","month":"11","has_accepted_license":"1","oa_version":"Published Version","scopus_import":"1","language":[{"iso":"eng"}],"external_id":{"isi":["001583892100002"],"pmid":["40946811"]},"PlanS_conform":"1","date_updated":"2026-01-05T13:09:08Z","project":[{"name":"The highjacking of meiosis for asexual reproduction","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","grant_number":"F8810"}],"OA_place":"publisher","ddc":["570"],"date_published":"2025-11-01T00:00:00Z","author":[{"first_name":"Yoshihiro","full_name":"Ishikawa, Yoshihiro","last_name":"Ishikawa"},{"first_name":"Melissa A","orcid":"0000-0002-9752-7380","last_name":"Toups","full_name":"Toups, Melissa A","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-5328-7231","first_name":"Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","full_name":"Elkrewi, Marwan N","last_name":"Elkrewi"},{"first_name":"Allison L.","last_name":"Zajac","full_name":"Zajac, Allison L."},{"first_name":"Sally","last_name":"Horne-Badovinac","full_name":"Horne-Badovinac, Sally"},{"first_name":"Yutaka","full_name":"Matsubayashi, Yutaka","last_name":"Matsubayashi"}],"isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"department":[{"_id":"BeVi"}],"publication_identifier":{"issn":["0945-053X"],"eissn":["1569-1802"]},"acknowledgement":"This project was supported by the All May See Foundation 7031,182 to YI, the Louisiana Board of Regents Support Fund: Research Competitiveness Subprogram to MAT, Austrian science fund (FWF) as part of the SFB Meiosis consortium FWF SFB F88-10 to Beatriz Vicoso (supported ME), American Heart Association 16POST2726018 and American Cancer Society 132,123-PF-18–025–01-CSM postdoctoral fellowships to ALZ, National Institutes of Health R01 GM136961 and R35 GM148485 to SH-B, and the Academy of Medical Sciences/the Wellcome Trust/ the Government Department of Business, Energy and Industrial Strategy/the British Heart Foundation/Diabetes UK Springboard Award SBF008\\1115 to YM. \r\nComputational analyses of single-nucleus transcriptome data were performed on the high performance computer (HPC) at Bournemouth University, the HPC at Institute of Science and Technology Austria, and the high-performance computational resources provided by the Louisiana Optical Network Infrastructure (http://www.loni.org). The authors are grateful to the researchers who published the transcriptome datasets [48,49,52,55] that became the essential bases for this study, to FlyBase for curating the datasets in an easily accessible format, and the Drosophila Genomics Resource Center (DGRC), supported by NIH grant 2P40OD010949, for providing the D17 cell line used in this research. The authors thank Kristian Koski (University of Oulu, Finland) for crucial advice on the domain structure of collagen P4H⍺s, and Ryusuke Niwa and Ryo Hoshino (University of Tsukuba, Japan) for helpful discussions on SP.","doi":"10.1016/j.matbio.2025.09.002"},{"doi":"10.1111/brv.70103","acknowledgement":"We thank Brian Charlesworth, Deborah Charlesworth, and Sally Otto for extensive comments and suggestions. We also thank Göran Arnqvist, Adam Eyre-Walker, Philip Hedrick, Jitka Polechová, and Henrique Teotónio for further helpful comments on the manuscript. This work was supported by a H2020 Marie Skłodowska-Curie COFUND Action fellowship (#101034413, to F. R.), the Birgitta Sintring Foundation (#S2024-0007, to M. K. Z.), the Research Council of Norway (302619, to D. G.), the Alexander von Humboldt Foundation (to H. K.), the Swiss National Science Foundation (#211549, to X. L. R.), the Swedish Research Council (#2022-03603, to CO; #2020-03123, to E. I. S.) and the European Research Council (ERC-2023-STG-#101117517, to C. O.). We are particularly grateful to the European Society for Evolutionary Biology for funding a Special Topics Network workshop (to T. C., H. K., E. I. S.), from which this review began. Open Access funding provided by Institute of Science and Technology Austria/KEMÖ.","license":"https://creativecommons.org/licenses/by-nc/4.0/","publication_identifier":{"issn":["1464-7931"],"eissn":["1469-185X"]},"article_number":"brv.70103","tmp":{"image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"isi":1,"department":[{"_id":"BeVi"}],"author":[{"id":"347955dd-57b0-11ee-9095-c28bdd368f4b","full_name":"Ruzicka, Filip","last_name":"Ruzicka","first_name":"Filip"},{"first_name":"Martyna K.","last_name":"Zwoinska","full_name":"Zwoinska, Martyna K."},{"first_name":"Debora","last_name":"Goedert","full_name":"Goedert, Debora"},{"full_name":"Kokko, Hanna","last_name":"Kokko","first_name":"Hanna"},{"last_name":"Li Richter","full_name":"Li Richter, Xiang‐Yi","first_name":"Xiang‐Yi"},{"full_name":"Moodie, Iain R.","last_name":"Moodie","first_name":"Iain R."},{"first_name":"Sofie","full_name":"Nilén, Sofie","last_name":"Nilén"},{"first_name":"Colin","last_name":"Olito","full_name":"Olito, Colin"},{"first_name":"Erik I.","last_name":"Svensson","full_name":"Svensson, Erik I."},{"first_name":"Peter","last_name":"Czuppon","full_name":"Czuppon, Peter"},{"full_name":"Connallon, Tim","last_name":"Connallon","first_name":"Tim"}],"ddc":["570"],"date_published":"2025-11-14T00:00:00Z","project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413"}],"date_updated":"2025-12-01T15:28:22Z","OA_place":"publisher","external_id":{"isi":["001614285900001"],"pmid":["41235821 "]},"PlanS_conform":"1","language":[{"iso":"eng"}],"has_accepted_license":"1","scopus_import":"1","oa_version":"Published Version","month":"11","article_type":"original","quality_controlled":"1","corr_author":"1","year":"2025","date_created":"2025-11-19T09:43:50Z","citation":{"ama":"Ruzicka F, Zwoinska MK, Goedert D, et al. A century of theories of balancing selection. <i>Biological Reviews</i>. 2025. doi:<a href=\"https://doi.org/10.1111/brv.70103\">10.1111/brv.70103</a>","ista":"Ruzicka F, Zwoinska MK, Goedert D, Kokko H, Li Richter X, Moodie IR, Nilén S, Olito C, Svensson EI, Czuppon P, Connallon T. 2025. A century of theories of balancing selection. Biological Reviews., brv. 70103.","apa":"Ruzicka, F., Zwoinska, M. K., Goedert, D., Kokko, H., Li Richter, X., Moodie, I. R., … Connallon, T. (2025). A century of theories of balancing selection. <i>Biological Reviews</i>. Wiley. <a href=\"https://doi.org/10.1111/brv.70103\">https://doi.org/10.1111/brv.70103</a>","chicago":"Ruzicka, Filip, Martyna K. Zwoinska, Debora Goedert, Hanna Kokko, Xiang‐Yi Li Richter, Iain R. Moodie, Sofie Nilén, et al. “A Century of Theories of Balancing Selection.” <i>Biological Reviews</i>. Wiley, 2025. <a href=\"https://doi.org/10.1111/brv.70103\">https://doi.org/10.1111/brv.70103</a>.","mla":"Ruzicka, Filip, et al. “A Century of Theories of Balancing Selection.” <i>Biological Reviews</i>, brv. 70103, Wiley, 2025, doi:<a href=\"https://doi.org/10.1111/brv.70103\">10.1111/brv.70103</a>.","short":"F. Ruzicka, M.K. Zwoinska, D. Goedert, H. Kokko, X. Li Richter, I.R. Moodie, S. Nilén, C. Olito, E.I. Svensson, P. Czuppon, T. Connallon, Biological Reviews (2025).","ieee":"F. Ruzicka <i>et al.</i>, “A century of theories of balancing selection,” <i>Biological Reviews</i>. Wiley, 2025."},"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ec_funded":1,"title":"A century of theories of balancing selection","publication_status":"epub_ahead","main_file_link":[{"url":"https://doi.org/10.1111/brv.70103","open_access":"1"}],"status":"public","_id":"20655","pmid":1,"abstract":[{"text":"Traits that affect organismal fitness are often highly genetically variable. This genetic variation is vital for populations to adapt to their environments, but it is also surprising given that nature – after all – ‘selects’ the best genotypes at the expense of those that fall short. Explaining the extensive genetic variation of fitness‐related traits is thus a longstanding puzzle in evolutionary biology, with cascading implications for ecology, conservation, and human health. Balancing selection – an umbrella term for scenarios in which natural selection maintains genetic variation – is a century‐old explanation to resolve this puzzle that has gained recent momentum from genome‐scale methods for detecting it. Yet evaluating whether balancing selection can, in fact, resolve the puzzle is challenging, given the logistical constraints of distinguishing balancing selection from alternative hypotheses and the daunting collection of theoretical models that formally underpin this debate. Here, we track the development of balancing selection theory over the last century and provide an accessible review of this rich collection of models. We first outline the range of biological scenarios that can generate balancing selection. We then examine how fundamental features of genetic systems – non‐random mating between individuals, ploidy levels, genetic drift, linkage, and genetic architectures of traits – have been progressively incorporated into the theory. We end by linking these theoretical predictions to ongoing empirical efforts to understand the evolutionary processes that explain genetic variation.","lang":"eng"}],"article_processing_charge":"Yes (via OA deal)","OA_type":"hybrid","publisher":"Wiley","publication":"Biological Reviews","day":"14","type":"journal_article"},{"oa":1,"citation":{"ista":"Layana Franco LA, Toups MA, Vicoso B. 2025. Causes and consequences of sex-chromosome turnovers in Diptera, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT-ISTA-20780\">10.15479/AT-ISTA-20780</a>.","ama":"Layana Franco LA, Toups MA, Vicoso B. Causes and consequences of sex-chromosome turnovers in Diptera. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20780\">10.15479/AT-ISTA-20780</a>","chicago":"Layana Franco, Lorena Alexandra, Melissa A Toups, and Beatriz Vicoso. “Causes and Consequences of Sex-Chromosome Turnovers in Diptera.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20780\">https://doi.org/10.15479/AT-ISTA-20780</a>.","apa":"Layana Franco, L. A., Toups, M. A., &#38; Vicoso, B. (2025). Causes and consequences of sex-chromosome turnovers in Diptera. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20780\">https://doi.org/10.15479/AT-ISTA-20780</a>","ieee":"L. A. Layana Franco, M. A. Toups, and B. Vicoso, “Causes and consequences of sex-chromosome turnovers in Diptera.” Institute of Science and Technology Austria, 2025.","short":"L.A. Layana Franco, M.A. Toups, B. Vicoso, (2025).","mla":"Layana Franco, Lorena Alexandra, et al. <i>Causes and Consequences of Sex-Chromosome Turnovers in Diptera</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20780\">10.15479/AT-ISTA-20780</a>."},"date_created":"2025-12-10T23:40:14Z","doi":"10.15479/AT-ISTA-20780","year":"2025","corr_author":"1","file_date_updated":"2025-12-11T11:00:53Z","title":"Causes and consequences of sex-chromosome turnovers in Diptera","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"department":[{"_id":"BeVi"}],"user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","_id":"20780","abstract":[{"lang":"eng","text":"Sex-chromosome systems are highly variable across animals, but how they transition from one to another is not well understood. Diptera have undergone multiple sex-chromosome turnovers and expansions while maintaining their general chromosomal content, which makes them an ideal clade to study such transitions. We analysed more than 100 dipteran whole-genome assemblies and identified 4 new lineages that underwent sex-chromosome turnover (in addition to the 5 previously reported). We find the majority of turnovers happened in the group Schizophora, which tend to have fewer genes on the F element (the chromosome homologous to the ancestral insect X chromosome) than lower dipterans, a factor previously hypothesized to facilitate turnover. Most derived X chromosomes have higher GC content than autosomes, consistent with a high prevalence of male-achiasmy in Diptera. In addition, an excess of gene movement out of the X is detected for most of these new X chromosomes, and many of these moved genes have high testis expression in Drosophila, suggesting that out-of-X gene movement contributes to the long-term demasculinization of X chromosomes."}],"status":"public","date_updated":"2025-12-15T11:13:32Z","date_published":"2025-12-01T00:00:00Z","file":[{"creator":"llayanaf","success":1,"date_updated":"2025-12-11T10:47:15Z","relation":"main_file","content_type":"application/zip","file_name":"Perl_scripts.zip","date_created":"2025-12-11T10:47:15Z","file_id":"20799","access_level":"open_access","file_size":4575,"checksum":"251e7aab01917c2ad2fbccf465492ea1"},{"checksum":"daf1c03149dd170b14e5c8e109ee3c77","file_size":19052849,"access_level":"open_access","file_id":"20800","date_created":"2025-12-11T10:52:17Z","file_name":"Supplementary_Datasets.zip","relation":"main_file","content_type":"application/zip","date_updated":"2025-12-11T10:52:17Z","success":1,"creator":"llayanaf"},{"file_id":"20801","access_level":"open_access","file_size":566476,"checksum":"658d6e95a361b0a3db058b7b4e1733d4","creator":"llayanaf","success":1,"date_updated":"2025-12-11T10:52:11Z","content_type":"application/zip","relation":"main_file","date_created":"2025-12-11T10:52:11Z","file_name":"Supplementary_Tables.zip"},{"relation":"main_file","content_type":"text/plain","file_name":"README.txt","date_created":"2025-12-11T11:00:53Z","creator":"llayanaf","success":1,"date_updated":"2025-12-11T11:00:53Z","checksum":"2a2b92eb9fade0015719190596a8c5b7","file_size":1204,"file_id":"20802","access_level":"open_access"}],"author":[{"orcid":"0000-0002-1253-6297","first_name":"Lorena Alexandra","id":"02814589-eb8f-11eb-b029-a70074f3f18f","full_name":"Layana Franco, Lorena Alexandra","last_name":"Layana Franco"},{"id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","full_name":"Toups, Melissa A","last_name":"Toups","orcid":"0000-0002-9752-7380","first_name":"Melissa A"},{"orcid":"0000-0002-4579-8306","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz","last_name":"Vicoso"}],"month":"12","type":"research_data","oa_version":"None","has_accepted_license":"1","keyword":["Schizophora","sex chromosomes","sex-chromosome turnover","Diptera","genomic features","out-of-X movement."],"acknowledged_ssus":[{"_id":"ScienComp"}],"publisher":"Institute of Science and Technology Austria","article_processing_charge":"No"},{"status":"public","intvolume":"        16","_id":"20796","abstract":[{"lang":"eng","text":"Rapid prophase chromosome movements ensure faithful alignment of the parental homologous chromosomes and successful synapsis formation during meiosis. These movements are driven by cytoplasmic forces transmitted to the nuclear periphery, where chromosome ends are attached through transmembrane proteins. During many developmental stages a specific genome architecture with chromatin nuclear periphery contacts mediates specific gene expression. Whether chromatin is removed from the nuclear periphery as a consequence of chromosome motions or by a specific mechanism is not fully understood. Here, we identify a mechanism to remove chromatin from the nuclear periphery through vaccinia related kinase (VRK-1)–dependent phosphorylation of Barrier to Autointegration Factor 1 (BAF-1) in Caenorhabditis elegans early prophase of meiosis. Interfering with chromatin removal delays chromosome pairing, impairs synapsis, produces oocytes with abnormal chromosomes and elevated apoptosis. Long read sequencing reveals deletions and duplications in offspring lacking VRK-1 underscoring the importance of the BAF-1–VRK-1 module in preserving genome stability in gametes during rapid chromosome movements."}],"pmid":1,"file":[{"relation":"main_file","content_type":"application/pdf","file_name":"2025_NatureComm_Paouneskou.pdf","date_created":"2025-12-15T09:25:51Z","creator":"dernst","success":1,"date_updated":"2025-12-15T09:25:51Z","checksum":"a952f7ea050242b79008540de49a0e61","file_size":8096309,"file_id":"20823","access_level":"open_access"}],"publication_status":"published","type":"journal_article","DOAJ_listed":"1","day":"25","volume":16,"publisher":"Springer Nature","publication":"Nature Communications","article_processing_charge":"Yes","OA_type":"gold","oa":1,"citation":{"ieee":"D. Paouneskou <i>et al.</i>, “BAF-1–VRK-1 mediated release of meiotic chromosomes from the nuclear periphery is important for genome integrity,” <i>Nature Communications</i>, vol. 16. Springer Nature, 2025.","short":"D. Paouneskou, A. Baudrimont, R.K. Kelemen, M.N. Elkrewi, A. Graf, S. Moukbel Ali Aldawla, C. Kölbl, I. Tiemann-Boege, B. Vicoso, V. Jantsch, Nature Communications 16 (2025).","mla":"Paouneskou, Dimitra, et al. “BAF-1–VRK-1 Mediated Release of Meiotic Chromosomes from the Nuclear Periphery Is Important for Genome Integrity.” <i>Nature Communications</i>, vol. 16, 10446, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1038/s41467-025-65420-9\">10.1038/s41467-025-65420-9</a>.","ista":"Paouneskou D, Baudrimont A, Kelemen RK, Elkrewi MN, Graf A, Moukbel Ali Aldawla S, Kölbl C, Tiemann-Boege I, Vicoso B, Jantsch V. 2025. BAF-1–VRK-1 mediated release of meiotic chromosomes from the nuclear periphery is important for genome integrity. Nature Communications. 16, 10446.","ama":"Paouneskou D, Baudrimont A, Kelemen RK, et al. BAF-1–VRK-1 mediated release of meiotic chromosomes from the nuclear periphery is important for genome integrity. <i>Nature Communications</i>. 2025;16. doi:<a href=\"https://doi.org/10.1038/s41467-025-65420-9\">10.1038/s41467-025-65420-9</a>","chicago":"Paouneskou, Dimitra, Antoine Baudrimont, Réka K Kelemen, Marwan N Elkrewi, Angela Graf, Shehab Moukbel Ali Aldawla, Claudia Kölbl, Irene Tiemann-Boege, Beatriz Vicoso, and Verena Jantsch. “BAF-1–VRK-1 Mediated Release of Meiotic Chromosomes from the Nuclear Periphery Is Important for Genome Integrity.” <i>Nature Communications</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41467-025-65420-9\">https://doi.org/10.1038/s41467-025-65420-9</a>.","apa":"Paouneskou, D., Baudrimont, A., Kelemen, R. K., Elkrewi, M. N., Graf, A., Moukbel Ali Aldawla, S., … Jantsch, V. (2025). BAF-1–VRK-1 mediated release of meiotic chromosomes from the nuclear periphery is important for genome integrity. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-025-65420-9\">https://doi.org/10.1038/s41467-025-65420-9</a>"},"year":"2025","date_created":"2025-12-11T10:45:06Z","article_type":"original","quality_controlled":"1","title":"BAF-1–VRK-1 mediated release of meiotic chromosomes from the nuclear periphery is important for genome integrity","file_date_updated":"2025-12-15T09:25:51Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-12-15T09:28:37Z","project":[{"grant_number":"F8810","name":"The highjacking of meiosis for asexual reproduction","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396"}],"OA_place":"publisher","ddc":["570"],"date_published":"2025-11-25T00:00:00Z","author":[{"first_name":"Dimitra","full_name":"Paouneskou, Dimitra","last_name":"Paouneskou"},{"first_name":"Antoine","full_name":"Baudrimont, Antoine","last_name":"Baudrimont"},{"id":"48D3F8DE-F248-11E8-B48F-1D18A9856A87","full_name":"Kelemen, Réka K","last_name":"Kelemen","orcid":"0000-0002-8489-9281","first_name":"Réka K"},{"id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","last_name":"Elkrewi","full_name":"Elkrewi, Marwan N","first_name":"Marwan N","orcid":"0000-0002-5328-7231"},{"last_name":"Graf","full_name":"Graf, Angela","first_name":"Angela"},{"last_name":"Moukbel Ali Aldawla","full_name":"Moukbel Ali Aldawla, Shehab","first_name":"Shehab"},{"first_name":"Claudia","full_name":"Kölbl, Claudia","last_name":"Kölbl"},{"first_name":"Irene","full_name":"Tiemann-Boege, Irene","last_name":"Tiemann-Boege"},{"last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz","first_name":"Beatriz","orcid":"0000-0002-4579-8306"},{"full_name":"Jantsch, Verena","last_name":"Jantsch","first_name":"Verena"}],"month":"11","has_accepted_license":"1","oa_version":"Published Version","scopus_import":"1","language":[{"iso":"eng"}],"external_id":{"pmid":["41290579"]},"PlanS_conform":"1","publication_identifier":{"eissn":["2041-1723"]},"acknowledgement":"We are grateful to Monique Zetka, Nicola Silva, and Yumi Kim, Needhi Bhalla, George Krohne and Rueyling Lin for providing reagents; Scott Kennedy for sharing the multiplexed FISH library; and members of the Max Perutz Labs’ BioOptics facility (Irmgard Fischer, Josef Gotzmann, Thomas Peterbauer, Clara Bodner, and Nick Wedige) for training and support in image acquisition. We also thank the members of the NGS facility at the Vienna Biocenter. This work was funded by the Austrian Science Fund (FWF) SFB projects F 8805-B (VJ), https://doi.org/10.55776/F88, F 8809-B (ITB), and F8810-B (BV). We are also grateful to members of the V. Jantsch laboratory for helpful discussions. Some strains were provided by the Caenorhabditis Genetics Center, which is funded by the National Institutes of Health Office of Research Infrastructure Programs (P40OD010440).","doi":"10.1038/s41467-025-65420-9","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"department":[{"_id":"BeVi"}],"article_number":"10446"},{"OA_place":"publisher","date_updated":"2025-09-30T10:49:17Z","author":[{"first_name":"Andrea","full_name":"Mrnjavac, Andrea","last_name":"Mrnjavac","id":"353FAC84-AE61-11E9-8BFC-00D3E5697425"},{"last_name":"Vicoso","full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","first_name":"Beatriz"}],"date_published":"2025-02-01T00:00:00Z","ddc":["570"],"oa_version":"Published Version","scopus_import":"1","has_accepted_license":"1","month":"02","external_id":{"pmid":["39913672"],"isi":["001423671400001"]},"language":[{"iso":"eng"}],"acknowledgement":"The authors would like to thank three anonymous reviewers for comments and suggestions. We are also grateful to Christelle Fraïsse, Marwan Elkrewi, and Filip Ruzicka for the help in this project.","publication_identifier":{"eissn":["1759-6653"]},"doi":"10.1093/gbe/evaf021","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"isi":1,"department":[{"_id":"BeVi"}],"article_number":"evaf021","_id":"19370","abstract":[{"lang":"eng","text":"Sex-linked and autosomal loci experience different selective pressures and evolutionary dynamics. X (or Z) chromosomes are often hemizygous in males (or females), as Y (or W) chromosomes often degenerate. Such hemizygous regions can be under greater efficacy of selection, as recessive mutations are immediately exposed to selection in the heterogametic sex leading to faster adaptation and faster divergence on the X chromosome (the so-called Faster-X or Faster-Z effect). However, in young nonrecombining regions, Y/W chromosomes often have many functional genes, and many X/Z-linked loci are therefore diploid. The sheltering of recessive mutations on the X/Z by the Y/W homolog is expected to drive slower adaptation for diploid X/Z loci, i.e. a reduction in the efficacy of selection. While the Faster-X effect has been studied extensively, much less is known empirically about the evolutionary dynamics of diploid X or Z chromosomes. Here, we took advantage of published population genomic data in the female-heterogametic human parasite Schistosoma japonicum to characterize the gene content and diversity levels of the diploid and hemizygous regions of the Z chromosome. We used different metrics of selective pressures acting on genes to test for differences in the efficacy of selection in hemizygous and diploid Z regions, relative to autosomes. We found consistent patterns suggesting reduced Ne, and reduced efficacy of purifying selection, on both hemizygous and diploid Z regions. Moreover, relaxed selection was particularly pronounced for female-biased genes on the diploid Z, as predicted by recent theoretical work."}],"intvolume":"        17","pmid":1,"status":"public","publication_status":"published","file":[{"success":1,"creator":"dernst","date_updated":"2025-03-10T08:25:59Z","content_type":"application/pdf","relation":"main_file","date_created":"2025-03-10T08:25:59Z","file_name":"2025_GBE_Mrnjavac.pdf","file_id":"19378","access_level":"open_access","file_size":768371,"checksum":"e3aa993e3d6dad10cb806c243fa57408"}],"volume":17,"day":"01","type":"journal_article","OA_type":"gold","article_processing_charge":"Yes","publication":"Genome Biology and Evolution","issue":"2","publisher":"Oxford University Press","citation":{"mla":"Mrnjavac, Andrea, and Beatriz Vicoso. “Reduced Efficacy of Selection on a Young Z Chromosome Region of Schistosoma Japonicum.” <i>Genome Biology and Evolution</i>, vol. 17, no. 2, evaf021, Oxford University Press, 2025, doi:<a href=\"https://doi.org/10.1093/gbe/evaf021\">10.1093/gbe/evaf021</a>.","short":"A. Mrnjavac, B. Vicoso, Genome Biology and Evolution 17 (2025).","ieee":"A. Mrnjavac and B. Vicoso, “Reduced efficacy of selection on a young Z chromosome region of schistosoma japonicum,” <i>Genome Biology and Evolution</i>, vol. 17, no. 2. Oxford University Press, 2025.","chicago":"Mrnjavac, Andrea, and Beatriz Vicoso. “Reduced Efficacy of Selection on a Young Z Chromosome Region of Schistosoma Japonicum.” <i>Genome Biology and Evolution</i>. Oxford University Press, 2025. <a href=\"https://doi.org/10.1093/gbe/evaf021\">https://doi.org/10.1093/gbe/evaf021</a>.","apa":"Mrnjavac, A., &#38; Vicoso, B. (2025). Reduced efficacy of selection on a young Z chromosome region of schistosoma japonicum. <i>Genome Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/gbe/evaf021\">https://doi.org/10.1093/gbe/evaf021</a>","ista":"Mrnjavac A, Vicoso B. 2025. Reduced efficacy of selection on a young Z chromosome region of schistosoma japonicum. Genome Biology and Evolution. 17(2), evaf021.","ama":"Mrnjavac A, Vicoso B. Reduced efficacy of selection on a young Z chromosome region of schistosoma japonicum. <i>Genome Biology and Evolution</i>. 2025;17(2). doi:<a href=\"https://doi.org/10.1093/gbe/evaf021\">10.1093/gbe/evaf021</a>"},"oa":1,"corr_author":"1","quality_controlled":"1","article_type":"original","date_created":"2025-03-09T23:01:27Z","year":"2025","related_material":{"record":[{"status":"public","id":"18549","relation":"earlier_version"}],"link":[{"relation":"software","url":"https://git.ista.ac.at/amrnjava/schistosomes_slower_z"}]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","file_date_updated":"2025-03-10T08:25:59Z","title":"Reduced efficacy of selection on a young Z chromosome region of schistosoma japonicum"},{"publication":"Molecular Biology and Evolution","issue":"5","publisher":"Oxford University Press","OA_type":"gold","article_processing_charge":"Yes","type":"journal_article","DOAJ_listed":"1","volume":42,"day":"01","publication_status":"published","file":[{"creator":"dernst","success":1,"date_updated":"2025-05-28T09:34:36Z","relation":"main_file","content_type":"application/pdf","date_created":"2025-05-28T09:34:36Z","file_name":"2025_MBE_Bett.pdf","file_id":"19756","access_level":"open_access","file_size":1282772,"checksum":"6c14b03f94b4aadf8869be2c4366d077"}],"_id":"19735","abstract":[{"lang":"eng","text":"The males and females of the brine shrimp Artemia franciscana are highly dimorphic, and this dimorphism is associated with substantial sex-biased gene expression in heads and gonads. How these sex-specific patterns of expression are regulated at the molecular level is unknown. A. franciscana also has differentiated ZW sex chromosomes, with complete dosage compensation, but the molecular mechanism through which compensation is achieved is unknown. Here, we conducted CUT&TAG assays targeting 7 post-translational histone modifications (H3K27me3, H3K9me2, H3K9me3, H3K36me3, H3K27ac, H3K4me3, and H4K16ac) in heads and gonads of A. franciscana, allowing us to divide the genome into 12 chromatin states. We further defined functional chromatin signatures for all genes, which were correlated with transcript level abundances. Differences in the occupancy of the profiled epigenetic marks between sexes were associated with differential gene expression between males and females. Finally, we found a significant enrichment of the permissive H4K16ac histone mark in the Z-specific region in both tissues of females but not males, supporting the role of this histone mark in mediating dosage compensation of the Z chromosome."}],"pmid":1,"intvolume":"        42","status":"public","file_date_updated":"2025-05-28T09:34:36Z","title":"Chromatin landscape is associated with sex-biased expression and Drosophila-like dosage compensation of the Z chromosome in Artemia franciscana","related_material":{"record":[{"status":"private","relation":"dissertation_contains","id":"20444"},{"status":"public","relation":"dissertation_contains","id":"20449"}],"link":[{"url":"https://github.com/vkb25/Chromatin-landscape-in-Artemia-franciscana.git","relation":"software"}]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2025-05-25T22:16:56Z","year":"2025","corr_author":"1","quality_controlled":"1","article_type":"original","oa":1,"citation":{"mla":"Bett, Vincent K., et al. “Chromatin Landscape Is Associated with Sex-Biased Expression and Drosophila-like Dosage Compensation of the Z Chromosome in Artemia Franciscana.” <i>Molecular Biology and Evolution</i>, vol. 42, no. 5, msaf085, Oxford University Press, 2025, doi:<a href=\"https://doi.org/10.1093/molbev/msaf085\">10.1093/molbev/msaf085</a>.","short":"V.K. Bett, M.S. Trejo Arellano, B. Vicoso, Molecular Biology and Evolution 42 (2025).","ieee":"V. K. Bett, M. S. Trejo Arellano, and B. Vicoso, “Chromatin landscape is associated with sex-biased expression and Drosophila-like dosage compensation of the Z chromosome in Artemia franciscana,” <i>Molecular Biology and Evolution</i>, vol. 42, no. 5. Oxford University Press, 2025.","chicago":"Bett, Vincent K, Minerva S Trejo Arellano, and Beatriz Vicoso. “Chromatin Landscape Is Associated with Sex-Biased Expression and Drosophila-like Dosage Compensation of the Z Chromosome in Artemia Franciscana.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2025. <a href=\"https://doi.org/10.1093/molbev/msaf085\">https://doi.org/10.1093/molbev/msaf085</a>.","apa":"Bett, V. K., Trejo Arellano, M. S., &#38; Vicoso, B. (2025). Chromatin landscape is associated with sex-biased expression and Drosophila-like dosage compensation of the Z chromosome in Artemia franciscana. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msaf085\">https://doi.org/10.1093/molbev/msaf085</a>","ista":"Bett VK, Trejo Arellano MS, Vicoso B. 2025. Chromatin landscape is associated with sex-biased expression and Drosophila-like dosage compensation of the Z chromosome in Artemia franciscana. Molecular Biology and Evolution. 42(5), msaf085.","ama":"Bett VK, Trejo Arellano MS, Vicoso B. Chromatin landscape is associated with sex-biased expression and Drosophila-like dosage compensation of the Z chromosome in Artemia franciscana. <i>Molecular Biology and Evolution</i>. 2025;42(5). doi:<a href=\"https://doi.org/10.1093/molbev/msaf085\">10.1093/molbev/msaf085</a>"},"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"external_id":{"isi":["001483460200001"],"pmid":["40202086"]},"month":"05","scopus_import":"1","oa_version":"Published Version","has_accepted_license":"1","date_published":"2025-05-01T00:00:00Z","ddc":["570"],"author":[{"first_name":"Vincent K","last_name":"Bett","full_name":"Bett, Vincent K","id":"57854184-AAE0-11E9-8D04-98D6E5697425"},{"first_name":"Minerva S","orcid":"0000-0002-1982-3475","id":"2b681148-eed5-11eb-b81b-ae229e8620f8","full_name":"Trejo Arellano, Minerva S","last_name":"Trejo Arellano"},{"full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","first_name":"Beatriz","orcid":"0000-0002-4579-8306"}],"OA_place":"publisher","date_updated":"2026-04-07T12:28:15Z","project":[{"grant_number":"PAT 8748323","_id":"8ed82125-16d5-11f0-9cad-fbcae312235b","name":"Sex chromosomes in evolution and development"},{"grant_number":"F8810","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","name":"The highjacking of meiosis for asexual reproduction"}],"article_number":"msaf085","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"department":[{"_id":"BeVi"},{"_id":"DaZi"}],"isi":1,"doi":"10.1093/molbev/msaf085","publication_identifier":{"issn":["0737-4038"],"eissn":["1537-1719"]},"acknowledgement":"We thank the Vicoso lab for their help in maintaining Artemia and for their valuable feedback and suggestions. We thank Marwan Elkrewi for his useful technical advice and discussions. We are also grateful to the Scientific Unit at ISTA Austria for computational resources and assistance. This work was supported by Austrian science fund (FWF) grants PAT8748323 and SFB F88-10 (as part of the SFB Meiosis consortium https://sfbmeiosis.org) to BV and Swedish Research Council (Vetenskapsrådet, grant number 2020-06424) to MSTA."},{"OA_place":"publisher","degree_awarded":"PhD","date_updated":"2026-04-07T12:28:15Z","project":[{"_id":"8ed82125-16d5-11f0-9cad-fbcae312235b","name":"Sex chromosomes in evolution and development","grant_number":"PAT 8748323"},{"grant_number":"F8810","name":"The highjacking of meiosis for asexual reproduction","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396"}],"date_published":"2025-10-10T00:00:00Z","alternative_title":["ISTA Thesis"],"ddc":["576"],"author":[{"first_name":"Vincent K","last_name":"Bett","full_name":"Bett, Vincent K","id":"57854184-AAE0-11E9-8D04-98D6E5697425"}],"month":"10","oa_version":"Published Version","has_accepted_license":"1","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"supervisor":[{"last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","first_name":"Beatriz"}],"publication_identifier":{"issn":["2663-337X"]},"acknowledgement":"This work was supported by the Austrian Science Fund (FWF) through grants PAT8748323\r\nand SFB F88-10 awarded to Professor Beatriz Vicoso.","doi":"10.15479/AT-ISTA-20449","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"_id":"20449","status":"public","publication_status":"published","file":[{"file_size":18507283,"checksum":"26905c22bca417198a733d792d8ce422","embargo_to":"open_access","file_id":"20507","access_level":"closed","relation":"main_file","content_type":"application/pdf","date_created":"2025-10-20T13:32:29Z","file_name":"2025_Bett_Vincent_Thesis.pdf","embargo":"2026-06-01","creator":"vbett","date_updated":"2025-10-20T13:32:29Z"},{"checksum":"6a09a8d126d3628bfd8a35202735f267","file_size":17163921,"access_level":"closed","file_id":"20508","date_created":"2025-10-20T13:35:34Z","file_name":"2025_Bett_Vincent_Thesis.docx","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2025-11-06T12:42:09Z","creator":"vbett"}],"type":"dissertation","page":"114","day":"10","publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","citation":{"short":"V.K. Bett, Evolution and Regulation of the Z Chromosome, Institute of Science and Technology Austria, 2025.","ieee":"V. K. Bett, “Evolution and regulation of the Z chromosome,” Institute of Science and Technology Austria, 2025.","mla":"Bett, Vincent K. <i>Evolution and Regulation of the Z Chromosome</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20449\">10.15479/AT-ISTA-20449</a>.","ista":"Bett VK. 2025. Evolution and regulation of the Z chromosome. Institute of Science and Technology Austria.","ama":"Bett VK. Evolution and regulation of the Z chromosome. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20449\">10.15479/AT-ISTA-20449</a>","chicago":"Bett, Vincent K. “Evolution and Regulation of the Z Chromosome.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20449\">https://doi.org/10.15479/AT-ISTA-20449</a>.","apa":"Bett, V. K. (2025). <i>Evolution and regulation of the Z chromosome</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20449\">https://doi.org/10.15479/AT-ISTA-20449</a>"},"date_created":"2025-10-11T08:18:51Z","year":"2025","corr_author":"1","file_date_updated":"2025-11-06T12:42:09Z","title":"Evolution and regulation of the Z chromosome","related_material":{"record":[{"relation":"part_of_dissertation","id":"19735","status":"public"},{"id":"15009","relation":"part_of_dissertation","status":"public"}]},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd"},{"oa_version":"Published Version","has_accepted_license":"1","month":"03","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"degree_awarded":"PhD","OA_place":"publisher","project":[{"name":"The highjacking of meiosis for asexual reproduction","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","grant_number":"F8810"}],"date_updated":"2026-04-16T12:20:41Z","author":[{"last_name":"Elkrewi","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","full_name":"Elkrewi, Marwan N","first_name":"Marwan N","orcid":"0000-0002-5328-7231"}],"date_published":"2025-03-14T00:00:00Z","alternative_title":["ISTA Thesis"],"ddc":["570","576"],"department":[{"_id":"GradSch"},{"_id":"BeVi"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"acknowledgement":"My PhD work was funded by the Austrian science fund (FWF), as part of the SFB Meiosis consortium (https://sfbmeiosis.org/, grant ID FWF SFB F88-10).","supervisor":[{"orcid":"0000-0002-4579-8306","first_name":"Beatriz","last_name":"Vicoso","full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"publication_identifier":{"isbn":["9783990780534"],"eissn":["2663-337X"]},"doi":"10.15479/AT-ISTA-19386","page":"170","day":"14","type":"dissertation","article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","abstract":[{"text":"Crustaceans are a large group of arthropods with a great diversity of species and\r\ndifferent types of sex determination systems and reproductive modes (Subramoniam, 2017).\r\nThis makes them a great model for exploring the evolution of sex chromosomes and sexual\r\ndimorphism and investigating the evolutionary mechanisms driving and maintaining the\r\ndiversity of reproductive systems. Within this taxon, Brine shrimp of the genus Artemia, a\r\nbranchiopod crustacean, are well suited for such explorations, as they have both highly\r\ndimorphic traits and closely related sexual and asexual species. Although brine shrimp are\r\nknown to have ZW sex chromosomes (Bowen, 1963; Parraguez et al., 2009), the sex\r\nchromosomes are still not well characterized at the genomic level, the sex-determination gene\r\nis unknown, and it is still unclear whether the same sex chromosomes as shared by the\r\ndifferent species.\r\nThe first part of this thesis was to characterize the Z and W chromosomes in Artemia\r\nusing an array of methods, from generating multiple chromosome and contig level genome\r\nassemblies to identifying W-linked scaffolds and transcripts in multiple species using k-mer\r\nbased approaches.\r\nThe second part tackles the conservation of the cell type specific regulatory pathways\r\nin the female reproductive system between Artemia and Drosophila, and the expression of the\r\nZ-specific region throughout meiosis using single-nucleus RNA-seq data. Our results show\r\nthat germline cells lack dosage compensation, with a subset of cells showing evidence of\r\nextreme repression of the Z chromosome.\r\nWith multiple sexual species and several asexual lineages of parthenogenetic females\r\nthat produce rare males at low frequencies, Brine shrimp present the perfect opportunity to\r\nexplore the transition to asexuality and shed light on the prerequisites and repercussions of\r\nthe form of modified meiosis maintaining the asexual lineages. The last chapter is an\r\ninvestigation of the molecular pathways involved in asexual reproduction in Artemia using\r\nnewly generated single nucleus RNAseq and WGS data and previously published data. ","lang":"eng"}],"_id":"19386","status":"public","publication_status":"published","file":[{"creator":"melkrewi","date_updated":"2026-03-26T23:30:03Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","file_name":"Thesis_Marwan_Elkrewi.docx","date_created":"2025-03-26T07:06:56Z","file_id":"19462","access_level":"closed","file_size":25019680,"checksum":"5549a8216c07e4c39281648912d72246","embargo_to":"open_access"},{"embargo":"2026-03-26","creator":"melkrewi","date_updated":"2026-03-26T23:30:03Z","relation":"main_file","content_type":"application/pdf","file_name":"Thesis_Marwan_Elkrewi.pdf","date_created":"2025-03-26T07:06:22Z","file_id":"19463","access_level":"open_access","checksum":"aed2ba9965aa89b3414deae1ae9f4321","file_size":17294844}],"related_material":{"record":[{"id":"12248","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"10167"},{"relation":"part_of_dissertation","id":"10767","status":"public"},{"relation":"part_of_dissertation","id":"15009","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"14613"},{"status":"public","relation":"part_of_dissertation","id":"17890"}]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","file_date_updated":"2026-03-26T23:30:03Z","title":"Evolution of sex chromosomes, sex determination and asexuality in Artemia brine shrimp","citation":{"mla":"Elkrewi, Marwan N. <i>Evolution of Sex Chromosomes, Sex Determination and Asexuality in Artemia Brine Shrimp</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19386\">10.15479/AT-ISTA-19386</a>.","short":"M.N. Elkrewi, Evolution of Sex Chromosomes, Sex Determination and Asexuality in Artemia Brine Shrimp, Institute of Science and Technology Austria, 2025.","ieee":"M. N. Elkrewi, “Evolution of sex chromosomes, sex determination and asexuality in Artemia brine shrimp,” Institute of Science and Technology Austria, 2025.","apa":"Elkrewi, M. N. (2025). <i>Evolution of sex chromosomes, sex determination and asexuality in Artemia brine shrimp</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-19386\">https://doi.org/10.15479/AT-ISTA-19386</a>","chicago":"Elkrewi, Marwan N. “Evolution of Sex Chromosomes, Sex Determination and Asexuality in Artemia Brine Shrimp.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-19386\">https://doi.org/10.15479/AT-ISTA-19386</a>.","ama":"Elkrewi MN. Evolution of sex chromosomes, sex determination and asexuality in Artemia brine shrimp. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-19386\">10.15479/AT-ISTA-19386</a>","ista":"Elkrewi MN. 2025. Evolution of sex chromosomes, sex determination and asexuality in Artemia brine shrimp. Institute of Science and Technology Austria."},"oa":1,"OA_embargo":"12","corr_author":"1","date_created":"2025-03-11T12:54:31Z","year":"2025"},{"article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","day":"02","keyword":["sex chromosome evolution","genome assembly","dosage compensation"],"has_accepted_license":"1","oa_version":"Published Version","type":"research_data","contributor":[{"contributor_type":"researcher","last_name":"Bett","id":"57854184-AAE0-11E9-8D04-98D6E5697425","first_name":"Vincent K"},{"contributor_type":"project_member","last_name":"Macon","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","first_name":"Ariana"},{"first_name":"Beatriz","orcid":"0000-0002-4579-8306","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","contributor_type":"supervisor"},{"contributor_type":"researcher","orcid":"0000-0002-5328-7231","first_name":"Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","last_name":"Elkrewi"}],"month":"01","file":[{"creator":"melkrewi","success":1,"date_updated":"2023-12-22T13:54:21Z","content_type":"text/plain","relation":"main_file","file_name":"readme.txt.txt","date_created":"2023-12-22T13:54:21Z","file_id":"14707","access_level":"open_access","checksum":"bdaf1392867786634ec5466d528c36ca","file_size":847},{"file_id":"14708","access_level":"open_access","checksum":"973e1cbdab923a71709782177980829f","file_size":343632753,"creator":"melkrewi","success":1,"date_updated":"2023-12-22T14:14:06Z","relation":"main_file","content_type":"application/x-zip-compressed","file_name":"data_artemia_franciscana_genome.zip","date_created":"2023-12-22T14:14:06Z"}],"author":[{"id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","full_name":"Elkrewi, Marwan N","last_name":"Elkrewi","first_name":"Marwan N","orcid":"0000-0002-5328-7231"}],"ddc":["576"],"date_published":"2024-01-02T00:00:00Z","status":"public","date_updated":"2025-09-04T12:05:42Z","project":[{"grant_number":"F8810","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","name":"The highjacking of meiosis for asexual reproduction"}],"abstract":[{"lang":"eng","text":"Since the commercialization of brine shrimp (genus Artemia) in the 1950s, this lineage, and in particular the model species Artemia franciscana, has been the subject of extensive research. However, our understanding of the genetic mechanisms underlying various aspects of their reproductive biology, including sex determination, are still lacking. This is partly due to the scarcity of genomic resources for Artemia species and crustaceans in general. Here, we present a chromosome-level genome assembly of Artemia franciscana (Kellogg 1906), from the Great Salt Lake, USA. The genome is 1GB, and the majority of the genome (81%) is scaffolded into 21 linkage groups using a previously published high-density linkage map. We performed coverage and FST analyses using male and female genomic and transcriptomic reads to quantify the extent of differentiation between the Z and W chromosomes. Additionally, we quantified the expression levels in male and female heads and gonads and found further evidence for dosage compensation in this species."}],"_id":"14705","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"relation":"used_in_publication","id":"15009","status":"public"}]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"department":[{"_id":"GradSch"},{"_id":"BeVi"}],"title":"Data from \"Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation\"","file_date_updated":"2023-12-22T14:14:06Z","corr_author":"1","year":"2024","date_created":"2023-12-22T13:40:48Z","doi":"10.15479/AT:ISTA:14705","citation":{"short":"M.N. Elkrewi, (2024).","mla":"Elkrewi, Marwan N. <i>Data from “Chromosome-Level Assembly of Artemia Franciscana Sheds Light on Sex-Chromosome Differentiation.”</i> Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:14705\">10.15479/AT:ISTA:14705</a>.","ieee":"M. N. Elkrewi, “Data from ‘Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation.’” Institute of Science and Technology Austria, 2024.","ama":"Elkrewi MN. Data from “Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation.” 2024. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:14705\">10.15479/AT:ISTA:14705</a>","ista":"Elkrewi MN. 2024. Data from ‘Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:14705\">10.15479/AT:ISTA:14705</a>.","apa":"Elkrewi, M. N. (2024). Data from “Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:14705\">https://doi.org/10.15479/AT:ISTA:14705</a>","chicago":"Elkrewi, Marwan N. “Data from ‘Chromosome-Level Assembly of Artemia Franciscana Sheds Light on Sex-Chromosome Differentiation.’” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/AT:ISTA:14705\">https://doi.org/10.15479/AT:ISTA:14705</a>."},"oa":1},{"doi":"10.1073/pnas.2406335121","publication_identifier":{"eissn":["1091-6490"]},"acknowledgement":"This work was supported by funds from the Australian Research Council and The School of Biological Sciences at Monash University. F.R. was funded by a H2020 Marie Skłodowska-Curie COFUND Action (No. 101034413). We thank three anonymous reviewers for suggestions that substantially improved the paper and breadth of the analysis.","article_number":"e2406335121","department":[{"_id":"BeVi"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"isi":1,"date_published":"2024-10-29T00:00:00Z","ddc":["570"],"author":[{"last_name":"Mcdonough","full_name":"Mcdonough, Yasmine","first_name":"Yasmine"},{"first_name":"Filip","full_name":"Ruzicka, Filip","last_name":"Ruzicka","id":"347955dd-57b0-11ee-9095-c28bdd368f4b"},{"full_name":"Connallon, Tim","last_name":"Connallon","first_name":"Tim"}],"OA_place":"publisher","date_updated":"2025-09-08T14:31:58Z","project":[{"name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413"}],"language":[{"iso":"eng"}],"external_id":{"pmid":["39436652"],"isi":["001359216400017"]},"month":"10","scopus_import":"1","oa_version":"Published Version","has_accepted_license":"1","date_created":"2024-10-27T23:01:44Z","year":"2024","quality_controlled":"1","article_type":"original","oa":1,"citation":{"mla":"Mcdonough, Yasmine, et al. “Reconciling Theories of Dominance with the Relative Rates of Adaptive Substitution on Sex Chromosomes and Autosomes.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 44, e2406335121, National Academy of Sciences, 2024, doi:<a href=\"https://doi.org/10.1073/pnas.2406335121\">10.1073/pnas.2406335121</a>.","short":"Y. Mcdonough, F. Ruzicka, T. Connallon, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","ieee":"Y. Mcdonough, F. Ruzicka, and T. Connallon, “Reconciling theories of dominance with the relative rates of adaptive substitution on sex chromosomes and autosomes,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 44. National Academy of Sciences, 2024.","ama":"Mcdonough Y, Ruzicka F, Connallon T. Reconciling theories of dominance with the relative rates of adaptive substitution on sex chromosomes and autosomes. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2024;121(44). doi:<a href=\"https://doi.org/10.1073/pnas.2406335121\">10.1073/pnas.2406335121</a>","ista":"Mcdonough Y, Ruzicka F, Connallon T. 2024. Reconciling theories of dominance with the relative rates of adaptive substitution on sex chromosomes and autosomes. Proceedings of the National Academy of Sciences of the United States of America. 121(44), e2406335121.","apa":"Mcdonough, Y., Ruzicka, F., &#38; Connallon, T. (2024). Reconciling theories of dominance with the relative rates of adaptive substitution on sex chromosomes and autosomes. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2406335121\">https://doi.org/10.1073/pnas.2406335121</a>","chicago":"Mcdonough, Yasmine, Filip Ruzicka, and Tim Connallon. “Reconciling Theories of Dominance with the Relative Rates of Adaptive Substitution on Sex Chromosomes and Autosomes.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2024. <a href=\"https://doi.org/10.1073/pnas.2406335121\">https://doi.org/10.1073/pnas.2406335121</a>."},"file_date_updated":"2024-11-04T10:29:43Z","title":"Reconciling theories of dominance with the relative rates of adaptive substitution on sex chromosomes and autosomes","ec_funded":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_status":"published","file":[{"date_updated":"2024-11-04T10:29:43Z","creator":"dernst","success":1,"date_created":"2024-11-04T10:29:43Z","file_name":"2024_PNAS_McDonough.pdf","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_id":"18501","file_size":1299095,"checksum":"73db3c87b35753e0f4324417f164a35e"}],"pmid":1,"_id":"18479","abstract":[{"text":"The dominance of beneficial mutations is a key evolutionary parameter affecting the rate and genetic basis of adaptation, yet it is notoriously difficult to estimate. A leading method to infer it is to compare the relative rates of adaptive substitution for X-linked and autosomal genes, which—according to a classic model by Charlesworth et al. (1987)—is a simple function of the dominance of new beneficial mutations. Recent evidence that rates of adaptive substitution are faster for X-linked genes implies, accordingly, that beneficial mutations are usually recessive. However, this conclusion is incompatible with leading theories of dominance, which predict that beneficial mutations tend to be dominant or overdominant with respect to fitness. To address this incompatibility, we use Fisher’s geometric model to predict the distribution of fitness effects of new mutations and the relative rates of positively selected substitution on the X and autosomes. Previous predictions of faster-X theory emerge as a special case of our model in which the phenotypic effects of mutations are small relative to the distance to the phenotypic optimum. But as mutational effects become large relative to the optimum, we observe an elevated tempo of positively selected substitutions on the X relative to the autosomes across a broader range of dominance conditions, including those predicted by theories of dominance. Our results imply that, contrary to previous models, dominant and overdominant beneficial mutations can plausibly generate patterns of faster-X adaptation. We discuss resulting implications for genomic studies of adaptation and inferences of dominance.","lang":"eng"}],"intvolume":"       121","status":"public","publication":"Proceedings of the National Academy of Sciences of the United States of America","issue":"44","publisher":"National Academy of Sciences","OA_type":"hybrid","article_processing_charge":"Yes (in subscription journal)","type":"journal_article","volume":121,"day":"29"}]