[{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","scopus_import":"1","date_updated":"2026-09-24T11:05:40Z","title":"Compensation of gene dosage on the mammalian X","oa":1,"license":"https://creativecommons.org/licenses/by/4.0/","file":[{"checksum":"5e428bda0440d3f957c694b315a8f2a9","creator":"cchlebak","success":1,"file_name":"2024_Development_Cecalev.pdf","content_type":"application/pdf","relation":"main_file","file_id":"17464","file_size":2085135,"date_updated":"2024-08-28T10:32:16Z","access_level":"open_access","date_created":"2024-08-28T10:32:16Z"}],"citation":{"short":"D. Cecalev, B. Vicoso, R. Galupa, Development 151 (2024).","ista":"Cecalev D, Vicoso B, Galupa R. 2024. Compensation of gene dosage on the mammalian X. Development. 151(15), dev202891.","mla":"Cecalev, Daniela, et al. “Compensation of Gene Dosage on the Mammalian X.” <i>Development</i>, vol. 151, no. 15, dev202891, Company of Biologists, 2024, doi:<a href=\"https://doi.org/10.1242/dev.202891\">10.1242/dev.202891</a>.","ieee":"D. Cecalev, B. Vicoso, and R. Galupa, “Compensation of gene dosage on the mammalian X,” <i>Development</i>, vol. 151, no. 15. Company of Biologists, 2024.","ama":"Cecalev D, Vicoso B, Galupa R. Compensation of gene dosage on the mammalian X. <i>Development</i>. 2024;151(15). doi:<a href=\"https://doi.org/10.1242/dev.202891\">10.1242/dev.202891</a>","chicago":"Cecalev, Daniela, Beatriz Vicoso, and Rafael Galupa. “Compensation of Gene Dosage on the Mammalian X.” <i>Development</i>. Company of Biologists, 2024. <a href=\"https://doi.org/10.1242/dev.202891\">https://doi.org/10.1242/dev.202891</a>.","apa":"Cecalev, D., Vicoso, B., &#38; Galupa, R. (2024). Compensation of gene dosage on the mammalian X. <i>Development</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/dev.202891\">https://doi.org/10.1242/dev.202891</a>"},"publication":"Development","_id":"17458","volume":151,"quality_controlled":"1","popular_science":"1","acknowledgement":"We thank Estelle Nicolas for critical feedback on the manuscript and Ikuhiro Okamoto for critical feedback on the figures. We apologise to authors whose work we overlooked or did not discuss or cite due to limits in the number of references. We thank the anonymous reviewers for pointing us to additional literature and for their constructive feedback. Figures were prepared with BioRender.com. D.C. is supported by a fellowship from Ligue Contre le Cancer (LNCC_TAJT25850) and R.G. holds a tenured research position from the Centre National de la Recherche Scientifique (France). Research in the Galupa lab is supported by a grant from the Fondation pour la Recherche Médicale (AJE202305017142). Open Access funding provided by Fondation pour la Recherche Médicale. Deposited in PMC for immediate release.","date_created":"2024-08-25T22:01:07Z","article_number":"dev202891","issue":"15","pmid":1,"external_id":{"pmid":["39140247"],"isi":["001292608800003"]},"intvolume":"       151","isi":1,"ddc":["599"],"doi":"10.1242/dev.202891","language":[{"iso":"eng"}],"das_tickbox":"0","day":"14","has_accepted_license":"1","supplementarymaterial":"no","oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_identifier":{"eissn":["1477-9129"],"issn":["0950-1991"]},"researchdata_availability":"no","department":[{"_id":"BeVi"}],"author":[{"first_name":"Daniela","full_name":"Cecalev, Daniela","last_name":"Cecalev"},{"full_name":"Vicoso, Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","first_name":"Beatriz"},{"full_name":"Galupa, Rafael","last_name":"Galupa","first_name":"Rafael"}],"article_type":"original","fulldoi":"https://doi.org/10.1242/dev.202891","month":"08","article_processing_charge":"Yes (in subscription journal)","year":"2024","publisher":"Company of Biologists","abstract":[{"lang":"eng","text":"Changes in gene dosage can have tremendous evolutionary potential (e.g. whole-genome duplications), but without compensatory mechanisms, they can also lead to gene dysregulation and pathologies. Sex chromosomes are a paradigmatic example of naturally occurring gene dosage differences and their compensation. In species with chromosome-based sex determination, individuals within the same population necessarily show ‘natural’ differences in gene dosage for the sex chromosomes. In this Review, we focus on the mammalian X chromosome and discuss recent new insights into the dosage-compensation mechanisms that evolved along with the emergence of sex chromosomes, namely X-inactivation and X-upregulation. We also discuss the evolution of the genetic loci and molecular players involved, as well as the regulatory diversity and potentially different requirements for dosage compensation across mammalian species."}],"status":"public","date_published":"2024-08-14T00:00:00Z","publication_status":"published","type":"journal_article","file_date_updated":"2024-08-28T10:32:16Z"},{"type":"journal_article","file_date_updated":"2024-11-04T10:29:43Z","dataavailabilitystatement":"All study data are included in the article and/or supporting information.","status":"public","date_published":"2024-10-29T00:00:00Z","publication_status":"published","year":"2024","article_processing_charge":"Yes (in subscription journal)","publisher":"National Academy of Sciences","project":[{"call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413"}],"abstract":[{"lang":"eng","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."}],"month":"10","fulldoi":"https://doi.org/10.1073/pnas.2406335121","ec_funded":1,"OA_place":"publisher","researchdata_availability":"yes (supplementary data)","department":[{"_id":"BeVi"}],"author":[{"last_name":"Mcdonough","full_name":"Mcdonough, Yasmine","first_name":"Yasmine"},{"full_name":"Ruzicka, Filip","last_name":"Ruzicka","first_name":"Filip","id":"347955dd-57b0-11ee-9095-c28bdd368f4b"},{"first_name":"Tim","full_name":"Connallon, Tim","last_name":"Connallon"}],"article_type":"original","supplementarymaterial":"yes","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"oa_version":"Published Version","publication_identifier":{"eissn":["1091-6490"]},"das_tickbox":"1","has_accepted_license":"1","day":"29","doi":"10.1073/pnas.2406335121","language":[{"iso":"eng"}],"intvolume":"       121","isi":1,"ddc":["570"],"issue":"44","article_number":"e2406335121","pmid":1,"external_id":{"isi":["001359216400017"],"pmid":["39436652"]},"quality_controlled":"1","date_created":"2024-10-27T23:01:44Z","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.","_id":"18479","volume":121,"file":[{"access_level":"open_access","date_created":"2024-11-04T10:29:43Z","file_name":"2024_PNAS_McDonough.pdf","content_type":"application/pdf","relation":"main_file","file_id":"18501","file_size":1299095,"date_updated":"2024-11-04T10:29:43Z","success":1,"checksum":"73db3c87b35753e0f4324417f164a35e","creator":"dernst"}],"citation":{"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>.","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>","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.","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>.","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.","short":"Y. Mcdonough, F. Ruzicka, T. Connallon, Proceedings of the National Academy of Sciences of the United States of America 121 (2024)."},"publication":"Proceedings of the National Academy of Sciences of the United States of America","scopus_import":"1","date_updated":"2026-09-24T11:12:56Z","title":"Reconciling theories of dominance with the relative rates of adaptive substitution on sex chromosomes and autosomes","OA_type":"hybrid","oa":1,"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"has_accepted_license":"1","day":"01","das_tickbox":"1","publication_identifier":{"eissn":["1759-6653"]},"oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"supplementarymaterial":"yes","article_type":"original","department":[{"_id":"BeVi"}],"author":[{"first_name":"Roxanne","full_name":"Fraser, Roxanne","last_name":"Fraser"},{"first_name":"Ruth","full_name":"Moraa, Ruth","last_name":"Moraa"},{"last_name":"Djolai","full_name":"Djolai, Annika","first_name":"Annika"},{"first_name":"Nils","last_name":"Meisenheimer","full_name":"Meisenheimer, Nils"},{"full_name":"Laube, Sophie","last_name":"Laube","first_name":"Sophie"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","orcid":"0000-0002-4579-8306","last_name":"Vicoso","full_name":"Vicoso, Beatriz"},{"last_name":"Huylmans","full_name":"Huylmans, Ann K","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","first_name":"Ann K","orcid":"0000-0001-8871-4961"}],"researchdata_availability":"yes","OA_place":"publisher","fulldoi":"https://doi.org/10.1093/gbe/evae265","corr_author":"1","month":"12","abstract":[{"text":"Termites, together with cockroaches, belong to the Blattodea. They possess an XX/XY sex determination system which has evolved from an XX/X0 system present in other Blattodean species, such as cockroaches and wood roaches. Little is currently known about the sex chromosomes of termites, their gene content, or their evolution. We here investigate the X chromosome of multiple termite species and compare them with the X chromosome of cockroaches using genomic and transcriptomic data. We find that the X chromosome of the termite Macrotermes natalensis is large and differentiated showing hall marks of sex chromosome evolution such as dosage compensation, while this does not seem to be the case in the other two termite species investigated here where sex chromosomes may be evolutionary younger. Furthermore, the X chromosome in M. natalensis is different from the X chromosome found in the cockroach Blattella germanica indicating that sex chromosome turn-over events may have happened during termite evolution.","lang":"eng"}],"project":[{"grant_number":"M02484","name":"Sex Determination in Termites","call_identifier":"FWF","_id":"26641CAC-B435-11E9-9278-68D0E5697425"}],"publisher":"Oxford University Press","year":"2024","article_processing_charge":"Yes","publication_status":"published","date_published":"2024-12-01T00:00:00Z","status":"public","dataavailabilitystatement":"Male and female DNAseq reads for the termites C. secundus, M. natalensis, and R. flavipes can be found in the NCBI SRA under accession codes SRR30467421-SRR30467422, SRR30467423-SRR30467424, and SRR30467425-SRR30467426, respectively (all BioProject PRJNA1153745)","file_date_updated":"2025-01-08T08:28:07Z","type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","license":"https://creativecommons.org/licenses/by-nc/4.0/","DOAJ_listed":"1","title":"Evidence for a novel X chromosome in termites","oa":1,"OA_type":"gold","date_updated":"2026-09-24T11:16:00Z","acknowledged_ssus":[{"_id":"ScienComp"}],"scopus_import":"1","publication":"Genome Biology and Evolution","file":[{"creator":"dernst","checksum":"9cf8fd14580dd694dd810ccca808ad0e","success":1,"date_updated":"2025-01-08T08:28:07Z","content_type":"application/pdf","relation":"main_file","file_name":"2024_GBE_Fraser.pdf","file_id":"18772","file_size":795106,"access_level":"open_access","date_created":"2025-01-08T08:28:07Z"}],"citation":{"chicago":"Fraser, Roxanne, Ruth Moraa, Annika Djolai, Nils Meisenheimer, Sophie Laube, Beatriz Vicoso, and Ann K Huylmans. “Evidence for a Novel X Chromosome in Termites.” <i>Genome Biology and Evolution</i>. Oxford University Press, 2024. <a href=\"https://doi.org/10.1093/gbe/evae265\">https://doi.org/10.1093/gbe/evae265</a>.","ama":"Fraser R, Moraa R, Djolai A, et al. Evidence for a novel X chromosome in termites. <i>Genome Biology and Evolution</i>. 2024;16(12). doi:<a href=\"https://doi.org/10.1093/gbe/evae265\">10.1093/gbe/evae265</a>","apa":"Fraser, R., Moraa, R., Djolai, A., Meisenheimer, N., Laube, S., Vicoso, B., &#38; Huylmans, A. K. (2024). Evidence for a novel X chromosome in termites. <i>Genome Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/gbe/evae265\">https://doi.org/10.1093/gbe/evae265</a>","ista":"Fraser R, Moraa R, Djolai A, Meisenheimer N, Laube S, Vicoso B, Huylmans AK. 2024. Evidence for a novel X chromosome in termites. Genome Biology and Evolution. 16(12), evae265.","short":"R. Fraser, R. Moraa, A. Djolai, N. Meisenheimer, S. Laube, B. Vicoso, A.K. Huylmans, Genome Biology and Evolution 16 (2024).","ieee":"R. Fraser <i>et al.</i>, “Evidence for a novel X chromosome in termites,” <i>Genome Biology and Evolution</i>, vol. 16, no. 12. Oxford University Press, 2024.","mla":"Fraser, Roxanne, et al. “Evidence for a Novel X Chromosome in Termites.” <i>Genome Biology and Evolution</i>, vol. 16, no. 12, evae265, Oxford University Press, 2024, doi:<a href=\"https://doi.org/10.1093/gbe/evae265\">10.1093/gbe/evae265</a>."},"_id":"18761","volume":16,"date_created":"2025-01-05T23:01:58Z","acknowledgement":"urthermore, we thank all lab members and collaborators for feedback on the project. Specifically, Dino McMahon provided R. flavipes males and females, Judith Korb provided C. secundus males and females, gave feedback on the project and discussed questions on termite reproduction, Mireille Vasseur-Cognet provided M. natalensis males and females, Ariana Macon performed the lab work for sequencing and the Vicoso group gave critical feedback on the project. We furthermore thank the HPC group at IST Austria and Christian Meesters at JGU Mainz for their technical support.\r\nThis work was supported by a Österreichischer Wissenschaftsfonds (FWF) grant of the Meitner Programme to A.K.H. (project number M 2484), funding by the Deutsche Forschungsgemeinschaft (DFG) of the Research Training Group GenEvo (project number 407023052) to A.K.H., R.F., and A.D., and funding of the DFG within the Schwerpunktprogramm Gevol to A.K.H. and R.M. (project number 503256468).","quality_controlled":"1","external_id":{"pmid":["39658246"],"isi":["001380841100001"]},"pmid":1,"issue":"12","article_number":"evae265","ddc":["570"],"isi":1,"intvolume":"        16","language":[{"iso":"eng"}],"doi":"10.1093/gbe/evae265"},{"has_accepted_license":"1","day":"05","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_updated":"2026-09-24T11:17:37Z","oa_version":"Published Version","acknowledged_ssus":[{"_id":"ScienComp"}],"title":"Data for: \"Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome\"","oa":1,"department":[{"_id":"GradSch"},{"_id":"BeVi"}],"author":[{"orcid":"0000-0002-5328-7231","first_name":"Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","last_name":"Elkrewi","full_name":"Elkrewi, Marwan N"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","orcid":"0000-0002-4579-8306","last_name":"Vicoso","full_name":"Vicoso, Beatriz"}],"file":[{"access_level":"open_access","date_created":"2024-08-05T22:24:18Z","content_type":"text/plain","file_name":"README.txt","relation":"main_file","file_size":2465,"file_id":"17394","date_updated":"2024-08-05T22:24:18Z","success":1,"checksum":"26b5d41b3103f4284dd97d56e370a5b6","creator":"melkrewi"},{"date_created":"2024-08-05T23:28:52Z","access_level":"open_access","date_updated":"2024-08-05T23:28:52Z","file_id":"17395","file_size":2526735400,"relation":"main_file","file_name":"Data_artemia_single_nucleus_atlas.zip","content_type":"application/x-zip-compressed","success":1,"creator":"melkrewi","checksum":"95adab5e36148015da313505e3910707"}],"related_material":{"record":[{"id":"17890","relation":"used_in_publication","status":"public"}]},"citation":{"mla":"Elkrewi, Marwan N., and Beatriz Vicoso. <i>Data for: “Single-Nucleus Atlas of the Artemia Female Reproductive System Suggests Germline Repression of the Z Chromosome.”</i> Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:17362\">10.15479/AT:ISTA:17362</a>.","ieee":"M. N. Elkrewi and B. Vicoso, “Data for: ‘Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome.’” Institute of Science and Technology Austria, 2024.","ista":"Elkrewi MN, Vicoso B. 2024. Data for: ‘Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:17362\">10.15479/AT:ISTA:17362</a>.","short":"M.N. Elkrewi, B. Vicoso, (2024).","apa":"Elkrewi, M. N., &#38; Vicoso, B. (2024). Data for: “Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:17362\">https://doi.org/10.15479/AT:ISTA:17362</a>","chicago":"Elkrewi, Marwan N, and Beatriz Vicoso. “Data for: ‘Single-Nucleus Atlas of the Artemia Female Reproductive System Suggests Germline Repression of the Z Chromosome.’” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/AT:ISTA:17362\">https://doi.org/10.15479/AT:ISTA:17362</a>.","ama":"Elkrewi MN, Vicoso B. Data for: “Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome.” 2024. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:17362\">10.15479/AT:ISTA:17362</a>"},"fulldoi":"https://doi.org/10.15479/AT:ISTA:17362","corr_author":"1","_id":"17362","month":"08","date_created":"2024-08-02T07:27:45Z","publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","year":"2024","abstract":[{"lang":"eng","text":"This is the supplementary data for the paper titled \"Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome\", where we described the generation and analysis of single-nucleus expression and chromatin-accessibility data from the female reproductive system of Artemia franciscana. We compared our dataset to the published Drosophila single-nucleus data (over 400 million years of divergence) and highlighted the extreme conservation of several of the molecular pathways of oogenesis and meiosis. We found evidence of global transcriptional quiescence and chromatin condensation in late germ cells, highlighting the conserved role of this repressive stage in arthropod oogenesis. Additionally, we explored the expression patterns of the ZW sex chromosomes during oogenesis. Our data shows that the Z-chromosome is consistently downregulated in germline cells. While this is partly driven by a lack of dosage compensation in the germline, a subset of cells show stronger repression of the Z chromosome."}],"project":[{"grant_number":"F8810","name":"The highjacking of meiosis for asexual reproduction","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396"}],"date_published":"2024-08-05T00:00:00Z","status":"public","ddc":["576"],"type":"research_data","doi":"10.15479/AT:ISTA:17362","file_date_updated":"2024-08-05T23:28:52Z"},{"status":"public","date_published":"2024-01-02T00:00:00Z","file_date_updated":"2023-12-22T14:14:06Z","doi_confirm":"1","type":"research_data","contributor":[{"contributor_type":"researcher","last_name":"Bett","id":"57854184-AAE0-11E9-8D04-98D6E5697425","first_name":"Vincent K"},{"last_name":"Macon","contributor_type":"project_member","first_name":"Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-4579-8306","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","contributor_type":"supervisor"},{"orcid":"0000-0002-5328-7231","first_name":"Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","last_name":"Elkrewi","contributor_type":"researcher"}],"month":"01","project":[{"_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","name":"The highjacking of meiosis for asexual reproduction","grant_number":"F8810"}],"abstract":[{"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.","lang":"eng"}],"year":"2024","article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"15009"}]},"department":[{"_id":"GradSch"},{"_id":"BeVi"}],"author":[{"full_name":"Elkrewi, Marwan N","last_name":"Elkrewi","first_name":"Marwan N","orcid":"0000-0002-5328-7231","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425"}],"corr_author":"1","fulldoi":"https://doi.org/10.15479/AT:ISTA:14705","has_accepted_license":"1","day":"02","oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"ddc":["576"],"doi":"10.15479/AT:ISTA:14705","date_created":"2023-12-22T13:40:48Z","keyword":["sex chromosome evolution","genome assembly","dosage compensation"],"file":[{"success":1,"checksum":"bdaf1392867786634ec5466d528c36ca","creator":"melkrewi","date_created":"2023-12-22T13:54:21Z","access_level":"open_access","file_id":"14707","file_size":847,"file_name":"readme.txt.txt","relation":"main_file","content_type":"text/plain","date_updated":"2023-12-22T13:54:21Z"},{"access_level":"open_access","date_created":"2023-12-22T14:14:06Z","date_updated":"2023-12-22T14:14:06Z","file_name":"data_artemia_franciscana_genome.zip","content_type":"application/x-zip-compressed","relation":"main_file","file_id":"14708","file_size":343632753,"success":1,"creator":"melkrewi","checksum":"973e1cbdab923a71709782177980829f"}],"citation":{"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>","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>.","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>","short":"M.N. Elkrewi, (2024).","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>.","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."},"_id":"14705","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa":1,"title":"Data from \"Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation\"","date_updated":"2026-10-02T11:13:43Z"},{"date_created":"2024-07-05T14:15:29Z","degree_awarded":"PhD","ddc":["570"],"doi":"10.15479/at:ista:17206","language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2026-09-24T11:19:04Z","acknowledged_ssus":[{"_id":"ScienComp"}],"license":"https://creativecommons.org/licenses/by-sa/4.0/","oa":1,"title":"Novel approaches to studying alternative splicing in Drosophila Melanogaster : Insights into sex-specific gene expression and the evolution of sex determination","citation":{"apa":"Raices, J. (2024). <i>Novel approaches to studying alternative splicing in Drosophila Melanogaster : Insights into sex-specific gene expression and the evolution of sex determination</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17206\">https://doi.org/10.15479/at:ista:17206</a>","chicago":"Raices, Julia. “Novel Approaches to Studying Alternative Splicing in Drosophila Melanogaster : Insights into Sex-Specific Gene Expression and the Evolution of Sex Determination.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17206\">https://doi.org/10.15479/at:ista:17206</a>.","ama":"Raices J. Novel approaches to studying alternative splicing in Drosophila Melanogaster : Insights into sex-specific gene expression and the evolution of sex determination. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17206\">10.15479/at:ista:17206</a>","mla":"Raices, Julia. <i>Novel Approaches to Studying Alternative Splicing in Drosophila Melanogaster : Insights into Sex-Specific Gene Expression and the Evolution of Sex Determination</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17206\">10.15479/at:ista:17206</a>.","ieee":"J. Raices, “Novel approaches to studying alternative splicing in Drosophila Melanogaster : Insights into sex-specific gene expression and the evolution of sex determination,” Institute of Science and Technology Austria, 2024.","ista":"Raices J. 2024. Novel approaches to studying alternative splicing in Drosophila Melanogaster : Insights into sex-specific gene expression and the evolution of sex determination. Institute of Science and Technology Austria.","short":"J. Raices, Novel Approaches to Studying Alternative Splicing in Drosophila Melanogaster : Insights into Sex-Specific Gene Expression and the Evolution of Sex Determination, Institute of Science and Technology Austria, 2024."},"file":[{"date_updated":"2025-01-11T23:30:04Z","file_size":13788479,"file_id":"17223","relation":"source_file","file_name":"ThesisRaices2024_postDefense.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2024-07-11T07:18:01Z","access_level":"closed","creator":"cchlebak","checksum":"d5e9234bde8667b005a8cfe18bb467d3","embargo_to":"open_access"},{"file_id":"17224","file_size":5580296,"content_type":"application/pdf","relation":"main_file","file_name":"ThesisRaices2024_nosignature.pdf","date_updated":"2025-01-11T23:30:04Z","date_created":"2024-07-11T07:22:32Z","access_level":"open_access","checksum":"f5ed0139aa3e11ce58369f0915647c5c","embargo":"2025-01-11","creator":"cchlebak"}],"page":"82","_id":"17206","month":"07","publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","year":"2024","abstract":[{"lang":"eng","text":"Males and females exhibit numerous differences, from the initial stages of sex determination to the\r\ndevelopment of secondary sexual characteristics. In Drosophila, these differences have been\r\nthoroughly studied. Extensive research has been performed to understand the role and molecular\r\nmode of action of central sex in determining switch genes, such as transformer (tra) and Sex-lethal\r\n(Sxl). Furthermore, studies have highlighted differential gene expression as an essential mechanism to\r\ncreate sexual dimorphism. An alternative path to sexual dimorphism that has been less explored is\r\nalternative splicing, the mechanism through which genes can produce multiple transcripts with\r\ndistinct properties and functions. The primary switch sex-determining gene Sxl is a good example of\r\nthe role of alternative splicing for sex-specific functions: the inclusion of a specific exon determines\r\nthe male or female form of the protein, which in turn switches on either the male or female\r\ndevelopmental pathway. The genes that act upstream of Sxl and determine which form is expressed -\r\nthe counter genes - have received less attention. This thesis addresses two critical questions about\r\nthe molecular encoding of sexes in the Drosophila melanogaster genome: First, the use of splice forms\r\nin male and female tissues in D. melanogaster is examined, inferring the molecular and evolutionary\r\nparameters shaping the diversity of the splicing landscape. Second, the behaviour of counter genes in\r\nDrosophila-related species is investigated, shedding light on potential changes leading to their\r\nincorporation into the sex-determination pathway.\r\nFor the alternative splicing analyses, long-read RNA sequencing of testes, ovaries, female and male\r\nmidguts, heads, and whole bodies was performed. A novel pipeline was developed to assign unique\r\ntranscript identifiers for each sequence of exons and introns in the read, enabling detailed\r\ncomparisons of splicing variants in each tissue/sex. Alternative splicing was found to be more\r\npervasive in females than males (22,201 exclusive splice forms in females versus 12,631 in males),\r\nespecially when comparing ovaries to other tissues. The ovaries alone displayed 15,299 exclusive\r\nsplice forms, suggesting most female exclusive splice forms originate there. Genome location and gene\r\nage were also correlated with the number of splice forms per gene. In particular, the X and 4th\r\nchromosomes (Muller elements A and F) showed more splice forms per gene than other\r\nchromosomes. Additionally, genes older than 63 million years exhibited more splice forms per gene\r\nthan younger genes. Our results suggest that alternative splicing is more prevalent than previously\r\nbelieved, with numerous female-exclusive forms, age, and location playing significant roles in shaping\r\nits prevalence.\r\nFor the counter genes analyses, we combined published gene expression, genomic, and gene\r\ninteraction data from various clades (Bactrocera jarvisi, B. oleae, Ceratitis capitata, Mus musculus,\r\nCaenorhabditis elegans, Homo sapiens, and D. melanogaster). The counter genes scute (sc), extra\r\nmacrochaetae (emc), groucho (gro), deadpan (dpn), daughterless (da), runt (run), Sxl, hermaphrodite\r\n(her), and tra maintain conserved Muller element locations between C. capitata and D. melanogaster,\r\nwhich are most of the counter genes identified in the C. capitata genome. Their expression patterns\r\nduring early embryogenesis in B. jarvisi and D. melanogaster are also similar for counter genes dpn,\r\ngro, da, and emc. However, Sxl and sc are also found to have more extreme expression ratios between\r\nthe species. Lastly, gene interactions within the counter genes are conserved, with da-sc and gro-dpn\r\ninteractions occurring in Drosophila, worms, humans, and mice. Interactions such as dpn-sc, dpn-da,\r\nda-emc, and gro-run are present in Drosophila, mice, and humans, suggesting these genes were\r\nrecruited by ancestral characteristics, primarily during embryogenesis. The conserved expression,\r\nlocation, and interactions of counter genes suggest serendipitous recruitment of such genes instead\r\nof a change in those characteristics as they were recruited for this function. "}],"project":[{"name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","call_identifier":"H2020","_id":"250BDE62-B435-11E9-9278-68D0E5697425","grant_number":"715257"}],"date_published":"2024-07-05T00:00:00Z","status":"public","supervisor":[{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","first_name":"Beatriz","full_name":"Vicoso, Beatriz","last_name":"Vicoso"}],"publication_status":"published","type":"dissertation","doi_confirm":"1","file_date_updated":"2025-01-11T23:30:04Z","das_tickbox":"0","has_accepted_license":"1","day":"05","tmp":{"image":"/images/cc_by_sa.png","short":"CC BY-SA (4.0)","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode"},"oa_version":"Published Version","supplementarymaterial":"no","publication_identifier":{"issn":["2663-337X"]},"department":[{"_id":"BeVi"},{"_id":"GradSch"}],"author":[{"id":"3EE67F22-F248-11E8-B48F-1D18A9856A87","first_name":"Julia","last_name":"Raices","full_name":"Raices, Julia"}],"researchdata_availability":"no","alternative_title":["ISTA Thesis"],"fulldoi":"https://doi.org/10.15479/at:ista:17206","corr_author":"1","ec_funded":1,"OA_place":"publisher"},{"publication_identifier":{"issn":["1553-7390"],"eissn":["1553-7404"]},"supplementarymaterial":"yes","oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"has_accepted_license":"1","day":"30","das_tickbox":"1","OA_place":"publisher","corr_author":"1","fulldoi":"https://doi.org/10.1371/journal.pgen.1011376","article_type":"original","related_material":{"record":[{"relation":"research_data","id":"17362","status":"public"},{"status":"public","relation":"dissertation_contains","id":"19386"}],"link":[{"relation":"software","url":"https://github.com/Melkrewi/Artemia-snRNAseq-Project"}]},"researchdata_availability":"yes","author":[{"id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","orcid":"0000-0002-5328-7231","first_name":"Marwan N","last_name":"Elkrewi","full_name":"Elkrewi, Marwan N"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","orcid":"0000-0002-4579-8306","last_name":"Vicoso","full_name":"Vicoso, Beatriz"}],"department":[{"_id":"BeVi"}],"project":[{"name":"FWF Open Access Fund","call_identifier":"FWF","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1"},{"grant_number":"F8810","name":"The highjacking of meiosis for asexual reproduction","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396"}],"abstract":[{"text":"Our understanding of the molecular pathways that regulate oogenesis and define cellular identity in the Arthropod female reproductive system and the extent of their conservation is currently very limited. This is due to the focus on model systems, including Drosophila and Daphnia, which do not reflect the observed diversity of morphologies, reproductive modes, and sex chromosome systems. We use single-nucleus RNA and ATAC sequencing to produce a comprehensive single nucleus atlas of the adult Artemia franciscana female reproductive system. We map our data to the Fly Cell Atlas single-nucleus dataset of the Drosophila melanogaster ovary, shedding light on the conserved regulatory programs between the two distantly related Arthropod species. We identify the major cell types known to be present in the Artemia ovary, including germ cells, follicle cells, and ovarian muscle cells. Additionally, we use the germ cells to explore gene regulation and expression of the Z chromosome during meiosis, highlighting its unique regulatory dynamics and allowing us to explore the presence of meiotic sex chromosome silencing in this group.","lang":"eng"}],"article_processing_charge":"Yes","year":"2024","publisher":"Public Library of Science","month":"08","file_date_updated":"2024-09-11T07:54:12Z","type":"journal_article","publication_status":"published","dataavailabilitystatement":"The scripts used in the analysis can be accessed on the GitHub page: https://github.com/Melkrewi/Artemia-snRNAseq Project. The raw data are available on the NCBI short read archive (BioProject number PRJNA1128544). The Seurat objects produced in the analysis, the loom files generated by Velocyto, the reciprocal best hits used for the SAMap analysis, and the module tables and their GO enrichment results are available for download on ISTA Research Explorer (ISTA REx) using the following link: https://doi.org/10.15479/AT: ISTA:17362. The single nucleus atlas can be viewed with this link on the UCSC Cell Browser: https://brine-shrimp-repro.cells.ucsc.edu","status":"public","date_published":"2024-08-30T00:00:00Z","OA_type":"gold","oa":1,"title":"Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome","DOAJ_listed":"1","APC_amount":"3145,39 EUR","acknowledged_ssus":[{"_id":"ScienComp"}],"scopus_import":"1","date_updated":"2026-10-14T22:31:12Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"17890","volume":20,"publication":"PLoS Genetics","file":[{"date_created":"2024-09-11T07:54:12Z","access_level":"open_access","file_id":"18056","file_size":8962687,"file_name":"2024_PloSGenetics_Elkrewi.pdf","content_type":"application/pdf","relation":"main_file","date_updated":"2024-09-11T07:54:12Z","success":1,"checksum":"f5d96b9af57126fc1063e951440477d6","creator":"dernst"}],"citation":{"chicago":"Elkrewi, Marwan N, and Beatriz Vicoso. “Single-Nucleus Atlas of the Artemia Female Reproductive System Suggests Germline Repression of the Z Chromosome.” <i>PLoS Genetics</i>. Public Library of Science, 2024. <a href=\"https://doi.org/10.1371/journal.pgen.1011376\">https://doi.org/10.1371/journal.pgen.1011376</a>.","ama":"Elkrewi MN, Vicoso B. Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome. <i>PLoS Genetics</i>. 2024;20(8). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1011376\">10.1371/journal.pgen.1011376</a>","apa":"Elkrewi, M. N., &#38; Vicoso, B. (2024). Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1011376\">https://doi.org/10.1371/journal.pgen.1011376</a>","ista":"Elkrewi MN, Vicoso B. 2024. Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome. PLoS Genetics. 20(8), e1011376.","short":"M.N. Elkrewi, B. Vicoso, PLoS Genetics 20 (2024).","ieee":"M. N. Elkrewi and B. Vicoso, “Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome,” <i>PLoS Genetics</i>, vol. 20, no. 8. Public Library of Science, 2024.","mla":"Elkrewi, Marwan N., and Beatriz Vicoso. “Single-Nucleus Atlas of the Artemia Female Reproductive System Suggests Germline Repression of the Z Chromosome.” <i>PLoS Genetics</i>, vol. 20, no. 8, e1011376, Public Library of Science, 2024, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1011376\">10.1371/journal.pgen.1011376</a>."},"pmid":1,"external_id":{"isi":["001304090200001"],"pmid":["39213449"]},"issue":"8","article_number":"e1011376","date_created":"2024-09-08T22:01:11Z","acknowledgement":"We thank the Vicoso group for their valuable comments on the earlier draft of the manuscript. We would also like to thank the Vienna BioCenter Next Generation Sequencing (NGS) facility staff, and in particular, Thomas Grentzinger for his support with the handling and sequencing of the samples, the scientific computing unit at ISTA for the computational resources, Brittney Wick for the help with hosting our data on the UCSC Cell Browser, and Lora B. Sweeney for her valuable input at the different stages of the project.\r\nThis research was funded by the Austrian science fund (FWF), as part of the SFB Meiosis consortium https://sfbmeiosis.org/, grant ID FWF SFB F88-10) to BV. ","quality_controlled":"1","language":[{"iso":"eng"}],"doi":"10.1371/journal.pgen.1011376","ddc":["570"],"intvolume":"        20","isi":1},{"ddc":["570"],"isi":1,"intvolume":"        16","language":[{"iso":"eng"}],"doi":"10.1093/gbe/evae006","date_created":"2024-02-18T23:01:02Z","quality_controlled":"1","external_id":{"isi":["001153952800001"],"pmid":["38245839"]},"pmid":1,"issue":"1","article_number":"evae006","publication":"Genome Biology and Evolution","file":[{"success":1,"checksum":"106a40f10443b2e7ba66749844ebbdf1","creator":"dernst","date_created":"2024-02-26T09:54:59Z","access_level":"open_access","file_size":5213306,"file_id":"15029","content_type":"application/pdf","relation":"main_file","file_name":"2024_GBE_Bett.pdf","date_updated":"2024-02-26T09:54:59Z"}],"citation":{"ama":"Bett VK, Macon A, Vicoso B, Elkrewi MN. Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation. <i>Genome Biology and Evolution</i>. 2024;16(1). doi:<a href=\"https://doi.org/10.1093/gbe/evae006\">10.1093/gbe/evae006</a>","chicago":"Bett, Vincent K, Ariana Macon, Beatriz Vicoso, and Marwan N Elkrewi. “Chromosome-Level Assembly of Artemia Franciscana Sheds Light on Sex Chromosome Differentiation.” <i>Genome Biology and Evolution</i>. Oxford University Press, 2024. <a href=\"https://doi.org/10.1093/gbe/evae006\">https://doi.org/10.1093/gbe/evae006</a>.","apa":"Bett, V. K., Macon, A., Vicoso, B., &#38; Elkrewi, M. N. (2024). Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation. <i>Genome Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/gbe/evae006\">https://doi.org/10.1093/gbe/evae006</a>","short":"V.K. Bett, A. Macon, B. Vicoso, M.N. Elkrewi, Genome Biology and Evolution 16 (2024).","ista":"Bett VK, Macon A, Vicoso B, Elkrewi MN. 2024. Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation. Genome Biology and Evolution. 16(1), evae006.","mla":"Bett, Vincent K., et al. “Chromosome-Level Assembly of Artemia Franciscana Sheds Light on Sex Chromosome Differentiation.” <i>Genome Biology and Evolution</i>, vol. 16, no. 1, evae006, Oxford University Press, 2024, doi:<a href=\"https://doi.org/10.1093/gbe/evae006\">10.1093/gbe/evae006</a>.","ieee":"V. K. Bett, A. Macon, B. Vicoso, and M. N. Elkrewi, “Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation,” <i>Genome Biology and Evolution</i>, vol. 16, no. 1. Oxford University Press, 2024."},"_id":"15009","volume":16,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","DOAJ_listed":"1","oa":1,"title":"Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation","OA_type":"gold","date_updated":"2026-10-14T22:31:14Z","scopus_import":"1","publication_status":"published","date_published":"2024-01-20T00:00:00Z","status":"public","dataavailabilitystatement":"The assembly pipeline and the scripts used in the analysis can be accessed on the gitpage (https://github.com/Melkrewi/Artemia_franciscana_genome/). The raw data are available on the National Center for Biotechnology Information (NCBI) short-read archive (BioProject number PRJNA1017357). The final assembly, the annotation, and the supplementary data sets are available on (https://doi.org/10.15479/AT:ISTA:14705). All genomic and transcriptomic samples used for this study and the steps of the analysis they were used in are described in supplementary table S3, Supplementary Material online.","file_date_updated":"2024-02-26T09:54:59Z","type":"journal_article","month":"01","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, is 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 A. franciscana (Kellogg 1906), from the Great Salt Lake, United States. The genome is 1 GB, 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."}],"publisher":"Oxford University Press","year":"2024","article_processing_charge":"Yes","article_type":"original","department":[{"_id":"BeVi"}],"author":[{"first_name":"Vincent K","id":"57854184-AAE0-11E9-8D04-98D6E5697425","full_name":"Bett, Vincent K","last_name":"Bett"},{"id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","first_name":"Ariana","last_name":"Macon","full_name":"Macon, Ariana"},{"first_name":"Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz","last_name":"Vicoso"},{"last_name":"Elkrewi","full_name":"Elkrewi, Marwan N","first_name":"Marwan N","orcid":"0000-0002-5328-7231","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425"}],"researchdata_availability":"yes","related_material":{"record":[{"relation":"research_data","id":"14705","status":"public"},{"status":"public","id":"19386","relation":"dissertation_contains"},{"id":"20449","relation":"dissertation_contains","status":"public"},{"relation":"dissertation_contains","id":"20444","status":"deleted"}]},"OA_place":"publisher","fulldoi":"https://doi.org/10.1093/gbe/evae006","corr_author":"1","day":"20","has_accepted_license":"1","das_tickbox":"1","publication_identifier":{"eissn":["1759-6653"]},"oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"supplementarymaterial":"yes"},{"abstract":[{"lang":"eng","text":"Sex chromosomes and autosomes exhibit very different evolutionary dynamics.\r\nThe Y chromosome usually degenerates, leaving many X-linked loci hemizygous in\r\nmales. Since recessive X-linked mutations are always exposed to selection in males,\r\nselection is more efficient on the X chromosome than on autosomes on recessive\r\nmutations, leading to faster adaptation on the X chromosome than other genomic\r\nregions, if beneficial mutations are on average recessive (known as the Faster-X\r\neffect). In the presence of the functional, but non-recombining gametolog on the Y (as\r\nis often the case in young non-recombining regions), recessive mutations are\r\nsheltered from selection on the X chromosome. We model this scenario and show that\r\nthe efficiency of selection is reduced on diploid X loci due to sheltering by the Y\r\nchromosome. Reduced efficiency of selection leads to slower adaptation and\r\nincreased accumulation of deleterious mutations (Slower-X effect). We extended this\r\nmodel to explore the effect of sex-specific selection on degeneration of sex\r\nchromosomes, showing theoretically that male-limited genes degenerate on the X\r\nchromosome and female-biased genes degenerate on the Y chromosome. This\r\nprediction depends on the effective population size and the mutation rate, explaining\r\nthe variety of sex chromosome degeneration patterns observed in nature.\r\nTo test for direct evidence of a Slower-X (or Slower-Z) effect, we analyzed the\r\nZW sex chromosomes of the flatworm Schistosoma japonicum, which have a very\r\nyoung non-recombining region with non-degenerated W. Diploid Z-linked genes have\r\nhigher ratios of non-synonymous to synonymous polymorphisms than autosomal\r\ngenes, supporting reduced efficiency of selection on the diploid Z region. These results\r\nprovide evidence of sheltering by the W chromosome, a mechanism that could\r\ncontribute to Z (X) chromosome degeneration, and illustrate contrasting evolutionary\r\npatterns in old and young sex chromosome regions. In addition, genes with sexspecific patterns of expression show opposite patterns of selection in the young\r\n(diploid) and old (hemizygous) Z, showing the complex manner in which sex-specific selection shapes the evolutionary patterns of sex chromosomes. "}],"year":"2024","article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","month":"11","file_date_updated":"2025-05-11T22:30:04Z","doi_confirm":"1","type":"dissertation","publication_status":"published","supervisor":[{"first_name":"Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","full_name":"Vicoso, Beatriz"}],"status":"public","date_published":"2024-11-11T00:00:00Z","publication_identifier":{"issn":["2663-337X"]},"supplementarymaterial":"unclear","oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"has_accepted_license":"1","day":"11","OA_place":"publisher","OA_embargo":"6","corr_author":"1","fulldoi":"https://doi.org/10.15479/at:ista:18531","alternative_title":["ISTA Thesis"],"related_material":{"record":[{"id":"12521","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"18549","relation":"part_of_dissertation"}]},"researchdata_availability":"unclear","author":[{"last_name":"Mrnjavac","full_name":"Mrnjavac, Andrea","id":"353FAC84-AE61-11E9-8BFC-00D3E5697425","first_name":"Andrea"}],"department":[{"_id":"GradSch"},{"_id":"BeVi"}],"date_created":"2024-11-11T08:40:45Z","keyword":["Sex chromosomes","evolution","selection","sheltering"],"language":[{"iso":"eng"}],"doi":"10.15479/at:ista:18531","degree_awarded":"PhD","ddc":["576"],"oa":1,"title":"Early stages of sex chromosome evolution","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"CampIT"}],"date_updated":"2026-10-02T11:14:08Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"18531","page":"181","file":[{"embargo_to":"open_access","checksum":"3e48b163c22114ef5d5371f758668289","creator":"amrnjava","access_level":"closed","date_created":"2024-11-13T12:15:28Z","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"AMrnjavac_thesis_library.docx","file_id":"18551","title":"Early stages of sex chromosome evolution","file_size":26870629,"date_updated":"2025-05-11T22:30:04Z"},{"access_level":"open_access","date_created":"2024-11-13T12:15:54Z","date_updated":"2025-05-11T22:30:04Z","relation":"main_file","content_type":"application/pdf","file_name":"AMrnjavac_thesis_library.pdf","title":"Early stages of sex chromosome evolution","file_id":"18552","file_size":4228766,"creator":"amrnjava","checksum":"3ead60c1b678e7dcf018043aef3b5db2","embargo":"2025-05-11"}],"citation":{"apa":"Mrnjavac, A. (2024). <i>Early stages of sex chromosome evolution</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18531\">https://doi.org/10.15479/at:ista:18531</a>","chicago":"Mrnjavac, Andrea. “Early Stages of Sex Chromosome Evolution.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18531\">https://doi.org/10.15479/at:ista:18531</a>.","ama":"Mrnjavac A. Early stages of sex chromosome evolution. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18531\">10.15479/at:ista:18531</a>","ieee":"A. Mrnjavac, “Early stages of sex chromosome evolution,” Institute of Science and Technology Austria, 2024.","mla":"Mrnjavac, Andrea. <i>Early Stages of Sex Chromosome Evolution</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18531\">10.15479/at:ista:18531</a>.","ista":"Mrnjavac A. 2024. Early stages of sex chromosome evolution. Institute of Science and Technology Austria.","short":"A. Mrnjavac, Early Stages of Sex Chromosome Evolution, Institute of Science and Technology Austria, 2024."}},{"day":"04","das_tickbox":"0","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"oa_version":"Preprint","supplementarymaterial":"yes","department":[{"_id":"BeVi"}],"author":[{"full_name":"Mrnjavac, Andrea","last_name":"Mrnjavac","id":"353FAC84-AE61-11E9-8BFC-00D3E5697425","first_name":"Andrea"},{"full_name":"Vicoso, Beatriz","last_name":"Vicoso","orcid":"0000-0002-4579-8306","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"researchdata_availability":"no","related_material":{"record":[{"status":"public","relation":"later_version","id":"19370"},{"status":"public","relation":"dissertation_contains","id":"18531"}]},"OA_place":"repository","fulldoi":"https://doi.org/10.1101/2024.07.02.601697","corr_author":"1","month":"07","abstract":[{"text":"Sex-linked and autosomal loci experience different selective pressures and\r\nevolutionary dynamics. X (or Z) chromosomes are often hemizygous, as Y (or W)\r\nchromosomes often degenerate. Such hemizygous regions can be under greater\r\nefficacy of selection, as recessive mutations are immediately exposed to selection in\r\nthe heterogametic sex (the so-called Faster-X or Faster-Z effect). However, in young\r\nnon-recombining regions, Y/W chromosomes often have many functional genes, and\r\nmany X/Z-linked loci are therefore diploid. The sheltering of recessive mutations on\r\nthe X/Z by the Y/W homolog is expected to drive a Slower-X (Slower-Z) effect for\r\ndiploid X/Z loci, i.e. a reduction in the efficacy of selection. While the Faster-X effect\r\nhas been studied extensively, much less is known empirically about the evolutionary\r\ndynamics of diploid X or Z chromosomes. Here, we took advantage of published\r\npopulation genomic data in the female-heterogametic human parasite Schistosoma\r\njaponicum to characterize the gene content and diversity levels of the diploid and\r\nhemizygous regions of the Z chromosome. We used different metrics of selective\r\npressures acting on genes to test for differences in the efficacy of selection in\r\nhemizygous and diploid Z regions, relative to autosomes. We found consistent\r\npatterns suggesting reduced Ne, and reduced efficacy of purifying selection, on both\r\nhemizygous and diploid Z regions. Moreover, relaxed selection was particularly\r\npronounced for female-biased genes on the diploid Z, as predicted by Slower-Z\r\ntheory.\r\n","lang":"eng"}],"article_processing_charge":"No","year":"2024","publication_status":"draft","date_published":"2024-07-04T00:00:00Z","status":"public","type":"preprint","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2024.07.02.601697"}],"oa":1,"title":"Evidence of a Slower-Z effect in Schistosoma japonicum","date_updated":"2026-10-14T22:31:15Z","publication":"bioRxiv","citation":{"ieee":"A. Mrnjavac and B. Vicoso, “Evidence of a Slower-Z effect in Schistosoma japonicum,” <i>bioRxiv</i>. .","mla":"Mrnjavac, Andrea, and Beatriz Vicoso. “Evidence of a Slower-Z Effect in Schistosoma Japonicum.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2024.07.02.601697\">10.1101/2024.07.02.601697</a>.","ista":"Mrnjavac A, Vicoso B. Evidence of a Slower-Z effect in Schistosoma japonicum. bioRxiv, <a href=\"https://doi.org/10.1101/2024.07.02.601697\">10.1101/2024.07.02.601697</a>.","short":"A. Mrnjavac, B. Vicoso, BioRxiv (n.d.).","apa":"Mrnjavac, A., &#38; Vicoso, B. (n.d.). Evidence of a Slower-Z effect in Schistosoma japonicum. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2024.07.02.601697\">https://doi.org/10.1101/2024.07.02.601697</a>","chicago":"Mrnjavac, Andrea, and Beatriz Vicoso. “Evidence of a Slower-Z Effect in Schistosoma Japonicum.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2024.07.02.601697\">https://doi.org/10.1101/2024.07.02.601697</a>.","ama":"Mrnjavac A, Vicoso B. Evidence of a Slower-Z effect in Schistosoma japonicum. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2024.07.02.601697\">10.1101/2024.07.02.601697</a>"},"_id":"18549","biorxivid":1,"date_created":"2024-11-13T09:12:08Z","external_id":{"biorxivid":["10.1101/2024.07.02.601697"]},"language":[{"iso":"eng"}],"doi":"10.1101/2024.07.02.601697"},{"doi":"10.15479/at:ista:17119","language":[{"iso":"eng"}],"ddc":["576"],"degree_awarded":"PhD","keyword":["meiotic driver","neofunctionalization","single nucleus sequencing"],"date_created":"2024-06-07T16:14:13Z","page":"105","_id":"17119","file":[{"embargo_to":"open_access","creator":"rkelemen","checksum":"fab59146e3b3dc2e5d214576984a2a63","date_created":"2024-06-07T16:09:17Z","access_level":"closed","date_updated":"2025-01-10T23:30:10Z","file_id":"17121","file_size":180557931,"content_type":"application/zip","relation":"source_file","file_name":"thesis.zip"},{"date_updated":"2025-01-10T23:30:10Z","file_size":19405484,"file_id":"17213","relation":"main_file","content_type":"application/pdf","file_name":"thesis_to_archive.pdf","date_created":"2024-07-10T08:00:20Z","access_level":"open_access","creator":"rkelemen","checksum":"91cc4c25a792239e8a7688e8aec7c62a","embargo":"2025-01-10"}],"citation":{"ama":"Kelemen RK. Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17119\">10.15479/at:ista:17119</a>","chicago":"Kelemen, Réka K. “Characterizing the Sequence and Expression Evolution of the T-Haplotype, a Model Meiotic Driver.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17119\">https://doi.org/10.15479/at:ista:17119</a>.","apa":"Kelemen, R. K. (2024). <i>Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17119\">https://doi.org/10.15479/at:ista:17119</a>","short":"R.K. Kelemen, Characterizing the Sequence and Expression Evolution of the T-Haplotype, a Model Meiotic Driver, Institute of Science and Technology Austria, 2024.","ista":"Kelemen RK. 2024. Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver. Institute of Science and Technology Austria.","ieee":"R. K. Kelemen, “Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver,” Institute of Science and Technology Austria, 2024.","mla":"Kelemen, Réka K. <i>Characterizing the Sequence and Expression Evolution of the T-Haplotype, a Model Meiotic Driver</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17119\">10.15479/at:ista:17119</a>."},"date_updated":"2026-10-02T11:14:33Z","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","oa":1,"title":"Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"dissertation","doi_confirm":"1","file_date_updated":"2025-01-10T23:30:10Z","date_published":"2024-06-20T00:00:00Z","status":"public","supervisor":[{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","first_name":"Beatriz","full_name":"Vicoso, Beatriz","last_name":"Vicoso"}],"publication_status":"published","publisher":"Institute of Science and Technology Austria","year":"2024","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Genomes are shaped by natural selection at the level of the organism, as genomic variants that\r\nhave a beneficial effect on the viability or fecundity of their carriers are on average expected\r\nto be passed on to more offspring than less beneficial alleles. However, selection also favors\r\ngenomic variants that drive their own transmission to the next generation above the mendelian\r\nexpectation of 50 percent in heterozygotes, even if these self-promoting variants are less\r\nbeneficial to the organism than other variants at the same locus. Such variants, called meiotic\r\ndrivers, are found in diverse taxa, and often impose fitness costs on their host organisms. As\r\nmeiotic drivers often require multiple genes and sequences for transmission ratio distortion,\r\nthey are often found in regions of low recombination, such as inversions, which prevent their\r\nrecombination with the non-driving homologous regions. Reduced recombination rates are\r\nexpected to lead to the accumulation of deleterious mutations, which may affect hundreds\r\nof genes trapped in the inversions of meiotic drivers. Although the observed fitness costs of\r\nself-promoting haplotypes are thought to possibly reflect sequence degeneration, no study has\r\nsystematically investigated the level of degeneration on a meiotic driver. Further, the low\r\nrates of recombination between driving and non-driving haplotypes have limited the power of\r\ntraditional genetic studies in uncovering the gene content of meiotic drivers, and made the\r\nthe identification of the genes causing transmission ratio distortion difficult.\r\nAfter an introduction to meiotic drivers in Chapter 1, this thesis presents three studies that\r\nmake use of next generation sequencing data to characterize the sequence and expression\r\nevolution of genes on the t-haplotype, a large and ancient meiotic driver in house mice that is\r\ntransmitted to up to 100% of the offspring in males heterozygous for it. Chapter 2 presents\r\na comprehensive assessment of the t-haplotype’s sequence evolution, which shows signs of\r\nsequence degeneration counteracted by occasional recombination with the non-driving homolog\r\nover large parts of the meiotic driver, proposing an explanation for its long-term survival.\r\nChapter 3 investigates the sequence and expression evolution of genes on the t-haplotype,\r\nand finds widespread expression and copy number changes and signs of less efficient purifying\r\nselection compared to the genes on the non-driving homolog. Further, this chapter finds\r\ncandidates for involvment in drive: two positively selected genes on the t-haplotype, and\r\nthe discovery of a t-specific gene duplicate, which was gained from another chromosome,\r\nand which acquired novel sequence and testis-specific expression on the t-haplotype. Finally,\r\nChapter 4 provides unprecedented insights into the gene expression landscape in testes of\r\nt-carrier mice, using single nucleus sequencing. Cell-resolved RNA-sequencing allows the\r\ncomparison of expression in spermatids carrying or not carrying the t-haplotype as well as the\r\ntiming of t-haplotype-induced expression changes along spermatogenesis. This study shows\r\nthe timing of previously found drive-associated genes, and uncovers novel candidate genes and\r\nbiological processes that may underlie the complex biology of transmission ratio distortion of\r\nthe t-haplotype. Chapter 5 synthesizes the findings of the three studies, and discusses them in\r\nthe context of the current state of meiotic drive research."}],"project":[{"grant_number":"715257","_id":"250BDE62-B435-11E9-9278-68D0E5697425","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","call_identifier":"H2020"},{"grant_number":"F8810","name":"The highjacking of meiosis for asexual reproduction","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396"}],"month":"06","fulldoi":"https://doi.org/10.15479/at:ista:17119","corr_author":"1","ec_funded":1,"OA_place":"publisher","author":[{"id":"48D3F8DE-F248-11E8-B48F-1D18A9856A87","first_name":"Réka K","orcid":"0000-0002-8489-9281","last_name":"Kelemen","full_name":"Kelemen, Réka K"}],"department":[{"_id":"GradSch"},{"_id":"BeVi"}],"related_material":{"record":[{"status":"public","id":"542","relation":"part_of_dissertation"},{"status":"public","id":"10767","relation":"part_of_dissertation"}]},"researchdata_availability":"unclear","alternative_title":["ISTA Thesis"],"tmp":{"image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode"},"oa_version":"Published Version","supplementarymaterial":"unclear","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-039-8"]},"day":"20","has_accepted_license":"1"},{"type":"journal_article","file_date_updated":"2023-02-27T07:10:17Z","date_published":"2023-02-01T00:00:00Z","status":"public","publication_status":"published","year":"2023","article_processing_charge":"No","publisher":"Wiley","abstract":[{"lang":"eng","text":"Understanding population divergence that eventually leads to speciation is essential for evolutionary biology. High species diversity in the sea was regarded as a paradox when strict allopatry was considered necessary for most speciation events because geographical barriers seemed largely absent in the sea, and many marine species have high dispersal capacities. Combining genome-wide data with demographic modelling to infer the demographic history of divergence has introduced new ways to address this classical issue. These models assume an ancestral population that splits into two subpopulations diverging according to different scenarios that allow tests for periods of gene flow. Models can also test for heterogeneities in population sizes and migration rates along the genome to account, respectively, for background selection and selection against introgressed ancestry. To investigate how barriers to gene flow arise in the sea, we compiled studies modelling the demographic history of divergence in marine organisms and extracted preferred demographic scenarios together with estimates of demographic parameters. These studies show that geographical barriers to gene flow do exist in the sea but that divergence can also occur without strict isolation. Heterogeneity of gene flow was detected in most population pairs suggesting the predominance of semipermeable barriers during divergence. We found a weak positive relationship between the fraction of the genome experiencing reduced gene flow and levels of genome-wide differentiation. Furthermore, we found that the upper bound of the ‘grey zone of speciation’ for our dataset extended beyond that found before, implying that gene flow between diverging taxa is possible at higher levels of divergence than previously thought. Finally, we list recommendations for further strengthening the use of demographic modelling in speciation research. These include a more balanced representation of taxa, more consistent and comprehensive modelling, clear reporting of results and simulation studies to rule out nonbiological explanations for general results."}],"month":"02","fulldoi":"https://doi.org/10.1111/eva.13428","author":[{"last_name":"De Jode","full_name":"De Jode, Aurélien","first_name":"Aurélien"},{"last_name":"Le Moan","full_name":"Le Moan, Alan","first_name":"Alan"},{"first_name":"Kerstin","last_name":"Johannesson","full_name":"Johannesson, Kerstin"},{"full_name":"Faria, Rui","last_name":"Faria","first_name":"Rui"},{"id":"43161670-5719-11EA-8025-FABC3DDC885E","first_name":"Sean","full_name":"Stankowski, Sean","last_name":"Stankowski"},{"last_name":"Westram","full_name":"Westram, Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M","orcid":"0000-0003-1050-4969"},{"first_name":"Roger K.","last_name":"Butlin","full_name":"Butlin, Roger K."},{"full_name":"Rafajlović, Marina","last_name":"Rafajlović","first_name":"Marina"},{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle","orcid":"0000-0001-8441-5075","last_name":"Fraisse","full_name":"Fraisse, Christelle"}],"department":[{"_id":"NiBa"},{"_id":"BeVi"}],"article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa_version":"Published Version","publication_identifier":{"eissn":["1752-4571"]},"day":"01","has_accepted_license":"1","doi":"10.1111/eva.13428","language":[{"iso":"eng"}],"intvolume":"        16","isi":1,"ddc":["576"],"issue":"2","pmid":1,"external_id":{"isi":["000815663700001"],"pmid":["36793688"]},"quality_controlled":"1","acknowledgement":"We greatly thank all the corresponding authors of the studies that were included in our synthesis for the sharing of additional data: Thomas Broquet, Dmitry Filatov, Quentin Rougemont, Paolo Momigliano, Pierre-Alexandre Gagnaire, Carlos Prada, Ahmed Souissi, Michael Møller Hansen, Sylvie Lapègue, Joseph Di Battista, Michael Hellberg and Carlos Prada. RKB and ADJ were supported by the European Research Council. MR was supported by the Swedish Research Council Vetenskapsrådet (grant number 2021-05243; to MR) and Formas (grant number 2019-00882; to KJ and MR), and by additional grants from the European Research Council (to RKB) and Vetenskapsrådet (to KJ) through the Centre for Marine Evolutionary Biology (https://www.gu.se/en/cemeb-marine-evolutionary-biology).","date_created":"2022-07-03T22:01:33Z","page":"542-559","volume":16,"_id":"11479","file":[{"access_level":"open_access","date_created":"2023-02-27T07:10:17Z","date_updated":"2023-02-27T07:10:17Z","relation":"main_file","content_type":"application/pdf","file_name":"2023_EvolutionaryApplications_DeJode.pdf","file_size":2269822,"file_id":"12685","success":1,"creator":"dernst","checksum":"d4d6fa9ddf36643af994a6a757919afb"}],"citation":{"ieee":"A. De Jode <i>et al.</i>, “Ten years of demographic modelling of divergence and speciation in the sea,” <i>Evolutionary Applications</i>, vol. 16, no. 2. Wiley, pp. 542–559, 2023.","mla":"De Jode, Aurélien, et al. “Ten Years of Demographic Modelling of Divergence and Speciation in the Sea.” <i>Evolutionary Applications</i>, vol. 16, no. 2, Wiley, 2023, pp. 542–59, doi:<a href=\"https://doi.org/10.1111/eva.13428\">10.1111/eva.13428</a>.","ista":"De Jode A, Le Moan A, Johannesson K, Faria R, Stankowski S, Westram AM, Butlin RK, Rafajlović M, Fraisse C. 2023. Ten years of demographic modelling of divergence and speciation in the sea. Evolutionary Applications. 16(2), 542–559.","short":"A. De Jode, A. Le Moan, K. Johannesson, R. Faria, S. Stankowski, A.M. Westram, R.K. Butlin, M. Rafajlović, C. Fraisse, Evolutionary Applications 16 (2023) 542–559.","apa":"De Jode, A., Le Moan, A., Johannesson, K., Faria, R., Stankowski, S., Westram, A. M., … Fraisse, C. (2023). Ten years of demographic modelling of divergence and speciation in the sea. <i>Evolutionary Applications</i>. Wiley. <a href=\"https://doi.org/10.1111/eva.13428\">https://doi.org/10.1111/eva.13428</a>","chicago":"De Jode, Aurélien, Alan Le Moan, Kerstin Johannesson, Rui Faria, Sean Stankowski, Anja M Westram, Roger K. Butlin, Marina Rafajlović, and Christelle Fraisse. “Ten Years of Demographic Modelling of Divergence and Speciation in the Sea.” <i>Evolutionary Applications</i>. Wiley, 2023. <a href=\"https://doi.org/10.1111/eva.13428\">https://doi.org/10.1111/eva.13428</a>.","ama":"De Jode A, Le Moan A, Johannesson K, et al. Ten years of demographic modelling of divergence and speciation in the sea. <i>Evolutionary Applications</i>. 2023;16(2):542-559. doi:<a href=\"https://doi.org/10.1111/eva.13428\">10.1111/eva.13428</a>"},"publication":"Evolutionary Applications","scopus_import":"1","date_updated":"2025-04-23T08:49:14Z","title":"Ten years of demographic modelling of divergence and speciation in the sea","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"file_date_updated":"2023-05-11T12:50:18Z","doi":"10.15479/AT:ISTA:12933","type":"research_data","ddc":["570"],"status":"public","date_published":"2023-05-15T00:00:00Z","abstract":[{"text":"Datasets of the publication \"Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster\".","lang":"eng"}],"article_processing_charge":"No","year":"2023","publisher":"Institute of Science and Technology Austria","date_created":"2023-05-10T10:00:49Z","contributor":[{"last_name":"Macon","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","first_name":"Ariana"},{"last_name":"Vicoso","orcid":"0000-0002-4579-8306","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"month":"05","_id":"12933","corr_author":"1","fulldoi":"https://doi.org/10.15479/AT:ISTA:12933","file":[{"date_updated":"2023-05-10T09:41:43Z","file_size":8029982,"file_id":"12934","file_name":"Dataset_S1.csv","relation":"main_file","content_type":"text/csv","date_created":"2023-05-10T09:41:43Z","access_level":"open_access","creator":"gpuixeus","checksum":"0ba0bcd0bb8b18d84792136a4370df90","success":1},{"success":1,"checksum":"a62aa9a6d4904e0fdb699cf752640863","creator":"gpuixeus","access_level":"open_access","date_created":"2023-05-10T09:41:43Z","relation":"main_file","content_type":"text/csv","file_name":"Dataset_S2.csv","file_size":13667640,"file_id":"12935","date_updated":"2023-05-10T09:41:43Z"},{"creator":"gpuixeus","checksum":"e20ea7f4f8a9bdf1b3849a44664ae58b","success":1,"date_updated":"2023-05-10T09:41:48Z","file_name":"Dataset_S3.csv","content_type":"text/csv","relation":"main_file","file_id":"12936","file_size":8369141,"access_level":"open_access","date_created":"2023-05-10T09:41:48Z"},{"creator":"gpuixeus","checksum":"f6156e5fc44446c907ddd0d7289d4cf8","success":1,"date_updated":"2023-05-10T09:41:50Z","content_type":"text/csv","relation":"main_file","file_name":"Dataset_S4.csv","file_id":"12937","file_size":19543247,"access_level":"open_access","date_created":"2023-05-10T09:41:50Z"},{"success":1,"creator":"gpuixeus","checksum":"ae9f54c77a1c42b666ae6c1dfd33ac86","access_level":"open_access","date_created":"2023-05-11T12:50:18Z","date_updated":"2023-05-11T12:50:18Z","content_type":"text/plain","file_name":"readme.txt","relation":"main_file","file_id":"12944","file_size":4566}],"citation":{"mla":"Puixeu Sala, Gemma. <i>Data from: Sex-Specific Estimation of Cis and Trans Regulation of Gene Expression in Heads and Gonads of Drosophila Melanogaster</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:12933\">10.15479/AT:ISTA:12933</a>.","ieee":"G. Puixeu Sala, “Data from: Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster.” Institute of Science and Technology Austria, 2023.","short":"G. Puixeu Sala, (2023).","ista":"Puixeu Sala G. 2023. Data from: Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:12933\">10.15479/AT:ISTA:12933</a>.","apa":"Puixeu Sala, G. (2023). Data from: Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:12933\">https://doi.org/10.15479/AT:ISTA:12933</a>","ama":"Puixeu Sala G. Data from: Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster. 2023. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:12933\">10.15479/AT:ISTA:12933</a>","chicago":"Puixeu Sala, Gemma. “Data from: Sex-Specific Estimation of Cis and Trans Regulation of Gene Expression in Heads and Gonads of Drosophila Melanogaster.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/AT:ISTA:12933\">https://doi.org/10.15479/AT:ISTA:12933</a>."},"related_material":{"record":[{"relation":"used_in_publication","id":"14077","status":"public"},{"status":"public","relation":"used_in_publication","id":"14058"}]},"department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"BeVi"}],"author":[{"full_name":"Puixeu Sala, Gemma","last_name":"Puixeu Sala","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8330-1754","first_name":"Gemma"}],"title":"Data from: Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster","oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa_version":"Published Version","date_updated":"2026-04-07T13:25:33Z","has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"15"},{"ddc":["570"],"intvolume":"        15","isi":1,"language":[{"iso":"eng"}],"doi":"10.1093/gbe/evad113","date_created":"2023-07-23T22:01:11Z","acknowledgement":"This work was supported by the Vienna Science and Technology Fund (WWTF)(10.47379/MA16061). C.K. received funding from the Royal Society (RG170315) and the Carnegie Trust (RIG007474). M.G.R. and R.R.S. have been supported by NERC (UK) grants NE/I014632/1 and NE/V001566/1. Bioinformatics analyses were performed on the computer cluster at the University of St Andrews Bioinformatics Unit, which is funded by Wellcome Trust ISSF awards 105621/Z/14/Z. Complementary data parsing was carried out with the computational resources provided by the Research/Scientific Computing teams at The James Hutton Institute and the National Institute of Agricultural Botany (NIAB)—UK’s Crop Diversity Bioinformatics HPC, BBSRC grant BB/S019669/1. We are thankful to Paris Veltsos and R. Axel W. Wiberg for useful discussions about the project as well as providing us with the resequencing data they had produced as a result of previous work on this experiment. We are especially grateful to Tanya Sneddon for her help with the DNA extraction process and shipping.","quality_controlled":"1","pmid":1,"external_id":{"pmid":["37341535"],"isi":["001023444700003"]},"issue":"7","article_number":"evad113","publication":"Genome biology and evolution","citation":{"ista":"de Castro Barbosa Rodrigues Barata C, Snook RR, Ritchie MG, Kosiol C. 2023. Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura. Genome biology and evolution. 15(7), evad113.","short":"C. de Castro Barbosa Rodrigues Barata, R.R. Snook, M.G. Ritchie, C. Kosiol, Genome Biology and Evolution 15 (2023).","mla":"de Castro Barbosa Rodrigues Barata, Carolina, et al. “Selection on the Fly: Short-Term Adaptation to an Altered Sexual Selection Regime in Drosophila Pseudoobscura.” <i>Genome Biology and Evolution</i>, vol. 15, no. 7, evad113, Oxford University Press, 2023, doi:<a href=\"https://doi.org/10.1093/gbe/evad113\">10.1093/gbe/evad113</a>.","ieee":"C. de Castro Barbosa Rodrigues Barata, R. R. Snook, M. G. Ritchie, and C. Kosiol, “Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura,” <i>Genome biology and evolution</i>, vol. 15, no. 7. Oxford University Press, 2023.","chicago":"Castro Barbosa Rodrigues Barata, Carolina de, Rhonda R. Snook, Michael G. Ritchie, and Carolin Kosiol. “Selection on the Fly: Short-Term Adaptation to an Altered Sexual Selection Regime in Drosophila Pseudoobscura.” <i>Genome Biology and Evolution</i>. Oxford University Press, 2023. <a href=\"https://doi.org/10.1093/gbe/evad113\">https://doi.org/10.1093/gbe/evad113</a>.","ama":"de Castro Barbosa Rodrigues Barata C, Snook RR, Ritchie MG, Kosiol C. Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura. <i>Genome biology and evolution</i>. 2023;15(7). doi:<a href=\"https://doi.org/10.1093/gbe/evad113\">10.1093/gbe/evad113</a>","apa":"de Castro Barbosa Rodrigues Barata, C., Snook, R. R., Ritchie, M. G., &#38; Kosiol, C. (2023). Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura. <i>Genome Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/gbe/evad113\">https://doi.org/10.1093/gbe/evad113</a>"},"file":[{"success":1,"creator":"dernst","checksum":"70de3c4878de6efe00dc56de2df8812f","date_created":"2023-08-01T06:58:34Z","access_level":"open_access","date_updated":"2023-08-01T06:58:34Z","file_size":2382587,"file_id":"13339","file_name":"2023_GBE_Barata.pdf","relation":"main_file","content_type":"application/pdf"}],"volume":15,"_id":"13260","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"title":"Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura","scopus_import":"1","date_updated":"2025-05-14T11:08:37Z","publication_status":"published","status":"public","date_published":"2023-07-01T00:00:00Z","file_date_updated":"2023-08-01T06:58:34Z","type":"journal_article","month":"07","abstract":[{"text":"Experimental evolution studies are powerful approaches to examine the evolutionary history of lab populations. Such studies have shed light on how selection changes phenotypes and genotypes. Most of these studies have not examined the time course of adaptation under sexual selection manipulation, by resequencing the populations’ genomes at multiple time points. Here, we analyze allele frequency trajectories in Drosophila pseudoobscura where we altered their sexual selection regime for 200 generations and sequenced pooled populations at 5 time points. The intensity of sexual selection was either relaxed in monogamous populations (M) or elevated in polyandrous lines (E). We present a comprehensive study of how selection alters population genetics parameters at the chromosome and gene level. We investigate differences in the effective population size—Ne—between the treatments, and perform a genome-wide scan to identify signatures of selection from the time-series data. We found genomic signatures of adaptation to both regimes in D. pseudoobscura. There are more significant variants in E lines as expected from stronger sexual selection. However, we found that the response on the X chromosome was substantial in both treatments, more pronounced in E and restricted to the more recently sex-linked chromosome arm XR in M. In the first generations of experimental evolution, we estimate Ne to be lower on the X in E lines, which might indicate a swift adaptive response at the onset of selection. Additionally, the third chromosome was affected by elevated polyandry whereby its distal end harbors a region showing a strong signal of adaptive evolution especially in E lines.","lang":"eng"}],"year":"2023","article_processing_charge":"Yes","publisher":"Oxford University Press","article_type":"original","related_material":{"link":[{"relation":"software","url":"https://github.com/carolbarata/dpseudo-n-beyond"}]},"department":[{"_id":"BeVi"}],"author":[{"full_name":"De Castro Barbosa Rodrigues Barata, Carolina","last_name":"De Castro Barbosa Rodrigues Barata","id":"20565186-803f-11ed-ab7e-96a4ff7694ef","orcid":"0000-0003-1945-2245","first_name":"Carolina"},{"last_name":"Snook","full_name":"Snook, Rhonda R.","first_name":"Rhonda R."},{"full_name":"Ritchie, Michael G.","last_name":"Ritchie","first_name":"Michael G."},{"first_name":"Carolin","full_name":"Kosiol, Carolin","last_name":"Kosiol"}],"corr_author":"1","fulldoi":"https://doi.org/10.1093/gbe/evad113","has_accepted_license":"1","day":"01","publication_identifier":{"eissn":["1759-6653"]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa_version":"Published Version"},{"page":"230","_id":"14058","citation":{"chicago":"Puixeu Sala, Gemma. “The Molecular Basis of Sexual Dimorphism: Experimental and Theoretical Characterization of Phenotypic, Transcriptomic and Genetic Patterns of Sex-Specific Adaptation.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14058\">https://doi.org/10.15479/at:ista:14058</a>.","ama":"Puixeu Sala G. The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14058\">10.15479/at:ista:14058</a>","apa":"Puixeu Sala, G. (2023). <i>The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14058\">https://doi.org/10.15479/at:ista:14058</a>","ista":"Puixeu Sala G. 2023. The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation. Institute of Science and Technology Austria.","short":"G. Puixeu Sala, The Molecular Basis of Sexual Dimorphism: Experimental and Theoretical Characterization of Phenotypic, Transcriptomic and Genetic Patterns of Sex-Specific Adaptation, Institute of Science and Technology Austria, 2023.","mla":"Puixeu Sala, Gemma. <i>The Molecular Basis of Sexual Dimorphism: Experimental and Theoretical Characterization of Phenotypic, Transcriptomic and Genetic Patterns of Sex-Specific Adaptation</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14058\">10.15479/at:ista:14058</a>.","ieee":"G. Puixeu Sala, “The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation,” Institute of Science and Technology Austria, 2023."},"file":[{"creator":"gpuixeus","checksum":"4e44e169f2724ee8c9324cd60bcc2b71","access_level":"closed","date_created":"2023-08-16T18:15:17Z","date_updated":"2023-08-17T06:55:24Z","content_type":"application/zip","file_name":"Thesis_latex_forpdfa.zip","relation":"source_file","file_size":10891454,"file_id":"14075"},{"file_id":"14079","file_size":19856686,"relation":"main_file","file_name":"PhDThesis_PuixeuG.pdf","content_type":"application/pdf","date_updated":"2023-08-18T10:47:55Z","date_created":"2023-08-18T10:47:55Z","access_level":"open_access","checksum":"e10b04cd8f3fecc0d9ef6e6868b6e1e8","creator":"gpuixeus","success":1}],"date_updated":"2026-04-07T13:25:34Z","oa":1,"title":"The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","doi":"10.15479/at:ista:14058","language":[{"iso":"eng"}],"ddc":["576"],"degree_awarded":"PhD","date_created":"2023-08-15T10:20:40Z","corr_author":"1","fulldoi":"https://doi.org/10.15479/at:ista:14058","OA_place":"publisher","ec_funded":1,"related_material":{"record":[{"status":"public","relation":"research_data","id":"9803"},{"status":"public","id":"12933","relation":"research_data"},{"id":"6831","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"14077"}]},"department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"BeVi"}],"author":[{"orcid":"0000-0001-8330-1754","first_name":"Gemma","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","last_name":"Puixeu Sala","full_name":"Puixeu Sala, Gemma"}],"alternative_title":["ISTA Thesis"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa_version":"Published Version","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-035-0"]},"day":"15","has_accepted_license":"1","type":"dissertation","file_date_updated":"2023-08-18T10:47:55Z","supervisor":[{"full_name":"Vicoso, Beatriz","last_name":"Vicoso","first_name":"Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton"}],"status":"public","date_published":"2023-08-15T00:00:00Z","publication_status":"published","article_processing_charge":"No","year":"2023","publisher":"Institute of Science and Technology Austria","project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385"},{"grant_number":"25817","_id":"9B9DFC9E-BA93-11EA-9121-9846C619BF3A","name":"Sexual conflict: resolution, constraints and biomedical implications"}],"abstract":[{"lang":"eng","text":"Females and males across species are subject to divergent selective pressures arising\r\nfrom di↵erent reproductive interests and ecological niches. This often translates into a\r\nintricate array of sex-specific natural and sexual selection on traits that have a shared\r\ngenetic basis between both sexes, causing a genetic sexual conflict. The resolution of\r\nthis conflict mostly relies on the evolution of sex-specific expression of the shared genes,\r\nleading to phenotypic sexual dimorphism. Such sex-specific gene expression is thought\r\nto evolve via modifications of the genetic networks ultimately linked to sex-determining\r\ntranscription factors. Although much empirical and theoretical evidence supports this\r\nstandard picture of the molecular basis of sexual conflict resolution, there still are a\r\nfew open questions regarding the complex array of selective forces driving phenotypic\r\ndi↵erentiation between the sexes, as well as the molecular mechanisms underlying sexspecific adaptation. I address some of these open questions in my PhD thesis.\r\nFirst, how do patterns of phenotypic sexual dimorphism vary within populations,\r\nas a response to the temporal and spatial changes in sex-specific selective forces? To\r\ntackle this question, I analyze the patterns of sex-specific phenotypic variation along\r\nthree life stages and across populations spanning the whole geographical range of Rumex\r\nhastatulus, a wind-pollinated angiosperm, in the first Chapter of the thesis.\r\nSecond, how do gene expression patterns lead to phenotypic dimorphism, and what\r\nare the molecular mechanisms underlying the observed transcriptomic variation? I\r\naddress this question by examining the sex- and tissue-specific expression variation in\r\nnewly-generated datasets of sex-specific expression in heads and gonads of Drosophila\r\nmelanogaster. I additionally used two complementary approaches for the study of the\r\ngenetic basis of sex di↵erences in gene expression in the second and third Chapters of\r\nthe thesis.\r\nThird, how does intersex correlation, thought to be one of the main aspects constraining the ability for the two sexes to decouple, interact with the evolution of sexual\r\ndimorphism? I develop models of sex-specific stabilizing selection, mutation and drift\r\nto formalize common intuition regarding the patterns of covariation between intersex\r\ncorrelation and sexual dimorphism in the fourth Chapter of the thesis.\r\nAlltogether, the work described in this PhD thesis provides useful insights into the\r\nlinks between genetic, transcriptomic and phenotypic layers of sex-specific variation,\r\nand contributes to our general understanding of the dynamics of sexual dimorphism\r\nevolution."}],"month":"08"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-04-07T13:25:34Z","scopus_import":"1","acknowledged_ssus":[{"_id":"ScienComp"}],"oa":1,"title":"Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster","file":[{"date_created":"2023-11-07T09:00:19Z","access_level":"open_access","file_id":"14498","file_size":845642,"file_name":"2023_G3_Puixeu.pdf","content_type":"application/pdf","relation":"main_file","date_updated":"2023-11-07T09:00:19Z","success":1,"checksum":"c62e29fc7c5efbf8356f4c60cab4a2d1","creator":"dernst"}],"citation":{"ama":"Puixeu Sala G, Macon A, Vicoso B. Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster. <i>G3: Genes, Genomes, Genetics</i>. 2023;13(8). doi:<a href=\"https://doi.org/10.1093/g3journal/jkad121\">10.1093/g3journal/jkad121</a>","chicago":"Puixeu Sala, Gemma, Ariana Macon, and Beatriz Vicoso. “Sex-Specific Estimation of Cis and Trans Regulation of Gene Expression in Heads and Gonads of Drosophila Melanogaster.” <i>G3: Genes, Genomes, Genetics</i>. Oxford University Press, 2023. <a href=\"https://doi.org/10.1093/g3journal/jkad121\">https://doi.org/10.1093/g3journal/jkad121</a>.","apa":"Puixeu Sala, G., Macon, A., &#38; Vicoso, B. (2023). Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster. <i>G3: Genes, Genomes, Genetics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/g3journal/jkad121\">https://doi.org/10.1093/g3journal/jkad121</a>","short":"G. Puixeu Sala, A. Macon, B. Vicoso, G3: Genes, Genomes, Genetics 13 (2023).","ista":"Puixeu Sala G, Macon A, Vicoso B. 2023. Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster. G3: Genes, Genomes, Genetics. 13(8).","ieee":"G. Puixeu Sala, A. Macon, and B. Vicoso, “Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster,” <i>G3: Genes, Genomes, Genetics</i>, vol. 13, no. 8. Oxford University Press, 2023.","mla":"Puixeu Sala, Gemma, et al. “Sex-Specific Estimation of Cis and Trans Regulation of Gene Expression in Heads and Gonads of Drosophila Melanogaster.” <i>G3: Genes, Genomes, Genetics</i>, vol. 13, no. 8, Oxford University Press, 2023, doi:<a href=\"https://doi.org/10.1093/g3journal/jkad121\">10.1093/g3journal/jkad121</a>."},"publication":"G3: Genes, Genomes, Genetics","volume":13,"_id":"14077","quality_controlled":"1","keyword":["Genetics (clinical)","Genetics","Molecular Biology"],"acknowledgement":"We thank members of the Vicoso Group for comments on the manuscript, the Scientific Computing Unit at ISTA for technical support, and 2 anonymous reviewers for useful feedback. 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).","date_created":"2023-08-18T06:52:14Z","issue":"8","external_id":{"isi":["001002997200001"],"pmid":["37259621"]},"pmid":1,"isi":1,"intvolume":"        13","ddc":["570"],"doi":"10.1093/g3journal/jkad121","language":[{"iso":"eng"}],"day":"01","has_accepted_license":"1","oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_identifier":{"issn":["2160-1836"]},"department":[{"_id":"BeVi"},{"_id":"NiBa"},{"_id":"GradSch"}],"author":[{"full_name":"Puixeu Sala, Gemma","last_name":"Puixeu Sala","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8330-1754","first_name":"Gemma"},{"full_name":"Macon, Ariana","last_name":"Macon","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","first_name":"Ariana"},{"full_name":"Vicoso, Beatriz","last_name":"Vicoso","first_name":"Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"relation":"research_data","id":"12933","status":"public"},{"id":"14058","relation":"dissertation_contains","status":"public"}]},"article_type":"original","fulldoi":"https://doi.org/10.1093/g3journal/jkad121","corr_author":"1","ec_funded":1,"month":"08","publisher":"Oxford University Press","article_processing_charge":"Yes","year":"2023","abstract":[{"lang":"eng","text":"The regulatory architecture of gene expression is known to differ substantially between sexes in Drosophila, but most studies performed\r\nso far used whole-body data and only single crosses, which may have limited their scope to detect patterns that are robust across tissues\r\nand biological replicates. Here, we use allele-specific gene expression of parental and reciprocal hybrid crosses between 6 Drosophila\r\nmelanogaster inbred lines to quantify cis- and trans-regulatory variation in heads and gonads of both sexes separately across 3 replicate\r\ncrosses. Our results suggest that female and male heads, as well as ovaries, have a similar regulatory architecture. On the other hand,\r\ntestes display more and substantially different cis-regulatory effects, suggesting that sex differences in the regulatory architecture that\r\nhave been previously observed may largely derive from testis-specific effects. We also examine the difference in cis-regulatory variation\r\nof genes across different levels of sex bias in gonads and heads. Consistent with the idea that intersex correlations constrain expression\r\nand can lead to sexual antagonism, we find more cis variation in unbiased and moderately biased genes in heads. In ovaries, reduced cis\r\nvariation is observed for male-biased genes, suggesting that cis variants acting on these genes in males do not lead to changes in ovary\r\nexpression. Finally, we examine the dominance patterns of gene expression and find that sex- and tissue-specific patterns of inheritance\r\nas well as trans-regulatory variation are highly variable across biological crosses, although these were performed in highly controlled\r\nexperimental conditions. This highlights the importance of using various genetic backgrounds to infer generalizable patterns."}],"project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"},{"_id":"9B9DFC9E-BA93-11EA-9121-9846C619BF3A","name":"Sexual conflict: resolution, constraints and biomedical implications","grant_number":"25817"}],"status":"public","date_published":"2023-08-01T00:00:00Z","publication_status":"published","type":"journal_article","file_date_updated":"2023-11-07T09:00:19Z"},{"date_updated":"2025-09-09T13:32:06Z","scopus_import":"1","oa":1,"title":"The X chromosome of insects likely predates the origin of class Insecta","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","page":"2504-2511","_id":"14604","volume":77,"file":[{"success":1,"checksum":"b66dc10edae92d38918d534e64dda77c","creator":"dernst","date_created":"2023-11-28T08:12:15Z","access_level":"open_access","file_size":1399102,"file_id":"14618","file_name":"2023_Evolution_Toups.pdf","content_type":"application/pdf","relation":"main_file","date_updated":"2023-11-28T08:12:15Z"}],"citation":{"apa":"Toups, M. A., &#38; Vicoso, B. (2023). The X chromosome of insects likely predates the origin of class Insecta. <i>Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/evolut/qpad169\">https://doi.org/10.1093/evolut/qpad169</a>","chicago":"Toups, Melissa A, and Beatriz Vicoso. “The X Chromosome of Insects Likely Predates the Origin of Class Insecta.” <i>Evolution</i>. Oxford University Press, 2023. <a href=\"https://doi.org/10.1093/evolut/qpad169\">https://doi.org/10.1093/evolut/qpad169</a>.","ama":"Toups MA, Vicoso B. The X chromosome of insects likely predates the origin of class Insecta. <i>Evolution</i>. 2023;77(11):2504-2511. doi:<a href=\"https://doi.org/10.1093/evolut/qpad169\">10.1093/evolut/qpad169</a>","ieee":"M. A. Toups and B. Vicoso, “The X chromosome of insects likely predates the origin of class Insecta,” <i>Evolution</i>, vol. 77, no. 11. Oxford University Press, pp. 2504–2511, 2023.","mla":"Toups, Melissa A., and Beatriz Vicoso. “The X Chromosome of Insects Likely Predates the Origin of Class Insecta.” <i>Evolution</i>, vol. 77, no. 11, Oxford University Press, 2023, pp. 2504–11, doi:<a href=\"https://doi.org/10.1093/evolut/qpad169\">10.1093/evolut/qpad169</a>.","ista":"Toups MA, Vicoso B. 2023. The X chromosome of insects likely predates the origin of class Insecta. Evolution. 77(11), 2504–2511.","short":"M.A. Toups, B. Vicoso, Evolution 77 (2023) 2504–2511."},"publication":"Evolution","issue":"11","external_id":{"pmid":["37738212"],"isi":["001170341900014"]},"pmid":1,"quality_controlled":"1","acknowledgement":"All computational analyses were performed on the server at Institute of Science and Technology Austria. We thank Marwan Elkrewi and Vincent Bett for analytical advice, and Tanja Schwander and Vincent Merel for useful discussions. We also thank Matthew Hahn for comments on an earlier version of the manuscript.","date_created":"2023-11-26T23:00:54Z","doi":"10.1093/evolut/qpad169","language":[{"iso":"eng"}],"isi":1,"intvolume":"        77","ddc":["570"],"oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_identifier":{"eissn":["1558-5646"]},"day":"02","has_accepted_license":"1","fulldoi":"https://doi.org/10.1093/evolut/qpad169","department":[{"_id":"BeVi"}],"author":[{"last_name":"Toups","full_name":"Toups, Melissa A","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9752-7380","first_name":"Melissa A"},{"first_name":"Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","full_name":"Vicoso, Beatriz"}],"related_material":{"link":[{"relation":"software","url":"https://git.ista.ac.at/bvicoso/veryoldx"}],"record":[{"status":"public","id":"14616","relation":"research_data"},{"id":"14617","relation":"research_data","status":"public"}]},"article_type":"original","publisher":"Oxford University Press","year":"2023","article_processing_charge":"Yes (in subscription journal)","abstract":[{"text":"Sex chromosomes have evolved independently multiple times, but why some are conserved for more than 100 million years whereas others turnover rapidly remains an open question. Here, we examine the homology of sex chromosomes across nine orders of insects, plus the outgroup springtails. We find that the X chromosome is likely homologous across insects and springtails; the only exception is in the Lepidoptera, which has lost the X and now has a ZZ/ZW sex-chromosome system. These results suggest the ancestral insect X chromosome has persisted for more than 450 million years—the oldest known sex chromosome to date. Further, we propose that the shrinking of gene content the dipteran X chromosome has allowed for a burst of sex-chromosome turnover that is absent from other speciose insect orders.","lang":"eng"}],"month":"11","type":"journal_article","file_date_updated":"2023-11-28T08:12:15Z","status":"public","date_published":"2023-11-02T00:00:00Z","publication_status":"published"},{"title":"The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome","oa":1,"date_updated":"2025-09-09T13:33:22Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa_version":"Published Version","day":"01","has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14614","fulldoi":"https://doi.org/10.15479/AT:ISTA:14614","corr_author":"1","author":[{"full_name":"Lasne, Clementine","last_name":"Lasne","first_name":"Clementine","orcid":"0000-0002-1197-8616","id":"02225f57-50d2-11eb-9ed8-8c92b9a34237"},{"full_name":"Elkrewi, Marwan N","last_name":"Elkrewi","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","first_name":"Marwan N","orcid":"0000-0002-5328-7231"}],"department":[{"_id":"BeVi"}],"file":[{"date_updated":"2023-11-28T13:15:26Z","file_size":404968272,"file_id":"14625","content_type":"application/zip","file_name":"panorpaX.zip","relation":"main_file","date_created":"2023-11-28T13:15:26Z","access_level":"open_access","creator":"clasne","checksum":"cd0f13322b5156819ecaebd2bc8e7d12","success":1},{"date_created":"2023-11-30T14:16:59Z","access_level":"open_access","date_updated":"2023-11-30T14:16:59Z","file_size":2625,"file_id":"14634","file_name":"panorpa_readme.txt","relation":"main_file","content_type":"text/plain","success":1,"creator":"clasne","checksum":"9ff600416577687a737cb3c96dfcb26c"}],"citation":{"chicago":"Lasne, Clementine, and Marwan N Elkrewi. “The Scorpionfly (Panorpa Cognata) Genome Highlights Conserved and Derived Features of the Peculiar Dipteran X Chromosome.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/AT:ISTA:14614\">https://doi.org/10.15479/AT:ISTA:14614</a>.","ama":"Lasne C, Elkrewi MN. The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome. 2023. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:14614\">10.15479/AT:ISTA:14614</a>","apa":"Lasne, C., &#38; Elkrewi, M. N. (2023). The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:14614\">https://doi.org/10.15479/AT:ISTA:14614</a>","ista":"Lasne C, Elkrewi MN. 2023. The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:14614\">10.15479/AT:ISTA:14614</a>.","short":"C. Lasne, M.N. Elkrewi, (2023).","ieee":"C. Lasne and M. N. Elkrewi, “The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome.” Institute of Science and Technology Austria, 2023.","mla":"Lasne, Clementine, and Marwan N. Elkrewi. <i>The Scorpionfly (Panorpa Cognata) Genome Highlights Conserved and Derived Features of the Peculiar Dipteran X Chromosome</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:14614\">10.15479/AT:ISTA:14614</a>."},"related_material":{"record":[{"status":"public","id":"14613","relation":"used_in_publication"}]},"abstract":[{"text":"Many insects carry an ancient X chromosome—the Drosophila Muller element F—that likely predates their origin. Interestingly, the X has undergone turnover in multiple fly species (Diptera) after being conserved for more than 450 My. The long evolutionary distance between Diptera and other sequenced insect clades makes it difficult to infer what could have contributed to this sudden increase in rate of turnover. Here, we produce the first genome and transcriptome of scorpionflies (genus Panorpa), an insect belonging to a long overlooked sister-order to Diptera: Mecoptera. Combining our genome assembly with genomic short-read data, we obtain genome coverage and identify X-linked super-scaffolds. We further perform a gene homology analysis between the Panorpa X and a closely related Diptera species, and we assess the conservation of the Panorpa X-linked gene content with that of more distantly related insect species. We explored the structure of the Panorpa X by determining its repeat content, GC content, and nucleotide diversity. Finally, we used RNAseq data to detect the presence of dosage compensation in somatic tissues, as well as to explore gene expression tissue-specificity, and sex-bias in gene expression. We find high conservation of gene content between the mecopteran X and the dipteran Muller F element, as well as several shared biological features, such as the presence of dosage compensation and a low amount of genetic diversity, consistent with a low recombination rate. However, the 2 homologous X chromosomes differ strikingly in their size and number of genes they carry. Our results therefore support a common ancestry of the mecopteran and ancestral dipteran X chromosomes, and suggest that Muller element F shrank in size and gene content after the split of Diptera and Mecoptera, which may have contributed to its turnover in dipteran insects.","lang":"eng"}],"publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","year":"2023","keyword":["Panorpa","scorpionfly","genome","transcriptome"],"date_created":"2023-11-27T16:39:19Z","contributor":[{"orcid":"0000-0002-5328-7231","first_name":"Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","last_name":"Elkrewi","contributor_type":"researcher"}],"month":"12","file_date_updated":"2023-11-30T14:16:59Z","type":"research_data","doi":"10.15479/AT:ISTA:14614","ddc":["576"],"date_published":"2023-12-01T00:00:00Z","status":"public"},{"doi":"10.5061/DRYAD.HX3FFBGKT","type":"research_data_reference","ddc":["570"],"date_published":"2023-09-15T00:00:00Z","status":"public","abstract":[{"lang":"eng","text":"Sex chromosomes have evolved independently multiple times, but why some are conserved for more than 100 million years whereas others turnover rapidly remains an open question. Here, we examine the homology of sex chromosomes across nine orders of insects, plus the outgroup springtails. We find that the X chromosome is likely homologous across insects and springtails; the only exception is in the Lepidoptera, which has lost the X and now has a ZZ/ZW sex chromosome system. These results suggest the ancestral insect X chromosome has persisted for more than 450 million years – the oldest known sex chromosome to date. Further, we propose that the shrinking of gene content of the Dipteran X chromosome has allowed for a burst of sex-chromosome turnover that is absent from other speciose insect orders."}],"year":"2023","article_processing_charge":"No","publisher":"Dryad","date_created":"2023-11-28T08:01:53Z","month":"09","_id":"14616","fulldoi":"https://doi.org/10.5061/DRYAD.HX3FFBGKT","related_material":{"record":[{"id":"14604","relation":"used_in_publication","status":"public"}]},"citation":{"apa":"Toups, M. A., &#38; Vicoso, B. (2023). The X chromosome of insects likely predates the origin of Class Insecta. Dryad. <a href=\"https://doi.org/10.5061/DRYAD.HX3FFBGKT\">https://doi.org/10.5061/DRYAD.HX3FFBGKT</a>","chicago":"Toups, Melissa A, and Beatriz Vicoso. “The X Chromosome of Insects Likely Predates the Origin of Class Insecta.” Dryad, 2023. <a href=\"https://doi.org/10.5061/DRYAD.HX3FFBGKT\">https://doi.org/10.5061/DRYAD.HX3FFBGKT</a>.","ama":"Toups MA, Vicoso B. The X chromosome of insects likely predates the origin of Class Insecta. 2023. doi:<a href=\"https://doi.org/10.5061/DRYAD.HX3FFBGKT\">10.5061/DRYAD.HX3FFBGKT</a>","mla":"Toups, Melissa A., and Beatriz Vicoso. <i>The X Chromosome of Insects Likely Predates the Origin of Class Insecta</i>. Dryad, 2023, doi:<a href=\"https://doi.org/10.5061/DRYAD.HX3FFBGKT\">10.5061/DRYAD.HX3FFBGKT</a>.","ieee":"M. A. Toups and B. Vicoso, “The X chromosome of insects likely predates the origin of Class Insecta.” Dryad, 2023.","ista":"Toups MA, Vicoso B. 2023. The X chromosome of insects likely predates the origin of Class Insecta, Dryad, <a href=\"https://doi.org/10.5061/DRYAD.HX3FFBGKT\">10.5061/DRYAD.HX3FFBGKT</a>.","short":"M.A. Toups, B. Vicoso, (2023)."},"department":[{"_id":"BeVi"}],"author":[{"id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9752-7380","first_name":"Melissa A","last_name":"Toups","full_name":"Toups, Melissa A"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","orcid":"0000-0002-4579-8306","last_name":"Vicoso","full_name":"Vicoso, Beatriz"}],"title":"The X chromosome of insects likely predates the origin of Class Insecta","oa":1,"license":"https://creativecommons.org/publicdomain/zero/1.0/","tmp":{"image":"/images/cc_0.png","short":"CC0 (1.0)","name":"Creative Commons Public Domain Dedication (CC0 1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode"},"date_updated":"2025-09-09T13:32:05Z","oa_version":"Published Version","has_accepted_license":"1","day":"15","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"https://doi.org/10.5061/dryad.hx3ffbgkt","open_access":"1"}]},{"type":"research_data_reference","doi":"10.5281/ZENODO.8138705","ddc":["570"],"date_published":"2023-09-15T00:00:00Z","status":"public","abstract":[{"lang":"eng","text":"Sex chromosomes have evolved independently multiple times, but why some are conserved for more than 100 million years whereas others turnover rapidly remains an open question. Here, we examine the homology of sex chromosomes across nine orders of insects, plus the outgroup springtails. We find that the X chromosome is likely homologous across insects and springtails; the only exception is in the Lepidoptera, which has lost the X and now has a ZZ/ZW sex chromosome system. These results suggest the ancestral insect X chromosome has persisted for more than 450 million years – the oldest known sex chromosome to date. Further, we propose that the shrinking of gene content of the Dipteran X chromosome has allowed for a burst of sex-chromosome turnover that is absent from other speciose insect orders."}],"publisher":"Zenodo","year":"2023","article_processing_charge":"No","date_created":"2023-11-28T08:04:03Z","month":"09","_id":"14617","fulldoi":"https://doi.org/10.5281/ZENODO.8138705","author":[{"first_name":"Melissa A","orcid":"0000-0002-9752-7380","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","last_name":"Toups","full_name":"Toups, Melissa A"},{"orcid":"0000-0002-4579-8306","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","full_name":"Vicoso, Beatriz"}],"department":[{"_id":"BeVi"}],"citation":{"ieee":"M. A. Toups and B. Vicoso, “The X chromosome of insects likely predates the origin of Class Insecta.” Zenodo, 2023.","mla":"Toups, Melissa A., and Beatriz Vicoso. <i>The X Chromosome of Insects Likely Predates the Origin of Class Insecta</i>. Zenodo, 2023, doi:<a href=\"https://doi.org/10.5281/ZENODO.8138705\">10.5281/ZENODO.8138705</a>.","short":"M.A. Toups, B. Vicoso, (2023).","ista":"Toups MA, Vicoso B. 2023. The X chromosome of insects likely predates the origin of Class Insecta, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.8138705\">10.5281/ZENODO.8138705</a>.","apa":"Toups, M. A., &#38; Vicoso, B. (2023). The X chromosome of insects likely predates the origin of Class Insecta. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.8138705\">https://doi.org/10.5281/ZENODO.8138705</a>","ama":"Toups MA, Vicoso B. The X chromosome of insects likely predates the origin of Class Insecta. 2023. doi:<a href=\"https://doi.org/10.5281/ZENODO.8138705\">10.5281/ZENODO.8138705</a>","chicago":"Toups, Melissa A, and Beatriz Vicoso. “The X Chromosome of Insects Likely Predates the Origin of Class Insecta.” Zenodo, 2023. <a href=\"https://doi.org/10.5281/ZENODO.8138705\">https://doi.org/10.5281/ZENODO.8138705</a>."},"related_material":{"record":[{"id":"14604","relation":"used_in_publication","status":"public"}]},"title":"The X chromosome of insects likely predates the origin of Class Insecta","oa":1,"date_updated":"2025-09-09T13:32:05Z","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"15","has_accepted_license":"1","main_file_link":[{"url":"https://doi.org/10.5281/zenodo.8138705","open_access":"1"}],"other_data_license":"MIT License"}]