[{"oa_version":"Published Version","type":"research_data","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, 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."}],"date_updated":"2025-07-24T11:06:43Z","date_created":"2023-12-22T13:40:48Z","file_date_updated":"2023-12-22T14:14:06Z","year":"2024","_id":"14705","oa":1,"has_accepted_license":"1","ddc":["576"],"date_published":"2024-01-02T00:00:00Z","status":"public","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"15009"}]},"citation":{"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.","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>.","short":"M.N. Elkrewi, (2024).","ama":"Elkrewi MN. Data from “Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation.” 2024. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:14705\">10.15479/AT:ISTA:14705</a>","ista":"Elkrewi MN. 2024. Data from ‘Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:14705\">10.15479/AT:ISTA:14705</a>.","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>.","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>"},"author":[{"first_name":"Marwan N","last_name":"Elkrewi","full_name":"Elkrewi, Marwan N","orcid":"0000-0002-5328-7231","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425"}],"license":"https://creativecommons.org/licenses/by/4.0/","day":"02","file":[{"checksum":"bdaf1392867786634ec5466d528c36ca","file_id":"14707","date_updated":"2023-12-22T13:54:21Z","access_level":"open_access","date_created":"2023-12-22T13:54:21Z","file_name":"readme.txt.txt","success":1,"creator":"melkrewi","file_size":847,"content_type":"text/plain","relation":"main_file"},{"success":1,"file_name":"data_artemia_franciscana_genome.zip","relation":"main_file","content_type":"application/x-zip-compressed","file_size":343632753,"creator":"melkrewi","date_updated":"2023-12-22T14:14:06Z","file_id":"14708","checksum":"973e1cbdab923a71709782177980829f","date_created":"2023-12-22T14:14:06Z","access_level":"open_access"}],"title":"Data from \"Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation\"","publisher":"Institute of Science and Technology Austria","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_processing_charge":"No","retracted":"1","contributor":[{"contributor_type":"researcher","first_name":"Vincent K","last_name":"Bett","id":"57854184-AAE0-11E9-8D04-98D6E5697425"},{"id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member","first_name":"Ariana","last_name":"Macon"},{"orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","contributor_type":"supervisor","last_name":"Vicoso"},{"last_name":"Elkrewi","first_name":"Marwan N","contributor_type":"researcher","orcid":"0000-0002-5328-7231","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425"}],"doi":"10.15479/AT:ISTA:14705","project":[{"name":"The highjacking of meiosis for asexual reproduction","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","grant_number":"F8810"}],"keyword":["sex chromosome evolution","genome assembly","dosage compensation"]},{"oa_version":"Published Version","month":"01","type":"journal_article","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, 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.","lang":"eng"}],"date_updated":"2025-07-24T11:06:42Z","date_created":"2024-02-18T23:01:02Z","file_date_updated":"2024-02-26T09:54:59Z","volume":16,"year":"2024","_id":"15009","has_accepted_license":"1","publication_status":"published","oa":1,"ddc":["570"],"date_published":"2024-01-20T00:00:00Z","external_id":{"pmid":["38245839"]},"status":"public","citation":{"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>.","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.","short":"V.K. Bett, A. Macon, B. Vicoso, M.N. Elkrewi, Genome Biology and Evolution 16 (2024).","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>","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>","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>."},"related_material":{"record":[{"id":"14705","status":"public","relation":"research_data"}]},"intvolume":"        16","file":[{"date_updated":"2024-02-26T09:54:59Z","file_id":"15029","checksum":"106a40f10443b2e7ba66749844ebbdf1","date_created":"2024-02-26T09:54:59Z","access_level":"open_access","success":1,"file_name":"2024_GBE_Bett.pdf","relation":"main_file","content_type":"application/pdf","file_size":5213306,"creator":"dernst"}],"day":"20","author":[{"first_name":"Vincent K","last_name":"Bett","full_name":"Bett, Vincent K","id":"57854184-AAE0-11E9-8D04-98D6E5697425"},{"last_name":"Macon","first_name":"Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","full_name":"Macon, Ariana"},{"last_name":"Vicoso","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz"},{"last_name":"Elkrewi","first_name":"Marwan N","full_name":"Elkrewi, Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","orcid":"0000-0002-5328-7231"}],"article_number":"evae006","title":"Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation","department":[{"_id":"BeVi"}],"pmid":1,"publisher":"Oxford University Press","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"scopus_import":"1","article_processing_charge":"Yes","publication":"Genome Biology and Evolution","publication_identifier":{"eissn":["1759-6653"]},"quality_controlled":"1","doi":"10.1093/gbe/evae006","issue":"1","language":[{"iso":"eng"}]},{"issue":"2","language":[{"iso":"eng"}],"isi":1,"publication_identifier":{"eissn":["1752-4571"]},"quality_controlled":"1","doi":"10.1111/eva.13428","department":[{"_id":"NiBa"},{"_id":"BeVi"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Wiley","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","article_processing_charge":"No","scopus_import":"1","publication":"Evolutionary Applications","file":[{"date_created":"2023-02-27T07:10:17Z","access_level":"open_access","date_updated":"2023-02-27T07:10:17Z","file_id":"12685","checksum":"d4d6fa9ddf36643af994a6a757919afb","content_type":"application/pdf","relation":"main_file","file_size":2269822,"creator":"dernst","success":1,"file_name":"2023_EvolutionaryApplications_DeJode.pdf"}],"day":"01","author":[{"full_name":"De Jode, Aurélien","last_name":"De Jode","first_name":"Aurélien"},{"full_name":"Le Moan, Alan","first_name":"Alan","last_name":"Le Moan"},{"full_name":"Johannesson, Kerstin","last_name":"Johannesson","first_name":"Kerstin"},{"first_name":"Rui","last_name":"Faria","full_name":"Faria, Rui"},{"first_name":"Sean","last_name":"Stankowski","id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean"},{"first_name":"Anja M","last_name":"Westram","full_name":"Westram, Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969"},{"first_name":"Roger K.","last_name":"Butlin","full_name":"Butlin, Roger K."},{"last_name":"Rafajlović","first_name":"Marina","full_name":"Rafajlović, Marina"},{"first_name":"Christelle","last_name":"Fraisse","full_name":"Fraisse, Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075"}],"title":"Ten years of demographic modelling of divergence and speciation in the sea","external_id":{"isi":["000815663700001"]},"status":"public","citation":{"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.","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>.","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.","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>","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.","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>.","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>"},"intvolume":"        16","has_accepted_license":"1","publication_status":"published","oa":1,"ddc":["576"],"date_published":"2023-02-01T00:00:00Z","year":"2023","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).","_id":"11479","type":"journal_article","oa_version":"Published Version","month":"02","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."}],"date_updated":"2023-08-01T12:25:44Z","page":"542-559","date_created":"2022-07-03T22:01:33Z","file_date_updated":"2023-02-27T07:10:17Z","volume":16},{"file":[{"date_created":"2023-11-28T08:12:15Z","access_level":"open_access","file_id":"14618","date_updated":"2023-11-28T08:12:15Z","checksum":"b66dc10edae92d38918d534e64dda77c","file_size":1399102,"relation":"main_file","content_type":"application/pdf","creator":"dernst","file_name":"2023_Evolution_Toups.pdf","success":1}],"day":"02","author":[{"full_name":"Toups, Melissa A","orcid":"0000-0002-9752-7380","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","first_name":"Melissa A","last_name":"Toups"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","last_name":"Vicoso","first_name":"Beatriz"}],"title":"The X chromosome of insects likely predates the origin of class Insecta","pmid":1,"department":[{"_id":"BeVi"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Oxford University Press","article_processing_charge":"Yes (in subscription journal)","scopus_import":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","publication":"Evolution","publication_identifier":{"eissn":["1558-5646"]},"quality_controlled":"1","doi":"10.1093/evolut/qpad169","language":[{"iso":"eng"}],"issue":"11","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 the dipteran X chromosome has allowed for a burst of sex-chromosome turnover that is absent from other speciose insect orders."}],"date_updated":"2023-11-28T08:25:28Z","oa_version":"Published Version","type":"journal_article","month":"11","page":"2504-2511","date_created":"2023-11-26T23:00:54Z","file_date_updated":"2023-11-28T08:12:15Z","volume":77,"year":"2023","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.","_id":"14604","has_accepted_license":"1","oa":1,"publication_status":"published","ddc":["570"],"date_published":"2023-11-02T00:00:00Z","external_id":{"pmid":["37738212"]},"status":"public","citation":{"short":"M.A. Toups, B. Vicoso, Evolution 77 (2023) 2504–2511.","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.","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>.","ista":"Toups MA, Vicoso B. 2023. The X chromosome of insects likely predates the origin of class Insecta. Evolution. 77(11), 2504–2511.","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>.","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>","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>"},"intvolume":"        77","related_material":{"link":[{"url":"https://git.ista.ac.at/bvicoso/veryoldx","relation":"software"}],"record":[{"id":"14616","status":"public","relation":"research_data"},{"relation":"research_data","status":"public","id":"14617"}]}},{"acknowledgement":"We thank the Vicoso lab for their assistance with specimen collection, and Tim Connallon for valuable comments and suggestions on earlier versions of the manuscript. Computational resources and support were provided by the Scientific Computing unit at the ISTA. This research was supported by grants from the Austrian Science Foundation to C.L.\r\n(FWF ESP 39), and to B.V. (FWF SFB F88-10).","year":"2023","_id":"14613","month":"12","type":"journal_article","oa_version":"Published Version","date_updated":"2024-02-21T12:18:35Z","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 a long overlooked sister-order to Diptera: Mecoptera. We compare the scorpionfly Panorpa cognata X-chromosome gene content, expression, and structure, to that of several dipteran species as well as more distantly-related insect orders (Orthoptera and Blattodea). We find high conservation of gene content between the mecopteran X and the dipteran Muller F element, as well as several shared biological features, such as the presence of dosage compensation and a low amount of genetic diversity, consistent with a low recombination rate. However, the two homologous X chromosomes differ strikingly in their size and number of genes they carry. Our results therefore support a common ancestry of the mecopteran and ancestral dipteran X chromosomes, and suggest that Muller element F shrank in size and gene content after the split of Diptera and Mecoptera, which may have contributed to its turnover in dipteran insects.","lang":"eng"}],"volume":40,"file_date_updated":"2024-01-02T11:39:38Z","date_created":"2023-11-27T16:14:37Z","external_id":{"pmid":["37988296"]},"status":"public","intvolume":"        40","related_material":{"record":[{"relation":"research_data","id":"14614","status":"public"}],"link":[{"url":"https://ista.ac.at/en/news/on-the-hunt/","description":"News on ISTA webpage","relation":"press_release"}]},"citation":{"ista":"Lasne C, Elkrewi MN, Toups MA, Layana Franco LA, Macon A, Vicoso B. 2023. The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome. Molecular Biology and Evolution. 40(12), msad245.","mla":"Lasne, Clementine, et al. “The Scorpionfly (Panorpa Cognata) Genome Highlights Conserved and Derived Features of the Peculiar Dipteran X Chromosome.” <i>Molecular Biology and Evolution</i>, vol. 40, no. 12, msad245, Oxford University Press, 2023, doi:<a href=\"https://doi.org/10.1093/molbev/msad245\">10.1093/molbev/msad245</a>.","apa":"Lasne, C., Elkrewi, M. N., Toups, M. A., Layana Franco, L. A., Macon, A., &#38; Vicoso, B. (2023). The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msad245\">https://doi.org/10.1093/molbev/msad245</a>","ama":"Lasne C, Elkrewi MN, Toups MA, Layana Franco LA, Macon A, Vicoso B. The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome. <i>Molecular Biology and Evolution</i>. 2023;40(12). doi:<a href=\"https://doi.org/10.1093/molbev/msad245\">10.1093/molbev/msad245</a>","short":"C. Lasne, M.N. Elkrewi, M.A. Toups, L.A. Layana Franco, A. Macon, B. Vicoso, Molecular Biology and Evolution 40 (2023).","ieee":"C. Lasne, M. N. Elkrewi, M. A. Toups, L. A. Layana Franco, A. Macon, and B. Vicoso, “The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome,” <i>Molecular Biology and Evolution</i>, vol. 40, no. 12. Oxford University Press, 2023.","chicago":"Lasne, Clementine, Marwan N Elkrewi, Melissa A Toups, Lorena Alexandra Layana Franco, Ariana Macon, and Beatriz Vicoso. “The Scorpionfly (Panorpa Cognata) Genome Highlights Conserved and Derived Features of the Peculiar Dipteran X Chromosome.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2023. <a href=\"https://doi.org/10.1093/molbev/msad245\">https://doi.org/10.1093/molbev/msad245</a>."},"publication_status":"published","oa":1,"has_accepted_license":"1","ddc":["570"],"date_published":"2023-12-01T00:00:00Z","acknowledged_ssus":[{"_id":"ScienComp"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Oxford University Press","department":[{"_id":"BeVi"}],"pmid":1,"publication":"Molecular Biology and Evolution","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","scopus_import":"1","article_processing_charge":"Yes (via OA deal)","author":[{"last_name":"Lasne","first_name":"Clementine","orcid":"0000-0002-1197-8616","id":"02225f57-50d2-11eb-9ed8-8c92b9a34237","full_name":"Lasne, Clementine"},{"first_name":"Marwan N","last_name":"Elkrewi","orcid":"0000-0002-5328-7231","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","full_name":"Elkrewi, Marwan N"},{"id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9752-7380","full_name":"Toups, Melissa A","first_name":"Melissa A","last_name":"Toups"},{"full_name":"Layana Franco, Lorena Alexandra","id":"02814589-eb8f-11eb-b029-a70074f3f18f","orcid":"0000-0002-1253-6297","last_name":"Layana Franco","first_name":"Lorena Alexandra"},{"full_name":"Macon, Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","last_name":"Macon","first_name":"Ariana"},{"full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","last_name":"Vicoso","first_name":"Beatriz"}],"day":"01","file":[{"date_created":"2024-01-02T11:39:38Z","access_level":"open_access","date_updated":"2024-01-02T11:39:38Z","file_id":"14727","checksum":"47c1c72fb499f26ea52d216b242208c8","content_type":"application/pdf","relation":"main_file","file_size":8623505,"creator":"dernst","success":1,"file_name":"2023_MolecularBioEvo_Lasne.pdf"}],"article_number":"msad245","title":"The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome","project":[{"name":"The highjacking of meiosis for asexual reproduction","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","grant_number":"F8810"},{"grant_number":"ESP39 49461","_id":"ebb230e0-77a9-11ec-83b8-87a37e0241d3","name":"Mechanisms and Evolution of Reproductive Plasticity"}],"keyword":["Genetics","Molecular Biology","Ecology","Evolution","Behavior and Systematics"],"issue":"12","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1537-1719"],"issn":["0737-4038"]},"doi":"10.1093/molbev/msad245","quality_controlled":"1"},{"citation":{"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>","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>.","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>.","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>","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.","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>.","short":"C. Lasne, M.N. Elkrewi, (2023)."},"related_material":{"record":[{"id":"14613","status":"public","relation":"used_in_publication"}]},"keyword":["Panorpa","scorpionfly","genome","transcriptome"],"status":"public","ddc":["576"],"doi":"10.15479/AT:ISTA:14614","contributor":[{"id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","orcid":"0000-0002-5328-7231","contributor_type":"researcher","first_name":"Marwan N","last_name":"Elkrewi"}],"date_published":"2023-12-01T00:00:00Z","has_accepted_license":"1","oa":1,"article_processing_charge":"No","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"14614","department":[{"_id":"BeVi"}],"year":"2023","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Institute of Science and Technology Austria","date_created":"2023-11-27T16:39:19Z","file_date_updated":"2023-11-30T14:16:59Z","title":"The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome","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"}],"file":[{"file_name":"panorpaX.zip","success":1,"file_size":404968272,"relation":"main_file","content_type":"application/zip","creator":"clasne","file_id":"14625","date_updated":"2023-11-28T13:15:26Z","checksum":"cd0f13322b5156819ecaebd2bc8e7d12","date_created":"2023-11-28T13:15:26Z","access_level":"open_access"},{"file_name":"panorpa_readme.txt","success":1,"creator":"clasne","file_size":2625,"content_type":"text/plain","relation":"main_file","checksum":"9ff600416577687a737cb3c96dfcb26c","file_id":"14634","date_updated":"2023-11-30T14:16:59Z","access_level":"open_access","date_created":"2023-11-30T14:16:59Z"}],"day":"01","date_updated":"2024-02-21T12:18:35Z","oa_version":"Published Version","month":"12","type":"research_data","author":[{"id":"02225f57-50d2-11eb-9ed8-8c92b9a34237","orcid":"0000-0002-1197-8616","full_name":"Lasne, Clementine","last_name":"Lasne","first_name":"Clementine"},{"first_name":"Marwan N","last_name":"Elkrewi","full_name":"Elkrewi, Marwan N","orcid":"0000-0002-5328-7231","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425"}]},{"article_processing_charge":"No","tmp":{"name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode"},"_id":"14616","year":"2023","department":[{"_id":"BeVi"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Dryad","date_created":"2023-11-28T08:01:53Z","title":"The X chromosome of insects likely predates the origin of Class Insecta","date_updated":"2023-11-28T08:17:31Z","license":"https://creativecommons.org/publicdomain/zero/1.0/","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 of the Dipteran X chromosome has allowed for a burst of sex-chromosome turnover that is absent from other speciose insect orders.","lang":"eng"}],"day":"15","month":"09","oa_version":"Published Version","type":"research_data_reference","author":[{"id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9752-7380","full_name":"Toups, Melissa A","last_name":"Toups","first_name":"Melissa A"},{"orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz","last_name":"Vicoso","first_name":"Beatriz"}],"citation":{"ieee":"M. A. Toups and B. Vicoso, “The X chromosome of insects likely predates the origin of Class Insecta.” Dryad, 2023.","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>.","short":"M.A. Toups, B. Vicoso, (2023).","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>.","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>.","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>"},"related_material":{"record":[{"relation":"used_in_publication","id":"14604","status":"public"}]},"status":"public","main_file_link":[{"url":"https://doi.org/10.5061/dryad.hx3ffbgkt","open_access":"1"}],"date_published":"2023-09-15T00:00:00Z","ddc":["570"],"doi":"10.5061/DRYAD.HX3FFBGKT","has_accepted_license":"1","oa":1},{"date_created":"2023-11-28T08:04:03Z","title":"The X chromosome of insects likely predates the origin of Class Insecta","month":"09","oa_version":"Published Version","type":"research_data_reference","date_updated":"2023-11-28T08:25:28Z","day":"15","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 of the Dipteran X chromosome has allowed for a burst of sex-chromosome turnover that is absent from other speciose insect orders.","lang":"eng"}],"author":[{"id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9752-7380","full_name":"Toups, Melissa A","first_name":"Melissa A","last_name":"Toups"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","first_name":"Beatriz","last_name":"Vicoso"}],"article_processing_charge":"No","_id":"14617","department":[{"_id":"BeVi"}],"year":"2023","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Zenodo","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.8138705"}],"doi":"10.5281/ZENODO.8138705","date_published":"2023-09-15T00:00:00Z","ddc":["570"],"has_accepted_license":"1","oa":1,"other_data_license":"MIT License","citation":{"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>.","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>","short":"M.A. Toups, B. Vicoso, (2023).","ieee":"M. A. Toups and B. Vicoso, “The X chromosome of insects likely predates the origin of Class Insecta.” Zenodo, 2023.","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":[{"status":"public","id":"14604","relation":"used_in_publication"}]},"status":"public"},{"quality_controlled":"1","doi":"10.1101/cshperspect.a041447","publication_identifier":{"issn":["1943-0264"]},"issue":"11","language":[{"iso":"eng"}],"keyword":["General Biochemistry","Genetics and Molecular Biology"],"article_number":"a041447","title":"The impact of chromosomal rearrangements in speciation: From micro- to macroevolution","day":"01","author":[{"last_name":"Lucek","first_name":"Kay","full_name":"Lucek, Kay"},{"last_name":"Giménez","first_name":"Mabel D.","full_name":"Giménez, Mabel D."},{"full_name":"Joron, Mathieu","first_name":"Mathieu","last_name":"Joron"},{"first_name":"Marina","last_name":"Rafajlović","full_name":"Rafajlović, Marina"},{"full_name":"Searle, Jeremy B.","first_name":"Jeremy B.","last_name":"Searle"},{"first_name":"Nora","last_name":"Walden","full_name":"Walden, Nora"},{"full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M","last_name":"Westram"},{"last_name":"Faria","first_name":"Rui","full_name":"Faria, Rui"}],"article_type":"original","scopus_import":"1","article_processing_charge":"No","publication":"Cold Spring Harbor Perspectives in Biology","department":[{"_id":"NiBa"},{"_id":"BeVi"}],"pmid":1,"publisher":"Cold Spring Harbor Laboratory","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/cshperspect.a041447"}],"date_published":"2023-11-01T00:00:00Z","publication_status":"published","oa":1,"citation":{"short":"K. Lucek, M.D. Giménez, M. Joron, M. Rafajlović, J.B. Searle, N. Walden, A.M. Westram, R. Faria, Cold Spring Harbor Perspectives in Biology 15 (2023).","chicago":"Lucek, Kay, Mabel D. Giménez, Mathieu Joron, Marina Rafajlović, Jeremy B. Searle, Nora Walden, Anja M Westram, and Rui Faria. “The Impact of Chromosomal Rearrangements in Speciation: From Micro- to Macroevolution.” <i>Cold Spring Harbor Perspectives in Biology</i>. Cold Spring Harbor Laboratory, 2023. <a href=\"https://doi.org/10.1101/cshperspect.a041447\">https://doi.org/10.1101/cshperspect.a041447</a>.","ieee":"K. Lucek <i>et al.</i>, “The impact of chromosomal rearrangements in speciation: From micro- to macroevolution,” <i>Cold Spring Harbor Perspectives in Biology</i>, vol. 15, no. 11. Cold Spring Harbor Laboratory, 2023.","apa":"Lucek, K., Giménez, M. D., Joron, M., Rafajlović, M., Searle, J. B., Walden, N., … Faria, R. (2023). The impact of chromosomal rearrangements in speciation: From micro- to macroevolution. <i>Cold Spring Harbor Perspectives in Biology</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/cshperspect.a041447\">https://doi.org/10.1101/cshperspect.a041447</a>","ista":"Lucek K, Giménez MD, Joron M, Rafajlović M, Searle JB, Walden N, Westram AM, Faria R. 2023. The impact of chromosomal rearrangements in speciation: From micro- to macroevolution. Cold Spring Harbor Perspectives in Biology. 15(11), a041447.","mla":"Lucek, Kay, et al. “The Impact of Chromosomal Rearrangements in Speciation: From Micro- to Macroevolution.” <i>Cold Spring Harbor Perspectives in Biology</i>, vol. 15, no. 11, a041447, Cold Spring Harbor Laboratory, 2023, doi:<a href=\"https://doi.org/10.1101/cshperspect.a041447\">10.1101/cshperspect.a041447</a>.","ama":"Lucek K, Giménez MD, Joron M, et al. The impact of chromosomal rearrangements in speciation: From micro- to macroevolution. <i>Cold Spring Harbor Perspectives in Biology</i>. 2023;15(11). doi:<a href=\"https://doi.org/10.1101/cshperspect.a041447\">10.1101/cshperspect.a041447</a>"},"intvolume":"        15","external_id":{"pmid":["37604585"]},"status":"public","date_created":"2024-01-08T12:43:48Z","volume":15,"type":"journal_article","oa_version":"Published Version","month":"11","abstract":[{"text":"Chromosomal rearrangements (CRs) have been known since almost the beginning of genetics.\r\nWhile an important role for CRs in speciation has been suggested, evidence primarily stems\r\nfrom theoretical and empirical studies focusing on the microevolutionary level (i.e., on taxon\r\npairs where speciation is often incomplete). Although the role of CRs in eukaryotic speciation at\r\na macroevolutionary level has been supported by associations between species diversity and\r\nrates of evolution of CRs across phylogenies, these findings are limited to a restricted range of\r\nCRs and taxa. Now that more broadly applicable and precise CR detection approaches have\r\nbecome available, we address the challenges in filling some of the conceptual and empirical\r\ngaps between micro- and macroevolutionary studies on the role of CRs in speciation. We\r\nsynthesize what is known about the macroevolutionary impact of CRs and suggest new research avenues to overcome the pitfalls of previous studies to gain a more comprehensive understanding of the evolutionary significance of CRs in speciation across the tree of life.","lang":"eng"}],"date_updated":"2024-01-08T12:52:29Z","_id":"14742","year":"2023","acknowledgement":"K.L. was funded by a Swiss National Science Foundation Eccellenza project: The evolution of strong reproductive barriers towards the completion of speciation (PCEFP3_202869). R.F.\r\nwas funded by an FCT CEEC (Fundação para a Ciênca e a Tecnologia, Concurso Estímulo ao\r\nEmprego Científico) contract (2020.00275. CEECIND) and by an FCT research project\r\n(PTDC/BIA-EVL/1614/2021). M.R. was funded by the Swedish Research Council Vetenskapsrådet (grant number 2021-05243). A.M.W. was partly funded by the Norwegian Research Council RCN. We thank Luis Silva for his help preparing Figure 1. We are grateful to Maren Wellenreuther, Daniel Bolnick, and two anonymous reviewers for their constructive feedback on an earlier version of this paper."},{"quality_controlled":"1","doi":"10.1093/gbe/evad113","publication_identifier":{"eissn":["1759-6653"]},"language":[{"iso":"eng"}],"issue":"7","isi":1,"title":"Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura","article_number":"evad113","day":"01","file":[{"access_level":"open_access","date_created":"2023-08-01T06:58:34Z","checksum":"70de3c4878de6efe00dc56de2df8812f","file_id":"13339","date_updated":"2023-08-01T06:58:34Z","creator":"dernst","file_size":2382587,"content_type":"application/pdf","relation":"main_file","file_name":"2023_GBE_Barata.pdf","success":1}],"author":[{"first_name":"Carolina","last_name":"De Castro Barbosa Rodrigues Barata","id":"20565186-803f-11ed-ab7e-96a4ff7694ef","full_name":"De Castro Barbosa Rodrigues Barata, Carolina"},{"full_name":"Snook, Rhonda R.","first_name":"Rhonda R.","last_name":"Snook"},{"full_name":"Ritchie, Michael G.","first_name":"Michael G.","last_name":"Ritchie"},{"first_name":"Carolin","last_name":"Kosiol","full_name":"Kosiol, Carolin"}],"scopus_import":"1","article_processing_charge":"Yes","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"publication":"Genome biology and evolution","pmid":1,"department":[{"_id":"BeVi"}],"publisher":"Oxford Academic","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["570"],"date_published":"2023-07-01T00:00:00Z","has_accepted_license":"1","oa":1,"publication_status":"published","citation":{"short":"C. de Castro Barbosa Rodrigues Barata, R.R. Snook, M.G. Ritchie, C. Kosiol, Genome Biology and Evolution 15 (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 Academic, 2023. <a href=\"https://doi.org/10.1093/gbe/evad113\">https://doi.org/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 Academic, 2023.","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 Academic. <a href=\"https://doi.org/10.1093/gbe/evad113\">https://doi.org/10.1093/gbe/evad113</a>","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.","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 Academic, 2023, doi:<a href=\"https://doi.org/10.1093/gbe/evad113\">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>"},"intvolume":"        15","related_material":{"link":[{"relation":"software","url":"https://github.com/carolbarata/dpseudo-n-beyond"}]},"external_id":{"pmid":["37341535"],"isi":["001023444700003"]},"status":"public","file_date_updated":"2023-08-01T06:58:34Z","date_created":"2023-07-23T22:01:11Z","volume":15,"date_updated":"2023-08-02T06:42:35Z","abstract":[{"lang":"eng","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."}],"type":"journal_article","month":"07","oa_version":"Published Version","_id":"13260","year":"2023","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."},{"title":"The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation","degree_awarded":"PhD","author":[{"orcid":"0000-0001-8330-1754","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","full_name":"Puixeu Sala, Gemma","first_name":"Gemma","last_name":"Puixeu Sala"}],"day":"15","file":[{"file_name":"Thesis_latex_forpdfa.zip","creator":"gpuixeus","content_type":"application/zip","relation":"source_file","file_size":10891454,"checksum":"4e44e169f2724ee8c9324cd60bcc2b71","date_updated":"2023-08-17T06:55:24Z","file_id":"14075","access_level":"closed","date_created":"2023-08-16T18:15:17Z"},{"creator":"gpuixeus","relation":"main_file","content_type":"application/pdf","file_size":19856686,"success":1,"file_name":"PhDThesis_PuixeuG.pdf","access_level":"open_access","date_created":"2023-08-18T10:47:55Z","checksum":"e10b04cd8f3fecc0d9ef6e6868b6e1e8","date_updated":"2023-08-18T10:47:55Z","file_id":"14079"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ec_funded":1,"article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"BeVi"}],"doi":"10.15479/at:ista:14058","publication_identifier":{"isbn":["978-3-99078-035-0"],"issn":["2663-337X"]},"language":[{"iso":"eng"}],"project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385"},{"_id":"9B9DFC9E-BA93-11EA-9121-9846C619BF3A","name":"Sexual conflict: resolution, constraints and biomedical implications","grant_number":"25817"}],"file_date_updated":"2023-08-18T10:47:55Z","date_created":"2023-08-15T10:20:40Z","page":"230","oa_version":"Published Version","type":"dissertation","month":"08","date_updated":"2023-12-13T12:15:36Z","abstract":[{"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.","lang":"eng"}],"_id":"14058","year":"2023","date_published":"2023-08-15T00:00:00Z","ddc":["576"],"supervisor":[{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","first_name":"Beatriz","last_name":"Vicoso"},{"last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"publication_status":"published","has_accepted_license":"1","related_material":{"record":[{"id":"9803","status":"public","relation":"research_data"},{"status":"public","id":"12933","relation":"research_data"},{"relation":"part_of_dissertation","id":"6831","status":"public"},{"status":"public","id":"14077","relation":"part_of_dissertation"}]},"citation":{"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.","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>.","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.","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>","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>.","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.","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>"},"alternative_title":["ISTA Thesis"],"status":"public"},{"department":[{"_id":"BeVi"},{"_id":"NiBa"},{"_id":"GradSch"}],"publisher":"Oxford University Press","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ec_funded":1,"scopus_import":"1","article_processing_charge":"Yes","publication":"G3: Genes, Genomes, Genetics","day":"01","file":[{"date_created":"2023-11-07T09:00:19Z","access_level":"open_access","date_updated":"2023-11-07T09:00:19Z","file_id":"14498","checksum":"c62e29fc7c5efbf8356f4c60cab4a2d1","content_type":"application/pdf","relation":"main_file","file_size":845642,"creator":"dernst","success":1,"file_name":"2023_G3_Puixeu.pdf"}],"author":[{"first_name":"Gemma","last_name":"Puixeu Sala","orcid":"0000-0001-8330-1754","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","full_name":"Puixeu Sala, Gemma"},{"id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","full_name":"Macon, Ariana","last_name":"Macon","first_name":"Ariana"},{"orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz","first_name":"Beatriz","last_name":"Vicoso"}],"title":"Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster","project":[{"grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program"},{"grant_number":"25817","name":"Sexual conflict: resolution, constraints and biomedical implications","_id":"9B9DFC9E-BA93-11EA-9121-9846C619BF3A"}],"issue":"8","language":[{"iso":"eng"}],"keyword":["Genetics (clinical)","Genetics","Molecular Biology"],"isi":1,"publication_identifier":{"issn":["2160-1836"]},"quality_controlled":"1","doi":"10.1093/g3journal/jkad121","year":"2023","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).","_id":"14077","type":"journal_article","month":"08","oa_version":"Published Version","date_updated":"2023-12-13T12:15:37Z","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."}],"file_date_updated":"2023-11-07T09:00:19Z","date_created":"2023-08-18T06:52:14Z","volume":13,"external_id":{"isi":["001002997200001"]},"status":"public","citation":{"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).","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>.","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>","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>","short":"G. Puixeu Sala, A. Macon, B. Vicoso, G3: Genes, Genomes, Genetics 13 (2023).","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.","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>."},"related_material":{"record":[{"relation":"research_data","status":"public","id":"12933"},{"relation":"dissertation_contains","status":"public","id":"14058"}]},"intvolume":"        13","has_accepted_license":"1","publication_status":"published","oa":1,"acknowledged_ssus":[{"_id":"ScienComp"}],"ddc":["570"],"date_published":"2023-08-01T00:00:00Z"},{"publication_identifier":{"issn":["2056-3744"]},"quality_controlled":"1","doi":"10.1093/evlett/qrac004","project":[{"grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics","_id":"256E75B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"250BDE62-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","grant_number":"715257"}],"issue":"1","language":[{"iso":"eng"}],"keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"isi":1,"file":[{"date_updated":"2023-08-16T11:43:33Z","file_id":"14068","checksum":"a240a041cb9b9b7c8ba93a4706674a3f","date_created":"2023-08-16T11:43:33Z","access_level":"open_access","success":1,"file_name":"2023_EvLetters_Mrnjavac.pdf","relation":"main_file","content_type":"application/pdf","file_size":2592189,"creator":"dernst"}],"day":"01","author":[{"first_name":"Andrea","last_name":"Mrnjavac","full_name":"Mrnjavac, Andrea","id":"353FAC84-AE61-11E9-8BFC-00D3E5697425"},{"last_name":"Khudiakova","first_name":"Kseniia","full_name":"Khudiakova, Kseniia","id":"4E6DC800-AE37-11E9-AC72-31CAE5697425","orcid":"0000-0002-6246-1465"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","last_name":"Vicoso","first_name":"Beatriz"}],"article_number":"qrac004","title":"Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"pmid":1,"publisher":"Oxford University Press","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","scopus_import":"1","ec_funded":1,"article_processing_charge":"Yes (via OA deal)","publication":"Evolution Letters","has_accepted_license":"1","oa":1,"publication_status":"published","date_published":"2023-02-01T00:00:00Z","ddc":["570"],"external_id":{"pmid":["37065438"],"isi":["001021692200001"]},"status":"public","citation":{"short":"A. Mrnjavac, K. Khudiakova, N.H. Barton, B. Vicoso, Evolution Letters 7 (2023).","chicago":"Mrnjavac, Andrea, Kseniia Khudiakova, Nicholas H Barton, and Beatriz Vicoso. “Slower-X: Reduced Efficiency of Selection in the Early Stages of X Chromosome Evolution.” <i>Evolution Letters</i>. Oxford University Press, 2023. <a href=\"https://doi.org/10.1093/evlett/qrac004\">https://doi.org/10.1093/evlett/qrac004</a>.","ieee":"A. Mrnjavac, K. Khudiakova, N. H. Barton, and B. Vicoso, “Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution,” <i>Evolution Letters</i>, vol. 7, no. 1. Oxford University Press, 2023.","apa":"Mrnjavac, A., Khudiakova, K., Barton, N. H., &#38; Vicoso, B. (2023). Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution. <i>Evolution Letters</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/evlett/qrac004\">https://doi.org/10.1093/evlett/qrac004</a>","ista":"Mrnjavac A, Khudiakova K, Barton NH, Vicoso B. 2023. Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution. Evolution Letters. 7(1), qrac004.","mla":"Mrnjavac, Andrea, et al. “Slower-X: Reduced Efficiency of Selection in the Early Stages of X Chromosome Evolution.” <i>Evolution Letters</i>, vol. 7, no. 1, qrac004, Oxford University Press, 2023, doi:<a href=\"https://doi.org/10.1093/evlett/qrac004\">10.1093/evlett/qrac004</a>.","ama":"Mrnjavac A, Khudiakova K, Barton NH, Vicoso B. Slower-X: Reduced efficiency of selection in the early stages of X chromosome evolution. <i>Evolution Letters</i>. 2023;7(1). doi:<a href=\"https://doi.org/10.1093/evlett/qrac004\">10.1093/evlett/qrac004</a>"},"intvolume":"         7","oa_version":"Published Version","type":"journal_article","month":"02","abstract":[{"lang":"eng","text":"Differentiated X chromosomes are expected to have higher rates of adaptive divergence than autosomes, if new beneficial mutations are recessive (the “faster-X effect”), largely because these mutations are immediately exposed to selection in males. The evolution of X chromosomes after they stop recombining in males, but before they become hemizygous, has not been well explored theoretically. We use the diffusion approximation to infer substitution rates of beneficial and deleterious mutations under such a scenario. Our results show that selection is less efficient on diploid X loci than on autosomal and hemizygous X loci under a wide range of parameters. This “slower-X” effect is stronger for genes affecting primarily (or only) male fitness, and for sexually antagonistic genes. These unusual dynamics suggest that some of the peculiar features of X chromosomes, such as the differential accumulation of genes with sex-specific functions, may start arising earlier than previously appreciated."}],"date_updated":"2023-08-16T11:44:32Z","date_created":"2023-02-06T13:59:12Z","file_date_updated":"2023-08-16T11:43:33Z","volume":7,"year":"2023","acknowledgement":"We thank the Vicoso and Barton groups and ISTA Scientific Computing Unit. We also thank two anonymous reviewers for their valuable comments. This work was supported by the European Research Council under the European Union’s Horizon 2020 research and innovation program (grant agreements no. 715257 and no. 716117).","_id":"12521"},{"oa":1,"has_accepted_license":"1","date_published":"2023-05-15T00:00:00Z","ddc":["570"],"contributor":[{"id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","first_name":"Ariana","last_name":"Macon"},{"last_name":"Vicoso","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306"}],"doi":"10.15479/AT:ISTA:12933","status":"public","related_material":{"record":[{"relation":"used_in_publication","id":"14058","status":"public"},{"relation":"used_in_publication","status":"public","id":"14077"}]},"citation":{"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>.","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>.","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>","short":"G. Puixeu Sala, (2023).","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.","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>."},"author":[{"orcid":"0000-0001-8330-1754","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","full_name":"Puixeu Sala, Gemma","last_name":"Puixeu Sala","first_name":"Gemma"}],"month":"05","oa_version":"Published Version","type":"research_data","day":"15","abstract":[{"lang":"eng","text":"Datasets of the publication \"Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster\"."}],"date_updated":"2023-12-13T12:15:36Z","file":[{"date_created":"2023-05-10T09:41:43Z","access_level":"open_access","date_updated":"2023-05-10T09:41:43Z","file_id":"12934","checksum":"0ba0bcd0bb8b18d84792136a4370df90","content_type":"text/csv","relation":"main_file","file_size":8029982,"creator":"gpuixeus","success":1,"file_name":"Dataset_S1.csv"},{"access_level":"open_access","date_created":"2023-05-10T09:41:43Z","checksum":"a62aa9a6d4904e0fdb699cf752640863","date_updated":"2023-05-10T09:41:43Z","file_id":"12935","creator":"gpuixeus","relation":"main_file","content_type":"text/csv","file_size":13667640,"success":1,"file_name":"Dataset_S2.csv"},{"file_name":"Dataset_S3.csv","success":1,"file_size":8369141,"content_type":"text/csv","relation":"main_file","creator":"gpuixeus","file_id":"12936","date_updated":"2023-05-10T09:41:48Z","checksum":"e20ea7f4f8a9bdf1b3849a44664ae58b","date_created":"2023-05-10T09:41:48Z","access_level":"open_access"},{"date_created":"2023-05-10T09:41:50Z","access_level":"open_access","file_id":"12937","date_updated":"2023-05-10T09:41:50Z","checksum":"f6156e5fc44446c907ddd0d7289d4cf8","file_size":19543247,"relation":"main_file","content_type":"text/csv","creator":"gpuixeus","file_name":"Dataset_S4.csv","success":1},{"access_level":"open_access","date_created":"2023-05-11T12:50:18Z","checksum":"ae9f54c77a1c42b666ae6c1dfd33ac86","file_id":"12944","date_updated":"2023-05-11T12:50:18Z","creator":"gpuixeus","file_size":4566,"relation":"main_file","content_type":"text/plain","file_name":"readme.txt","success":1}],"title":"Data from: Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster","file_date_updated":"2023-05-11T12:50:18Z","date_created":"2023-05-10T10:00:49Z","publisher":"Institute of Science and Technology Austria","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2023","department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"BeVi"}],"_id":"12933","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_processing_charge":"No"},{"title":"Novel patterns of expression and recruitment of new genes on the t-haplotype, a mouse selfish chromosome","author":[{"id":"48D3F8DE-F248-11E8-B48F-1D18A9856A87","full_name":"Kelemen, Réka K","first_name":"Réka K","last_name":"Kelemen"},{"orcid":"0000-0002-5328-7231","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","full_name":"Elkrewi, Marwan N","last_name":"Elkrewi","first_name":"Marwan N"},{"first_name":"Anna K.","last_name":"Lindholm","full_name":"Lindholm, Anna K."},{"first_name":"Beatriz","last_name":"Vicoso","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"day":"09","file":[{"access_level":"open_access","date_created":"2022-02-21T08:17:38Z","checksum":"27042a3706ae52a919fed1ac114bf7bb","file_id":"10779","date_updated":"2022-02-21T08:17:38Z","creator":"dernst","file_size":2366976,"content_type":"application/pdf","relation":"main_file","file_name":"2022_ProceedingsRoyalSocB_Kelemen.pdf","success":1}],"publication":"Proceedings of the Royal Society B: Biological Sciences","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","ec_funded":1,"scopus_import":"1","article_processing_charge":"No","publisher":"The Royal Society","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"BeVi"}],"pmid":1,"doi":"10.1098/rspb.2021.1985","quality_controlled":"1","publication_identifier":{"eissn":["14712954"]},"isi":1,"issue":"1968","language":[{"iso":"eng"}],"project":[{"name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","_id":"250BDE62-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"715257"}],"volume":289,"file_date_updated":"2022-02-21T08:17:38Z","date_created":"2022-02-20T23:01:31Z","page":"20211985","type":"journal_article","month":"02","oa_version":"Published Version","abstract":[{"text":"The t-haplotype of mice is a classical model for autosomal transmission distortion. A largely non-recombining variant of the proximal region of chromosome 17, it is transmitted to more than 90% of the progeny of heterozygous males through the disabling of sperm carrying a standard chromosome. While extensive genetic and functional work has shed light on individual genes involved in drive, much less is known about the evolution and function of the rest of its hundreds of genes. Here, we characterize the sequence and expression of dozens of t-specific transcripts and of their chromosome 17 homologues. Many genes showed reduced expression of the t-allele, but an equal number of genes showed increased expression of their t-copy, consistent with increased activity or a newly evolved function. Genes on the t-haplotype had a significantly higher non-synonymous substitution rate than their homologues on the standard chromosome, with several genes harbouring dN/dS ratios above 1. Finally, the t-haplotype has acquired at least two genes from other chromosomes, which show high and tissue-specific expression. These results provide a first overview of the gene content of this selfish element, and support a more dynamic evolutionary scenario than expected of a large genomic region with almost no recombination.","lang":"eng"}],"date_updated":"2023-08-02T14:26:07Z","_id":"10767","acknowledgement":"This project has received funding from the European Research Council under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 715257) and from the Swiss National Science Foundation (grant no. 310030_189145).\r\nWe thank Jari Garbely of the Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland, for conducting the PCR verification. Barbara\r\nKonig, Gabi Stichel and A.K.L. collected mouse tissue samples, from the field study led by R.K.K. ","year":"2022","ddc":["570"],"date_published":"2022-02-09T00:00:00Z","publication_status":"published","oa":1,"has_accepted_license":"1","intvolume":"       289","citation":{"chicago":"Kelemen, Réka K, Marwan N Elkrewi, Anna K. Lindholm, and Beatriz Vicoso. “Novel Patterns of Expression and Recruitment of New Genes on the T-Haplotype, a Mouse Selfish Chromosome.” <i>Proceedings of the Royal Society B: Biological Sciences</i>. The Royal Society, 2022. <a href=\"https://doi.org/10.1098/rspb.2021.1985\">https://doi.org/10.1098/rspb.2021.1985</a>.","ieee":"R. K. Kelemen, M. N. Elkrewi, A. K. Lindholm, and B. Vicoso, “Novel patterns of expression and recruitment of new genes on the t-haplotype, a mouse selfish chromosome,” <i>Proceedings of the Royal Society B: Biological Sciences</i>, vol. 289, no. 1968. The Royal Society, p. 20211985, 2022.","short":"R.K. Kelemen, M.N. Elkrewi, A.K. Lindholm, B. Vicoso, Proceedings of the Royal Society B: Biological Sciences 289 (2022) 20211985.","ama":"Kelemen RK, Elkrewi MN, Lindholm AK, Vicoso B. Novel patterns of expression and recruitment of new genes on the t-haplotype, a mouse selfish chromosome. <i>Proceedings of the Royal Society B: Biological Sciences</i>. 2022;289(1968):20211985. doi:<a href=\"https://doi.org/10.1098/rspb.2021.1985\">10.1098/rspb.2021.1985</a>","apa":"Kelemen, R. K., Elkrewi, M. N., Lindholm, A. K., &#38; Vicoso, B. (2022). Novel patterns of expression and recruitment of new genes on the t-haplotype, a mouse selfish chromosome. <i>Proceedings of the Royal Society B: Biological Sciences</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rspb.2021.1985\">https://doi.org/10.1098/rspb.2021.1985</a>","ista":"Kelemen RK, Elkrewi MN, Lindholm AK, Vicoso B. 2022. Novel patterns of expression and recruitment of new genes on the t-haplotype, a mouse selfish chromosome. Proceedings of the Royal Society B: Biological Sciences. 289(1968), 20211985.","mla":"Kelemen, Réka K., et al. “Novel Patterns of Expression and Recruitment of New Genes on the T-Haplotype, a Mouse Selfish Chromosome.” <i>Proceedings of the Royal Society B: Biological Sciences</i>, vol. 289, no. 1968, The Royal Society, 2022, p. 20211985, doi:<a href=\"https://doi.org/10.1098/rspb.2021.1985\">10.1098/rspb.2021.1985</a>."},"status":"public","external_id":{"pmid":["35135349"],"isi":["000752812800012"]}},{"department":[{"_id":"BeVi"}],"publisher":"Oxford Academic","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_type":"original","article_processing_charge":"No","scopus_import":"1","publication":"Journal of Molluscan Studies","day":"01","author":[{"first_name":"Samuel","last_name":"Perini","full_name":"Perini, Samuel"},{"full_name":"Butlin, Rogerk","first_name":"Rogerk","last_name":"Butlin"},{"first_name":"Anja M","last_name":"Westram","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Kerstin","last_name":"Johannesson","full_name":"Johannesson, Kerstin"}],"article_number":"eyab049","title":"Very short mountings are enough for sperm transfer in Littorina saxatilis","issue":"1","language":[{"iso":"eng"}],"isi":1,"publication_identifier":{"eissn":["1464-3766"],"issn":["0260-1230"]},"quality_controlled":"1","doi":"10.1093/mollus/eyab049","year":"2022","_id":"10926","type":"journal_article","month":"03","oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Conflict over reproduction between females and males exists because of anisogamy and promiscuity. Together they generate differences in fitness optima between the sexes and result in antagonistic coevolution of female and male reproductive traits. Mounting duration is likely to be a compromise between male and female interests whose outcome depends on the intensity of sexual selection. The timing of sperm transfer during mounting is critical. For example, mountings may be interrupted before sperm is transferred as a consequence of female or male choice, or they may be prolonged to function as mate guarding. In the highly promiscuous intertidal snail Littorina saxatilis, mountings vary substantially in duration, from less than a minute to more than an hour, and it has been assumed that mountings of a few minutes do not result in any sperm being transferred. Here, we examined the timing of sperm transfer, a reproductive trait that is likely affected by sexual conflict. We performed time-controlled mounting trials using L. saxatilis males and virgin females, aiming to examine indirectly when the transfer of sperm starts. We observed the relationship between mounting duration and the proportion of developing embryos out of all eggs and embryos in the brood pouch. Developing embryos were observed in similar proportions in all treatments (i.e. 1, 5 and 10 or more minutes at which mountings were artificially interrupted), suggesting that sperm transfer begins rapidly (within 1 min) in L. saxatilis and very short matings do not result in sperm shortage in the females. We discuss how the observed pattern can be influenced by predation risk, population density, and female status and receptivity."}],"date_updated":"2023-08-03T06:23:13Z","date_created":"2022-03-27T22:01:46Z","volume":88,"status":"public","external_id":{"isi":["000759081600002"]},"citation":{"ista":"Perini S, Butlin R, Westram AM, Johannesson K. 2022. Very short mountings are enough for sperm transfer in Littorina saxatilis. Journal of Molluscan Studies. 88(1), eyab049.","mla":"Perini, Samuel, et al. “Very Short Mountings Are Enough for Sperm Transfer in Littorina Saxatilis.” <i>Journal of Molluscan Studies</i>, vol. 88, no. 1, eyab049, Oxford Academic, 2022, doi:<a href=\"https://doi.org/10.1093/mollus/eyab049\">10.1093/mollus/eyab049</a>.","apa":"Perini, S., Butlin, R., Westram, A. M., &#38; Johannesson, K. (2022). Very short mountings are enough for sperm transfer in Littorina saxatilis. <i>Journal of Molluscan Studies</i>. Oxford Academic. <a href=\"https://doi.org/10.1093/mollus/eyab049\">https://doi.org/10.1093/mollus/eyab049</a>","ama":"Perini S, Butlin R, Westram AM, Johannesson K. Very short mountings are enough for sperm transfer in Littorina saxatilis. <i>Journal of Molluscan Studies</i>. 2022;88(1). doi:<a href=\"https://doi.org/10.1093/mollus/eyab049\">10.1093/mollus/eyab049</a>","short":"S. Perini, R. Butlin, A.M. Westram, K. Johannesson, Journal of Molluscan Studies 88 (2022).","ieee":"S. Perini, R. Butlin, A. M. Westram, and K. Johannesson, “Very short mountings are enough for sperm transfer in Littorina saxatilis,” <i>Journal of Molluscan Studies</i>, vol. 88, no. 1. Oxford Academic, 2022.","chicago":"Perini, Samuel, Rogerk Butlin, Anja M Westram, and Kerstin Johannesson. “Very Short Mountings Are Enough for Sperm Transfer in Littorina Saxatilis.” <i>Journal of Molluscan Studies</i>. Oxford Academic, 2022. <a href=\"https://doi.org/10.1093/mollus/eyab049\">https://doi.org/10.1093/mollus/eyab049</a>."},"intvolume":"        88","publication_status":"published","oa":1,"main_file_link":[{"url":"https://eprints.whiterose.ac.uk/187332/","open_access":"1"}],"date_published":"2022-03-01T00:00:00Z"},{"publication_identifier":{"eissn":["1558-5646"],"issn":["0014-3820"]},"doi":"10.1111/evo.14462","quality_controlled":"1","project":[{"grant_number":"797747","name":"Theoretical and empirical approaches to understanding Parallel Adaptation","_id":"265B41B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"isi":1,"issue":"5","language":[{"iso":"eng"}],"author":[{"full_name":"Freitas, Susana","first_name":"Susana","last_name":"Freitas"},{"orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","full_name":"Westram, Anja M","last_name":"Westram","first_name":"Anja M"},{"last_name":"Schwander","first_name":"Tanja","full_name":"Schwander, Tanja"},{"last_name":"Arakelyan","first_name":"Marine","full_name":"Arakelyan, Marine"},{"full_name":"Ilgaz, Çetin","first_name":"Çetin","last_name":"Ilgaz"},{"first_name":"Yusuf","last_name":"Kumlutas","full_name":"Kumlutas, Yusuf"},{"first_name":"David James","last_name":"Harris","full_name":"Harris, David James"},{"last_name":"Carretero","first_name":"Miguel A.","full_name":"Carretero, Miguel A."},{"first_name":"Roger K.","last_name":"Butlin","full_name":"Butlin, Roger K."}],"file":[{"file_name":"2022_Evolution_Freitas.pdf","success":1,"file_size":2855214,"content_type":"application/pdf","relation":"main_file","creator":"dernst","file_id":"11729","date_updated":"2022-08-05T06:19:28Z","checksum":"c27c025ae9afcf6c804d46a909775ee5","date_created":"2022-08-05T06:19:28Z","access_level":"open_access"}],"license":"https://creativecommons.org/licenses/by-nc/4.0/","day":"01","title":"Parthenogenesis in Darevskia lizards: A rare outcome of common hybridization, not a common outcome of rare hybridization","publisher":"Wiley","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"NiBa"},{"_id":"BeVi"}],"pmid":1,"publication":"Evolution","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"article_type":"original","article_processing_charge":"No","scopus_import":"1","ec_funded":1,"publication_status":"published","oa":1,"has_accepted_license":"1","date_published":"2022-05-01T00:00:00Z","ddc":["570"],"external_id":{"isi":["000781632500001"],"pmid":["35323995"]},"status":"public","intvolume":"        76","citation":{"short":"S. Freitas, A.M. Westram, T. Schwander, M. Arakelyan, Ç. Ilgaz, Y. Kumlutas, D.J. Harris, M.A. Carretero, R.K. Butlin, Evolution 76 (2022) 899–914.","ieee":"S. Freitas <i>et al.</i>, “Parthenogenesis in Darevskia lizards: A rare outcome of common hybridization, not a common outcome of rare hybridization,” <i>Evolution</i>, vol. 76, no. 5. Wiley, pp. 899–914, 2022.","chicago":"Freitas, Susana, Anja M Westram, Tanja Schwander, Marine Arakelyan, Çetin Ilgaz, Yusuf Kumlutas, David James Harris, Miguel A. Carretero, and Roger K. Butlin. “Parthenogenesis in Darevskia Lizards: A Rare Outcome of Common Hybridization, Not a Common Outcome of Rare Hybridization.” <i>Evolution</i>. Wiley, 2022. <a href=\"https://doi.org/10.1111/evo.14462\">https://doi.org/10.1111/evo.14462</a>.","mla":"Freitas, Susana, et al. “Parthenogenesis in Darevskia Lizards: A Rare Outcome of Common Hybridization, Not a Common Outcome of Rare Hybridization.” <i>Evolution</i>, vol. 76, no. 5, Wiley, 2022, pp. 899–914, doi:<a href=\"https://doi.org/10.1111/evo.14462\">10.1111/evo.14462</a>.","ista":"Freitas S, Westram AM, Schwander T, Arakelyan M, Ilgaz Ç, Kumlutas Y, Harris DJ, Carretero MA, Butlin RK. 2022. Parthenogenesis in Darevskia lizards: A rare outcome of common hybridization, not a common outcome of rare hybridization. Evolution. 76(5), 899–914.","apa":"Freitas, S., Westram, A. M., Schwander, T., Arakelyan, M., Ilgaz, Ç., Kumlutas, Y., … Butlin, R. K. (2022). Parthenogenesis in Darevskia lizards: A rare outcome of common hybridization, not a common outcome of rare hybridization. <i>Evolution</i>. Wiley. <a href=\"https://doi.org/10.1111/evo.14462\">https://doi.org/10.1111/evo.14462</a>","ama":"Freitas S, Westram AM, Schwander T, et al. Parthenogenesis in Darevskia lizards: A rare outcome of common hybridization, not a common outcome of rare hybridization. <i>Evolution</i>. 2022;76(5):899-914. doi:<a href=\"https://doi.org/10.1111/evo.14462\">10.1111/evo.14462</a>"},"page":"899-914","oa_version":"Published Version","month":"05","type":"journal_article","abstract":[{"text":"Hybridization is a common evolutionary process with multiple possible outcomes. In vertebrates, interspecific hybridization has repeatedly generated parthenogenetic hybrid species. However, it is unknown whether the generation of parthenogenetic hybrids is a rare outcome of frequent hybridization between sexual species within a genus or the typical outcome of rare hybridization events. Darevskia is a genus of rock lizards with both hybrid parthenogenetic and sexual species. Using capture sequencing, we estimate phylogenetic relationships and gene flow among the sexual species, to determine how introgressive hybridization relates to the origins of parthenogenetic hybrids. We find evidence for widespread hybridization with gene flow, both between recently diverged species and deep branches. Surprisingly, we find no signal of gene flow between parental species of the parthenogenetic hybrids, suggesting that the parental pairs were either reproductively or geographically isolated early in their divergence. The generation of parthenogenetic hybrids in Darevskia is, then, a rare outcome of the total occurrence of hybridization within the genus, but the typical outcome when specific species pairs hybridize. Our results question the conventional view that parthenogenetic lineages are generated by hybridization in a window of divergence. Instead, they suggest that some lineages possess specific properties that underpin successful parthenogenetic reproduction.","lang":"eng"}],"date_updated":"2023-08-03T07:00:28Z","volume":76,"file_date_updated":"2022-08-05T06:19:28Z","date_created":"2022-04-24T22:01:44Z","acknowledgement":"The authors thank A. van der Meijden and F. Ahmadzadeh for providing specimens and tissue samples, and A. Vardanyan, C. Corti, F. Jorge, and S. Drovetski for support during field work. The authors also thank S. Qiu for assistance with python scripting, S. Rocha for her support in BEAST analysis, and B. Wielstra for his comments on\r\na previous version of the manuscript. SF was funded by FCT grant SFRH/BD/81483/2011 (a PhD individual grant). AMW was funded by the European Union’s Horizon 2020 research and innovation programme under Marie Skłodowska-Curie grant agreement no. 797747. TS acknowledges funding from the Swiss National Science Foundation (grants\r\nPP00P3_170627 and 31003A_182495). The work was carried out under financial support of the projects “Preserving Armenian biodiversity: Joint Portuguese – Armenian program for training in modern conservation biology” of Gulbenkian Foundation (Portugal) and PTDC/BIABEC/101256/2008 of Fundação para a Ciência e a Tecnologia (FCT, Portugal).","year":"2022","_id":"11334"},{"date_published":"2022-08-01T00:00:00Z","ddc":["570"],"has_accepted_license":"1","publication_status":"published","oa":1,"citation":{"mla":"Westram, Anja M., et al. “Inversions and Parallel Evolution.” <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>, vol. 377, no. 1856, 20210203, Royal Society of London, 2022, doi:<a href=\"https://doi.org/10.1098/rstb.2021.0203\">10.1098/rstb.2021.0203</a>.","ista":"Westram AM, Faria R, Johannesson K, Butlin R, Barton NH. 2022. Inversions and parallel evolution. Philosophical Transactions of the Royal Society B: Biological Sciences. 377(1856), 20210203.","apa":"Westram, A. M., Faria, R., Johannesson, K., Butlin, R., &#38; Barton, N. H. (2022). Inversions and parallel evolution. <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>. Royal Society of London. <a href=\"https://doi.org/10.1098/rstb.2021.0203\">https://doi.org/10.1098/rstb.2021.0203</a>","ama":"Westram AM, Faria R, Johannesson K, Butlin R, Barton NH. Inversions and parallel evolution. <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>. 2022;377(1856). doi:<a href=\"https://doi.org/10.1098/rstb.2021.0203\">10.1098/rstb.2021.0203</a>","short":"A.M. Westram, R. Faria, K. Johannesson, R. Butlin, N.H. Barton, Philosophical Transactions of the Royal Society B: Biological Sciences 377 (2022).","ieee":"A. M. Westram, R. Faria, K. Johannesson, R. Butlin, and N. H. Barton, “Inversions and parallel evolution,” <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>, vol. 377, no. 1856. Royal Society of London, 2022.","chicago":"Westram, Anja M, Rui Faria, Kerstin Johannesson, Roger Butlin, and Nicholas H Barton. “Inversions and Parallel Evolution.” <i>Philosophical Transactions of the Royal Society B: Biological Sciences</i>. Royal Society of London, 2022. <a href=\"https://doi.org/10.1098/rstb.2021.0203\">https://doi.org/10.1098/rstb.2021.0203</a>."},"intvolume":"       377","external_id":{"isi":["000812317300005"]},"status":"public","file_date_updated":"2023-02-02T08:20:29Z","date_created":"2022-07-08T11:41:56Z","volume":377,"date_updated":"2023-08-03T11:55:42Z","abstract":[{"lang":"eng","text":"Local adaptation leads to differences between populations within a species. In many systems, similar environmental contrasts occur repeatedly, sometimes driving parallel phenotypic evolution. Understanding the genomic basis of local adaptation and parallel evolution is a major goal of evolutionary genomics. It is now known that by preventing the break-up of favourable combinations of alleles across multiple loci, genetic architectures that reduce recombination, like chromosomal inversions, can make an important contribution to local adaptation. However, little is known about whether inversions also contribute disproportionately to parallel evolution. Our aim here is to highlight this knowledge gap, to showcase existing studies, and to illustrate the differences between genomic architectures with and without inversions using simple models. We predict that by generating stronger effective selection, inversions can sometimes speed up the parallel adaptive process or enable parallel adaptation where it would be impossible otherwise, but this is highly dependent on the spatial setting. We highlight that further empirical work is needed, in particular to cover a broader taxonomic range and to understand the relative importance of inversions compared to genomic regions without inversions."}],"oa_version":"Published Version","month":"08","type":"journal_article","_id":"11546","year":"2022","acknowledgement":"We thank the editor and two anonymous reviewers for their helpful and interesting comments on this manuscript.","quality_controlled":"1","doi":"10.1098/rstb.2021.0203","publication_identifier":{"issn":["0962-8436"],"eissn":["1471-2970"]},"language":[{"iso":"eng"}],"issue":"1856","isi":1,"keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology"],"project":[{"grant_number":"P32166","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","name":"The maintenance of alternative adaptive peaks in snapdragons"}],"title":"Inversions and parallel evolution","article_number":"20210203","file":[{"file_name":"2022_PhilosophicalTransactionsB_Westram.pdf","success":1,"creator":"dernst","file_size":920304,"relation":"main_file","content_type":"application/pdf","checksum":"49f69428f3dcf5ce3ff281f7d199e9df","file_id":"12479","date_updated":"2023-02-02T08:20:29Z","access_level":"open_access","date_created":"2023-02-02T08:20:29Z"}],"day":"01","author":[{"last_name":"Westram","first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M"},{"last_name":"Faria","first_name":"Rui","full_name":"Faria, Rui"},{"full_name":"Johannesson, Kerstin","last_name":"Johannesson","first_name":"Kerstin"},{"full_name":"Butlin, Roger","first_name":"Roger","last_name":"Butlin"},{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H"}],"scopus_import":"1","article_processing_charge":"Yes (via OA deal)","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","publication":"Philosophical Transactions of the Royal Society B: Biological Sciences","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"publisher":"Royal Society of London","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"date_created":"2022-07-26T11:01:47Z","file_date_updated":"2022-08-08T22:30:04Z","title":"Data from Elkrewi, Khauratovich, Toups et al. 2022, \"ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp\"","oa_version":"Published Version","month":"08","type":"research_data","date_updated":"2024-02-21T12:35:53Z","abstract":[{"text":"Eurasian brine shrimp (genus Artemia) have closely related sexual and asexual lineages of parthenogenetic females, which produce rare males at low frequencies. Although they are known to have ZW chromosomes, these are not well characterized, and it is unclear whether they are shared across the clade. Furthermore, the underlying genetic architecture of the transmission of asexuality, which can occur when rare males mate with closely related sexual females, is not well understood. We produced a chromosome-level assembly for the sexual Eurasian species A. sinica and characterized in detail the pair of sex chromosomes of this species. We combined this new assembly with short-read genomic data for the sexual species A. sp. Kazakhstan and several asexual lineages of A. parthenogenetica, allowing us to perform an in-depth characterization of sex-chromosome evolution across the genus. We identified a small differentiated region of the ZW pair that is shared by all sexual and asexual lineages, supporting the shared ancestry of the sex chromosomes. We also inferred that recombination suppression has spread to larger sections of the chromosome independently in the American and Eurasian lineages. Finally, we took advantage of a rare male, which we backcrossed to sexual females, to explore the genetic basis of asexuality. Our results suggest that parthenogenesis is likely partly controlled by a locus on the Z chromosome, highlighting the interplay between sex determination and asexuality.","lang":"eng"}],"day":"05","file":[{"checksum":"5f1d7c6d7ab5375ed2564521432bed0c","description":"The folder contains the following datasets (fasta files, and text files):\nSup. Dataset 1: Genome assemblies: A. sinica male high quality assembly, A. sp. Kazakhstan\nmale draft assembly\nSup. Dataset 2: Male transcriptome assemblies for A. sinica and A. franciscana\nSup. Dataset 3: Male and female coverage for A. sinica, A. sp. Kazakhstan, A. urmiana, and\nA. parthenogenetica females and rare male.\nSup. Dataset 4: Artemia sinica Male:female FST per 1Kb window\nSup. Dataset 5: FASTA file with candidate W scaffolds\nSup. Dataset 6: Candidate W-derived transcripts and alignments\nSup. Dataset 7: Gene expression with genomic location\nSup. Dataset 8: VCF for asexual female and rare male\nSup. Dataset 9: FST between backcrossed asexual and control females (pooled analysis)\nSup. Dataset 10: VCF of backcrossed asexual and control females (individual analysis using\nA. sp. Kazakhstan as the reference), and inferred ancestry\nSup. Dataset 11: GO and DE annotations of all the Artemia sinica transcripts and their\nlocations in the Artemia sinica male genome.\n","date_updated":"2022-08-08T22:30:04Z","file_id":"11655","title":"Supplementary Datasets","access_level":"open_access","date_created":"2022-07-26T12:37:52Z","file_name":"Data.zip","creator":"melkrewi","relation":"main_file","content_type":"application/x-zip-compressed","embargo":"2022-08-07","file_size":2209382998}],"author":[{"id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","orcid":"0000-0002-5328-7231","full_name":"Elkrewi, Marwan N","first_name":"Marwan N","last_name":"Elkrewi"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_processing_charge":"No","_id":"11653","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"year":"2022","publisher":"Institute of Science and Technology Austria","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2022-08-05T00:00:00Z","doi":"10.15479/AT:ISTA:11653","contributor":[{"first_name":"Marwan N","last_name":"Elkrewi","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","orcid":"0000-0002-5328-7231"},{"first_name":"Uladzislava","last_name":"Khauratovich"},{"id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","first_name":"Melissa A","last_name":"Toups"},{"last_name":"Bett","first_name":"Vincent K","id":"57854184-AAE0-11E9-8D04-98D6E5697425"},{"first_name":"Andrea","last_name":"Mrnjavac","id":"353FAC84-AE61-11E9-8BFC-00D3E5697425"},{"id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","last_name":"Macon","first_name":"Ariana"},{"first_name":"Christelle","last_name":"Fraisse","orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sax","first_name":"Luca"},{"last_name":"Huylmans","first_name":"Ann K","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hontoria ","first_name":"Francisco"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","last_name":"Vicoso","first_name":"Beatriz"}],"ddc":["570"],"has_accepted_license":"1","oa":1,"citation":{"ama":"Elkrewi MN. Data from Elkrewi, Khauratovich, Toups et al. 2022, “ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp.” 2022. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:11653\">10.15479/AT:ISTA:11653</a>","apa":"Elkrewi, M. N. (2022). Data from Elkrewi, Khauratovich, Toups et al. 2022, “ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:11653\">https://doi.org/10.15479/AT:ISTA:11653</a>","ista":"Elkrewi MN. 2022. Data from Elkrewi, Khauratovich, Toups et al. 2022, ‘ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:11653\">10.15479/AT:ISTA:11653</a>.","mla":"Elkrewi, Marwan N. <i>Data from Elkrewi, Khauratovich, Toups et Al. 2022, “ZW Sex-Chromosome Evolution and Contagious Parthenogenesis in Artemia Brine Shrimp.”</i> Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:11653\">10.15479/AT:ISTA:11653</a>.","chicago":"Elkrewi, Marwan N. “Data from Elkrewi, Khauratovich, Toups et Al. 2022, ‘ZW Sex-Chromosome Evolution and Contagious Parthenogenesis in Artemia Brine Shrimp.’” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/AT:ISTA:11653\">https://doi.org/10.15479/AT:ISTA:11653</a>.","ieee":"M. N. Elkrewi, “Data from Elkrewi, Khauratovich, Toups et al. 2022, ‘ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp.’” Institute of Science and Technology Austria, 2022.","short":"M.N. Elkrewi, (2022)."},"related_material":{"record":[{"status":"public","id":"12248","relation":"used_in_publication"}]},"status":"public"},{"language":[{"iso":"eng"}],"issue":"7","isi":1,"project":[{"call_identifier":"H2020","_id":"250BDE62-B435-11E9-9278-68D0E5697425","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","grant_number":"715257"}],"quality_controlled":"1","doi":"10.1371/journal.pgen.1010226","publication_identifier":{"eissn":["1553-7404"]},"scopus_import":"1","article_processing_charge":"No","ec_funded":1,"article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"publication":"PLoS Genetics","pmid":1,"department":[{"_id":"BeVi"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Public Library of Science","title":"Dioecy and chromosomal sex determination are maintained through allopolyploid speciation in the plant genus Mercurialis","article_number":"e1010226","file":[{"file_name":"2022_PLoSGenetics_Toups.pdf","success":1,"file_size":1620272,"content_type":"application/pdf","relation":"main_file","creator":"dernst","file_id":"11708","date_updated":"2022-08-01T07:49:25Z","checksum":"aa4c137f82635e700856c359dccfaa0a","date_created":"2022-08-01T07:49:25Z","access_level":"open_access"}],"day":"06","author":[{"full_name":"Toups, Melissa A","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9752-7380","last_name":"Toups","first_name":"Melissa A"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","first_name":"Beatriz","last_name":"Vicoso"},{"last_name":"Pannell","first_name":"John R.","full_name":"Pannell, John R."}],"citation":{"ista":"Toups MA, Vicoso B, Pannell JR. 2022. Dioecy and chromosomal sex determination are maintained through allopolyploid speciation in the plant genus Mercurialis. PLoS Genetics. 18(7), e1010226.","mla":"Toups, Melissa A., et al. “Dioecy and Chromosomal Sex Determination Are Maintained through Allopolyploid Speciation in the Plant Genus Mercurialis.” <i>PLoS Genetics</i>, vol. 18, no. 7, e1010226, Public Library of Science, 2022, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1010226\">10.1371/journal.pgen.1010226</a>.","apa":"Toups, M. A., Vicoso, B., &#38; Pannell, J. R. (2022). Dioecy and chromosomal sex determination are maintained through allopolyploid speciation in the plant genus Mercurialis. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1010226\">https://doi.org/10.1371/journal.pgen.1010226</a>","ama":"Toups MA, Vicoso B, Pannell JR. Dioecy and chromosomal sex determination are maintained through allopolyploid speciation in the plant genus Mercurialis. <i>PLoS Genetics</i>. 2022;18(7). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1010226\">10.1371/journal.pgen.1010226</a>","short":"M.A. Toups, B. Vicoso, J.R. Pannell, PLoS Genetics 18 (2022).","ieee":"M. A. Toups, B. Vicoso, and J. R. Pannell, “Dioecy and chromosomal sex determination are maintained through allopolyploid speciation in the plant genus Mercurialis,” <i>PLoS Genetics</i>, vol. 18, no. 7. Public Library of Science, 2022.","chicago":"Toups, Melissa A, Beatriz Vicoso, and John R. Pannell. “Dioecy and Chromosomal Sex Determination Are Maintained through Allopolyploid Speciation in the Plant Genus Mercurialis.” <i>PLoS Genetics</i>. Public Library of Science, 2022. <a href=\"https://doi.org/10.1371/journal.pgen.1010226\">https://doi.org/10.1371/journal.pgen.1010226</a>."},"intvolume":"        18","status":"public","external_id":{"pmid":["35793353"],"isi":["000886643100006"]},"date_published":"2022-07-06T00:00:00Z","ddc":["570"],"has_accepted_license":"1","publication_status":"published","oa":1,"_id":"11703","year":"2022","acknowledgement":"JRP was supported by the Swiss National Science Foundation (https://www.snf.ch/en), Sinergia grant 26073998. BV was supported by the European Research Council (https://erc.europa.eu/) under the European Union’s Horizon 2020 research and innovation program, grant number 715257. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.\r\nPlants were grown in Lausanne by Aline Revel, and RNA extraction and library preparation were performed by Dessislava Savova Bianchi. All sequencing and the IsoSeq3 analysis were carried out by Center for Integrative Genomics at the University of Lausanne. All other computational analyses were performed on the server at IST Austria.","file_date_updated":"2022-08-01T07:49:25Z","date_created":"2022-07-31T22:01:48Z","volume":18,"abstract":[{"text":"Polyploidization may precipitate dramatic changes to the genome, including chromosome rearrangements, gene loss, and changes in gene expression. In dioecious plants, the sex-determining mechanism may also be disrupted by polyploidization, with the potential evolution of hermaphroditism. However, while dioecy appears to have persisted through a ploidy transition in some species, it is unknown whether the newly formed polyploid maintained its sex-determining system uninterrupted, or whether dioecy re-evolved after a period of hermaphroditism. Here, we develop a bioinformatic pipeline using RNA-sequencing data from natural populations to demonstrate that the allopolyploid plant Mercurialis canariensis directly inherited its sex-determining region from one of its diploid progenitor species, M. annua, and likely remained dioecious through the transition. The sex-determining region of M. canariensis is smaller than that of its diploid progenitor, suggesting that the non-recombining region of M. annua expanded subsequent to the polyploid origin of M. canariensis. Homeologous pairs show partial sexual subfunctionalization. We discuss the possibility that gene duplicates created by polyploidization might contribute to resolving sexual antagonism.","lang":"eng"}],"date_updated":"2023-08-03T12:17:12Z","oa_version":"Published Version","month":"07","type":"journal_article"}]