[{"publication":"Biology Letters","language":[{"iso":"eng"}],"status":"public","date_created":"2019-05-19T21:59:15Z","scopus_import":"1","pmid":1,"intvolume":"        15","_id":"6467","related_material":{"record":[{"status":"public","id":"9799","relation":"research_data"},{"relation":"research_data","id":"9798","status":"public"}],"link":[{"relation":"supplementary_material","url":"https://dx.doi.org/10.6084/m9.figshare.c.4461008"}]},"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Christelle","orcid":"0000-0001-8441-5075","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","full_name":"Fraisse, Christelle"},{"full_name":"Welch, John J.","last_name":"Welch","first_name":"John J."}],"type":"journal_article","issue":"4","external_id":{"pmid":["31014191"],"isi":["000465405300010"]},"quality_controlled":"1","project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"ec_funded":1,"day":"03","oa_version":"Published Version","volume":15,"article_type":"original","abstract":[{"text":"Fitness interactions between mutations can influence a population’s evolution in many different ways. While epistatic effects are difficult to measure precisely, important information is captured by the mean and variance of log fitnesses for individuals carrying different numbers of mutations. We derive predictions for these quantities from a class of simple fitness landscapes, based on models of optimizing selection on quantitative traits. We also explore extensions to the models, including modular pleiotropy, variable effect sizes, mutational bias and maladaptation of the wild type. We illustrate our approach by reanalysing a large dataset of mutant effects in a yeast snoRNA (small nucleolar RNA). Though characterized by some large epistatic effects, these data give a good overall fit to the non-epistatic null model, suggesting that epistasis might have limited influence on the evolutionary dynamics in this system. We also show how the amount of epistasis depends on both the underlying fitness landscape and the distribution of mutations, and so is expected to vary in consistent ways between new mutations, standing variation and fixed mutations.","lang":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1098/rsbl.2018.0881","open_access":"1"}],"publication_identifier":{"eissn":["1744-957X"],"issn":["1744-9561"]},"article_processing_charge":"No","publisher":"Royal Society of London","doi":"10.1098/rsbl.2018.0881","publication_status":"published","date_published":"2019-04-03T00:00:00Z","year":"2019","citation":{"short":"C. Fraisse, J.J. Welch, Biology Letters 15 (2019).","apa":"Fraisse, C., &#38; Welch, J. J. (2019). The distribution of epistasis on simple fitness landscapes. <i>Biology Letters</i>. Royal Society of London. <a href=\"https://doi.org/10.1098/rsbl.2018.0881\">https://doi.org/10.1098/rsbl.2018.0881</a>","ama":"Fraisse C, Welch JJ. The distribution of epistasis on simple fitness landscapes. <i>Biology Letters</i>. 2019;15(4). doi:<a href=\"https://doi.org/10.1098/rsbl.2018.0881\">10.1098/rsbl.2018.0881</a>","chicago":"Fraisse, Christelle, and John J. Welch. “The Distribution of Epistasis on Simple Fitness Landscapes.” <i>Biology Letters</i>. Royal Society of London, 2019. <a href=\"https://doi.org/10.1098/rsbl.2018.0881\">https://doi.org/10.1098/rsbl.2018.0881</a>.","ista":"Fraisse C, Welch JJ. 2019. The distribution of epistasis on simple fitness landscapes. Biology Letters. 15(4), 0881.","ieee":"C. Fraisse and J. J. Welch, “The distribution of epistasis on simple fitness landscapes,” <i>Biology Letters</i>, vol. 15, no. 4. Royal Society of London, 2019.","mla":"Fraisse, Christelle, and John J. Welch. “The Distribution of Epistasis on Simple Fitness Landscapes.” <i>Biology Letters</i>, vol. 15, no. 4, 0881, Royal Society of London, 2019, doi:<a href=\"https://doi.org/10.1098/rsbl.2018.0881\">10.1098/rsbl.2018.0881</a>."},"article_number":"0881","isi":1,"title":"The distribution of epistasis on simple fitness landscapes","date_updated":"2025-07-10T11:53:23Z","month":"04","department":[{"_id":"BeVi"},{"_id":"NiBa"}]},{"title":"On the power to detect rare recombination events","isi":1,"department":[{"_id":"BeVi"}],"month":"06","date_updated":"2025-05-14T10:56:48Z","publication_status":"published","doi":"10.1073/pnas.1905555116","publisher":"National Academy of Sciences","article_processing_charge":"No","citation":{"ieee":"A. E. Wright <i>et al.</i>, “On the power to detect rare recombination events,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 116, no. 26. National Academy of Sciences, pp. 12607–12608, 2019.","mla":"Wright, Alison E., et al. “On the Power to Detect Rare Recombination Events.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 116, no. 26, National Academy of Sciences, 2019, pp. 12607–08, doi:<a href=\"https://doi.org/10.1073/pnas.1905555116\">10.1073/pnas.1905555116</a>.","ista":"Wright AE, Darolti I, Bloch NI, Oostra V, Sandkam BA, Buechel SD, Kolm N, Breden F, Vicoso B, Mank JE. 2019. On the power to detect rare recombination events. Proceedings of the National Academy of Sciences of the United States of America. 116(26), 12607–12608.","ama":"Wright AE, Darolti I, Bloch NI, et al. On the power to detect rare recombination events. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2019;116(26):12607-12608. doi:<a href=\"https://doi.org/10.1073/pnas.1905555116\">10.1073/pnas.1905555116</a>","chicago":"Wright, Alison E., Iulia Darolti, Natasha I. Bloch, Vicencio Oostra, Benjamin A. Sandkam, Séverine D. Buechel, Niclas Kolm, Felix Breden, Beatriz Vicoso, and Judith E. Mank. “On the Power to Detect Rare Recombination Events.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2019. <a href=\"https://doi.org/10.1073/pnas.1905555116\">https://doi.org/10.1073/pnas.1905555116</a>.","short":"A.E. Wright, I. Darolti, N.I. Bloch, V. Oostra, B.A. Sandkam, S.D. Buechel, N. Kolm, F. Breden, B. Vicoso, J.E. Mank, Proceedings of the National Academy of Sciences of the United States of America 116 (2019) 12607–12608.","apa":"Wright, A. E., Darolti, I., Bloch, N. I., Oostra, V., Sandkam, B. A., Buechel, S. D., … Mank, J. E. (2019). On the power to detect rare recombination events. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1905555116\">https://doi.org/10.1073/pnas.1905555116</a>"},"date_published":"2019-06-25T00:00:00Z","year":"2019","abstract":[{"text":"We read with great interest the recent work in PNAS by Bergero et al. (1) describing differences in male and female recombination patterns on the guppy (Poecilia reticulata) sex chromosome. We fully agree that recombination in males is largely confined to the ends of the sex chromosome. Bergero et al. interpret these results to suggest that our previous findings of population-level variation in the degree of sex chromosome differentiation in this species (2) are incorrect. However, we suggest that their results are entirely consistent with our previous report, and that their interpretation presents a false controversy.","lang":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1073/pnas.1905555116","open_access":"1"}],"article_type":"letter_note","quality_controlled":"1","external_id":{"isi":["000472719100010"],"pmid":["31213531"]},"volume":116,"day":"25","oa_version":"Published Version","type":"journal_article","author":[{"first_name":"Alison E.","last_name":"Wright","full_name":"Wright, Alison E."},{"first_name":"Iulia","last_name":"Darolti","full_name":"Darolti, Iulia"},{"last_name":"Bloch","full_name":"Bloch, Natasha I.","first_name":"Natasha I."},{"first_name":"Vicencio","full_name":"Oostra, Vicencio","last_name":"Oostra"},{"first_name":"Benjamin A.","last_name":"Sandkam","full_name":"Sandkam, Benjamin A."},{"first_name":"Séverine D.","full_name":"Buechel, Séverine D.","last_name":"Buechel"},{"full_name":"Kolm, Niclas","last_name":"Kolm","first_name":"Niclas"},{"first_name":"Felix","full_name":"Breden, Felix","last_name":"Breden"},{"full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","orcid":"0000-0002-4579-8306","first_name":"Beatriz"},{"last_name":"Mank","full_name":"Mank, Judith E.","first_name":"Judith E."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"26","_id":"6621","oa":1,"pmid":1,"intvolume":"       116","page":"12607-12608","language":[{"iso":"eng"}],"publication":"Proceedings of the National Academy of Sciences of the United States of America","scopus_import":"1","status":"public","date_created":"2019-07-07T21:59:25Z"},{"department":[{"_id":"BeVi"}],"month":"07","date_updated":"2025-05-20T06:25:39Z","tmp":{"image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"license":"https://creativecommons.org/licenses/by-nc/4.0/","isi":1,"title":"Haploid selection drives new gene male germline expression","citation":{"short":"J. Raices, P. Otto, M. Vibranovski, Genome Research 29 (2019) 1115–1122.","apa":"Raices, J., Otto, P., &#38; Vibranovski, M. (2019). Haploid selection drives new gene male germline expression. <i>Genome Research</i>. Cold Spring Harbor Laboratory Press. <a href=\"https://doi.org/10.1101/gr.238824.118\">https://doi.org/10.1101/gr.238824.118</a>","ama":"Raices J, Otto P, Vibranovski M. Haploid selection drives new gene male germline expression. <i>Genome Research</i>. 2019;29(7):1115-1122. doi:<a href=\"https://doi.org/10.1101/gr.238824.118\">10.1101/gr.238824.118</a>","chicago":"Raices, Julia, Paulo Otto, and Maria Vibranovski. “Haploid Selection Drives New Gene Male Germline Expression.” <i>Genome Research</i>. Cold Spring Harbor Laboratory Press, 2019. <a href=\"https://doi.org/10.1101/gr.238824.118\">https://doi.org/10.1101/gr.238824.118</a>.","ista":"Raices J, Otto P, Vibranovski M. 2019. Haploid selection drives new gene male germline expression. Genome Research. 29(7), 1115–1122.","ieee":"J. Raices, P. Otto, and M. Vibranovski, “Haploid selection drives new gene male germline expression,” <i>Genome Research</i>, vol. 29, no. 7. Cold Spring Harbor Laboratory Press, pp. 1115–1122, 2019.","mla":"Raices, Julia, et al. “Haploid Selection Drives New Gene Male Germline Expression.” <i>Genome Research</i>, vol. 29, no. 7, Cold Spring Harbor Laboratory Press, 2019, pp. 1115–22, doi:<a href=\"https://doi.org/10.1101/gr.238824.118\">10.1101/gr.238824.118</a>."},"date_published":"2019-07-01T00:00:00Z","year":"2019","doi":"10.1101/gr.238824.118","article_processing_charge":"No","publication_identifier":{"eissn":[" 1549-5469"],"issn":["1088-9051"]},"publisher":"Cold Spring Harbor Laboratory Press","publication_status":"published","article_type":"original","OA_embargo":"6 months","abstract":[{"text":"New genes are a major source of novelties, and a disproportionate amount of them are known to show testis expression in later phases of male gametogenesis in different groups such as mammals and plants. Here, we propose that this enhanced expression is a consequence of haploid selection during the latter stages of male gametogenesis. Because emerging adaptive mutations will be fixed faster if their phenotypes are expressed by haploid rather than diploid genotypes, new genes with advantageous functions arising during this unique stage of development have a better chance to become fixed. To test this hypothesis, expression levels of genes of differing evolutionary age were examined at various stages of Drosophila spermatogenesis. We found, consistent with a model based on haploid selection, that new Drosophila genes are both expressed in later haploid phases of spermatogenesis and harbor a significant enrichment of adaptive mutations. Additionally, the observed overexpression of new genes in the latter phases of spermatogenesis was limited to the autosomes. Because all male cells exhibit hemizygous expression for X-linked genes (and therefore effectively haploid), there is no expectation that selection acting on late spermatogenesis will have a different effect on X-linked genes in comparison to initial diploid phases. Together, our proposed hypothesis and the analyzed data suggest that natural selection in haploid cells elucidates several aspects of the origin of new genes by explaining the general prevalence of their testis expression, and a parsimonious solution for new alleles to avoid being lost by genetic drift or pseudogenization. ","lang":"eng"}],"OA_type":"hybrid","day":"01","oa_version":"Published Version","volume":29,"external_id":{"isi":["000473730600007"]},"quality_controlled":"1","issue":"7","file_date_updated":"2020-07-14T12:47:35Z","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Raices, Julia","id":"3EE67F22-F248-11E8-B48F-1D18A9856A87","last_name":"Raices","first_name":"Julia"},{"last_name":"Otto","full_name":"Otto, Paulo","first_name":"Paulo"},{"last_name":"Vibranovski","full_name":"Vibranovski, Maria","first_name":"Maria"}],"oa":1,"OA_place":"publisher","_id":"6658","ddc":["576"],"file":[{"relation":"main_file","file_size":2319022,"access_level":"open_access","checksum":"4636f03a6750f90b88bf2bc3eb9d71ae","date_created":"2019-07-24T08:05:56Z","file_id":"6670","creator":"apreinsp","content_type":"application/pdf","date_updated":"2020-07-14T12:47:35Z","file_name":"2019_GenomeResearch_Raices.pdf"}],"page":"1115-1122","intvolume":"        29","date_created":"2019-07-21T21:59:15Z","status":"public","scopus_import":"1","language":[{"iso":"eng"}],"publication":"Genome Research","has_accepted_license":"1"},{"publication":"Annals of botany","language":[{"iso":"eng"}],"status":"public","scopus_import":"1","date_created":"2019-07-28T21:59:15Z","pmid":1,"page":"1119-1131","intvolume":"       123","_id":"6710","oa":1,"author":[{"last_name":"Cossard","full_name":"Cossard, Guillaume","first_name":"Guillaume"},{"orcid":"0000-0002-9752-7380","first_name":"Melissa A","full_name":"Toups, Melissa A","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","last_name":"Toups"},{"first_name":"John ","last_name":"Pannell","full_name":"Pannell, John "}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","issue":"7","quality_controlled":"1","external_id":{"isi":["000493043500004"],"pmid":["30289430"]},"oa_version":"Published Version","day":"04","volume":123,"article_type":"original","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/aob/mcy183"}],"abstract":[{"text":"Sexual dimorphism in morphology, physiology or life history traits is common in dioecious plants at reproductive maturity, but it is typically inconspicuous or absent in juveniles. Although plants of different sexes probably begin to diverge in gene expression both before their reproduction commences and before dimorphism becomes readily apparent, to our knowledge transcriptome-wide differential gene expression has yet to be demonstrated for any angiosperm species.","lang":"eng"}],"article_processing_charge":"No","publication_identifier":{"issn":["0305-7364"],"eissn":["1095-8290"]},"publisher":"Oxford University Press","doi":"10.1093/aob/mcy183","publication_status":"published","year":"2019","date_published":"2019-06-04T00:00:00Z","citation":{"ama":"Cossard G, Toups MA, Pannell J. Sexual dimorphism and rapid turnover in gene expression in pre-reproductive seedlings of a dioecious herb. <i>Annals of botany</i>. 2019;123(7):1119-1131. doi:<a href=\"https://doi.org/10.1093/aob/mcy183\">10.1093/aob/mcy183</a>","chicago":"Cossard, Guillaume, Melissa A Toups, and John  Pannell. “Sexual Dimorphism and Rapid Turnover in Gene Expression in Pre-Reproductive Seedlings of a Dioecious Herb.” <i>Annals of Botany</i>. Oxford University Press, 2019. <a href=\"https://doi.org/10.1093/aob/mcy183\">https://doi.org/10.1093/aob/mcy183</a>.","short":"G. Cossard, M.A. Toups, J. Pannell, Annals of Botany 123 (2019) 1119–1131.","apa":"Cossard, G., Toups, M. A., &#38; Pannell, J. (2019). Sexual dimorphism and rapid turnover in gene expression in pre-reproductive seedlings of a dioecious herb. <i>Annals of Botany</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/aob/mcy183\">https://doi.org/10.1093/aob/mcy183</a>","ieee":"G. Cossard, M. A. Toups, and J. Pannell, “Sexual dimorphism and rapid turnover in gene expression in pre-reproductive seedlings of a dioecious herb,” <i>Annals of botany</i>, vol. 123, no. 7. Oxford University Press, pp. 1119–1131, 2019.","mla":"Cossard, Guillaume, et al. “Sexual Dimorphism and Rapid Turnover in Gene Expression in Pre-Reproductive Seedlings of a Dioecious Herb.” <i>Annals of Botany</i>, vol. 123, no. 7, Oxford University Press, 2019, pp. 1119–31, doi:<a href=\"https://doi.org/10.1093/aob/mcy183\">10.1093/aob/mcy183</a>.","ista":"Cossard G, Toups MA, Pannell J. 2019. Sexual dimorphism and rapid turnover in gene expression in pre-reproductive seedlings of a dioecious herb. Annals of botany. 123(7), 1119–1131."},"isi":1,"title":"Sexual dimorphism and rapid turnover in gene expression in pre-reproductive seedlings of a dioecious herb","date_updated":"2023-08-29T06:42:22Z","department":[{"_id":"BeVi"}],"month":"06"},{"pmid":1,"page":"1909-1922","intvolume":"        11","ddc":["570"],"file":[{"file_size":580205,"relation":"main_file","access_level":"open_access","checksum":"f9e8f6863a406dcc5a36b2be001c138c","date_created":"2019-08-05T07:55:02Z","creator":"dernst","file_id":"6765","content_type":"application/pdf","file_name":"2019_GenomeBiology_Picard.pdf","date_updated":"2020-07-14T12:47:39Z"}],"language":[{"iso":"eng"}],"publication":"Genome biology and evolution","has_accepted_license":"1","acknowledged_ssus":[{"_id":"CampIT"}],"date_created":"2019-08-04T21:59:18Z","status":"public","scopus_import":"1","type":"journal_article","author":[{"id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","full_name":"Picard, Marion A L","last_name":"Picard","orcid":"0000-0002-8101-2518","first_name":"Marion A L"},{"orcid":"0000-0002-4579-8306","first_name":"Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz"},{"first_name":"David","last_name":"Roquis","full_name":"Roquis, David"},{"last_name":"Bulla","full_name":"Bulla, Ingo","first_name":"Ingo"},{"full_name":"Augusto, Ronaldo C.","last_name":"Augusto","first_name":"Ronaldo C."},{"last_name":"Arancibia","full_name":"Arancibia, Nathalie","first_name":"Nathalie"},{"first_name":"Christoph","last_name":"Grunau","full_name":"Grunau, Christoph"},{"last_name":"Boissier","full_name":"Boissier, Jérôme","first_name":"Jérôme"},{"last_name":"Cosseau","full_name":"Cosseau, Céline","first_name":"Céline"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"7","file_date_updated":"2020-07-14T12:47:39Z","_id":"6755","oa":1,"article_type":"original","abstract":[{"text":"Differentiated sex chromosomes are accompanied by a difference in gene dose between X/Z-specific and autosomal genes. At the transcriptomic level, these sex-linked genes can lead to expression imbalance, or gene dosage can be compensated by epigenetic mechanisms and results into expression level equalization. Schistosoma mansoni has been previously described as a ZW species (i.e., female heterogamety, in opposition to XY male heterogametic species) with a partial dosage compensation, but underlying mechanisms are still unexplored. Here, we combine transcriptomic (RNA-Seq) and epigenetic data (ChIP-Seq against H3K4me3, H3K27me3,andH4K20me1histonemarks) in free larval cercariae and intravertebrate parasitic stages. For the first time, we describe differences in dosage compensation status in ZW females, depending on the parasitic status: free cercariae display global dosage compensation, whereas intravertebrate stages show a partial dosage compensation. We also highlight regional differences of gene expression along the Z chromosome in cercariae, but not in the intravertebrate stages. Finally, we feature a consistent permissive chromatin landscape of the Z chromosome in both sexes and stages. We argue that dosage compensation in schistosomes is characterized by chromatin remodeling mechanisms in the Z-specific region.","lang":"eng"}],"external_id":{"pmid":["31273378"],"isi":["000484039500018"]},"quality_controlled":"1","day":"01","volume":11,"oa_version":"Published Version","isi":1,"title":"Dosage compensation throughout the Schistosoma mansoni lifecycle: Specific chromatin landscape of the Z chromosome","month":"07","department":[{"_id":"BeVi"}],"date_updated":"2025-05-14T11:08:50Z","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)"},"license":"https://creativecommons.org/licenses/by/4.0/","doi":"10.1093/gbe/evz133","article_processing_charge":"No","publisher":"Oxford University Press","publication_identifier":{"eissn":["1759-6653"]},"publication_status":"published","citation":{"ieee":"M. A. L. Picard <i>et al.</i>, “Dosage compensation throughout the Schistosoma mansoni lifecycle: Specific chromatin landscape of the Z chromosome,” <i>Genome biology and evolution</i>, vol. 11, no. 7. Oxford University Press, pp. 1909–1922, 2019.","mla":"Picard, Marion A. L., et al. “Dosage Compensation throughout the Schistosoma Mansoni Lifecycle: Specific Chromatin Landscape of the Z Chromosome.” <i>Genome Biology and Evolution</i>, vol. 11, no. 7, Oxford University Press, 2019, pp. 1909–22, doi:<a href=\"https://doi.org/10.1093/gbe/evz133\">10.1093/gbe/evz133</a>.","ista":"Picard MAL, Vicoso B, Roquis D, Bulla I, Augusto RC, Arancibia N, Grunau C, Boissier J, Cosseau C. 2019. Dosage compensation throughout the Schistosoma mansoni lifecycle: Specific chromatin landscape of the Z chromosome. Genome biology and evolution. 11(7), 1909–1922.","ama":"Picard MAL, Vicoso B, Roquis D, et al. Dosage compensation throughout the Schistosoma mansoni lifecycle: Specific chromatin landscape of the Z chromosome. <i>Genome biology and evolution</i>. 2019;11(7):1909-1922. doi:<a href=\"https://doi.org/10.1093/gbe/evz133\">10.1093/gbe/evz133</a>","chicago":"Picard, Marion A L, Beatriz Vicoso, David Roquis, Ingo Bulla, Ronaldo C. Augusto, Nathalie Arancibia, Christoph Grunau, Jérôme Boissier, and Céline Cosseau. “Dosage Compensation throughout the Schistosoma Mansoni Lifecycle: Specific Chromatin Landscape of the Z Chromosome.” <i>Genome Biology and Evolution</i>. Oxford University Press, 2019. <a href=\"https://doi.org/10.1093/gbe/evz133\">https://doi.org/10.1093/gbe/evz133</a>.","short":"M.A.L. Picard, B. Vicoso, D. Roquis, I. Bulla, R.C. Augusto, N. Arancibia, C. Grunau, J. Boissier, C. Cosseau, Genome Biology and Evolution 11 (2019) 1909–1922.","apa":"Picard, M. A. L., Vicoso, B., Roquis, D., Bulla, I., Augusto, R. C., Arancibia, N., … Cosseau, C. (2019). Dosage compensation throughout the Schistosoma mansoni lifecycle: Specific chromatin landscape of the Z chromosome. <i>Genome Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/gbe/evz133\">https://doi.org/10.1093/gbe/evz133</a>"},"year":"2019","date_published":"2019-07-01T00:00:00Z"},{"date_updated":"2023-08-29T07:10:44Z","department":[{"_id":"BeVi"}],"month":"11","title":"Diurnal variation in opsin expression and common housekeeping genes necessitates comprehensive normalization methods for quantitative real-time PCR analyses","isi":1,"date_published":"2019-11-01T00:00:00Z","year":"2019","citation":{"mla":"Yourick, Miranda R., et al. “Diurnal Variation in Opsin Expression and Common Housekeeping Genes Necessitates Comprehensive Normalization Methods for Quantitative Real-Time PCR Analyses.” <i>Molecular Ecology Resources</i>, vol. 19, no. 6, Wiley, 2019, pp. 1447–60, doi:<a href=\"https://doi.org/10.1111/1755-0998.13062\">10.1111/1755-0998.13062</a>.","ieee":"M. R. Yourick <i>et al.</i>, “Diurnal variation in opsin expression and common housekeeping genes necessitates comprehensive normalization methods for quantitative real-time PCR analyses,” <i>Molecular Ecology Resources</i>, vol. 19, no. 6. Wiley, pp. 1447–1460, 2019.","ista":"Yourick MR, Sandkam BA, Gammerdinger WJ, Escobar-Camacho D, Nandamuri SP, Clark FE, Joyce B, Conte MA, Kocher TD, Carleton KL. 2019. Diurnal variation in opsin expression and common housekeeping genes necessitates comprehensive normalization methods for quantitative real-time PCR analyses. Molecular Ecology Resources. 19(6), 1447–1460.","chicago":"Yourick, Miranda R., Benjamin A. Sandkam, William J Gammerdinger, Daniel Escobar-Camacho, Sri Pratima Nandamuri, Frances E. Clark, Brendan Joyce, Matthew A. Conte, Thomas D. Kocher, and Karen L. Carleton. “Diurnal Variation in Opsin Expression and Common Housekeeping Genes Necessitates Comprehensive Normalization Methods for Quantitative Real-Time PCR Analyses.” <i>Molecular Ecology Resources</i>. Wiley, 2019. <a href=\"https://doi.org/10.1111/1755-0998.13062\">https://doi.org/10.1111/1755-0998.13062</a>.","ama":"Yourick MR, Sandkam BA, Gammerdinger WJ, et al. Diurnal variation in opsin expression and common housekeeping genes necessitates comprehensive normalization methods for quantitative real-time PCR analyses. <i>Molecular Ecology Resources</i>. 2019;19(6):1447-1460. doi:<a href=\"https://doi.org/10.1111/1755-0998.13062\">10.1111/1755-0998.13062</a>","apa":"Yourick, M. R., Sandkam, B. A., Gammerdinger, W. J., Escobar-Camacho, D., Nandamuri, S. P., Clark, F. E., … Carleton, K. L. (2019). Diurnal variation in opsin expression and common housekeeping genes necessitates comprehensive normalization methods for quantitative real-time PCR analyses. <i>Molecular Ecology Resources</i>. Wiley. <a href=\"https://doi.org/10.1111/1755-0998.13062\">https://doi.org/10.1111/1755-0998.13062</a>","short":"M.R. Yourick, B.A. Sandkam, W.J. Gammerdinger, D. Escobar-Camacho, S.P. Nandamuri, F.E. Clark, B. Joyce, M.A. Conte, T.D. Kocher, K.L. Carleton, Molecular Ecology Resources 19 (2019) 1447–1460."},"publication_status":"published","publication_identifier":{"eissn":["1755-0998"]},"publisher":"Wiley","article_processing_charge":"No","doi":"10.1111/1755-0998.13062","abstract":[{"lang":"eng","text":"To determine the visual sensitivities of an organism of interest, quantitative reverse transcription–polymerase chain reaction (qRT–PCR) is often used to quantify expression of the light‐sensitive opsins in the retina. While qRT–PCR is an affordable, high‐throughput method for measuring expression, it comes with inherent normalization issues that affect the interpretation of results, especially as opsin expression can vary greatly based on developmental stage, light environment or diurnal cycles. We tested for diurnal cycles of opsin expression over a period of 24 hr at 1‐hr increments and examined how normalization affects a data set with fluctuating expression levels using qRT–PCR and transcriptome data from the retinae of the cichlid Pelmatolapia mariae. We compared five methods of normalizing opsin expression relative to (a) the average of three stably expressed housekeeping genes (Ube2z, EF1‐α and β‐actin), (b) total RNA concentration, (c) GNAT2, (the cone‐specific subunit of transducin), (d) total opsin expression and (e) only opsins expressed in the same cone type. Normalizing by proportion of cone type produced the least variation and would be best for removing time‐of‐day variation. In contrast, normalizing by housekeeping genes produced the highest daily variation in expression and demonstrated that the peak of cone opsin expression was in the late afternoon. A weighted correlation network analysis showed that the expression of different cone opsins follows a very similar daily cycle. With the knowledge of how these normalization methods affect opsin expression data, we make recommendations for designing sampling approaches and quantification methods based upon the scientific question being examined."}],"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6995727"}],"article_type":"original","volume":19,"day":"01","oa_version":"Submitted Version","external_id":{"isi":["000480196800001"],"pmid":["31325910"]},"quality_controlled":"1","issue":"6","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Yourick, Miranda R.","last_name":"Yourick","first_name":"Miranda R."},{"full_name":"Sandkam, Benjamin A.","last_name":"Sandkam","first_name":"Benjamin A."},{"orcid":"0000-0001-9638-1220","first_name":"William J","full_name":"Gammerdinger, William J","id":"3A7E01BC-F248-11E8-B48F-1D18A9856A87","last_name":"Gammerdinger"},{"first_name":"Daniel","last_name":"Escobar-Camacho","full_name":"Escobar-Camacho, Daniel"},{"last_name":"Nandamuri","full_name":"Nandamuri, Sri Pratima","first_name":"Sri Pratima"},{"first_name":"Frances E.","last_name":"Clark","full_name":"Clark, Frances E."},{"first_name":"Brendan","full_name":"Joyce, Brendan","last_name":"Joyce"},{"full_name":"Conte, Matthew A.","last_name":"Conte","first_name":"Matthew A."},{"last_name":"Kocher","full_name":"Kocher, Thomas D.","first_name":"Thomas D."},{"first_name":"Karen L.","last_name":"Carleton","full_name":"Carleton, Karen L."}],"type":"journal_article","oa":1,"_id":"6821","intvolume":"        19","page":"1447-1460","pmid":1,"date_created":"2019-08-18T22:00:41Z","status":"public","scopus_import":"1","publication":"Molecular Ecology Resources","language":[{"iso":"eng"}]},{"_id":"6983","oa":1,"author":[{"id":"48D3F8DE-F248-11E8-B48F-1D18A9856A87","full_name":"Kelemen, Réka K","last_name":"Kelemen","orcid":"0000-0002-8489-9281","first_name":"Réka K"},{"full_name":"Rajakaruna, H","last_name":"Rajakaruna","first_name":"H"},{"last_name":"Cockburn","full_name":"Cockburn, IA","first_name":"IA"},{"last_name":"Ganusov","full_name":"Ganusov, VV","first_name":"VV"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","file_date_updated":"2020-07-14T12:47:46Z","publication":"Frontiers in Immunology","language":[{"iso":"eng"}],"has_accepted_license":"1","date_created":"2019-11-04T15:50:06Z","scopus_import":"1","status":"public","pmid":1,"intvolume":"        10","ddc":["570"],"file":[{"content_type":"application/pdf","file_name":"2019_FrontiersImmonology_Kelemen.pdf","date_updated":"2020-07-14T12:47:46Z","file_id":"6984","creator":"dernst","checksum":"68d1708f7aa412544159b498ef17a6b9","date_created":"2019-11-04T15:54:00Z","file_size":2083061,"relation":"main_file","access_level":"open_access"}],"publication_identifier":{"issn":["1664-3224"]},"article_processing_charge":"No","publisher":"Frontiers","doi":"10.3389/fimmu.2019.02153","publication_status":"published","year":"2019","date_published":"2019-09-20T00:00:00Z","citation":{"mla":"Kelemen, Réka K., et al. “Clustering of Activated CD8 T Cells around Malaria-Infected Hepatocytes Is Rapid and Is Driven by Antigen-Specific Cells.” <i>Frontiers in Immunology</i>, vol. 10, 2153, Frontiers, 2019, doi:<a href=\"https://doi.org/10.3389/fimmu.2019.02153\">10.3389/fimmu.2019.02153</a>.","ieee":"R. K. Kelemen, H. Rajakaruna, I. Cockburn, and V. Ganusov, “Clustering of activated CD8 T cells around Malaria-infected hepatocytes is rapid and is driven by antigen-specific cells,” <i>Frontiers in Immunology</i>, vol. 10. Frontiers, 2019.","ista":"Kelemen RK, Rajakaruna H, Cockburn I, Ganusov V. 2019. Clustering of activated CD8 T cells around Malaria-infected hepatocytes is rapid and is driven by antigen-specific cells. Frontiers in Immunology. 10, 2153.","chicago":"Kelemen, Réka K, H Rajakaruna, IA Cockburn, and VV Ganusov. “Clustering of Activated CD8 T Cells around Malaria-Infected Hepatocytes Is Rapid and Is Driven by Antigen-Specific Cells.” <i>Frontiers in Immunology</i>. Frontiers, 2019. <a href=\"https://doi.org/10.3389/fimmu.2019.02153\">https://doi.org/10.3389/fimmu.2019.02153</a>.","ama":"Kelemen RK, Rajakaruna H, Cockburn I, Ganusov V. Clustering of activated CD8 T cells around Malaria-infected hepatocytes is rapid and is driven by antigen-specific cells. <i>Frontiers in Immunology</i>. 2019;10. doi:<a href=\"https://doi.org/10.3389/fimmu.2019.02153\">10.3389/fimmu.2019.02153</a>","apa":"Kelemen, R. K., Rajakaruna, H., Cockburn, I., &#38; Ganusov, V. (2019). Clustering of activated CD8 T cells around Malaria-infected hepatocytes is rapid and is driven by antigen-specific cells. <i>Frontiers in Immunology</i>. Frontiers. <a href=\"https://doi.org/10.3389/fimmu.2019.02153\">https://doi.org/10.3389/fimmu.2019.02153</a>","short":"R.K. Kelemen, H. Rajakaruna, I. Cockburn, V. Ganusov, Frontiers in Immunology 10 (2019)."},"article_number":"2153","isi":1,"title":"Clustering of activated CD8 T cells around Malaria-infected hepatocytes is rapid and is driven by antigen-specific cells","date_updated":"2023-08-30T07:18:23Z","department":[{"_id":"BeVi"}],"month":"09","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)"},"external_id":{"pmid":["31616407"],"isi":["000487187000001"]},"quality_controlled":"1","oa_version":"Published Version","volume":10,"day":"20","article_type":"original","abstract":[{"lang":"eng","text":"Malaria, a disease caused by parasites of the Plasmodium genus, begins when Plasmodium-infected mosquitoes inject malaria sporozoites while searching for blood. Sporozoites migrate from the skin via blood to the liver, infect hepatocytes, and form liver stages which in mice 48 h later escape into blood and cause clinical malaria. Vaccine-induced activated or memory CD8 T cells are capable of locating and eliminating all liver stages in 48 h, thus preventing the blood-stage disease. However, the rules of how CD8 T cells are able to locate all liver stages within a relatively short time period remains poorly understood. We recently reported formation of clusters consisting of variable numbers of activated CD8 T cells around Plasmodium yoelii (Py)-infected hepatocytes. Using a combination of experimental data and mathematical models we now provide additional insights into mechanisms of formation of these clusters. First, we show that a model in which cluster formation is driven exclusively by T-cell-extrinsic factors, such as variability in “attractiveness” of different liver stages, cannot explain distribution of cluster sizes in different experimental conditions. In contrast, the model in which cluster formation is driven by the positive feedback loop (i.e., larger clusters attract more CD8 T cells) can accurately explain the available data. Second, while both Py-specific CD8 T cells and T cells of irrelevant specificity (non-specific CD8 T cells) are attracted to the clusters, we found no evidence that non-specific CD8 T cells play a role in cluster formation. Third and finally, mathematical modeling suggested that formation of clusters occurs rapidly, within few hours after adoptive transfer of CD8 T cells, thus illustrating high efficiency of CD8 T cells in locating their targets in complex peripheral organs, such as the liver. Taken together, our analysis provides novel insights into and attempts to discriminate between alternative mechanisms driving the formation of clusters of antigen-specific CD8 T cells in the liver."}]},{"_id":"7146","author":[{"last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","first_name":"Beatriz"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","type":"journal_article","issue":"12","publication":"Nature Ecology & Evolution","language":[{"iso":"eng"}],"date_created":"2019-12-04T16:05:25Z","status":"public","scopus_import":"1","intvolume":"         3","page":"1632-1641","publication_status":"published","publisher":"Springer Nature","article_processing_charge":"No","publication_identifier":{"issn":["2397-334X"]},"doi":"10.1038/s41559-019-1050-8","date_published":"2019-11-25T00:00:00Z","year":"2019","citation":{"short":"B. Vicoso, Nature Ecology &#38; Evolution 3 (2019) 1632–1641.","apa":"Vicoso, B. (2019). Molecular and evolutionary dynamics of animal sex-chromosome turnover. <i>Nature Ecology &#38; Evolution</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41559-019-1050-8\">https://doi.org/10.1038/s41559-019-1050-8</a>","ama":"Vicoso B. Molecular and evolutionary dynamics of animal sex-chromosome turnover. <i>Nature Ecology &#38; Evolution</i>. 2019;3(12):1632-1641. doi:<a href=\"https://doi.org/10.1038/s41559-019-1050-8\">10.1038/s41559-019-1050-8</a>","chicago":"Vicoso, Beatriz. “Molecular and Evolutionary Dynamics of Animal Sex-Chromosome Turnover.” <i>Nature Ecology &#38; Evolution</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41559-019-1050-8\">https://doi.org/10.1038/s41559-019-1050-8</a>.","ista":"Vicoso B. 2019. Molecular and evolutionary dynamics of animal sex-chromosome turnover. Nature Ecology &#38; Evolution. 3(12), 1632–1641.","ieee":"B. Vicoso, “Molecular and evolutionary dynamics of animal sex-chromosome turnover,” <i>Nature Ecology &#38; Evolution</i>, vol. 3, no. 12. Springer Nature, pp. 1632–1641, 2019.","mla":"Vicoso, Beatriz. “Molecular and Evolutionary Dynamics of Animal Sex-Chromosome Turnover.” <i>Nature Ecology &#38; Evolution</i>, vol. 3, no. 12, Springer Nature, 2019, pp. 1632–41, doi:<a href=\"https://doi.org/10.1038/s41559-019-1050-8\">10.1038/s41559-019-1050-8</a>."},"title":"Molecular and evolutionary dynamics of animal sex-chromosome turnover","isi":1,"date_updated":"2025-04-14T07:41:21Z","department":[{"_id":"BeVi"}],"month":"11","quality_controlled":"1","external_id":{"isi":["000500728800009"]},"project":[{"grant_number":"715257","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","_id":"250BDE62-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"day":"25","oa_version":"None","volume":3,"ec_funded":1,"abstract":[{"text":"Prevailing models of sex-chromosome evolution were largely inspired by the stable and highly differentiated XY pairs of model organisms, such as those of mammals and flies. Recent work has uncovered an incredible diversity of sex-determining systems, bringing some of the assumptions of these traditional models into question. One particular question that has arisen is what drives some sex chromosomes to be maintained over millions of years and differentiate fully, while others are replaced by new sex-determining chromosomes before differentiation has occurred. Here, I review recent data on the variability of sex-determining genes and sex chromosomes in different non-model vertebrates and invertebrates, and discuss some theoretical models that have been put forward to account for this diversity.","lang":"eng"}],"article_type":"original"},{"date_updated":"2025-04-14T07:41:20Z","department":[{"_id":"BeVi"}],"month":"07","isi":1,"title":"Early sex-chromosome evolution in the diploid dioecious plant Mercurialis annua","year":"2019","date_published":"2019-07-01T00:00:00Z","citation":{"chicago":"Veltsos, Paris, Kate E. Ridout, Melissa A Toups, Santiago C. González-Martínez, Aline Muyle, Olivier Emery, Pasi Rastas, et al. “Early Sex-Chromosome Evolution in the Diploid Dioecious Plant Mercurialis Annua.” <i>Genetics</i>. Genetics Society of America, 2019. <a href=\"https://doi.org/10.1534/genetics.119.302045\">https://doi.org/10.1534/genetics.119.302045</a>.","ama":"Veltsos P, Ridout KE, Toups MA, et al. Early sex-chromosome evolution in the diploid dioecious plant Mercurialis annua. <i>Genetics</i>. 2019;212(3):815-835. doi:<a href=\"https://doi.org/10.1534/genetics.119.302045\">10.1534/genetics.119.302045</a>","apa":"Veltsos, P., Ridout, K. E., Toups, M. A., González-Martínez, S. C., Muyle, A., Emery, O., … Pannell, J. R. (2019). Early sex-chromosome evolution in the diploid dioecious plant Mercurialis annua. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.119.302045\">https://doi.org/10.1534/genetics.119.302045</a>","short":"P. Veltsos, K.E. Ridout, M.A. Toups, S.C. González-Martínez, A. Muyle, O. Emery, P. Rastas, V. Hudzieczek, R. Hobza, B. Vyskot, G.A.B. Marais, D.A. Filatov, J.R. Pannell, Genetics 212 (2019) 815–835.","mla":"Veltsos, Paris, et al. “Early Sex-Chromosome Evolution in the Diploid Dioecious Plant Mercurialis Annua.” <i>Genetics</i>, vol. 212, no. 3, Genetics Society of America, 2019, pp. 815–35, doi:<a href=\"https://doi.org/10.1534/genetics.119.302045\">10.1534/genetics.119.302045</a>.","ieee":"P. Veltsos <i>et al.</i>, “Early sex-chromosome evolution in the diploid dioecious plant Mercurialis annua,” <i>Genetics</i>, vol. 212, no. 3. Genetics Society of America, pp. 815–835, 2019.","ista":"Veltsos P, Ridout KE, Toups MA, González-Martínez SC, Muyle A, Emery O, Rastas P, Hudzieczek V, Hobza R, Vyskot B, Marais GAB, Filatov DA, Pannell JR. 2019. Early sex-chromosome evolution in the diploid dioecious plant Mercurialis annua. Genetics. 212(3), 815–835."},"publisher":"Genetics Society of America","article_processing_charge":"No","publication_identifier":{"eissn":["1943-2631"],"issn":["0016-6731"]},"doi":"10.1534/genetics.119.302045","publication_status":"published","article_type":"original","abstract":[{"lang":"eng","text":"Suppressed recombination allows divergence between homologous sex chromosomes and the functionality of their genes. Here, we reveal patterns of the earliest stages of sex-chromosome evolution in the diploid dioecious herb Mercurialis annua on the basis of cytological analysis, de novo genome assembly and annotation, genetic mapping, exome resequencing of natural populations, and transcriptome analysis. The genome assembly contained 34,105 expressed genes, of which 10,076 were assigned to linkage groups. Genetic mapping and exome resequencing of individuals across the species range both identified the largest linkage group, LG1, as the sex chromosome. Although the sex chromosomes of M. annua are karyotypically homomorphic, we estimate that about one-third of the Y chromosome, containing 568 transcripts and spanning 22.3 cM in the corresponding female map, has ceased recombining. Nevertheless, we found limited evidence for Y-chromosome degeneration in terms of gene loss and pseudogenization, and most X- and Y-linked genes appear to have diverged in the period subsequent to speciation between M. annua and its sister species M. huetii, which shares the same sex-determining region. Taken together, our results suggest that the M. annua Y chromosome has at least two evolutionary strata: a small old stratum shared with M. huetii, and a more recent larger stratum that is probably unique to M. annua and that stopped recombining ∼1 MYA. Patterns of gene expression within the nonrecombining region are consistent with the idea that sexually antagonistic selection may have played a role in favoring suppressed recombination."}],"main_file_link":[{"url":"https://doi.org/10.1534/genetics.119.302045","open_access":"1"}],"ec_funded":1,"volume":212,"oa_version":"Published Version","day":"01","external_id":{"pmid":["31113811"],"isi":["000474809300015"]},"quality_controlled":"1","project":[{"name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","_id":"250BDE62-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"715257"}],"issue":"3","author":[{"last_name":"Veltsos","full_name":"Veltsos, Paris","first_name":"Paris"},{"first_name":"Kate E.","last_name":"Ridout","full_name":"Ridout, Kate E."},{"last_name":"Toups","full_name":"Toups, Melissa A","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","first_name":"Melissa A","orcid":"0000-0002-9752-7380"},{"full_name":"González-Martínez, Santiago C.","last_name":"González-Martínez","first_name":"Santiago C."},{"first_name":"Aline","full_name":"Muyle, Aline","last_name":"Muyle"},{"last_name":"Emery","full_name":"Emery, Olivier","first_name":"Olivier"},{"first_name":"Pasi","last_name":"Rastas","full_name":"Rastas, Pasi"},{"first_name":"Vojtech","last_name":"Hudzieczek","full_name":"Hudzieczek, Vojtech"},{"last_name":"Hobza","full_name":"Hobza, Roman","first_name":"Roman"},{"last_name":"Vyskot","full_name":"Vyskot, Boris","first_name":"Boris"},{"full_name":"Marais, Gabriel A. B.","last_name":"Marais","first_name":"Gabriel A. B."},{"first_name":"Dmitry A.","full_name":"Filatov, Dmitry A.","last_name":"Filatov"},{"full_name":"Pannell, John R.","last_name":"Pannell","first_name":"John R."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","type":"journal_article","oa":1,"_id":"7400","intvolume":"       212","page":"815-835","pmid":1,"scopus_import":"1","date_created":"2020-01-29T16:15:44Z","status":"public","publication":"Genetics","language":[{"iso":"eng"}]},{"publication_identifier":{"eissn":["1365-294X"],"issn":["0962-1083"]},"publisher":"Wiley","article_processing_charge":"No","doi":"10.1111/mec.14990","publication_status":"published","year":"2019","date_published":"2019-04-01T00:00:00Z","citation":{"ama":"Toups MA, Rodrigues N, Perrin N, Kirkpatrick M. A reciprocal translocation radically reshapes sex‐linked inheritance in the common frog. <i>Molecular Ecology</i>. 2019;28(8):1877-1889. doi:<a href=\"https://doi.org/10.1111/mec.14990\">10.1111/mec.14990</a>","chicago":"Toups, Melissa A, Nicolas Rodrigues, Nicolas Perrin, and Mark Kirkpatrick. “A Reciprocal Translocation Radically Reshapes Sex‐linked Inheritance in the Common Frog.” <i>Molecular Ecology</i>. Wiley, 2019. <a href=\"https://doi.org/10.1111/mec.14990\">https://doi.org/10.1111/mec.14990</a>.","short":"M.A. Toups, N. Rodrigues, N. Perrin, M. Kirkpatrick, Molecular Ecology 28 (2019) 1877–1889.","apa":"Toups, M. A., Rodrigues, N., Perrin, N., &#38; Kirkpatrick, M. (2019). A reciprocal translocation radically reshapes sex‐linked inheritance in the common frog. <i>Molecular Ecology</i>. Wiley. <a href=\"https://doi.org/10.1111/mec.14990\">https://doi.org/10.1111/mec.14990</a>","ieee":"M. A. Toups, N. Rodrigues, N. Perrin, and M. Kirkpatrick, “A reciprocal translocation radically reshapes sex‐linked inheritance in the common frog,” <i>Molecular Ecology</i>, vol. 28, no. 8. Wiley, pp. 1877–1889, 2019.","mla":"Toups, Melissa A., et al. “A Reciprocal Translocation Radically Reshapes Sex‐linked Inheritance in the Common Frog.” <i>Molecular Ecology</i>, vol. 28, no. 8, Wiley, 2019, pp. 1877–89, doi:<a href=\"https://doi.org/10.1111/mec.14990\">10.1111/mec.14990</a>.","ista":"Toups MA, Rodrigues N, Perrin N, Kirkpatrick M. 2019. A reciprocal translocation radically reshapes sex‐linked inheritance in the common frog. Molecular Ecology. 28(8), 1877–1889."},"isi":1,"title":"A reciprocal translocation radically reshapes sex‐linked inheritance in the common frog","date_updated":"2023-09-06T15:00:13Z","month":"04","department":[{"_id":"BeVi"}],"external_id":{"pmid":["30576024"],"isi":["000468200800004"]},"quality_controlled":"1","day":"01","volume":28,"oa_version":"None","article_type":"original","abstract":[{"lang":"eng","text":"X and Y chromosomes can diverge when rearrangements block recombination between them. Here we present the first genomic view of a reciprocal translocation that causes two physically unconnected pairs of chromosomes to be coinherited as sex chromosomes. In a population of the common frog (Rana temporaria), both pairs of X and Y chromosomes show extensive sequence differentiation, but not degeneration of the Y chromosomes. A new method based on gene trees shows both chromosomes are sex‐linked. Furthermore, the gene trees from the two Y chromosomes have identical topologies, showing they have been coinherited since the reciprocal translocation occurred. Reciprocal translocations can thus reshape sex linkage on a much greater scale compared with inversions, the type of rearrangement that is much better known in sex chromosome evolution, and they can greatly amplify the power of sexually antagonistic selection to drive genomic rearrangement. Two more populations show evidence of other rearrangements, suggesting that this species has unprecedented structural polymorphism in its sex chromosomes."}],"_id":"7421","author":[{"id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","full_name":"Toups, Melissa A","last_name":"Toups","first_name":"Melissa A","orcid":"0000-0002-9752-7380"},{"first_name":"Nicolas","full_name":"Rodrigues, Nicolas","last_name":"Rodrigues"},{"first_name":"Nicolas","last_name":"Perrin","full_name":"Perrin, Nicolas"},{"first_name":"Mark","full_name":"Kirkpatrick, Mark","last_name":"Kirkpatrick"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","type":"journal_article","issue":"8","publication":"Molecular Ecology","language":[{"iso":"eng"}],"status":"public","date_created":"2020-01-30T10:33:05Z","intvolume":"        28","page":"1877-1889","pmid":1},{"project":[{"grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program"}],"quality_controlled":"1","external_id":{"isi":["000481376500001"]},"day":"01","volume":224,"oa_version":"Published Version","ec_funded":1,"abstract":[{"lang":"eng","text":"* Understanding the mechanisms causing phenotypic differences between females and males has long fascinated evolutionary biologists. An extensive literature exists on animal sexual dimorphism but less information is known about sex differences in plants, particularly the extent of geographical variation in sexual dimorphism and its life‐cycle dynamics.\r\n* Here, we investigated patterns of genetically based sexual dimorphism in vegetative and reproductive traits of a wind‐pollinated dioecious plant, Rumex hastatulus, across three life‐cycle stages using open‐pollinated families from 30 populations spanning the geographic range and chromosomal variation (XY and XY1Y2) of the species.\r\n* The direction and degree of sexual dimorphism was highly variable among populations and life‐cycle stages. Sex‐specific differences in reproductive function explained a significant amount of temporal change in sexual dimorphism. For several traits, geographical variation in sexual dimorphism was associated with bioclimatic parameters, likely due to the differential responses of the sexes to climate. We found no systematic differences in sexual dimorphism between chromosome races.\r\n* Sex‐specific trait differences in dioecious plants largely result from a balance between sexual and natural selection on resource allocation. Our results indicate that abiotic factors associated with geographical context also play a role in modifying sexual dimorphism during the plant life‐cycle."}],"article_type":"original","publication_status":"published","doi":"10.1111/nph.16050","publication_identifier":{"eissn":["1469-8137"]},"publisher":"Wiley","article_processing_charge":"Yes (via OA deal)","citation":{"ama":"Puixeu Sala G, Pickup M, Field D, Barrett SCH. Variation in sexual dimorphism in a wind-pollinated plant: The influence of geographical context and life-cycle dynamics. <i>New Phytologist</i>. 2019;224(3):1108-1120. doi:<a href=\"https://doi.org/10.1111/nph.16050\">10.1111/nph.16050</a>","chicago":"Puixeu Sala, Gemma, Melinda Pickup, David Field, and Spencer C.H. Barrett. “Variation in Sexual Dimorphism in a Wind-Pollinated Plant: The Influence of Geographical Context and Life-Cycle Dynamics.” <i>New Phytologist</i>. Wiley, 2019. <a href=\"https://doi.org/10.1111/nph.16050\">https://doi.org/10.1111/nph.16050</a>.","short":"G. Puixeu Sala, M. Pickup, D. Field, S.C.H. Barrett, New Phytologist 224 (2019) 1108–1120.","apa":"Puixeu Sala, G., Pickup, M., Field, D., &#38; Barrett, S. C. H. (2019). Variation in sexual dimorphism in a wind-pollinated plant: The influence of geographical context and life-cycle dynamics. <i>New Phytologist</i>. Wiley. <a href=\"https://doi.org/10.1111/nph.16050\">https://doi.org/10.1111/nph.16050</a>","ieee":"G. Puixeu Sala, M. Pickup, D. Field, and S. C. H. Barrett, “Variation in sexual dimorphism in a wind-pollinated plant: The influence of geographical context and life-cycle dynamics,” <i>New Phytologist</i>, vol. 224, no. 3. Wiley, pp. 1108–1120, 2019.","mla":"Puixeu Sala, Gemma, et al. “Variation in Sexual Dimorphism in a Wind-Pollinated Plant: The Influence of Geographical Context and Life-Cycle Dynamics.” <i>New Phytologist</i>, vol. 224, no. 3, Wiley, 2019, pp. 1108–20, doi:<a href=\"https://doi.org/10.1111/nph.16050\">10.1111/nph.16050</a>.","ista":"Puixeu Sala G, Pickup M, Field D, Barrett SCH. 2019. Variation in sexual dimorphism in a wind-pollinated plant: The influence of geographical context and life-cycle dynamics. New Phytologist. 224(3), 1108–1120."},"date_published":"2019-11-01T00:00:00Z","year":"2019","title":"Variation in sexual dimorphism in a wind-pollinated plant: The influence of geographical context and life-cycle dynamics","isi":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)"},"department":[{"_id":"NiBa"},{"_id":"BeVi"}],"month":"11","date_updated":"2026-04-07T13:25:33Z","has_accepted_license":"1","language":[{"iso":"eng"}],"publication":"New Phytologist","date_created":"2019-08-25T22:00:51Z","scopus_import":"1","status":"public","intvolume":"       224","page":"1108-1120","file":[{"checksum":"6370e7567d96b7b562e77d8b89653f80","date_created":"2019-08-27T12:44:54Z","relation":"main_file","file_size":2314016,"access_level":"open_access","content_type":"application/pdf","file_name":"2019_NewPhytologist_Puixeu.pdf","date_updated":"2020-07-14T12:47:42Z","file_id":"6833","creator":"apreinsp"}],"ddc":["570"],"_id":"6831","related_material":{"record":[{"relation":"research_data","id":"9803","status":"public"},{"status":"public","id":"14058","relation":"dissertation_contains"}]},"oa":1,"type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"id":"33AB266C-F248-11E8-B48F-1D18A9856A87","full_name":"Puixeu Sala, Gemma","last_name":"Puixeu Sala","orcid":"0000-0001-8330-1754","first_name":"Gemma"},{"first_name":"Melinda","orcid":"0000-0001-6118-0541","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","full_name":"Pickup, Melinda","last_name":"Pickup"},{"first_name":"David","orcid":"0000-0002-4014-8478","full_name":"Field, David","last_name":"Field"},{"last_name":"Barrett","full_name":"Barrett, Spencer C.H.","first_name":"Spencer C.H."}],"file_date_updated":"2020-07-14T12:47:42Z","issue":"3","corr_author":"1"},{"main_file_link":[{"url":"https://doi.org/10.5061/dryad.n1701c9","open_access":"1"}],"abstract":[{"lang":"eng","text":"Understanding the mechanisms causing phenotypic differences between females and males has long fascinated evolutionary biologists. An extensive literature exists on animal sexual dimorphism but less is known about sex differences in plants, particularly the extent of geographical variation in sexual dimorphism and its life-cycle dynamics. Here, we investigate patterns of genetically-based sexual dimorphism in vegetative and reproductive traits of a wind-pollinated dioecious plant, Rumex hastatulus, across three life-cycle stages using open-pollinated families from 30 populations spanning the geographic range and chromosomal variation (XY and XY1Y2) of the species. The direction and degree of sexual dimorphism was highly variable among populations and life-cycle stages. Sex-specific differences in reproductive function explained a significant amount of temporal change in sexual dimorphism. For several traits, geographical variation in sexual dimorphism was associated with bioclimatic parameters, likely due to the differential responses of the sexes to climate. We found no systematic differences in sexual dimorphism between chromosome races. Sex-specific trait differences in dioecious plants largely result from a balance between sexual and natural selection on resource allocation. Our results indicate that abiotic factors associated with geographical context also play a role in modifying sexual dimorphism during the plant life cycle."}],"day":"22","oa_version":"Published Version","status":"public","date_created":"2021-08-06T11:48:42Z","title":"Data from: Variation in sexual dimorphism in a wind-pollinated plant: the influence of geographical context and life-cycle dynamics","type":"research_data_reference","author":[{"full_name":"Puixeu Sala, Gemma","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","last_name":"Puixeu Sala","first_name":"Gemma","orcid":"0000-0001-8330-1754"},{"id":"2C78037E-F248-11E8-B48F-1D18A9856A87","full_name":"Pickup, Melinda","last_name":"Pickup","orcid":"0000-0001-6118-0541","first_name":"Melinda"},{"full_name":"Field, David","last_name":"Field","first_name":"David"},{"full_name":"Barrett, Spencer C.H.","last_name":"Barrett","first_name":"Spencer C.H."}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","month":"07","department":[{"_id":"NiBa"},{"_id":"BeVi"}],"date_updated":"2026-04-07T13:25:33Z","_id":"9803","doi":"10.5061/dryad.n1701c9","article_processing_charge":"No","publisher":"Dryad","citation":{"apa":"Puixeu Sala, G., Pickup, M., Field, D., &#38; Barrett, S. C. H. (2019). Data from: Variation in sexual dimorphism in a wind-pollinated plant: the influence of geographical context and life-cycle dynamics. Dryad. <a href=\"https://doi.org/10.5061/dryad.n1701c9\">https://doi.org/10.5061/dryad.n1701c9</a>","short":"G. Puixeu Sala, M. Pickup, D. Field, S.C.H. Barrett, (2019).","chicago":"Puixeu Sala, Gemma, Melinda Pickup, David Field, and Spencer C.H. Barrett. “Data from: Variation in Sexual Dimorphism in a Wind-Pollinated Plant: The Influence of Geographical Context and Life-Cycle Dynamics.” Dryad, 2019. <a href=\"https://doi.org/10.5061/dryad.n1701c9\">https://doi.org/10.5061/dryad.n1701c9</a>.","ama":"Puixeu Sala G, Pickup M, Field D, Barrett SCH. Data from: Variation in sexual dimorphism in a wind-pollinated plant: the influence of geographical context and life-cycle dynamics. 2019. doi:<a href=\"https://doi.org/10.5061/dryad.n1701c9\">10.5061/dryad.n1701c9</a>","ista":"Puixeu Sala G, Pickup M, Field D, Barrett SCH. 2019. Data from: Variation in sexual dimorphism in a wind-pollinated plant: the influence of geographical context and life-cycle dynamics, Dryad, <a href=\"https://doi.org/10.5061/dryad.n1701c9\">10.5061/dryad.n1701c9</a>.","mla":"Puixeu Sala, Gemma, et al. <i>Data from: Variation in Sexual Dimorphism in a Wind-Pollinated Plant: The Influence of Geographical Context and Life-Cycle Dynamics</i>. Dryad, 2019, doi:<a href=\"https://doi.org/10.5061/dryad.n1701c9\">10.5061/dryad.n1701c9</a>.","ieee":"G. Puixeu Sala, M. Pickup, D. Field, and S. C. H. Barrett, “Data from: Variation in sexual dimorphism in a wind-pollinated plant: the influence of geographical context and life-cycle dynamics.” Dryad, 2019."},"oa":1,"related_material":{"record":[{"id":"6831","status":"public","relation":"used_in_publication"},{"status":"public","id":"14058","relation":"used_in_publication"}]},"year":"2019","date_published":"2019-07-22T00:00:00Z"},{"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"orcid":"0000-0001-8441-5075","first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","full_name":"Fraisse, Christelle","last_name":"Fraisse"},{"full_name":"Roux, Camille","last_name":"Roux","first_name":"Camille"},{"first_name":"Pierre","full_name":"Gagnaire, Pierre","last_name":"Gagnaire"},{"first_name":"Jonathan","full_name":"Romiguier, Jonathan","last_name":"Romiguier"},{"full_name":"Faivre, Nicolas","last_name":"Faivre","first_name":"Nicolas"},{"first_name":"John","full_name":"Welch, John","last_name":"Welch"},{"first_name":"Nicolas","full_name":"Bierne, Nicolas","last_name":"Bierne"}],"file_date_updated":"2020-07-14T12:44:48Z","issue":"7","_id":"139","oa":1,"intvolume":"      2018","publist_id":"7784","file":[{"access_level":"open_access","file_size":1480792,"relation":"main_file","date_created":"2018-12-18T09:42:11Z","checksum":"7d55ae22598a1c70759cd671600cff53","file_id":"5739","creator":"dernst","file_name":"2018_PeerJ_Fraisse.pdf","date_updated":"2020-07-14T12:44:48Z","content_type":"application/pdf"}],"ddc":["576"],"has_accepted_license":"1","language":[{"iso":"eng"}],"publication":"PeerJ","status":"public","date_created":"2018-12-11T11:44:50Z","scopus_import":"1","title":"The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies","article_number":"30083438","isi":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)"},"department":[{"_id":"BeVi"},{"_id":"NiBa"}],"month":"07","date_updated":"2023-10-17T12:25:28Z","publication_status":"published","doi":"10.7717/peerj.5198","article_processing_charge":"No","publisher":"PeerJ","citation":{"chicago":"Fraisse, Christelle, Camille Roux, Pierre Gagnaire, Jonathan Romiguier, Nicolas Faivre, John Welch, and Nicolas Bierne. “The Divergence History of European Blue Mussel Species Reconstructed from Approximate Bayesian Computation: The Effects of Sequencing Techniques and Sampling Strategies.” <i>PeerJ</i>. PeerJ, 2018. <a href=\"https://doi.org/10.7717/peerj.5198\">https://doi.org/10.7717/peerj.5198</a>.","ama":"Fraisse C, Roux C, Gagnaire P, et al. The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies. <i>PeerJ</i>. 2018;2018(7). doi:<a href=\"https://doi.org/10.7717/peerj.5198\">10.7717/peerj.5198</a>","apa":"Fraisse, C., Roux, C., Gagnaire, P., Romiguier, J., Faivre, N., Welch, J., &#38; Bierne, N. (2018). The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies. <i>PeerJ</i>. PeerJ. <a href=\"https://doi.org/10.7717/peerj.5198\">https://doi.org/10.7717/peerj.5198</a>","short":"C. Fraisse, C. Roux, P. Gagnaire, J. Romiguier, N. Faivre, J. Welch, N. Bierne, PeerJ 2018 (2018).","mla":"Fraisse, Christelle, et al. “The Divergence History of European Blue Mussel Species Reconstructed from Approximate Bayesian Computation: The Effects of Sequencing Techniques and Sampling Strategies.” <i>PeerJ</i>, vol. 2018, no. 7, 30083438, PeerJ, 2018, doi:<a href=\"https://doi.org/10.7717/peerj.5198\">10.7717/peerj.5198</a>.","ieee":"C. Fraisse <i>et al.</i>, “The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies,” <i>PeerJ</i>, vol. 2018, no. 7. PeerJ, 2018.","ista":"Fraisse C, Roux C, Gagnaire P, Romiguier J, Faivre N, Welch J, Bierne N. 2018. The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies. PeerJ. 2018(7), 30083438."},"year":"2018","date_published":"2018-07-30T00:00:00Z","abstract":[{"lang":"eng","text":"Genome-scale diversity data are increasingly available in a variety of biological systems, and can be used to reconstruct the past evolutionary history of species divergence. However, extracting the full demographic information from these data is not trivial, and requires inferential methods that account for the diversity of coalescent histories throughout the genome. Here, we evaluate the potential and limitations of one such approach. We reexamine a well-known system of mussel sister species, using the joint site frequency spectrum (jSFS) of synonymousmutations computed either fromexome capture or RNA-seq, in an Approximate Bayesian Computation (ABC) framework. We first assess the best sampling strategy (number of: individuals, loci, and bins in the jSFS), and show that model selection is robust to variation in the number of individuals and loci. In contrast, different binning choices when summarizing the jSFS, strongly affect the results: including classes of low and high frequency shared polymorphisms can more effectively reveal recent migration events. We then take advantage of the flexibility of ABC to compare more realistic models of speciation, including variation in migration rates through time (i.e., periodic connectivity) and across genes (i.e., genome-wide heterogeneity in migration rates). We show that these models were consistently selected as the most probable, suggesting that mussels have experienced a complex history of gene flow during divergence and that the species boundary is semi-permeable. Our work provides a comprehensive evaluation of ABC demographic inference in mussels based on the coding jSFS, and supplies guidelines for employing different sequencing techniques and sampling strategies. We emphasize, perhaps surprisingly, that inferences are less limited by the volume of data, than by the way in which they are analyzed."}],"quality_controlled":"1","external_id":{"isi":["000440484800002"]},"day":"30","volume":2018,"oa_version":"Published Version"},{"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)"},"date_updated":"2025-04-15T08:18:37Z","department":[{"_id":"BeVi"}],"month":"08","title":"Evolution of gene dosage on the Z-chromosome of schistosome parasites","article_number":"e35684","isi":1,"year":"2018","date_published":"2018-08-13T00:00:00Z","citation":{"ista":"Picard MAL, Cosseau C, Ferré S, Quack T, Grevelding C, Couté Y, Vicoso B. 2018. Evolution of gene dosage on the Z-chromosome of schistosome parasites. eLife. 7, e35684.","mla":"Picard, Marion A. L., et al. “Evolution of Gene Dosage on the Z-Chromosome of Schistosome Parasites.” <i>ELife</i>, vol. 7, e35684, eLife Sciences Publications, 2018, doi:<a href=\"https://doi.org/10.7554/eLife.35684\">10.7554/eLife.35684</a>.","ieee":"M. A. L. Picard <i>et al.</i>, “Evolution of gene dosage on the Z-chromosome of schistosome parasites,” <i>eLife</i>, vol. 7. eLife Sciences Publications, 2018.","apa":"Picard, M. A. L., Cosseau, C., Ferré, S., Quack, T., Grevelding, C., Couté, Y., &#38; Vicoso, B. (2018). Evolution of gene dosage on the Z-chromosome of schistosome parasites. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.35684\">https://doi.org/10.7554/eLife.35684</a>","short":"M.A.L. Picard, C. Cosseau, S. Ferré, T. Quack, C. Grevelding, Y. Couté, B. Vicoso, ELife 7 (2018).","chicago":"Picard, Marion A L, Celine Cosseau, Sabrina Ferré, Thomas Quack, Christoph Grevelding, Yohann Couté, and Beatriz Vicoso. “Evolution of Gene Dosage on the Z-Chromosome of Schistosome Parasites.” <i>ELife</i>. eLife Sciences Publications, 2018. <a href=\"https://doi.org/10.7554/eLife.35684\">https://doi.org/10.7554/eLife.35684</a>.","ama":"Picard MAL, Cosseau C, Ferré S, et al. Evolution of gene dosage on the Z-chromosome of schistosome parasites. <i>eLife</i>. 2018;7. doi:<a href=\"https://doi.org/10.7554/eLife.35684\">10.7554/eLife.35684</a>"},"publication_status":"published","publisher":"eLife Sciences Publications","article_processing_charge":"No","doi":"10.7554/eLife.35684","abstract":[{"lang":"eng","text":"XY systems usually show chromosome-wide compensation of X-linked genes, while in many ZW systems, compensation is restricted to a minority of dosage-sensitive genes. Why such differences arose is still unclear. Here, we combine comparative genomics, transcriptomics and proteomics to obtain a complete overview of the evolution of gene dosage on the Z-chromosome of Schistosoma parasites. We compare the Z-chromosome gene content of African (Schistosoma mansoni and S. haematobium) and Asian (S. japonicum) schistosomes and describe lineage-specific evolutionary strata. We use these to assess gene expression evolution following sex-linkage. The resulting patterns suggest a reduction in expression of Z-linked genes in females, combined with upregulation of the Z in both sexes, in line with the first step of Ohno’s classic model of dosage compensation evolution. Quantitative proteomics suggest that post-transcriptional mechanisms do not play a major role in balancing the expression of Z-linked genes. "}],"article_type":"original","day":"13","oa_version":"Published Version","volume":7,"quality_controlled":"1","external_id":{"isi":["000441388200001"]},"project":[{"call_identifier":"FWF","_id":"250ED89C-B435-11E9-9278-68D0E5697425","name":"Sex chromosome evolution under male- and female- heterogamety","grant_number":"P28842-B22"}],"file_date_updated":"2020-07-14T12:44:43Z","acknowledgement":"We are grateful to Lu Dabing (Soochow University, Suzhou, China) for providing Schistosoma japonicum samples, to Ariana Macon (IST Austria) and Georgette Stovall (JLU Giessen) for technical assistance, to IT support at IST Austria for providing optimal environment to bioinformatic analyses, and to the Vicoso lab for comments on the manuscript.","author":[{"first_name":"Marion A","orcid":"0000-0002-8101-2518","last_name":"Picard","full_name":"Picard, Marion A","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Cosseau","full_name":"Cosseau, Celine","first_name":"Celine"},{"full_name":"Ferré, Sabrina","last_name":"Ferré","first_name":"Sabrina"},{"first_name":"Thomas","last_name":"Quack","full_name":"Quack, Thomas"},{"last_name":"Grevelding","full_name":"Grevelding, Christoph","first_name":"Christoph"},{"last_name":"Couté","full_name":"Couté, Yohann","first_name":"Yohann"},{"first_name":"Beatriz","orcid":"0000-0002-4579-8306","last_name":"Vicoso","full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","type":"journal_article","related_material":{"record":[{"relation":"popular_science","id":"5586","status":"public"}]},"oa":1,"_id":"131","file":[{"content_type":"application/pdf","file_name":"2018_eLife_Picard.pdf","date_updated":"2020-07-14T12:44:43Z","creator":"dernst","file_id":"5695","checksum":"d6331d4385b1fffd6b47b45d5949d841","date_created":"2018-12-17T11:55:05Z","relation":"main_file","file_size":3158125,"access_level":"open_access"}],"ddc":["570"],"intvolume":"         7","publist_id":"7792","date_created":"2018-12-11T11:44:47Z","status":"public","scopus_import":"1","has_accepted_license":"1","publication":"eLife","language":[{"iso":"eng"}]},{"file":[{"access_level":"open_access","relation":"main_file","file_size":3985796,"date_created":"2019-02-01T07:52:28Z","checksum":"423069beb1cd3cdd25bf3f464b38f1d7","file_id":"5905","creator":"dernst","date_updated":"2020-07-14T12:45:22Z","file_name":"2018_Genes_Ma.pdf","content_type":"application/pdf"}],"ddc":["570"],"intvolume":"         9","publist_id":"7714","status":"public","date_created":"2018-12-11T11:45:09Z","scopus_import":"1","has_accepted_license":"1","language":[{"iso":"eng"}],"publication":"Genes","file_date_updated":"2020-07-14T12:45:22Z","issue":"6","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Ma, Wen","last_name":"Ma","first_name":"Wen"},{"first_name":"Paris","last_name":"Veltsos","full_name":"Veltsos, Paris"},{"full_name":"Toups, Melissa A","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","last_name":"Toups","first_name":"Melissa A","orcid":"0000-0002-9752-7380"},{"full_name":"Rodrigues, Nicolas","last_name":"Rodrigues","first_name":"Nicolas"},{"first_name":"Roberto","last_name":"Sermier","full_name":"Sermier, Roberto"},{"last_name":"Jeffries","full_name":"Jeffries, Daniel","first_name":"Daniel"},{"full_name":"Perrin, Nicolas","last_name":"Perrin","first_name":"Nicolas"}],"oa":1,"_id":"199","abstract":[{"lang":"eng","text":"Sex-biased genes are central to the study of sexual selection, sexual antagonism, and sex chromosome evolution. We describe a comprehensive de novo assembled transcriptome in the common frog Rana temporaria based on five developmental stages and three adult tissues from both sexes, obtained from a population with karyotypically homomorphic but genetically differentiated sex chromosomes. This allows the study of sex-biased gene expression throughout development, and its effect on the rate of gene evolution while accounting for pleiotropic expression, which is known to negatively correlate with the evolutionary rate. Overall, sex-biased genes had little overlap among developmental stages and adult tissues. Late developmental stages and gonad tissues had the highest numbers of stage-or tissue-specific genes. We find that pleiotropic gene expression is a better predictor than sex bias for the evolutionary rate of genes, though it often interacts with sex bias. Although genetically differentiated, the sex chromosomes were not enriched in sex-biased genes, possibly due to a very recent arrest of XY recombination. These results extend our understanding of the developmental dynamics, tissue specificity, and genomic localization of sex-biased genes."}],"oa_version":"Published Version","volume":9,"day":"12","external_id":{"isi":["000436494200026"]},"quality_controlled":"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)"},"month":"06","department":[{"_id":"BeVi"}],"date_updated":"2024-12-11T13:13:35Z","title":"Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes","article_number":"294","isi":1,"citation":{"chicago":"Ma, Wen, Paris Veltsos, Melissa A Toups, Nicolas Rodrigues, Roberto Sermier, Daniel Jeffries, and Nicolas Perrin. “Tissue Specificity and Dynamics of Sex Biased Gene Expression in a Common Frog Population with Differentiated, yet Homomorphic, Sex Chromosomes.” <i>Genes</i>. MDPI, 2018. <a href=\"https://doi.org/10.3390/genes9060294\">https://doi.org/10.3390/genes9060294</a>.","ama":"Ma W, Veltsos P, Toups MA, et al. Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes. <i>Genes</i>. 2018;9(6). doi:<a href=\"https://doi.org/10.3390/genes9060294\">10.3390/genes9060294</a>","apa":"Ma, W., Veltsos, P., Toups, M. A., Rodrigues, N., Sermier, R., Jeffries, D., &#38; Perrin, N. (2018). Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes. <i>Genes</i>. MDPI. <a href=\"https://doi.org/10.3390/genes9060294\">https://doi.org/10.3390/genes9060294</a>","short":"W. Ma, P. Veltsos, M.A. Toups, N. Rodrigues, R. Sermier, D. Jeffries, N. Perrin, Genes 9 (2018).","mla":"Ma, Wen, et al. “Tissue Specificity and Dynamics of Sex Biased Gene Expression in a Common Frog Population with Differentiated, yet Homomorphic, Sex Chromosomes.” <i>Genes</i>, vol. 9, no. 6, 294, MDPI, 2018, doi:<a href=\"https://doi.org/10.3390/genes9060294\">10.3390/genes9060294</a>.","ieee":"W. Ma <i>et al.</i>, “Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes,” <i>Genes</i>, vol. 9, no. 6. MDPI, 2018.","ista":"Ma W, Veltsos P, Toups MA, Rodrigues N, Sermier R, Jeffries D, Perrin N. 2018. Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes. Genes. 9(6), 294."},"year":"2018","date_published":"2018-06-12T00:00:00Z","publication_status":"published","doi":"10.3390/genes9060294","article_processing_charge":"No","publisher":"MDPI"},{"publist_id":"7730","intvolume":"       330","pmid":1,"page":"254-264","status":"public","date_created":"2018-12-11T11:45:06Z","scopus_import":"1","language":[{"iso":"eng"}],"publication":"Journal of Experimental Zoology Part B: Molecular and Developmental Evolution","type":"journal_article","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"first_name":"Mark","last_name":"Harrison","full_name":"Harrison, Mark"},{"first_name":"Nicolas","last_name":"Arning","full_name":"Arning, Nicolas"},{"first_name":"Lucas","full_name":"Kremer, Lucas","last_name":"Kremer"},{"first_name":"Guillem","full_name":"Ylla, Guillem","last_name":"Ylla"},{"full_name":"Belles, Xavier","last_name":"Belles","first_name":"Xavier"},{"full_name":"Bornberg Bauer, Erich","last_name":"Bornberg Bauer","first_name":"Erich"},{"first_name":"Ann K","orcid":"0000-0001-8871-4961","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","full_name":"Huylmans, Ann K","last_name":"Huylmans"},{"last_name":"Jongepier","full_name":"Jongepier, Evelien","first_name":"Evelien"},{"first_name":"Maria","full_name":"Puilachs, Maria","last_name":"Puilachs"},{"full_name":"Richards, Stephen","last_name":"Richards","first_name":"Stephen"},{"first_name":"Coby","last_name":"Schal","full_name":"Schal, Coby"}],"oa":1,"_id":"190","article_type":"original","abstract":[{"text":"The German cockroach, Blattella germanica, is a worldwide pest that infests buildings, including homes, restaurants, and hospitals, often living in unsanitary conditions. As a disease vector and producer of allergens, this species has major health and economic impacts on humans. Factors contributing to the success of the German cockroach include its resistance to a broad range of insecticides, immunity to many pathogens, and its ability, as an extreme generalist omnivore, to survive on most food sources. The recently published genome shows that B. germanica has an exceptionally high number of protein coding genes. In this study, we investigate the functions of the 93 significantly expanded gene families with the aim to better understand the success of B. germanica as a major pest despite such inhospitable conditions. We find major expansions in gene families with functions related to the detoxification of insecticides and allelochemicals, defense against pathogens, digestion, sensory perception, and gene regulation. These expansions might have allowed B. germanica to develop multiple resistance mechanisms to insecticides and pathogens, and enabled a broad, flexible diet, thus explaining its success in unsanitary conditions and under recurrent chemical control. The findings and resources presented here provide insights for better understanding molecular mechanisms that will facilitate more effective cockroach control.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"https://onlinelibrary.wiley.com/doi/am-pdf/10.1002/jez.b.22824"}],"day":"11","volume":330,"oa_version":"Submitted Version","external_id":{"isi":["000443231000002"],"pmid":["29998472"]},"quality_controlled":"1","department":[{"_id":"BeVi"}],"month":"07","date_updated":"2023-09-11T13:59:54Z","isi":1,"title":"Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest","citation":{"ama":"Harrison M, Arning N, Kremer L, et al. Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest. <i>Journal of Experimental Zoology Part B: Molecular and Developmental Evolution</i>. 2018;330:254-264. doi:<a href=\"https://doi.org/10.1002/jez.b.22824\">10.1002/jez.b.22824</a>","chicago":"Harrison, Mark, Nicolas Arning, Lucas Kremer, Guillem Ylla, Xavier Belles, Erich Bornberg Bauer, Ann K Huylmans, et al. “Expansions of Key Protein Families in the German Cockroach Highlight the Molecular Basis of Its Remarkable Success as a Global Indoor Pest.” <i>Journal of Experimental Zoology Part B: Molecular and Developmental Evolution</i>. Wiley, 2018. <a href=\"https://doi.org/10.1002/jez.b.22824\">https://doi.org/10.1002/jez.b.22824</a>.","short":"M. Harrison, N. Arning, L. Kremer, G. Ylla, X. Belles, E. Bornberg Bauer, A.K. Huylmans, E. Jongepier, M. Puilachs, S. Richards, C. Schal, Journal of Experimental Zoology Part B: Molecular and Developmental Evolution 330 (2018) 254–264.","apa":"Harrison, M., Arning, N., Kremer, L., Ylla, G., Belles, X., Bornberg Bauer, E., … Schal, C. (2018). Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest. <i>Journal of Experimental Zoology Part B: Molecular and Developmental Evolution</i>. Wiley. <a href=\"https://doi.org/10.1002/jez.b.22824\">https://doi.org/10.1002/jez.b.22824</a>","ieee":"M. Harrison <i>et al.</i>, “Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest,” <i>Journal of Experimental Zoology Part B: Molecular and Developmental Evolution</i>, vol. 330. Wiley, pp. 254–264, 2018.","mla":"Harrison, Mark, et al. “Expansions of Key Protein Families in the German Cockroach Highlight the Molecular Basis of Its Remarkable Success as a Global Indoor Pest.” <i>Journal of Experimental Zoology Part B: Molecular and Developmental Evolution</i>, vol. 330, Wiley, 2018, pp. 254–64, doi:<a href=\"https://doi.org/10.1002/jez.b.22824\">10.1002/jez.b.22824</a>.","ista":"Harrison M, Arning N, Kremer L, Ylla G, Belles X, Bornberg Bauer E, Huylmans AK, Jongepier E, Puilachs M, Richards S, Schal C. 2018. Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution. 330, 254–264."},"year":"2018","date_published":"2018-07-11T00:00:00Z","doi":"10.1002/jez.b.22824","article_processing_charge":"No","publisher":"Wiley","publication_status":"published"},{"project":[{"call_identifier":"FWF","name":"Sex chromosome evolution under male- and female- heterogamety","_id":"250ED89C-B435-11E9-9278-68D0E5697425","grant_number":"P28842-B22"}],"oa_version":"Published Version","day":"24","abstract":[{"text":"Input files and scripts from \"Evolution of gene dosage on the Z-chromosome of schistosome parasites\" by Picard M.A.L., et al (2018).","lang":"eng"}],"article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","doi":"10.15479/AT:ISTA:109","date_published":"2018-07-24T00:00:00Z","year":"2018","citation":{"ista":"Vicoso B. 2018. Input files and scripts from ‘Evolution of gene dosage on the Z-chromosome of schistosome parasites’ by Picard M.A.L., et al (2018), Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:109\">10.15479/AT:ISTA:109</a>.","ieee":"B. Vicoso, “Input files and scripts from ‘Evolution of gene dosage on the Z-chromosome of schistosome parasites’ by Picard M.A.L., et al (2018).” Institute of Science and Technology Austria, 2018.","mla":"Vicoso, Beatriz. <i>Input Files and Scripts from “Evolution of Gene Dosage on the Z-Chromosome of Schistosome Parasites” by Picard M.A.L., et Al (2018)</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:109\">10.15479/AT:ISTA:109</a>.","short":"B. Vicoso, (2018).","apa":"Vicoso, B. (2018). Input files and scripts from “Evolution of gene dosage on the Z-chromosome of schistosome parasites” by Picard M.A.L., et al (2018). Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:109\">https://doi.org/10.15479/AT:ISTA:109</a>","ama":"Vicoso B. Input files and scripts from “Evolution of gene dosage on the Z-chromosome of schistosome parasites” by Picard M.A.L., et al (2018). 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:109\">10.15479/AT:ISTA:109</a>","chicago":"Vicoso, Beatriz. “Input Files and Scripts from ‘Evolution of Gene Dosage on the Z-Chromosome of Schistosome Parasites’ by Picard M.A.L., et Al (2018).” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:109\">https://doi.org/10.15479/AT:ISTA:109</a>."},"title":"Input files and scripts from \"Evolution of gene dosage on the Z-chromosome of schistosome parasites\" by Picard M.A.L., et al (2018)","license":"https://creativecommons.org/publicdomain/zero/1.0/","tmp":{"name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png"},"date_updated":"2025-04-15T08:18:37Z","month":"07","department":[{"_id":"BeVi"}],"contributor":[{"last_name":"Picard","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","first_name":"Marion A","orcid":"0000-0002-8101-2518"}],"has_accepted_license":"1","date_created":"2018-12-12T12:31:40Z","keyword":["schistosoma","Z-chromosome","gene expression"],"status":"public","datarep_id":"109","file":[{"checksum":"e60b484bd6f55c08eb66a189cb72c923","date_created":"2018-12-12T13:02:35Z","relation":"main_file","file_size":11918144,"access_level":"open_access","content_type":"application/zip","file_name":"IST-2018-109-v1+1_SupplementaryMethods.zip","date_updated":"2020-07-14T12:47:08Z","creator":"system","file_id":"5601"}],"ddc":["570"],"_id":"5586","oa":1,"related_material":{"record":[{"id":"131","status":"public","relation":"research_paper"}]},"author":[{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz","last_name":"Vicoso","first_name":"Beatriz","orcid":"0000-0002-4579-8306"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"research_data","file_date_updated":"2020-07-14T12:47:08Z"},{"file":[{"access_level":"open_access","file_size":369837892,"relation":"main_file","date_created":"2018-12-19T14:19:52Z","checksum":"aed7ee9ca3f4dc07d8a66945f68e13cd","creator":"cfraisse","file_id":"5758","date_updated":"2020-07-14T12:47:11Z","file_name":"FileS1.zip","content_type":"application/zip"},{"content_type":"application/zip","date_updated":"2020-07-14T12:47:11Z","file_name":"FileS2.zip","file_id":"5759","creator":"cfraisse","checksum":"3592e467b4d8206650860b612d6e12f3","date_created":"2018-12-19T14:19:49Z","relation":"main_file","file_size":84856909,"access_level":"open_access"},{"checksum":"c37ac5d5437c457338afc128c1240655","date_created":"2018-12-19T14:19:49Z","file_size":881133,"relation":"main_file","access_level":"open_access","content_type":"text/plain","file_name":"FileS3.txt","date_updated":"2020-07-14T12:47:11Z","creator":"cfraisse","file_id":"5760"},{"content_type":"text/plain","date_updated":"2020-07-14T12:47:11Z","file_name":"FileS4.txt","file_id":"5761","creator":"cfraisse","checksum":"943dfd14da61817441e33e3e3cb8cdb9","date_created":"2018-12-19T14:19:49Z","file_size":883742,"relation":"main_file","access_level":"open_access"},{"file_name":"FileS5.txt","date_updated":"2020-07-14T12:47:11Z","content_type":"text/plain","creator":"cfraisse","file_id":"5762","date_created":"2018-12-19T14:19:49Z","checksum":"1c669b6c4690ec1bbca3e2da9f566d17","access_level":"open_access","file_size":2495437,"relation":"main_file"},{"content_type":"text/plain","file_name":"FileS6.txt","date_updated":"2020-07-14T12:47:11Z","creator":"cfraisse","file_id":"5763","checksum":"f40f661b987ca6fb6b47f650cbbb04e6","date_created":"2018-12-19T14:19:50Z","relation":"main_file","file_size":15913457,"access_level":"open_access"},{"file_id":"5764","creator":"cfraisse","content_type":"text/plain","file_name":"FileS7.txt","date_updated":"2020-07-14T12:47:11Z","file_size":2584120,"relation":"main_file","access_level":"open_access","checksum":"25f41e5b8a075669c6c88d4c6713bf6f","date_created":"2018-12-19T14:19:50Z"},{"date_created":"2018-12-19T14:19:50Z","checksum":"f6c0bd3e63e14ddf5445bd69b43a9152","access_level":"open_access","file_size":2446059,"relation":"main_file","file_name":"FileS8.txt","date_updated":"2020-07-14T12:47:11Z","content_type":"text/plain","creator":"cfraisse","file_id":"5765"},{"access_level":"open_access","file_size":100737,"relation":"main_file","date_created":"2018-12-19T14:19:50Z","checksum":"0fe7a58a030b11bf3b9c8ff7a7addcae","creator":"cfraisse","file_id":"5766","date_updated":"2020-07-14T12:47:11Z","file_name":"FileS9.txt","content_type":"text/plain"}],"abstract":[{"lang":"eng","text":"File S1. Variant Calling Format file of the ingroup: 197 haploid sequences of D. melanogaster from Zambia (Africa) aligned to the D. melanogaster 5.57 reference genome.\r\n\r\nFile S2. Variant Calling Format file of the outgroup: 1 haploid sequence of D. simulans aligned to the D. melanogaster 5.57 reference genome.\r\n\r\nFile S3. Annotations of each transcript in coding regions with SNPeff: Ps (# of synonymous polymorphic sites); Pn (# of non-synonymous polymorphic sites); Ds (# of synonymous divergent sites); Dn (# of non-synonymous divergent sites); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S4. Annotations of each transcript in non-coding regions with SNPeff: Ps (# of synonymous polymorphic sites); Pu (# of UTR polymorphic sites); Ds (# of synonymous divergent sites); Du (# of UTR divergent sites); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S5. Annotations of each transcript in coding regions with SNPGenie: Ps (# of synonymous polymorphic sites); πs (synonymous diversity); Ss_p (total # of synonymous sites in the polymorphism data); Pn (# of non-synonymous polymorphic sites); πn (non-synonymous diversity); Sn_p (total # of non-synonymous sites in the polymorphism data); Ds (# of synonymous divergent sites); ks (synonymous evolutionary rate); Ss_d (total # of synonymous sites in the divergence data); Dn (# of non-synonymous divergent sites); kn (non-synonymous evolutionary rate); Sn_d (total # of non-\r\nsynonymous sites in the divergence data); DoS; ⍺ MK . All variants were included.\r\n\r\nFile S6. Gene expression values (RPKM summed over all transcripts) for each sample. Values were quantile-normalized across all samples.\r\n\r\nFile S7. Final dataset with all covariates, ⍺ MK , ωA MK and DoS for coding sites, excluding variants below 5% frequency.\r\n\r\nFile S8. Final dataset with all covariates, ⍺ MK , ωA MK and DoS for non-coding sites, excluding variants below 5%\r\nfrequency.\r\n\r\nFile S9. Final dataset with all covariates, ⍺ EWK , ωA EWK and deleterious SFS for coding sites obtained with the Eyre-Walker and Keightley method on binned data and using all variants."}],"ddc":["576"],"day":"19","oa_version":"Published Version","ec_funded":1,"status":"public","date_created":"2018-12-19T14:22:35Z","keyword":["(mal)adaptation","pleiotropy","selective constraint","evo-devo","gene expression","Drosophila melanogaster"],"has_accepted_license":"1","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734"}],"file_date_updated":"2020-07-14T12:47:11Z","contributor":[{"first_name":"Christelle","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Gemma","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","last_name":"Puixeu Sala"},{"last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","orcid":"0000-0002-4579-8306"}],"month":"12","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"date_updated":"2025-04-15T08:18:38Z","title":"Supplementary Files for \"Pleiotropy modulates the efficacy of selection in Drosophila melanogaster\"","type":"research_data","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Fraisse","full_name":"Fraisse, Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075","first_name":"Christelle"}],"citation":{"apa":"Fraisse, C. (2018). Supplementary Files for “Pleiotropy modulates the efficacy of selection in Drosophila melanogaster.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:/5757\">https://doi.org/10.15479/at:ista:/5757</a>","short":"C. Fraisse, (2018).","chicago":"Fraisse, Christelle. “Supplementary Files for ‘Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.’” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/at:ista:/5757\">https://doi.org/10.15479/at:ista:/5757</a>.","ama":"Fraisse C. Supplementary Files for “Pleiotropy modulates the efficacy of selection in Drosophila melanogaster.” 2018. doi:<a href=\"https://doi.org/10.15479/at:ista:/5757\">10.15479/at:ista:/5757</a>","ista":"Fraisse C. 2018. Supplementary Files for ‘Pleiotropy modulates the efficacy of selection in Drosophila melanogaster’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/at:ista:/5757\">10.15479/at:ista:/5757</a>.","mla":"Fraisse, Christelle. <i>Supplementary Files for “Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.”</i> Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/at:ista:/5757\">10.15479/at:ista:/5757</a>.","ieee":"C. Fraisse, “Supplementary Files for ‘Pleiotropy modulates the efficacy of selection in Drosophila melanogaster.’” Institute of Science and Technology Austria, 2018."},"oa":1,"date_published":"2018-12-19T00:00:00Z","year":"2018","related_material":{"record":[{"status":"public","id":"6089","relation":"research_paper"}]},"_id":"5757","doi":"10.15479/at:ista:/5757","publisher":"Institute of Science and Technology Austria","article_processing_charge":"No"},{"oa_version":"Published Version","day":"01","volume":10,"external_id":{"isi":["000429483700013"]},"quality_controlled":"1","abstract":[{"text":"Schistosomes are the causative agents of schistosomiasis, a neglected tropical disease affecting over 230 million people worldwide.Additionally to their major impact on human health, they are also models of choice in evolutionary biology. These parasitic flatwormsare unique among the common hermaphroditic trematodes as they have separate sexes. This so-called “evolutionary scandal”displays a female heterogametic genetic sex-determination system (ZZ males and ZW females), as well as a pronounced adult sexualdimorphism. These phenotypic differences are determined by a shared set of genes in both sexes, potentially leading to intralocussexual conflicts. To resolve these conflicts in sexually selected traits, molecular mechanisms such as sex-biased gene expression couldoccur, but parent-of-origin gene expression also provides an alternative. In this work we investigated the latter mechanism, that is,genes expressed preferentially from either the maternal or the paternal allele, inSchistosoma mansonispecies. To this end, tran-scriptomes from male and female hybrid adults obtained by strain crosses were sequenced. Strain-specific single nucleotide poly-morphism (SNP) markers allowed us to discriminate the parental origin, while reciprocal crosses helped to differentiate parentalexpression from strain-specific expression. We identified genes containing SNPs expressed in a parent-of-origin manner consistentwith paternal and maternal imprints. Although the majority of the SNPs was identified in mitochondrial and Z-specific loci, theremaining SNPs found in male and female transcriptomes were situated in genes that have the potential to explain sexual differencesin schistosome parasites. Furthermore, we identified and validated four new Z-specific scaffolds.","lang":"eng"}],"citation":{"short":"J. Kincaid-Smith, M.A.L. Picard, C. Cosseau, J. Boissier, D. Severac, C. Grunau, E. Toulza, Genome Biology and Evolution 10 (2018) 840–856.","apa":"Kincaid-Smith, J., Picard, M. A. L., Cosseau, C., Boissier, J., Severac, D., Grunau, C., &#38; Toulza, E. (2018). Parent-of-Origin-Dependent Gene Expression in Male and Female Schistosome Parasites. <i>Genome Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/gbe/evy037\">https://doi.org/10.1093/gbe/evy037</a>","ama":"Kincaid-Smith J, Picard MAL, Cosseau C, et al. Parent-of-Origin-Dependent Gene Expression in Male and Female Schistosome Parasites. <i>Genome Biology and Evolution</i>. 2018;10(3):840-856. doi:<a href=\"https://doi.org/10.1093/gbe/evy037\">10.1093/gbe/evy037</a>","chicago":"Kincaid-Smith, Julien, Marion A L Picard, Céline Cosseau, Jérôme Boissier, Dany Severac, Christoph Grunau, and Eve Toulza. “Parent-of-Origin-Dependent Gene Expression in Male and Female Schistosome Parasites.” <i>Genome Biology and Evolution</i>. Oxford University Press, 2018. <a href=\"https://doi.org/10.1093/gbe/evy037\">https://doi.org/10.1093/gbe/evy037</a>.","ista":"Kincaid-Smith J, Picard MAL, Cosseau C, Boissier J, Severac D, Grunau C, Toulza E. 2018. Parent-of-Origin-Dependent Gene Expression in Male and Female Schistosome Parasites. Genome Biology and Evolution. 10(3), 840–856.","ieee":"J. Kincaid-Smith <i>et al.</i>, “Parent-of-Origin-Dependent Gene Expression in Male and Female Schistosome Parasites,” <i>Genome Biology and Evolution</i>, vol. 10, no. 3. Oxford University Press, pp. 840–856, 2018.","mla":"Kincaid-Smith, Julien, et al. “Parent-of-Origin-Dependent Gene Expression in Male and Female Schistosome Parasites.” <i>Genome Biology and Evolution</i>, vol. 10, no. 3, Oxford University Press, 2018, pp. 840–56, doi:<a href=\"https://doi.org/10.1093/gbe/evy037\">10.1093/gbe/evy037</a>."},"date_published":"2018-03-01T00:00:00Z","year":"2018","publication_status":"published","doi":"10.1093/gbe/evy037","article_processing_charge":"No","publisher":"Oxford University Press","publication_identifier":{"issn":["1759-6653"]},"tmp":{"image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"month":"03","department":[{"_id":"BeVi"}],"date_updated":"2023-09-19T14:39:08Z","title":"Parent-of-Origin-Dependent Gene Expression in Male and Female Schistosome Parasites","isi":1,"status":"public","scopus_import":"1","date_created":"2019-02-14T12:13:52Z","has_accepted_license":"1","language":[{"iso":"eng"}],"publication":"Genome Biology and Evolution","file":[{"relation":"main_file","file_size":529755,"access_level":"open_access","checksum":"736a459cb77de5824354466bb0331caf","date_created":"2019-02-14T12:20:01Z","file_id":"5991","creator":"dernst","content_type":"application/pdf","file_name":"2018_GBE_Kincaid_Smith.pdf","date_updated":"2020-07-14T12:47:15Z"}],"ddc":["570"],"intvolume":"        10","page":"840-856","oa":1,"_id":"5989","file_date_updated":"2020-07-14T12:47:15Z","issue":"3","type":"journal_article","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"first_name":"Julien","last_name":"Kincaid-Smith","full_name":"Kincaid-Smith, Julien"},{"full_name":"Picard, Marion A L","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","last_name":"Picard","orcid":"0000-0002-8101-2518","first_name":"Marion A L"},{"last_name":"Cosseau","full_name":"Cosseau, Céline","first_name":"Céline"},{"last_name":"Boissier","full_name":"Boissier, Jérôme","first_name":"Jérôme"},{"last_name":"Severac","full_name":"Severac, Dany","first_name":"Dany"},{"first_name":"Christoph","last_name":"Grunau","full_name":"Grunau, Christoph"},{"first_name":"Eve","last_name":"Toulza","full_name":"Toulza, Eve"}]},{"isi":1,"article_number":"480","title":"Unusual diversity of sex chromosomes in African cichlid fishes","date_updated":"2025-04-15T06:50:01Z","month":"10","department":[{"_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)"},"publisher":"MDPI","article_processing_charge":"No","doi":"10.3390/genes9100480","publication_status":"published","date_published":"2018-10-04T00:00:00Z","year":"2018","citation":{"ama":"Gammerdinger WJ, Kocher T. Unusual diversity of sex chromosomes in African cichlid fishes. <i>Genes</i>. 2018;9(10). doi:<a href=\"https://doi.org/10.3390/genes9100480\">10.3390/genes9100480</a>","chicago":"Gammerdinger, William J, and Thomas Kocher. “Unusual Diversity of Sex Chromosomes in African Cichlid Fishes.” <i>Genes</i>. MDPI, 2018. <a href=\"https://doi.org/10.3390/genes9100480\">https://doi.org/10.3390/genes9100480</a>.","short":"W.J. Gammerdinger, T. Kocher, Genes 9 (2018).","apa":"Gammerdinger, W. J., &#38; Kocher, T. (2018). Unusual diversity of sex chromosomes in African cichlid fishes. <i>Genes</i>. MDPI. <a href=\"https://doi.org/10.3390/genes9100480\">https://doi.org/10.3390/genes9100480</a>","ieee":"W. J. Gammerdinger and T. Kocher, “Unusual diversity of sex chromosomes in African cichlid fishes,” <i>Genes</i>, vol. 9, no. 10. MDPI, 2018.","mla":"Gammerdinger, William J., and Thomas Kocher. “Unusual Diversity of Sex Chromosomes in African Cichlid Fishes.” <i>Genes</i>, vol. 9, no. 10, 480, MDPI, 2018, doi:<a href=\"https://doi.org/10.3390/genes9100480\">10.3390/genes9100480</a>.","ista":"Gammerdinger WJ, Kocher T. 2018. Unusual diversity of sex chromosomes in African cichlid fishes. Genes. 9(10), 480."},"abstract":[{"lang":"eng","text":"African cichlids display a remarkable assortment of jaw morphologies, pigmentation patterns, and mating behaviors. In addition to this previously documented diversity, recent studies have documented a rich diversity of sex chromosomes within these fishes. Here we review the known sex-determination network within vertebrates, and the extraordinary number of sex chromosomes systems segregating in African cichlids. We also propose a model for understanding the unusual number of sex chromosome systems within this clade."}],"external_id":{"isi":["000448656700018"]},"quality_controlled":"1","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"ec_funded":1,"day":"04","volume":9,"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Gammerdinger","full_name":"Gammerdinger, William J","id":"3A7E01BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9638-1220","first_name":"William J"},{"last_name":"Kocher","full_name":"Kocher, Thomas","first_name":"Thomas"}],"acknowledgement":"NSF DEB-1830753 and ISTPlus Fellowship","type":"journal_article","issue":"10","file_date_updated":"2020-07-14T12:47:27Z","_id":"63","oa":1,"publist_id":"7991","intvolume":"         9","ddc":["570"],"file":[{"date_created":"2018-12-18T09:54:46Z","checksum":"bec527692e2c9b56919c0429634ff337","access_level":"open_access","file_size":1415791,"relation":"main_file","file_name":"2018_Genes_Gammerdinger.pdf","date_updated":"2020-07-14T12:47:27Z","content_type":"application/pdf","creator":"dernst","file_id":"5743"}],"publication":"Genes","language":[{"iso":"eng"}],"has_accepted_license":"1","date_created":"2018-12-11T11:44:26Z","status":"public","scopus_import":"1"}]