[{"citation":{"ama":"Vicoso B. Supplementary data for “Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome” (Huylman, Toups et al., 2019). . 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6060\">10.15479/AT:ISTA:6060</a>","apa":"Vicoso, B. (2019). Supplementary data for “Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome” (Huylman, Toups et al., 2019). . Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6060\">https://doi.org/10.15479/AT:ISTA:6060</a>","mla":"Vicoso, Beatriz. <i>Supplementary Data for “Sex-Biased Gene Expression and Dosage Compensation on the Artemia Franciscana Z-Chromosome” (Huylman, Toups et Al., 2019). </i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6060\">10.15479/AT:ISTA:6060</a>.","ista":"Vicoso B. 2019. Supplementary data for ‘Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome’ (Huylman, Toups et al., 2019). , Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:6060\">10.15479/AT:ISTA:6060</a>.","chicago":"Vicoso, Beatriz. “Supplementary Data for ‘Sex-Biased Gene Expression and Dosage Compensation on the Artemia Franciscana Z-Chromosome’ (Huylman, Toups et Al., 2019). .” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:6060\">https://doi.org/10.15479/AT:ISTA:6060</a>.","ieee":"B. Vicoso, “Supplementary data for ‘Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome’ (Huylman, Toups et al., 2019). .” Institute of Science and Technology Austria, 2019.","short":"B. Vicoso, (2019)."},"related_material":{"record":[{"status":"public","id":"6418","relation":"research_paper"}]},"status":"public","date_published":"2019-02-28T00:00:00Z","doi":"10.15479/AT:ISTA:6060","has_accepted_license":"1","oa":1,"article_processing_charge":"No","_id":"6060","department":[{"_id":"BeVi"}],"year":"2019","publisher":"Institute of Science and Technology Austria","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2020-07-14T12:47:17Z","date_created":"2019-02-28T10:55:15Z","title":"Supplementary data for \"Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome\" (Huylman, Toups et al., 2019). ","oa_version":"Published Version","type":"research_data","month":"02","date_updated":"2024-02-21T12:45:42Z","file":[{"creator":"bvicoso","file_size":36646050,"content_type":"application/zip","relation":"main_file","file_name":"SupData.zip","access_level":"open_access","date_created":"2019-02-28T10:54:27Z","checksum":"a338a622d728af0e3199cb07e6dd64d3","file_id":"6061","date_updated":"2020-07-14T12:47:17Z"}],"day":"28","author":[{"last_name":"Vicoso","first_name":"Beatriz","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}]},{"date_published":"2019-03-01T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30590559"}],"publication_status":"published","oa":1,"intvolume":"        36","related_material":{"record":[{"id":"5757","status":"public","relation":"popular_science"}]},"citation":{"apa":"Fraisse, C., Puixeu Sala, G., &#38; Vicoso, B. (2019). Pleiotropy modulates the efficacy of selection in drosophila melanogaster. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msy246\">https://doi.org/10.1093/molbev/msy246</a>","ista":"Fraisse C, Puixeu Sala G, Vicoso B. 2019. Pleiotropy modulates the efficacy of selection in drosophila melanogaster. Molecular biology and evolution. 36(3), 500–515.","mla":"Fraisse, Christelle, et al. “Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.” <i>Molecular Biology and Evolution</i>, vol. 36, no. 3, Oxford University Press, 2019, pp. 500–15, doi:<a href=\"https://doi.org/10.1093/molbev/msy246\">10.1093/molbev/msy246</a>.","ama":"Fraisse C, Puixeu Sala G, Vicoso B. Pleiotropy modulates the efficacy of selection in drosophila melanogaster. <i>Molecular biology and evolution</i>. 2019;36(3):500-515. doi:<a href=\"https://doi.org/10.1093/molbev/msy246\">10.1093/molbev/msy246</a>","short":"C. Fraisse, G. Puixeu Sala, B. Vicoso, Molecular Biology and Evolution 36 (2019) 500–515.","chicago":"Fraisse, Christelle, Gemma Puixeu Sala, and Beatriz Vicoso. “Pleiotropy Modulates the Efficacy of Selection in Drosophila Melanogaster.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2019. <a href=\"https://doi.org/10.1093/molbev/msy246\">https://doi.org/10.1093/molbev/msy246</a>.","ieee":"C. Fraisse, G. Puixeu Sala, and B. Vicoso, “Pleiotropy modulates the efficacy of selection in drosophila melanogaster,” <i>Molecular biology and evolution</i>, vol. 36, no. 3. Oxford University Press, pp. 500–515, 2019."},"status":"public","external_id":{"isi":["000462585100006"],"pmid":["30590559"]},"volume":36,"date_created":"2019-03-10T22:59:19Z","page":"500-515","date_updated":"2024-02-21T13:59:17Z","abstract":[{"text":"Pleiotropy is the well-established idea that a single mutation affects multiple phenotypes. If a mutation has opposite effects on fitness when expressed in different contexts, then genetic conflict arises. Pleiotropic conflict is expected to reduce the efficacy of selection by limiting the fixation of beneficial mutations through adaptation, and the removal of deleterious mutations through purifying selection. Although this has been widely discussed, in particular in the context of a putative “gender load,” it has yet to be systematically quantified. In this work, we empirically estimate to which extent different pleiotropic regimes impede the efficacy of selection in Drosophila melanogaster. We use whole-genome polymorphism data from a single African population and divergence data from D. simulans to estimate the fraction of adaptive fixations (α), the rate of adaptation (ωA), and the direction of selection (DoS). After controlling for confounding covariates, we find that the different pleiotropic regimes have a relatively small, but significant, effect on selection efficacy. Specifically, our results suggest that pleiotropic sexual antagonism may restrict the efficacy of selection, but that this conflict can be resolved by limiting the expression of genes to the sex where they are beneficial. Intermediate levels of pleiotropy across tissues and life stages can also lead to maladaptation in D. melanogaster, due to inefficient purifying selection combined with low frequency of mutations that confer a selective advantage. Thus, our study highlights the need to consider the efficacy of selection in the context of antagonistic pleiotropy, and of genetic conflict in general.","lang":"eng"}],"type":"journal_article","month":"03","oa_version":"Submitted Version","_id":"6089","year":"2019","doi":"10.1093/molbev/msy246","quality_controlled":"1","publication_identifier":{"issn":["0737-4038"],"eissn":["1537-1719"]},"isi":1,"language":[{"iso":"eng"}],"issue":"3","project":[{"grant_number":"P28842-B22","call_identifier":"FWF","_id":"250ED89C-B435-11E9-9278-68D0E5697425","name":"Sex chromosome evolution under male- and female- heterogamety"}],"title":"Pleiotropy modulates the efficacy of selection in drosophila melanogaster","author":[{"first_name":"Christelle","last_name":"Fraisse","orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","full_name":"Fraisse, Christelle"},{"orcid":"0000-0001-8330-1754","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","full_name":"Puixeu Sala, Gemma","last_name":"Puixeu Sala","first_name":"Gemma"},{"orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz","last_name":"Vicoso","first_name":"Beatriz"}],"day":"01","publication":"Molecular biology and evolution","article_processing_charge":"No","scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Oxford University Press","pmid":1,"department":[{"_id":"BeVi"},{"_id":"NiBa"}]},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Oxford University Press","department":[{"_id":"BeVi"}],"publication":"Genome biology and evolution","ec_funded":1,"article_processing_charge":"No","scopus_import":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"author":[{"orcid":"0000-0001-8871-4961","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","full_name":"Huylmans, Ann K","last_name":"Huylmans","first_name":"Ann K"},{"orcid":"0000-0002-9752-7380","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","full_name":"Toups, Melissa A","last_name":"Toups","first_name":"Melissa A"},{"full_name":"Macon, Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","last_name":"Macon","first_name":"Ariana"},{"full_name":"Gammerdinger, William J","id":"3A7E01BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9638-1220","first_name":"William J","last_name":"Gammerdinger"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","last_name":"Vicoso","first_name":"Beatriz"}],"file":[{"file_name":"2019_GBE_Huylmans.pdf","creator":"dernst","file_size":1256303,"content_type":"application/pdf","relation":"main_file","checksum":"7d0ede297b6741f3dc89cd59017c7642","file_id":"6446","date_updated":"2020-07-14T12:47:29Z","access_level":"open_access","date_created":"2019-05-14T08:29:38Z"}],"day":"01","title":"Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome","project":[{"grant_number":"715257","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","_id":"250BDE62-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"isi":1,"language":[{"iso":"eng"}],"issue":"4","publication_identifier":{"eissn":["1759-6653"]},"doi":"10.1093/gbe/evz053","quality_controlled":"1","year":"2019","_id":"6418","page":"1033-1044","abstract":[{"lang":"eng","text":"Males and females of Artemia franciscana, a crustacean commonly used in the aquarium trade, are highly dimorphic. Sex is determined by a pair of ZW chromosomes, but the nature and extent of differentiation of these chromosomes is unknown. Here, we characterize the Z chromosome by detecting genomic regions that show lower genomic coverage in female than in male samples, and regions that harbor an excess of female-specific SNPs. We detect many Z-specific genes, which no longer have homologs on the W, but also Z-linked genes that appear to have diverged very recently from their existing W-linked homolog. We assess patterns of male and female expression in two tissues with extensive morphological dimorphism, gonads, and heads. In agreement with their morphology, sex-biased expression is common in both tissues. Interestingly, the Z chromosome is not enriched for sex-biased genes, and seems to in fact have a mechanism of dosage compensation that leads to equal expression in males and in females. Both of these patterns are contrary to most ZW systems studied so far, making A. franciscana an excellent model for investigating the interplay between the evolution of sexual dimorphism and dosage compensation, as well as Z chromosome evolution in general."}],"date_updated":"2024-02-21T12:45:41Z","month":"04","type":"journal_article","oa_version":"Published Version","volume":11,"file_date_updated":"2020-07-14T12:47:29Z","date_created":"2019-05-13T07:58:38Z","external_id":{"isi":["000476569800003"]},"status":"public","intvolume":"        11","related_material":{"record":[{"relation":"popular_science","status":"public","id":"6060"}]},"citation":{"mla":"Huylmans, Ann K., et al. “Sex-Biased Gene Expression and Dosage Compensation on the Artemia Franciscana Z-Chromosome.” <i>Genome Biology and Evolution</i>, vol. 11, no. 4, Oxford University Press, 2019, pp. 1033–44, doi:<a href=\"https://doi.org/10.1093/gbe/evz053\">10.1093/gbe/evz053</a>.","ista":"Huylmans AK, Toups MA, Macon A, Gammerdinger WJ, Vicoso B. 2019. Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome. Genome biology and evolution. 11(4), 1033–1044.","apa":"Huylmans, A. K., Toups, M. A., Macon, A., Gammerdinger, W. J., &#38; Vicoso, B. (2019). Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome. <i>Genome Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/gbe/evz053\">https://doi.org/10.1093/gbe/evz053</a>","ama":"Huylmans AK, Toups MA, Macon A, Gammerdinger WJ, Vicoso B. Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome. <i>Genome biology and evolution</i>. 2019;11(4):1033-1044. doi:<a href=\"https://doi.org/10.1093/gbe/evz053\">10.1093/gbe/evz053</a>","short":"A.K. Huylmans, M.A. Toups, A. Macon, W.J. Gammerdinger, B. Vicoso, Genome Biology and Evolution 11 (2019) 1033–1044.","ieee":"A. K. Huylmans, M. A. Toups, A. Macon, W. J. Gammerdinger, and B. Vicoso, “Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome,” <i>Genome biology and evolution</i>, vol. 11, no. 4. Oxford University Press, pp. 1033–1044, 2019.","chicago":"Huylmans, Ann K, Melissa A Toups, Ariana Macon, William J Gammerdinger, and Beatriz Vicoso. “Sex-Biased Gene Expression and Dosage Compensation on the Artemia Franciscana Z-Chromosome.” <i>Genome Biology and Evolution</i>. Oxford University Press, 2019. <a href=\"https://doi.org/10.1093/gbe/evz053\">https://doi.org/10.1093/gbe/evz053</a>."},"publication_status":"published","oa":1,"has_accepted_license":"1","ddc":["570"],"date_published":"2019-04-01T00:00:00Z","acknowledged_ssus":[{"_id":"ScienComp"}]},{"publisher":"Royal Society of London","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","pmid":1,"department":[{"_id":"BeVi"},{"_id":"NiBa"}],"publication":"Biology Letters","article_processing_charge":"No","ec_funded":1,"scopus_import":"1","article_type":"original","author":[{"last_name":"Fraisse","first_name":"Christelle","orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","full_name":"Fraisse, Christelle"},{"full_name":"Welch, John J.","last_name":"Welch","first_name":"John J."}],"day":"03","title":"The distribution of epistasis on simple fitness landscapes","article_number":"0881","project":[{"grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme"}],"isi":1,"language":[{"iso":"eng"}],"issue":"4","publication_identifier":{"issn":["17449561"],"eissn":["1744957X"]},"doi":"10.1098/rsbl.2018.0881","quality_controlled":"1","year":"2019","_id":"6467","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"}],"date_updated":"2023-08-25T10:34:41Z","month":"04","type":"journal_article","oa_version":"Published Version","volume":15,"date_created":"2019-05-19T21:59:15Z","status":"public","external_id":{"isi":["000465405300010"],"pmid":["31014191"]},"intvolume":"        15","related_material":{"record":[{"status":"public","id":"9798","relation":"research_data"},{"relation":"research_data","id":"9799","status":"public"}],"link":[{"relation":"supplementary_material","url":"https://dx.doi.org/10.6084/m9.figshare.c.4461008"}]},"citation":{"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>","ista":"Fraisse C, Welch JJ. 2019. The distribution of epistasis on simple fitness landscapes. Biology Letters. 15(4), 0881.","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>.","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>","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.","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>.","short":"C. Fraisse, J.J. Welch, Biology Letters 15 (2019)."},"publication_status":"published","oa":1,"date_published":"2019-04-03T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1098/rsbl.2018.0881"}]},{"oa_version":"Published Version","month":"07","type":"research_data_reference","day":"22","date_updated":"2023-08-29T07:17:07Z","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."}],"author":[{"first_name":"Gemma","last_name":"Puixeu Sala","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8330-1754","full_name":"Puixeu Sala, Gemma"},{"full_name":"Pickup, Melinda","orcid":"0000-0001-6118-0541","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","last_name":"Pickup","first_name":"Melinda"},{"last_name":"Field","first_name":"David","full_name":"Field, David"},{"last_name":"Barrett","first_name":"Spencer C.H.","full_name":"Barrett, Spencer C.H."}],"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","department":[{"_id":"NiBa"},{"_id":"BeVi"}],"year":"2019","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publisher":"Dryad","article_processing_charge":"No","_id":"9803","oa":1,"main_file_link":[{"url":"https://doi.org/10.5061/dryad.n1701c9","open_access":"1"}],"doi":"10.5061/dryad.n1701c9","date_published":"2019-07-22T00:00:00Z","status":"public","citation":{"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>","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>.","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>.","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>","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.","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>.","short":"G. Puixeu Sala, M. Pickup, D. Field, S.C.H. Barrett, (2019)."},"related_material":{"record":[{"status":"public","id":"14058","relation":"used_in_publication"},{"status":"public","id":"6831","relation":"used_in_publication"}]}},{"language":[{"iso":"eng"}],"isi":1,"quality_controlled":"1","doi":"10.1002/jez.b.22824","article_processing_charge":"No","scopus_import":"1","article_type":"original","publication":"Journal of Experimental Zoology Part B: Molecular and Developmental Evolution","pmid":1,"department":[{"_id":"BeVi"}],"publisher":"Wiley","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"7730","title":"Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest","day":"11","author":[{"full_name":"Harrison, Mark","last_name":"Harrison","first_name":"Mark"},{"last_name":"Arning","first_name":"Nicolas","full_name":"Arning, Nicolas"},{"last_name":"Kremer","first_name":"Lucas","full_name":"Kremer, Lucas"},{"full_name":"Ylla, Guillem","last_name":"Ylla","first_name":"Guillem"},{"last_name":"Belles","first_name":"Xavier","full_name":"Belles, Xavier"},{"first_name":"Erich","last_name":"Bornberg Bauer","full_name":"Bornberg Bauer, Erich"},{"first_name":"Ann K","last_name":"Huylmans","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8871-4961","full_name":"Huylmans, Ann K"},{"full_name":"Jongepier, Evelien","first_name":"Evelien","last_name":"Jongepier"},{"full_name":"Puilachs, Maria","last_name":"Puilachs","first_name":"Maria"},{"full_name":"Richards, Stephen","last_name":"Richards","first_name":"Stephen"},{"first_name":"Coby","last_name":"Schal","full_name":"Schal, Coby"}],"citation":{"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.","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>.","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.","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>","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.","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>.","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>"},"intvolume":"       330","status":"public","external_id":{"isi":["000443231000002"],"pmid":["29998472"]},"main_file_link":[{"open_access":"1","url":"https://onlinelibrary.wiley.com/doi/am-pdf/10.1002/jez.b.22824"}],"date_published":"2018-07-11T00:00:00Z","publication_status":"published","oa":1,"_id":"190","year":"2018","date_created":"2018-12-11T11:45:06Z","volume":330,"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"}],"date_updated":"2023-09-11T13:59:54Z","type":"journal_article","oa_version":"Submitted Version","month":"07","page":"254-264"},{"quality_controlled":"1","doi":"10.3390/genes9060294","issue":"6","language":[{"iso":"eng"}],"isi":1,"file":[{"checksum":"423069beb1cd3cdd25bf3f464b38f1d7","date_updated":"2020-07-14T12:45:22Z","file_id":"5905","access_level":"open_access","date_created":"2019-02-01T07:52:28Z","file_name":"2018_Genes_Ma.pdf","creator":"dernst","content_type":"application/pdf","relation":"main_file","file_size":3985796}],"day":"12","author":[{"first_name":"Wen","last_name":"Ma","full_name":"Ma, Wen"},{"last_name":"Veltsos","first_name":"Paris","full_name":"Veltsos, Paris"},{"full_name":"Toups, Melissa A","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9752-7380","last_name":"Toups","first_name":"Melissa A"},{"first_name":"Nicolas","last_name":"Rodrigues","full_name":"Rodrigues, Nicolas"},{"last_name":"Sermier","first_name":"Roberto","full_name":"Sermier, Roberto"},{"first_name":"Daniel","last_name":"Jeffries","full_name":"Jeffries, Daniel"},{"first_name":"Nicolas","last_name":"Perrin","full_name":"Perrin, Nicolas"}],"publist_id":"7714","article_number":"294","title":"Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes","department":[{"_id":"BeVi"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"MDPI AG","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_processing_charge":"No","scopus_import":"1","publication":"Genes","has_accepted_license":"1","oa":1,"publication_status":"published","date_published":"2018-06-12T00:00:00Z","ddc":["570"],"external_id":{"isi":["000436494200026"]},"status":"public","citation":{"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.","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 AG, 2018, 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 AG. <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>","short":"W. Ma, P. Veltsos, M.A. Toups, N. Rodrigues, R. Sermier, D. Jeffries, N. Perrin, Genes 9 (2018).","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 AG, 2018.","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 AG, 2018. <a href=\"https://doi.org/10.3390/genes9060294\">https://doi.org/10.3390/genes9060294</a>."},"intvolume":"         9","month":"06","type":"journal_article","oa_version":"Published Version","date_updated":"2023-09-19T10:15:31Z","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."}],"date_created":"2018-12-11T11:45:09Z","file_date_updated":"2020-07-14T12:45:22Z","volume":9,"year":"2018","_id":"199"},{"project":[{"name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","_id":"250BDE62-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"715257"}],"language":[{"iso":"eng"}],"issue":"1","isi":1,"pubrep_id":"1058","quality_controlled":"1","doi":"10.1534/genetics.117.300513","department":[{"_id":"BeVi"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Genetics Society of America","ec_funded":1,"article_processing_charge":"No","scopus_import":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","publication":"Genetics","day":"01","file":[{"date_updated":"2020-07-14T12:46:50Z","file_id":"5132","checksum":"2123845e7031a0cf043905be160f9e69","date_created":"2018-12-12T10:15:14Z","access_level":"open_access","file_name":"IST-2018-1058-v1+1_365.full__1_.pdf","relation":"main_file","content_type":"application/pdf","file_size":1311661,"creator":"system"}],"author":[{"orcid":"0000-0002-8489-9281","id":"48D3F8DE-F248-11E8-B48F-1D18A9856A87","full_name":"Kelemen, Réka K","first_name":"Réka K","last_name":"Kelemen"},{"full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","first_name":"Beatriz","last_name":"Vicoso"}],"publist_id":"7274","title":"Complex history and differentiation patterns of the t-haplotype, a mouse meiotic driver","status":"public","external_id":{"isi":["000419356300024"]},"citation":{"short":"R.K. Kelemen, B. Vicoso, Genetics 208 (2018) 365–375.","chicago":"Kelemen, Réka K, and Beatriz Vicoso. “Complex History and Differentiation Patterns of the T-Haplotype, a Mouse Meiotic Driver.” <i>Genetics</i>. Genetics Society of America, 2018. <a href=\"https://doi.org/10.1534/genetics.117.300513\">https://doi.org/10.1534/genetics.117.300513</a>.","ieee":"R. K. Kelemen and B. Vicoso, “Complex history and differentiation patterns of the t-haplotype, a mouse meiotic driver,” <i>Genetics</i>, vol. 208, no. 1. Genetics Society of America, pp. 365–375, 2018.","apa":"Kelemen, R. K., &#38; Vicoso, B. (2018). Complex history and differentiation patterns of the t-haplotype, a mouse meiotic driver. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.117.300513\">https://doi.org/10.1534/genetics.117.300513</a>","ista":"Kelemen RK, Vicoso B. 2018. Complex history and differentiation patterns of the t-haplotype, a mouse meiotic driver. Genetics. 208(1), 365–375.","mla":"Kelemen, Réka K., and Beatriz Vicoso. “Complex History and Differentiation Patterns of the T-Haplotype, a Mouse Meiotic Driver.” <i>Genetics</i>, vol. 208, no. 1, Genetics Society of America, 2018, pp. 365–75, doi:<a href=\"https://doi.org/10.1534/genetics.117.300513\">10.1534/genetics.117.300513</a>.","ama":"Kelemen RK, Vicoso B. Complex history and differentiation patterns of the t-haplotype, a mouse meiotic driver. <i>Genetics</i>. 2018;208(1):365-375. doi:<a href=\"https://doi.org/10.1534/genetics.117.300513\">10.1534/genetics.117.300513</a>"},"intvolume":"       208","related_material":{"record":[{"status":"public","id":"5571","relation":"popular_science"},{"status":"public","id":"5572","relation":"popular_science"}]},"has_accepted_license":"1","oa":1,"publication_status":"published","date_published":"2018-01-01T00:00:00Z","ddc":["576"],"year":"2018","_id":"542","abstract":[{"text":"The t-haplotype, a mouse meiotic driver found on chromosome 17, has been a model for autosomal segregation distortion for close to a century, but several questions remain regarding its biology and evolutionary history. A recently published set of population genomics resources for wild mice includes several individuals heterozygous for the t-haplotype, which we use to characterize this selfish element at the genomic and transcriptomic level. Our results show that large sections of the t-haplotype have been replaced by standard homologous sequences, possibly due to occasional events of recombination, and that this complicates the inference of its history. As expected for a long genomic segment of very low recombination, the t-haplotype carries an excess of fixed nonsynonymous mutations compared to the standard chromosome. This excess is stronger for regions that have not undergone recent recombination, suggesting that occasional gene flow between the t and the standard chromosome may provide a mechanism to regenerate coding sequences that have accumulated deleterious mutations. Finally, we find that t-complex genes with altered expression largely overlap with deleted or amplified regions, and that carrying a t-haplotype alters the testis expression of genes outside of the t-complex, providing new leads into the pathways involved in the biology of this segregation distorter.","lang":"eng"}],"date_updated":"2024-02-21T13:48:27Z","oa_version":"Published Version","month":"01","type":"journal_article","page":"365 - 375","file_date_updated":"2020-07-14T12:46:50Z","date_created":"2018-12-11T11:47:04Z","volume":208},{"doi":"10.15479/AT:ISTA:109","contributor":[{"id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8101-2518","first_name":"Marion A","last_name":"Picard"}],"project":[{"grant_number":"P28842-B22","_id":"250ED89C-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Sex chromosome evolution under male- and female- heterogamety"}],"keyword":["schistosoma","Z-chromosome","gene expression"],"author":[{"orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz","last_name":"Vicoso","first_name":"Beatriz"}],"file":[{"file_name":"IST-2018-109-v1+1_SupplementaryMethods.zip","file_size":11918144,"relation":"main_file","content_type":"application/zip","creator":"system","file_id":"5601","date_updated":"2020-07-14T12:47:08Z","checksum":"e60b484bd6f55c08eb66a189cb72c923","date_created":"2018-12-12T13:02:35Z","access_level":"open_access"}],"license":"https://creativecommons.org/publicdomain/zero/1.0/","day":"24","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)","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Institute of Science and Technology Austria","department":[{"_id":"BeVi"}],"article_processing_charge":"No","tmp":{"name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode"},"oa":1,"has_accepted_license":"1","date_published":"2018-07-24T00:00:00Z","ddc":["570"],"status":"public","related_material":{"record":[{"relation":"research_paper","id":"131","status":"public"}]},"citation":{"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>","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>","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>.","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>.","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>.","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.","short":"B. Vicoso, (2018)."},"date_updated":"2024-02-21T13:45:12Z","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"}],"oa_version":"Published Version","type":"research_data","month":"07","file_date_updated":"2020-07-14T12:47:08Z","date_created":"2018-12-12T12:31:40Z","datarep_id":"109","year":"2018","_id":"5586"},{"ddc":["576"],"date_published":"2018-12-19T00:00:00Z","doi":"10.15479/at:ista:/5757","contributor":[{"id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle","last_name":"Fraisse"},{"first_name":"Gemma","last_name":"Puixeu Sala","id":"33AB266C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306"}],"has_accepted_license":"1","oa":1,"citation":{"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>.","ieee":"C. Fraisse, “Supplementary Files for ‘Pleiotropy modulates the efficacy of selection in Drosophila melanogaster.’” Institute of Science and Technology Austria, 2018.","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>","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>.","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>.","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>"},"related_material":{"record":[{"relation":"research_paper","status":"public","id":"6089"}]},"keyword":["(mal)adaptation","pleiotropy","selective constraint","evo-devo","gene expression","Drosophila melanogaster"],"status":"public","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"file_date_updated":"2020-07-14T12:47:11Z","date_created":"2018-12-19T14:22:35Z","title":"Supplementary Files for \"Pleiotropy modulates the efficacy of selection in Drosophila melanogaster\"","date_updated":"2024-02-21T13:59:18Z","day":"19","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."}],"file":[{"file_name":"FileS1.zip","file_size":369837892,"content_type":"application/zip","relation":"main_file","creator":"cfraisse","file_id":"5758","date_updated":"2020-07-14T12:47:11Z","checksum":"aed7ee9ca3f4dc07d8a66945f68e13cd","date_created":"2018-12-19T14:19:52Z","access_level":"open_access"},{"creator":"cfraisse","relation":"main_file","content_type":"application/zip","file_size":84856909,"file_name":"FileS2.zip","access_level":"open_access","date_created":"2018-12-19T14:19:49Z","checksum":"3592e467b4d8206650860b612d6e12f3","date_updated":"2020-07-14T12:47:11Z","file_id":"5759"},{"file_name":"FileS3.txt","creator":"cfraisse","content_type":"text/plain","relation":"main_file","file_size":881133,"checksum":"c37ac5d5437c457338afc128c1240655","date_updated":"2020-07-14T12:47:11Z","file_id":"5760","access_level":"open_access","date_created":"2018-12-19T14:19:49Z"},{"creator":"cfraisse","file_size":883742,"relation":"main_file","content_type":"text/plain","file_name":"FileS4.txt","access_level":"open_access","date_created":"2018-12-19T14:19:49Z","checksum":"943dfd14da61817441e33e3e3cb8cdb9","file_id":"5761","date_updated":"2020-07-14T12:47:11Z"},{"creator":"cfraisse","relation":"main_file","content_type":"text/plain","file_size":2495437,"file_name":"FileS5.txt","access_level":"open_access","date_created":"2018-12-19T14:19:49Z","checksum":"1c669b6c4690ec1bbca3e2da9f566d17","date_updated":"2020-07-14T12:47:11Z","file_id":"5762"},{"file_name":"FileS6.txt","file_size":15913457,"content_type":"text/plain","relation":"main_file","creator":"cfraisse","file_id":"5763","date_updated":"2020-07-14T12:47:11Z","checksum":"f40f661b987ca6fb6b47f650cbbb04e6","date_created":"2018-12-19T14:19:50Z","access_level":"open_access"},{"date_updated":"2020-07-14T12:47:11Z","file_id":"5764","checksum":"25f41e5b8a075669c6c88d4c6713bf6f","date_created":"2018-12-19T14:19:50Z","access_level":"open_access","file_name":"FileS7.txt","relation":"main_file","content_type":"text/plain","file_size":2584120,"creator":"cfraisse"},{"creator":"cfraisse","file_size":2446059,"content_type":"text/plain","relation":"main_file","file_name":"FileS8.txt","access_level":"open_access","date_created":"2018-12-19T14:19:50Z","checksum":"f6c0bd3e63e14ddf5445bd69b43a9152","file_id":"5765","date_updated":"2020-07-14T12:47:11Z"},{"file_name":"FileS9.txt","creator":"cfraisse","file_size":100737,"relation":"main_file","content_type":"text/plain","checksum":"0fe7a58a030b11bf3b9c8ff7a7addcae","file_id":"5766","date_updated":"2020-07-14T12:47:11Z","access_level":"open_access","date_created":"2018-12-19T14:19:50Z"}],"oa_version":"Published Version","type":"research_data","month":"12","author":[{"orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","full_name":"Fraisse, Christelle","last_name":"Fraisse","first_name":"Christelle"}],"article_processing_charge":"No","ec_funded":1,"_id":"5757","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"year":"2018","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Institute of Science and Technology Austria"},{"status":"public","external_id":{"isi":["000429483700013"]},"citation":{"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>","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.","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>.","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>","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.","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>.","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."},"intvolume":"        10","has_accepted_license":"1","publication_status":"published","oa":1,"date_published":"2018-03-01T00:00:00Z","ddc":["570"],"year":"2018","_id":"5989","date_updated":"2023-09-19T14:39:08Z","abstract":[{"lang":"eng","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."}],"month":"03","type":"journal_article","oa_version":"Published Version","page":"840-856","date_created":"2019-02-14T12:13:52Z","file_date_updated":"2020-07-14T12:47:15Z","volume":10,"language":[{"iso":"eng"}],"issue":"3","isi":1,"publication_identifier":{"issn":["1759-6653"]},"quality_controlled":"1","doi":"10.1093/gbe/evy037","department":[{"_id":"BeVi"}],"publisher":"Oxford University Press","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","scopus_import":"1","article_processing_charge":"No","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"publication":"Genome Biology and Evolution","file":[{"date_updated":"2020-07-14T12:47:15Z","file_id":"5991","checksum":"736a459cb77de5824354466bb0331caf","date_created":"2019-02-14T12:20:01Z","access_level":"open_access","file_name":"2018_GBE_Kincaid_Smith.pdf","content_type":"application/pdf","relation":"main_file","file_size":529755,"creator":"dernst"}],"day":"01","author":[{"full_name":"Kincaid-Smith, Julien","first_name":"Julien","last_name":"Kincaid-Smith"},{"last_name":"Picard","first_name":"Marion A L","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8101-2518","full_name":"Picard, Marion A L"},{"first_name":"Céline","last_name":"Cosseau","full_name":"Cosseau, Céline"},{"last_name":"Boissier","first_name":"Jérôme","full_name":"Boissier, Jérôme"},{"full_name":"Severac, Dany","last_name":"Severac","first_name":"Dany"},{"last_name":"Grunau","first_name":"Christoph","full_name":"Grunau, Christoph"},{"full_name":"Toulza, Eve","last_name":"Toulza","first_name":"Eve"}],"title":"Parent-of-Origin-Dependent Gene Expression in Male and Female Schistosome Parasites"},{"_id":"63","acknowledgement":"NSF DEB-1830753 and ISTPlus Fellowship","year":"2018","volume":9,"date_created":"2018-12-11T11:44:26Z","file_date_updated":"2020-07-14T12:47:27Z","abstract":[{"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.","lang":"eng"}],"date_updated":"2023-09-19T10:37:03Z","oa_version":"Published Version","type":"journal_article","month":"10","intvolume":"         9","citation":{"apa":"Gammerdinger, W. J., &#38; Kocher, T. (2018). Unusual diversity of sex chromosomes in African cichlid fishes. <i>Genes</i>. MDPI AG. <a href=\"https://doi.org/10.3390/genes9100480\">https://doi.org/10.3390/genes9100480</a>","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 AG, 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.","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>","short":"W.J. Gammerdinger, T. Kocher, Genes 9 (2018).","chicago":"Gammerdinger, William J, and Thomas Kocher. “Unusual Diversity of Sex Chromosomes in African Cichlid Fishes.” <i>Genes</i>. MDPI AG, 2018. <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 AG, 2018."},"external_id":{"isi":["000448656700018"]},"status":"public","ddc":["570"],"date_published":"2018-10-04T00:00:00Z","oa":1,"publication_status":"published","has_accepted_license":"1","publication":"Genes","ec_funded":1,"article_processing_charge":"No","scopus_import":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"MDPI AG","department":[{"_id":"BeVi"}],"title":"Unusual diversity of sex chromosomes in African cichlid fishes","article_number":"480","publist_id":"7991","author":[{"last_name":"Gammerdinger","first_name":"William J","orcid":"0000-0001-9638-1220","id":"3A7E01BC-F248-11E8-B48F-1D18A9856A87","full_name":"Gammerdinger, William J"},{"full_name":"Kocher, Thomas","first_name":"Thomas","last_name":"Kocher"}],"day":"04","file":[{"file_name":"2018_Genes_Gammerdinger.pdf","content_type":"application/pdf","relation":"main_file","file_size":1415791,"creator":"dernst","date_updated":"2020-07-14T12:47:27Z","file_id":"5743","checksum":"bec527692e2c9b56919c0429634ff337","date_created":"2018-12-18T09:54:46Z","access_level":"open_access"}],"isi":1,"language":[{"iso":"eng"}],"issue":"10","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"doi":"10.3390/genes9100480","quality_controlled":"1"},{"quality_controlled":"1","doi":"10.7554/eLife.35684","language":[{"iso":"eng"}],"isi":1,"project":[{"call_identifier":"FWF","_id":"250ED89C-B435-11E9-9278-68D0E5697425","name":"Sex chromosome evolution under male- and female- heterogamety","grant_number":"P28842-B22"}],"publist_id":"7792","title":"Evolution of gene dosage on the Z-chromosome of schistosome parasites","article_number":"e35684","file":[{"checksum":"d6331d4385b1fffd6b47b45d5949d841","file_id":"5695","date_updated":"2020-07-14T12:44:43Z","access_level":"open_access","date_created":"2018-12-17T11:55:05Z","file_name":"2018_eLife_Picard.pdf","creator":"dernst","file_size":3158125,"content_type":"application/pdf","relation":"main_file"}],"day":"13","author":[{"first_name":"Marion A","last_name":"Picard","full_name":"Picard, Marion A","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8101-2518"},{"full_name":"Cosseau, Celine","first_name":"Celine","last_name":"Cosseau"},{"full_name":"Ferré, Sabrina","first_name":"Sabrina","last_name":"Ferré"},{"full_name":"Quack, Thomas","last_name":"Quack","first_name":"Thomas"},{"full_name":"Grevelding, Christoph","last_name":"Grevelding","first_name":"Christoph"},{"full_name":"Couté, Yohann","first_name":"Yohann","last_name":"Couté"},{"full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","first_name":"Beatriz"}],"scopus_import":"1","article_processing_charge":"No","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","publication":"eLife","department":[{"_id":"BeVi"}],"publisher":"eLife Sciences Publications","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_published":"2018-08-13T00:00:00Z","ddc":["570"],"has_accepted_license":"1","publication_status":"published","oa":1,"citation":{"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>","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>","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>.","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>.","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.","short":"M.A.L. Picard, C. Cosseau, S. Ferré, T. Quack, C. Grevelding, Y. Couté, B. Vicoso, ELife 7 (2018)."},"related_material":{"record":[{"relation":"popular_science","status":"public","id":"5586"}]},"intvolume":"         7","status":"public","external_id":{"isi":["000441388200001"]},"date_created":"2018-12-11T11:44:47Z","file_date_updated":"2020-07-14T12:44:43Z","volume":7,"abstract":[{"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. ","lang":"eng"}],"date_updated":"2024-02-21T13:45:12Z","oa_version":"Published Version","month":"08","type":"journal_article","_id":"131","year":"2018","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."},{"_id":"139","year":"2018","file_date_updated":"2020-07-14T12:44:48Z","date_created":"2018-12-11T11:44:50Z","volume":2018,"type":"journal_article","month":"07","oa_version":"Published Version","date_updated":"2023-10-17T12:25:28Z","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."}],"citation":{"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>","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.","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>.","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>","short":"C. Fraisse, C. Roux, P. Gagnaire, J. Romiguier, N. Faivre, J. Welch, N. Bierne, PeerJ 2018 (2018).","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>.","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."},"intvolume":"      2018","external_id":{"isi":["000440484800002"]},"status":"public","ddc":["576"],"date_published":"2018-07-30T00:00:00Z","has_accepted_license":"1","oa":1,"publication_status":"published","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"scopus_import":"1","article_processing_charge":"No","publication":"PeerJ","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"publisher":"PeerJ","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"7784","article_number":"30083438","title":"The divergence history of European blue mussel species reconstructed from Approximate Bayesian Computation: The effects of sequencing techniques and sampling strategies","file":[{"file_name":"2018_PeerJ_Fraisse.pdf","relation":"main_file","content_type":"application/pdf","file_size":1480792,"creator":"dernst","date_updated":"2020-07-14T12:44:48Z","file_id":"5739","checksum":"7d55ae22598a1c70759cd671600cff53","date_created":"2018-12-18T09:42:11Z","access_level":"open_access"}],"day":"30","author":[{"full_name":"Fraisse, Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075","first_name":"Christelle","last_name":"Fraisse"},{"first_name":"Camille","last_name":"Roux","full_name":"Roux, Camille"},{"full_name":"Gagnaire, Pierre","last_name":"Gagnaire","first_name":"Pierre"},{"full_name":"Romiguier, Jonathan","last_name":"Romiguier","first_name":"Jonathan"},{"full_name":"Faivre, Nicolas","last_name":"Faivre","first_name":"Nicolas"},{"full_name":"Welch, John","first_name":"John","last_name":"Welch"},{"full_name":"Bierne, Nicolas","last_name":"Bierne","first_name":"Nicolas"}],"issue":"7","language":[{"iso":"eng"}],"isi":1,"quality_controlled":"1","doi":"10.7717/peerj.5198"},{"date_created":"2021-08-09T13:13:48Z","title":"Data from: Hemimetabolous genomes reveal molecular basis of termite eusociality","type":"research_data_reference","oa_version":"Published Version","month":"12","day":"12","abstract":[{"text":"Around 150 million years ago, eusocial termites evolved from within the cockroaches, 50 million years before eusocial Hymenoptera, such as bees and ants, appeared. Here, we report the 2-Gb genome of the German cockroach, Blattella germanica, and the 1.3-Gb genome of the drywood termite Cryptotermes secundus. We show evolutionary signatures of termite eusociality by comparing the genomes and transcriptomes of three termites and the cockroach against the background of 16 other eusocial and non-eusocial insects. Dramatic adaptive changes in genes underlying the production and perception of pheromones confirm the importance of chemical communication in the termites. These are accompanied by major changes in gene regulation and the molecular evolution of caste determination. Many of these results parallel molecular mechanisms of eusocial evolution in Hymenoptera. However, the specific solutions are remarkably different, thus revealing a striking case of convergence in one of the major evolutionary transitions in biological complexity.","lang":"eng"}],"date_updated":"2023-09-11T14:10:56Z","author":[{"first_name":"Mark C.","last_name":"Harrison","full_name":"Harrison, Mark C."},{"last_name":"Jongepier","first_name":"Evelien","full_name":"Jongepier, Evelien"},{"full_name":"Robertson, Hugh M.","last_name":"Robertson","first_name":"Hugh M."},{"full_name":"Arning, Nicolas","first_name":"Nicolas","last_name":"Arning"},{"first_name":"Tristan","last_name":"Bitard-Feildel","full_name":"Bitard-Feildel, Tristan"},{"first_name":"Hsu","last_name":"Chao","full_name":"Chao, Hsu"},{"first_name":"Christopher P.","last_name":"Childers","full_name":"Childers, Christopher P."},{"last_name":"Dinh","first_name":"Huyen","full_name":"Dinh, Huyen"},{"first_name":"Harshavardhan","last_name":"Doddapaneni","full_name":"Doddapaneni, Harshavardhan"},{"last_name":"Dugan","first_name":"Shannon","full_name":"Dugan, Shannon"},{"full_name":"Gowin, Johannes","last_name":"Gowin","first_name":"Johannes"},{"full_name":"Greiner, Carolin","first_name":"Carolin","last_name":"Greiner"},{"full_name":"Han, Yi","first_name":"Yi","last_name":"Han"},{"last_name":"Hu","first_name":"Haofu","full_name":"Hu, Haofu"},{"full_name":"Hughes, Daniel S. T.","first_name":"Daniel S. T.","last_name":"Hughes"},{"last_name":"Huylmans","first_name":"Ann K","orcid":"0000-0001-8871-4961","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","full_name":"Huylmans, Ann K"},{"full_name":"Kemena, Carsten","last_name":"Kemena","first_name":"Carsten"},{"first_name":"Lukas P. M.","last_name":"Kremer","full_name":"Kremer, Lukas P. M."},{"full_name":"Lee, Sandra L.","first_name":"Sandra L.","last_name":"Lee"},{"last_name":"Lopez-Ezquerra","first_name":"Alberto","full_name":"Lopez-Ezquerra, Alberto"},{"full_name":"Mallet, Ludovic","last_name":"Mallet","first_name":"Ludovic"},{"full_name":"Monroy-Kuhn, Jose M.","first_name":"Jose M.","last_name":"Monroy-Kuhn"},{"last_name":"Moser","first_name":"Annabell","full_name":"Moser, Annabell"},{"first_name":"Shwetha C.","last_name":"Murali","full_name":"Murali, Shwetha C."},{"full_name":"Muzny, Donna M.","last_name":"Muzny","first_name":"Donna M."},{"first_name":"Saria","last_name":"Otani","full_name":"Otani, Saria"},{"full_name":"Piulachs, Maria-Dolors","last_name":"Piulachs","first_name":"Maria-Dolors"},{"full_name":"Poelchau, Monica","first_name":"Monica","last_name":"Poelchau"},{"full_name":"Qu, Jiaxin","first_name":"Jiaxin","last_name":"Qu"},{"first_name":"Florentine","last_name":"Schaub","full_name":"Schaub, Florentine"},{"full_name":"Wada-Katsumata, Ayako","first_name":"Ayako","last_name":"Wada-Katsumata"},{"first_name":"Kim C.","last_name":"Worley","full_name":"Worley, Kim C."},{"full_name":"Xie, Qiaolin","last_name":"Xie","first_name":"Qiaolin"},{"full_name":"Ylla, Guillem","first_name":"Guillem","last_name":"Ylla"},{"first_name":"Michael","last_name":"Poulsen","full_name":"Poulsen, Michael"},{"full_name":"Gibbs, Richard A.","first_name":"Richard A.","last_name":"Gibbs"},{"first_name":"Coby","last_name":"Schal","full_name":"Schal, Coby"},{"first_name":"Stephen","last_name":"Richards","full_name":"Richards, Stephen"},{"full_name":"Belles, Xavier","last_name":"Belles","first_name":"Xavier"},{"full_name":"Korb, Judith","first_name":"Judith","last_name":"Korb"},{"full_name":"Bornberg-Bauer, Erich","first_name":"Erich","last_name":"Bornberg-Bauer"}],"article_processing_charge":"No","_id":"9841","department":[{"_id":"BeVi"}],"year":"2018","publisher":"Dryad","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.51d4r"}],"doi":"10.5061/dryad.51d4r","date_published":"2018-12-12T00:00:00Z","oa":1,"citation":{"ama":"Harrison MC, Jongepier E, Robertson HM, et al. Data from: Hemimetabolous genomes reveal molecular basis of termite eusociality. 2018. doi:<a href=\"https://doi.org/10.5061/dryad.51d4r\">10.5061/dryad.51d4r</a>","ista":"Harrison MC, Jongepier E, Robertson HM, Arning N, Bitard-Feildel T, Chao H, Childers CP, Dinh H, Doddapaneni H, Dugan S, Gowin J, Greiner C, Han Y, Hu H, Hughes DST, Huylmans AK, Kemena C, Kremer LPM, Lee SL, Lopez-Ezquerra A, Mallet L, Monroy-Kuhn JM, Moser A, Murali SC, Muzny DM, Otani S, Piulachs M-D, Poelchau M, Qu J, Schaub F, Wada-Katsumata A, Worley KC, Xie Q, Ylla G, Poulsen M, Gibbs RA, Schal C, Richards S, Belles X, Korb J, Bornberg-Bauer E. 2018. Data from: Hemimetabolous genomes reveal molecular basis of termite eusociality, Dryad, <a href=\"https://doi.org/10.5061/dryad.51d4r\">10.5061/dryad.51d4r</a>.","mla":"Harrison, Mark C., et al. <i>Data from: Hemimetabolous Genomes Reveal Molecular Basis of Termite Eusociality</i>. Dryad, 2018, doi:<a href=\"https://doi.org/10.5061/dryad.51d4r\">10.5061/dryad.51d4r</a>.","apa":"Harrison, M. C., Jongepier, E., Robertson, H. M., Arning, N., Bitard-Feildel, T., Chao, H., … Bornberg-Bauer, E. (2018). Data from: Hemimetabolous genomes reveal molecular basis of termite eusociality. Dryad. <a href=\"https://doi.org/10.5061/dryad.51d4r\">https://doi.org/10.5061/dryad.51d4r</a>","ieee":"M. C. Harrison <i>et al.</i>, “Data from: Hemimetabolous genomes reveal molecular basis of termite eusociality.” Dryad, 2018.","chicago":"Harrison, Mark C., Evelien Jongepier, Hugh M. Robertson, Nicolas Arning, Tristan Bitard-Feildel, Hsu Chao, Christopher P. Childers, et al. “Data from: Hemimetabolous Genomes Reveal Molecular Basis of Termite Eusociality.” Dryad, 2018. <a href=\"https://doi.org/10.5061/dryad.51d4r\">https://doi.org/10.5061/dryad.51d4r</a>.","short":"M.C. Harrison, E. Jongepier, H.M. Robertson, N. Arning, T. Bitard-Feildel, H. Chao, C.P. Childers, H. Dinh, H. Doddapaneni, S. Dugan, J. Gowin, C. Greiner, Y. Han, H. Hu, D.S.T. Hughes, A.K. Huylmans, C. Kemena, L.P.M. Kremer, S.L. Lee, A. Lopez-Ezquerra, L. Mallet, J.M. Monroy-Kuhn, A. Moser, S.C. Murali, D.M. Muzny, S. Otani, M.-D. Piulachs, M. Poelchau, J. Qu, F. Schaub, A. Wada-Katsumata, K.C. Worley, Q. Xie, G. Ylla, M. Poulsen, R.A. Gibbs, C. Schal, S. Richards, X. Belles, J. Korb, E. Bornberg-Bauer, (2018)."},"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"448"}]},"status":"public"},{"_id":"9915","year":"2018","acknowledgement":"The authors express a special thanks to Dr Richard Willan at the Museum and Art Gallery of the Northern Territory for guidance and support in the field, and to Carole Smadja for reading and commenting on the manuscript. The authors thank the Government of Western Australia Department of Parks and Wildlife (license no. 009254) and Fishery Research Division (exemption no. 2262) for assistance with permits. Khalid Belkhir modified the coalescent sampler msnsam for the specific needs of this project and Martin Hirsch helped to set up the ABC pipeline and to modify the summary statistic calculator mscalc. The authors are grateful to the Crafoord Foundation for supporting this project. R.K.B., A.M.W., and L.D. were supported by grants from the Natural Environment Research Council, R.K.B. and A.M.W. were also supported by the European Research Council and R.K.B. and L.D. by the Leverhulme Trust. M.M.R. was supported by Consejo Nacional de Ciencia y Tecnología and Secretaría de Educación Pública, Mexico. G.B. was supported by the Centre for Animal Movement Research (CAnMove) financed by a Linnaeus grant (No. 349-2007-8690) from the Swedish Research Council and Lund University.","file_date_updated":"2021-08-16T07:37:28Z","date_created":"2021-08-16T07:30:00Z","volume":2,"type":"journal_article","oa_version":"Published Version","month":"12","date_updated":"2023-09-19T15:08:53Z","abstract":[{"lang":"eng","text":"The evolution of assortative mating is a key part of the speciation process. Stronger assortment, or greater divergence in mating traits, between species pairs with overlapping ranges is commonly observed, but possible causes of this pattern of reproductive character displacement are difficult to distinguish. We use a multidisciplinary approach to provide a rare example where it is possible to distinguish among hypotheses concerning the evolution of reproductive character displacement. We build on an earlier comparative analysis that illustrated a strong pattern of greater divergence in penis form between pairs of sister species with overlapping ranges than between allopatric sister-species pairs, in a large clade of marine gastropods (Littorinidae). We investigate both assortative mating and divergence in male genitalia in one of the sister-species pairs, discriminating among three contrasting processes each of which can generate a pattern of reproductive character displacement: reinforcement, reproductive interference and the Templeton effect. We demonstrate reproductive character displacement in assortative mating, but not in genital form between this pair of sister species and use demographic models to distinguish among the different processes. Our results support a model with no gene flow since secondary contact and thus favor reproductive interference as the cause of reproductive character displacement for mate choice, rather than reinforcement. High gene flow within species argues against the Templeton effect. Secondary contact appears to have had little impact on genital divergence."}],"page":"557-566","citation":{"apa":"Hollander, J., Montaño-Rendón, M., Bianco, G., Yang, X., Westram, A. M., Duvaux, L., … Butlin, R. K. (2018). Are assortative mating and genital divergence driven by reinforcement? <i>Evolution Letters</i>. Wiley. <a href=\"https://doi.org/10.1002/evl3.85\">https://doi.org/10.1002/evl3.85</a>","mla":"Hollander, Johan, et al. “Are Assortative Mating and Genital Divergence Driven by Reinforcement?” <i>Evolution Letters</i>, vol. 2, no. 6, Wiley, 2018, pp. 557–66, doi:<a href=\"https://doi.org/10.1002/evl3.85\">10.1002/evl3.85</a>.","ista":"Hollander J, Montaño-Rendón M, Bianco G, Yang X, Westram AM, Duvaux L, Reid DG, Butlin RK. 2018. Are assortative mating and genital divergence driven by reinforcement? Evolution Letters. 2(6), 557–566.","ama":"Hollander J, Montaño-Rendón M, Bianco G, et al. Are assortative mating and genital divergence driven by reinforcement? <i>Evolution Letters</i>. 2018;2(6):557-566. doi:<a href=\"https://doi.org/10.1002/evl3.85\">10.1002/evl3.85</a>","short":"J. Hollander, M. Montaño-Rendón, G. Bianco, X. Yang, A.M. Westram, L. Duvaux, D.G. Reid, R.K. Butlin, Evolution Letters 2 (2018) 557–566.","chicago":"Hollander, Johan, Mauricio Montaño-Rendón, Giuseppe Bianco, Xi Yang, Anja M Westram, Ludovic Duvaux, David G. Reid, and Roger K. Butlin. “Are Assortative Mating and Genital Divergence Driven by Reinforcement?” <i>Evolution Letters</i>. Wiley, 2018. <a href=\"https://doi.org/10.1002/evl3.85\">https://doi.org/10.1002/evl3.85</a>.","ieee":"J. Hollander <i>et al.</i>, “Are assortative mating and genital divergence driven by reinforcement?,” <i>Evolution Letters</i>, vol. 2, no. 6. Wiley, pp. 557–566, 2018."},"intvolume":"         2","related_material":{"record":[{"status":"public","id":"9929","relation":"research_data"}]},"external_id":{"pmid":["30564439"],"isi":["000452990000002"]},"status":"public","ddc":["570"],"date_published":"2018-12-13T00:00:00Z","has_accepted_license":"1","oa":1,"publication_status":"published","article_type":"letter_note","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_processing_charge":"Yes","publication":"Evolution Letters","department":[{"_id":"BeVi"}],"pmid":1,"publisher":"Wiley","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Are assortative mating and genital divergence driven by reinforcement?","file":[{"creator":"asandaue","relation":"main_file","content_type":"application/pdf","file_size":584606,"success":1,"file_name":"2018_EvolutionLetters_Hollander.pdf","access_level":"open_access","date_created":"2021-08-16T07:37:28Z","checksum":"997a78ac41c809975ca69cbdea441f88","date_updated":"2021-08-16T07:37:28Z","file_id":"9916"}],"day":"13","author":[{"full_name":"Hollander, Johan","last_name":"Hollander","first_name":"Johan"},{"first_name":"Mauricio","last_name":"Montaño-Rendón","full_name":"Montaño-Rendón, Mauricio"},{"full_name":"Bianco, Giuseppe","last_name":"Bianco","first_name":"Giuseppe"},{"first_name":"Xi","last_name":"Yang","full_name":"Yang, Xi"},{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","last_name":"Westram","first_name":"Anja M"},{"full_name":"Duvaux, Ludovic","first_name":"Ludovic","last_name":"Duvaux"},{"full_name":"Reid, David G.","last_name":"Reid","first_name":"David G."},{"full_name":"Butlin, Roger K.","first_name":"Roger K.","last_name":"Butlin"}],"issue":"6","language":[{"iso":"eng"}],"isi":1,"quality_controlled":"1","doi":"10.1002/evl3.85","publication_identifier":{"eissn":["2056-3744"],"issn":[" 2056-3744"]}},{"month":"08","oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Adaptive divergence and speciation may happen despite opposition by gene flow. Identifying the genomic basis underlying divergence with gene flow is a major task in evolutionary genomics. Most approaches (e.g., outlier scans) focus on genomic regions of high differentiation. However, not all genomic architectures potentially underlying divergence are expected to show extreme differentiation. Here, we develop an approach that combines hybrid zone analysis (i.e., focuses on spatial patterns of allele frequency change) with system-specific simulations to identify loci inconsistent with neutral evolution. We apply this to a genome-wide SNP set from an ideally suited study organism, the intertidal snail Littorina saxatilis, which shows primary divergence between ecotypes associated with different shore habitats. We detect many SNPs with clinal patterns, most of which are consistent with neutrality. Among non-neutral SNPs, most are located within three large putative inversions differentiating ecotypes. Many non-neutral SNPs show relatively low levels of differentiation. We discuss potential reasons for this pattern, including loose linkage to selected variants, polygenic adaptation and a component of balancing selection within populations (which may be expected for inversions). Our work is in line with theory predicting a role for inversions in divergence, and emphasizes that genomic regions contributing to divergence may not always be accessible with methods purely based on allele frequency differences. These conclusions call for approaches that take spatial patterns of allele frequency change into account in other systems."}],"date_updated":"2023-09-19T15:08:25Z","page":"297-309","date_created":"2021-08-16T07:45:38Z","file_date_updated":"2021-08-16T07:48:03Z","volume":2,"year":"2018","acknowledgement":"We are very grateful to people who helped with fieldwork, snail processing, and DNA extractions, particularly Laura Brettell, Mårten Duvetorp, Juan Galindo, Anne-Lise Liabot and Irena Senčić. We would also like to thank Magnus Alm Rosenblad and Mats Töpel for their contribution to assembling the Littorina saxatilis genome, Carl André, Pasi Rastas, and Romain Villoutreix for discussion, and two anonymous reviewers for their helpful comments on the manuscript. We are grateful to RapidGenomics for library preparation and sequencing. We thank the Natural Environment Research Council, the European Research Council and the Swedish Research Councils VR and Formas (Linnaeus grant to the Centre for Marine Evolutionary Biology and Tage Erlander Guest Professorship) for funding. P.C. was funded by the University of Sheffield Vice-chancellor's India scholarship. R.F. is funded by the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement no. 706376. M. Raf. was supported by the Adlerbert Research Foundation.","_id":"9917","has_accepted_license":"1","oa":1,"publication_status":"published","ddc":["570"],"date_published":"2018-08-20T00:00:00Z","status":"public","external_id":{"pmid":["30283683"],"isi":["000446774400004"]},"citation":{"ista":"Westram AM, Rafajlović M, Chaube P, Faria R, Larsson T, Panova M, Ravinet M, Blomberg A, Mehlig B, Johannesson K, Butlin R. 2018. Clines on the seashore: The genomic architecture underlying rapid divergence in the face of gene flow. Evolution Letters. 2(4), 297–309.","mla":"Westram, Anja M., et al. “Clines on the Seashore: The Genomic Architecture Underlying Rapid Divergence in the Face of Gene Flow.” <i>Evolution Letters</i>, vol. 2, no. 4, Wiley, 2018, pp. 297–309, doi:<a href=\"https://doi.org/10.1002/evl3.74\">10.1002/evl3.74</a>.","apa":"Westram, A. M., Rafajlović, M., Chaube, P., Faria, R., Larsson, T., Panova, M., … Butlin, R. (2018). Clines on the seashore: The genomic architecture underlying rapid divergence in the face of gene flow. <i>Evolution Letters</i>. Wiley. <a href=\"https://doi.org/10.1002/evl3.74\">https://doi.org/10.1002/evl3.74</a>","ama":"Westram AM, Rafajlović M, Chaube P, et al. Clines on the seashore: The genomic architecture underlying rapid divergence in the face of gene flow. <i>Evolution Letters</i>. 2018;2(4):297-309. doi:<a href=\"https://doi.org/10.1002/evl3.74\">10.1002/evl3.74</a>","short":"A.M. Westram, M. Rafajlović, P. Chaube, R. Faria, T. Larsson, M. Panova, M. Ravinet, A. Blomberg, B. Mehlig, K. Johannesson, R. Butlin, Evolution Letters 2 (2018) 297–309.","ieee":"A. M. Westram <i>et al.</i>, “Clines on the seashore: The genomic architecture underlying rapid divergence in the face of gene flow,” <i>Evolution Letters</i>, vol. 2, no. 4. Wiley, pp. 297–309, 2018.","chicago":"Westram, Anja M, Marina Rafajlović, Pragya Chaube, Rui Faria, Tomas Larsson, Marina Panova, Mark Ravinet, et al. “Clines on the Seashore: The Genomic Architecture Underlying Rapid Divergence in the Face of Gene Flow.” <i>Evolution Letters</i>. Wiley, 2018. <a href=\"https://doi.org/10.1002/evl3.74\">https://doi.org/10.1002/evl3.74</a>."},"related_material":{"record":[{"relation":"research_data","id":"9930","status":"public"}]},"intvolume":"         2","file":[{"success":1,"file_name":"2018_EvolutionLetters_Westram.pdf","content_type":"application/pdf","relation":"main_file","file_size":764299,"creator":"asandaue","date_updated":"2021-08-16T07:48:03Z","file_id":"9918","checksum":"8524e72507d521416be3f8ccfcd5e3f5","date_created":"2021-08-16T07:48:03Z","access_level":"open_access"}],"day":"20","author":[{"full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","last_name":"Westram","first_name":"Anja M"},{"last_name":"Rafajlović","first_name":"Marina","full_name":"Rafajlović, Marina"},{"last_name":"Chaube","first_name":"Pragya","full_name":"Chaube, Pragya"},{"full_name":"Faria, Rui","last_name":"Faria","first_name":"Rui"},{"first_name":"Tomas","last_name":"Larsson","full_name":"Larsson, Tomas"},{"first_name":"Marina","last_name":"Panova","full_name":"Panova, Marina"},{"first_name":"Mark","last_name":"Ravinet","full_name":"Ravinet, Mark"},{"first_name":"Anders","last_name":"Blomberg","full_name":"Blomberg, Anders"},{"full_name":"Mehlig, Bernhard","first_name":"Bernhard","last_name":"Mehlig"},{"full_name":"Johannesson, Kerstin","first_name":"Kerstin","last_name":"Johannesson"},{"first_name":"Roger","last_name":"Butlin","full_name":"Butlin, Roger"}],"title":"Clines on the seashore: The genomic architecture underlying rapid divergence in the face of gene flow","department":[{"_id":"BeVi"}],"pmid":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Wiley","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"letter_note","article_processing_charge":"Yes","publication":"Evolution Letters","publication_identifier":{"issn":["2056-3744"],"eissn":["2056-3744"]},"quality_controlled":"1","doi":"10.1002/evl3.74","issue":"4","language":[{"iso":"eng"}],"isi":1},{"status":"public","related_material":{"record":[{"id":"9915","status":"public","relation":"used_in_publication"}]},"citation":{"ieee":"J. Hollander <i>et al.</i>, “Data from: Are assortative mating and genital divergence driven by reinforcement?” Dryad, 2018.","chicago":"Hollander, Johan, Mauricio Montaño-Rendón, Giuseppe Bianco, Xi Yang, Anja M Westram, Ludovic Duvaux, David G. Reid, and Roger K. Butlin. “Data from: Are Assortative Mating and Genital Divergence Driven by Reinforcement?” Dryad, 2018. <a href=\"https://doi.org/10.5061/dryad.51sd2p5\">https://doi.org/10.5061/dryad.51sd2p5</a>.","short":"J. Hollander, M. Montaño-Rendón, G. Bianco, X. Yang, A.M. Westram, L. Duvaux, D.G. Reid, R.K. Butlin, (2018).","ama":"Hollander J, Montaño-Rendón M, Bianco G, et al. Data from: Are assortative mating and genital divergence driven by reinforcement? 2018. doi:<a href=\"https://doi.org/10.5061/dryad.51sd2p5\">10.5061/dryad.51sd2p5</a>","mla":"Hollander, Johan, et al. <i>Data from: Are Assortative Mating and Genital Divergence Driven by Reinforcement?</i> Dryad, 2018, doi:<a href=\"https://doi.org/10.5061/dryad.51sd2p5\">10.5061/dryad.51sd2p5</a>.","ista":"Hollander J, Montaño-Rendón M, Bianco G, Yang X, Westram AM, Duvaux L, Reid DG, Butlin RK. 2018. Data from: Are assortative mating and genital divergence driven by reinforcement?, Dryad, <a href=\"https://doi.org/10.5061/dryad.51sd2p5\">10.5061/dryad.51sd2p5</a>.","apa":"Hollander, J., Montaño-Rendón, M., Bianco, G., Yang, X., Westram, A. M., Duvaux, L., … Butlin, R. K. (2018). Data from: Are assortative mating and genital divergence driven by reinforcement? Dryad. <a href=\"https://doi.org/10.5061/dryad.51sd2p5\">https://doi.org/10.5061/dryad.51sd2p5</a>"},"oa":1,"date_published":"2018-10-17T00:00:00Z","doi":"10.5061/dryad.51sd2p5","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.51sd2p5"}],"publisher":"Dryad","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","department":[{"_id":"BeVi"}],"year":"2018","_id":"9929","article_processing_charge":"No","author":[{"first_name":"Johan","last_name":"Hollander","full_name":"Hollander, Johan"},{"full_name":"Montaño-Rendón, Mauricio","first_name":"Mauricio","last_name":"Montaño-Rendón"},{"last_name":"Bianco","first_name":"Giuseppe","full_name":"Bianco, Giuseppe"},{"full_name":"Yang, Xi","last_name":"Yang","first_name":"Xi"},{"last_name":"Westram","first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M"},{"full_name":"Duvaux, Ludovic","first_name":"Ludovic","last_name":"Duvaux"},{"full_name":"Reid, David G.","last_name":"Reid","first_name":"David G."},{"full_name":"Butlin, Roger K.","first_name":"Roger K.","last_name":"Butlin"}],"day":"17","abstract":[{"lang":"eng","text":"The evolution of assortative mating is a key part of the speciation process. Stronger assortment, or greater divergence in mating traits, between species pairs with overlapping ranges is commonly observed, but possible causes of this pattern of reproductive character displacement are difficult to distinguish. We use a multidisciplinary approach to provide a rare example where it is possible to distinguish among hypotheses concerning the evolution of reproductive character displacement. We build on an earlier comparative analysis that illustrated a strong pattern of greater divergence in penis form between pairs of sister species with overlapping ranges than between allopatric sister-species pairs, in a large clade of marine gastropods (Littorinidae). We investigate both assortative mating and divergence in male genitalia in one of the sister-species pairs, discriminating among three contrasting processes each of which can generate a pattern of reproductive character displacement: reinforcement, reproductive interference and the Templeton effect. We demonstrate reproductive character displacement in assortative mating, but not in genital form between this pair of sister species and use demographic models to distinguish among the different processes. Our results support a model with no gene flow since secondary contact and thus favour reproductive interference as the cause of reproductive character displacement for mate choice, rather than reinforcement. High gene flow within species argues against the Templeton effect. Secondary contact appears to have had little impact on genital divergence."}],"date_updated":"2023-09-19T15:08:53Z","oa_version":"Published Version","month":"10","type":"research_data_reference","title":"Data from: Are assortative mating and genital divergence driven by reinforcement?","date_created":"2021-08-17T08:51:06Z"},{"author":[{"first_name":"Anja M","last_name":"Westram","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Rafajlović, Marina","first_name":"Marina","last_name":"Rafajlović"},{"full_name":"Chaube, Pragya","last_name":"Chaube","first_name":"Pragya"},{"full_name":"Faria, Rui","last_name":"Faria","first_name":"Rui"},{"full_name":"Larsson, Tomas","first_name":"Tomas","last_name":"Larsson"},{"last_name":"Panova","first_name":"Marina","full_name":"Panova, Marina"},{"first_name":"Mark","last_name":"Ravinet","full_name":"Ravinet, Mark"},{"last_name":"Blomberg","first_name":"Anders","full_name":"Blomberg, Anders"},{"full_name":"Mehlig, Bernhard","last_name":"Mehlig","first_name":"Bernhard"},{"full_name":"Johannesson, Kerstin","last_name":"Johannesson","first_name":"Kerstin"},{"full_name":"Butlin, Roger","last_name":"Butlin","first_name":"Roger"}],"oa_version":"Published Version","month":"07","type":"research_data_reference","abstract":[{"text":"Adaptive divergence and speciation may happen despite opposition by gene flow. Identifying the genomic basis underlying divergence with gene flow is a major task in evolutionary genomics. Most approaches (e.g. outlier scans) focus on genomic regions of high differentiation. However, not all genomic architectures potentially underlying divergence are expected to show extreme differentiation. Here, we develop an approach that combines hybrid zone analysis (i.e. focuses on spatial patterns of allele frequency change) with system-specific simulations to identify loci inconsistent with neutral evolution. We apply this to a genome-wide SNP set from an ideally-suited study organism, the intertidal snail Littorina saxatilis, which shows primary divergence between ecotypes associated with different shore habitats. We detect many SNPs with clinal patterns, most of which are consistent with neutrality. Among non-neutral SNPs, most are located within three large putative inversions differentiating ecotypes. Many non-neutral SNPs show relatively low levels of differentiation. We discuss potential reasons for this pattern, including loose linkage to selected variants, polygenic adaptation and a component of balancing selection within populations (which may be expected for inversions). Our work is in line with theory predicting a role for inversions in divergence, and emphasises that genomic regions contributing to divergence may not always be accessible with methods purely based on allele frequency differences. These conclusions call for approaches that take spatial patterns of allele frequency change into account in other systems.","lang":"eng"}],"date_updated":"2023-09-19T15:08:24Z","day":"23","title":"Data from: Clines on the seashore: the genomic architecture underlying rapid divergence in the face of gene flow","date_created":"2021-08-17T08:58:47Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publisher":"Dryad","department":[{"_id":"BeVi"}],"year":"2018","_id":"9930","article_processing_charge":"No","oa":1,"doi":"10.5061/dryad.bp25b65","date_published":"2018-07-23T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.bp25b65"}],"status":"public","related_material":{"record":[{"id":"9917","status":"public","relation":"used_in_publication"}]},"citation":{"ama":"Westram AM, Rafajlović M, Chaube P, et al. Data from: Clines on the seashore: the genomic architecture underlying rapid divergence in the face of gene flow. 2018. doi:<a href=\"https://doi.org/10.5061/dryad.bp25b65\">10.5061/dryad.bp25b65</a>","apa":"Westram, A. M., Rafajlović, M., Chaube, P., Faria, R., Larsson, T., Panova, M., … Butlin, R. (2018). Data from: Clines on the seashore: the genomic architecture underlying rapid divergence in the face of gene flow. Dryad. <a href=\"https://doi.org/10.5061/dryad.bp25b65\">https://doi.org/10.5061/dryad.bp25b65</a>","mla":"Westram, Anja M., et al. <i>Data from: Clines on the Seashore: The Genomic Architecture Underlying Rapid Divergence in the Face of Gene Flow</i>. Dryad, 2018, doi:<a href=\"https://doi.org/10.5061/dryad.bp25b65\">10.5061/dryad.bp25b65</a>.","ista":"Westram AM, Rafajlović M, Chaube P, Faria R, Larsson T, Panova M, Ravinet M, Blomberg A, Mehlig B, Johannesson K, Butlin R. 2018. Data from: Clines on the seashore: the genomic architecture underlying rapid divergence in the face of gene flow, Dryad, <a href=\"https://doi.org/10.5061/dryad.bp25b65\">10.5061/dryad.bp25b65</a>.","chicago":"Westram, Anja M, Marina Rafajlović, Pragya Chaube, Rui Faria, Tomas Larsson, Marina Panova, Mark Ravinet, et al. “Data from: Clines on the Seashore: The Genomic Architecture Underlying Rapid Divergence in the Face of Gene Flow.” Dryad, 2018. <a href=\"https://doi.org/10.5061/dryad.bp25b65\">https://doi.org/10.5061/dryad.bp25b65</a>.","ieee":"A. M. Westram <i>et al.</i>, “Data from: Clines on the seashore: the genomic architecture underlying rapid divergence in the face of gene flow.” Dryad, 2018.","short":"A.M. Westram, M. Rafajlović, P. Chaube, R. Faria, T. Larsson, M. Panova, M. Ravinet, A. Blomberg, B. Mehlig, K. Johannesson, R. Butlin, (2018)."}},{"publist_id":"7375","title":"Hemimetabolous genomes reveal molecular basis of termite eusociality","file":[{"access_level":"open_access","date_created":"2018-12-12T10:09:08Z","checksum":"874953136ac125e65f37971d3cabc5b7","date_updated":"2020-07-14T12:46:30Z","file_id":"4731","creator":"system","content_type":"application/pdf","relation":"main_file","file_size":3730583,"file_name":"IST-2018-969-v1+1_2018_Huylmans_Hemimetabolous_genomes.pdf"}],"day":"05","author":[{"last_name":"Harrison","first_name":"Mark","full_name":"Harrison, Mark"},{"last_name":"Jongepier","first_name":"Evelien","full_name":"Jongepier, Evelien"},{"full_name":"Robertson, Hugh","last_name":"Robertson","first_name":"Hugh"},{"full_name":"Arning, Nicolas","last_name":"Arning","first_name":"Nicolas"},{"last_name":"Bitard Feildel","first_name":"Tristan","full_name":"Bitard Feildel, Tristan"},{"last_name":"Chao","first_name":"Hsu","full_name":"Chao, Hsu"},{"last_name":"Childers","first_name":"Christopher","full_name":"Childers, Christopher"},{"last_name":"Dinh","first_name":"Huyen","full_name":"Dinh, Huyen"},{"full_name":"Doddapaneni, Harshavardhan","last_name":"Doddapaneni","first_name":"Harshavardhan"},{"full_name":"Dugan, Shannon","last_name":"Dugan","first_name":"Shannon"},{"first_name":"Johannes","last_name":"Gowin","full_name":"Gowin, Johannes"},{"first_name":"Carolin","last_name":"Greiner","full_name":"Greiner, Carolin"},{"first_name":"Yi","last_name":"Han","full_name":"Han, Yi"},{"first_name":"Haofu","last_name":"Hu","full_name":"Hu, Haofu"},{"first_name":"Daniel","last_name":"Hughes","full_name":"Hughes, Daniel"},{"full_name":"Huylmans, Ann K","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8871-4961","first_name":"Ann K","last_name":"Huylmans"},{"first_name":"Karsten","last_name":"Kemena","full_name":"Kemena, Karsten"},{"first_name":"Lukas","last_name":"Kremer","full_name":"Kremer, Lukas"},{"last_name":"Lee","first_name":"Sandra","full_name":"Lee, Sandra"},{"full_name":"López Ezquerra, Alberto","last_name":"López Ezquerra","first_name":"Alberto"},{"full_name":"Mallet, Ludovic","last_name":"Mallet","first_name":"Ludovic"},{"full_name":"Monroy Kuhn, Jose","first_name":"Jose","last_name":"Monroy Kuhn"},{"first_name":"Annabell","last_name":"Moser","full_name":"Moser, Annabell"},{"full_name":"Murali, Shwetha","last_name":"Murali","first_name":"Shwetha"},{"last_name":"Muzny","first_name":"Donna","full_name":"Muzny, Donna"},{"last_name":"Otani","first_name":"Saria","full_name":"Otani, Saria"},{"last_name":"Piulachs","first_name":"Maria","full_name":"Piulachs, Maria"},{"first_name":"Monica","last_name":"Poelchau","full_name":"Poelchau, Monica"},{"first_name":"Jiaxin","last_name":"Qu","full_name":"Qu, Jiaxin"},{"last_name":"Schaub","first_name":"Florentine","full_name":"Schaub, Florentine"},{"full_name":"Wada Katsumata, Ayako","last_name":"Wada Katsumata","first_name":"Ayako"},{"first_name":"Kim","last_name":"Worley","full_name":"Worley, Kim"},{"full_name":"Xie, Qiaolin","first_name":"Qiaolin","last_name":"Xie"},{"full_name":"Ylla, Guillem","last_name":"Ylla","first_name":"Guillem"},{"last_name":"Poulsen","first_name":"Michael","full_name":"Poulsen, Michael"},{"first_name":"Richard","last_name":"Gibbs","full_name":"Gibbs, Richard"},{"last_name":"Schal","first_name":"Coby","full_name":"Schal, Coby"},{"full_name":"Richards, Stephen","last_name":"Richards","first_name":"Stephen"},{"full_name":"Belles, Xavier","last_name":"Belles","first_name":"Xavier"},{"full_name":"Korb, Judith","last_name":"Korb","first_name":"Judith"},{"full_name":"Bornberg Bauer, Erich","first_name":"Erich","last_name":"Bornberg Bauer"}],"article_processing_charge":"No","scopus_import":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"publication":"Nature Ecology and Evolution","department":[{"_id":"BeVi"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Springer Nature","quality_controlled":"1","doi":"10.1038/s41559-017-0459-1","pubrep_id":"969","language":[{"iso":"eng"}],"issue":"3","isi":1,"date_created":"2018-12-11T11:46:32Z","file_date_updated":"2020-07-14T12:46:30Z","volume":2,"date_updated":"2023-09-11T14:10:57Z","abstract":[{"lang":"eng","text":"Around 150 million years ago, eusocial termites evolved from within the cockroaches, 50 million years before eusocial Hymenoptera, such as bees and ants, appeared. Here, we report the 2-Gb genome of the German cockroach, Blattella germanica, and the 1.3-Gb genome of the drywood termite Cryptotermes secundus. We show evolutionary signatures of termite eusociality by comparing the genomes and transcriptomes of three termites and the cockroach against the background of 16 other eusocial and non-eusocial insects. Dramatic adaptive changes in genes underlying the production and perception of pheromones confirm the importance of chemical communication in the termites. These are accompanied by major changes in gene regulation and the molecular evolution of caste determination. Many of these results parallel molecular mechanisms of eusocial evolution in Hymenoptera. However, the specific solutions are remarkably different, thus revealing a striking case of convergence in one of the major evolutionary transitions in biological complexity."}],"month":"02","type":"journal_article","oa_version":"Published Version","page":"557-566","_id":"448","year":"2018","acknowledgement":"We thank O. Niehuis for allowing use of the unpublished E. danica genome, J. Gadau and C. Smith for comments and advice on the manuscript, and J. Schmitz for assistance with analyses and proofreading the manuscript. J.K. thanks Charles Darwin University (Australia), especially S. Garnett and the Horticulture and Aquaculture team, for providing logistic support to collect C. secundus. The Parks and Wildlife Commission, Northern Territory, the Department of the Environment, Water, Heritage and the Arts gave permission to collect (Permit number 36401) and export (Permit WT2010-6997) the termites. USDA is an equal opportunity provider and employer. M.C.H. and E.J. are supported by DFG grant BO2544/11-1 to E.B.-B. J.K. is supported by University of Osnabrück and DFG grant KO1895/16-1. X.B. and M.-D.P. are supported by Spanish Ministerio de Economía y Competitividad (CGL2012-36251 and CGL2015-64727-P to X.B., and CGL2016-76011-R to M.-D.P.), including FEDER funds, and by Catalan Government (2014 SGR 619). C.S. is supported by grants from the US Department of Housing and Urban Development (NCHHU-0017-13), the National Science Foundation (IOS-1557864), the Alfred P. Sloan Foundation (2013-5-35 MBE), the National Institute of Environmental Health Sciences (P30ES025128) to the Center for Human Health and the Environment, and the Blanton J. Whitmire Endowment. M.P. is supported by a Villum Kann Rasmussen Young Investigator Fellowship (VKR10101).","ddc":["576"],"date_published":"2018-02-05T00:00:00Z","has_accepted_license":"1","oa":1,"publication_status":"published","citation":{"short":"M. Harrison, E. Jongepier, H. Robertson, N. Arning, T. Bitard Feildel, H. Chao, C. Childers, H. Dinh, H. Doddapaneni, S. Dugan, J. Gowin, C. Greiner, Y. Han, H. Hu, D. Hughes, A.K. Huylmans, K. Kemena, L. Kremer, S. Lee, A. López Ezquerra, L. Mallet, J. Monroy Kuhn, A. Moser, S. Murali, D. Muzny, S. Otani, M. Piulachs, M. Poelchau, J. Qu, F. Schaub, A. Wada Katsumata, K. Worley, Q. Xie, G. Ylla, M. Poulsen, R. Gibbs, C. Schal, S. Richards, X. Belles, J. Korb, E. Bornberg Bauer, Nature Ecology and Evolution 2 (2018) 557–566.","ieee":"M. Harrison <i>et al.</i>, “Hemimetabolous genomes reveal molecular basis of termite eusociality,” <i>Nature Ecology and Evolution</i>, vol. 2, no. 3. Springer Nature, pp. 557–566, 2018.","chicago":"Harrison, Mark, Evelien Jongepier, Hugh Robertson, Nicolas Arning, Tristan Bitard Feildel, Hsu Chao, Christopher Childers, et al. “Hemimetabolous Genomes Reveal Molecular Basis of Termite Eusociality.” <i>Nature Ecology and Evolution</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1038/s41559-017-0459-1\">https://doi.org/10.1038/s41559-017-0459-1</a>.","ista":"Harrison M, Jongepier E, Robertson H, Arning N, Bitard Feildel T, Chao H, Childers C, Dinh H, Doddapaneni H, Dugan S, Gowin J, Greiner C, Han Y, Hu H, Hughes D, Huylmans AK, Kemena K, Kremer L, Lee S, López Ezquerra A, Mallet L, Monroy Kuhn J, Moser A, Murali S, Muzny D, Otani S, Piulachs M, Poelchau M, Qu J, Schaub F, Wada Katsumata A, Worley K, Xie Q, Ylla G, Poulsen M, Gibbs R, Schal C, Richards S, Belles X, Korb J, Bornberg Bauer E. 2018. Hemimetabolous genomes reveal molecular basis of termite eusociality. Nature Ecology and Evolution. 2(3), 557–566.","mla":"Harrison, Mark, et al. “Hemimetabolous Genomes Reveal Molecular Basis of Termite Eusociality.” <i>Nature Ecology and Evolution</i>, vol. 2, no. 3, Springer Nature, 2018, pp. 557–66, doi:<a href=\"https://doi.org/10.1038/s41559-017-0459-1\">10.1038/s41559-017-0459-1</a>.","apa":"Harrison, M., Jongepier, E., Robertson, H., Arning, N., Bitard Feildel, T., Chao, H., … Bornberg Bauer, E. (2018). Hemimetabolous genomes reveal molecular basis of termite eusociality. <i>Nature Ecology and Evolution</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41559-017-0459-1\">https://doi.org/10.1038/s41559-017-0459-1</a>","ama":"Harrison M, Jongepier E, Robertson H, et al. Hemimetabolous genomes reveal molecular basis of termite eusociality. <i>Nature Ecology and Evolution</i>. 2018;2(3):557-566. doi:<a href=\"https://doi.org/10.1038/s41559-017-0459-1\">10.1038/s41559-017-0459-1</a>"},"intvolume":"         2","related_material":{"record":[{"status":"public","id":"9841","relation":"research_data"}]},"status":"public","external_id":{"isi":["000426559600026"]}}]