[{"citation":{"ieee":"A. Mrnjavac, B. Vicoso, and T. Connallon, “An extension of Muller’s sheltering hypothesis for the evolution of sex chromosome gene content,” <i>Molecular Biology and Evolution</i>, vol. 42, no. 8. Oxford University Press, 2025.","chicago":"Mrnjavac, Andrea, Beatriz Vicoso, and Tim Connallon. “An Extension of Muller’s Sheltering Hypothesis for the Evolution of Sex Chromosome Gene Content.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2025. <a href=\"https://doi.org/10.1093/molbev/msaf177\">https://doi.org/10.1093/molbev/msaf177</a>.","ista":"Mrnjavac A, Vicoso B, Connallon T. 2025. An extension of Muller’s sheltering hypothesis for the evolution of sex chromosome gene content. Molecular Biology and Evolution. 42(8), msaf177.","short":"A. Mrnjavac, B. Vicoso, T. Connallon, Molecular Biology and Evolution 42 (2025).","mla":"Mrnjavac, Andrea, et al. “An Extension of Muller’s Sheltering Hypothesis for the Evolution of Sex Chromosome Gene Content.” <i>Molecular Biology and Evolution</i>, vol. 42, no. 8, msaf177, Oxford University Press, 2025, doi:<a href=\"https://doi.org/10.1093/molbev/msaf177\">10.1093/molbev/msaf177</a>.","ama":"Mrnjavac A, Vicoso B, Connallon T. An extension of Muller’s sheltering hypothesis for the evolution of sex chromosome gene content. <i>Molecular Biology and Evolution</i>. 2025;42(8). doi:<a href=\"https://doi.org/10.1093/molbev/msaf177\">10.1093/molbev/msaf177</a>","apa":"Mrnjavac, A., Vicoso, B., &#38; Connallon, T. (2025). An extension of Muller’s sheltering hypothesis for the evolution of sex chromosome gene content. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msaf177\">https://doi.org/10.1093/molbev/msaf177</a>"},"year":"2025","external_id":{"isi":["001547617100001"],"pmid":["40713898"]},"has_accepted_license":"1","month":"08","publication":"Molecular Biology and Evolution","acknowledged_ssus":[{"_id":"ScienComp"}],"date_updated":"2025-09-30T14:25:57Z","DOAJ_listed":"1","PlanS_conform":"1","publication_status":"published","status":"public","doi":"10.1093/molbev/msaf177","ddc":["570"],"OA_type":"gold","oa_version":"Published Version","oa":1,"file_date_updated":"2025-09-02T07:47:32Z","file":[{"date_created":"2025-09-02T07:47:32Z","success":1,"file_name":"2025_MolecularBioEvolution_Mrnjavac.pdf","file_id":"20274","checksum":"f40abffa56cb1e9ff65800f2a7d7b39a","access_level":"open_access","relation":"main_file","creator":"dernst","date_updated":"2025-09-02T07:47:32Z","file_size":1239841,"content_type":"application/pdf"}],"volume":42,"article_processing_charge":"Yes","day":"01","isi":1,"article_type":"original","publisher":"Oxford University Press","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}],"acknowledgement":"We thank Filip Ruzicka, Colin Olito, Akane Uesugi, Melissa Toups, Daniel Jeffries, the Associate Editor, and anonymous reviewers, for comments and suggestions on earlier versions of the paper. We are particularly grateful to Deborah Charlesworth and Brian Charlesworth for extensive comments on two different drafts of the manuscript. We also thank Aneil Agrawal and Thomas Lenormand for email correspondence about the data on dominance and ways to interpret it. Technical support was provided by ISTA Scientific Computing Unit.","date_created":"2025-08-24T22:01:31Z","issue":"8","OA_place":"publisher","scopus_import":"1","intvolume":"        42","_id":"20223","article_number":"msaf177","date_published":"2025-08-01T00:00:00Z","pmid":1,"type":"journal_article","publication_identifier":{"issn":["0737-4038"],"eissn":["1537-1719"]},"title":"An extension of Muller's sheltering hypothesis for the evolution of sex chromosome gene content","related_material":{"link":[{"relation":"software","url":"https://git.ista.ac.at/bvicoso/xydegenerate"}]},"author":[{"last_name":"Mrnjavac","id":"353FAC84-AE61-11E9-8BFC-00D3E5697425","first_name":"Andrea","full_name":"Mrnjavac, Andrea"},{"full_name":"Vicoso, Beatriz","last_name":"Vicoso","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz"},{"first_name":"Tim","last_name":"Connallon","full_name":"Connallon, Tim"}],"department":[{"_id":"BeVi"}],"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"quality_controlled":"1","abstract":[{"lang":"eng","text":"The first influential hypothesis for sex chromosome evolution was proposed in 1914 by H. J. Muller, who argued that once recombination was suppressed between the X and Y chromosomes, Y-linked genes become “sheltered” from selection, leading to accumulation of recessive loss-of-function (LOF) mutations and decay of Y-linked genes. The hypothesis fell out of favor in the 1970s because early mathematical models failed to support it and data on the dominance of lethal mutations were viewed as incompatible with the hypothesis. We reevaluate the main arguments against Muller's hypothesis and find that they do not conclusively exclude a role for sheltering in sex chromosome evolution. By relaxing restrictive assumptions of earlier models, we show that sheltering promotes fixation of LOF mutations with sexually dimorphic fitness effects, resulting in decay of X-linked genes that are exclusively expressed by males and Y-linked genes that are primarily, though not necessarily exclusively, expressed by females. We further show that drift and other processes contributing to Y degeneration (i.e. selective interference and regulatory evolution) expand conditions of Y-linked gene loss by sheltering. The actual contribution of sheltering to sex chromosome evolution hinges upon the distribution of dominance and sex-specific fitness effects of LOF mutations, which we discuss."}]},{"year":"2025","citation":{"ieee":"V. K. Bett, M. S. Trejo Arellano, and B. Vicoso, “Chromatin landscape is associated with sex-biased expression and Drosophila-like dosage compensation of the Z chromosome in Artemia franciscana,” <i>Molecular Biology and Evolution</i>, vol. 42, no. 5. Oxford University Press, 2025.","chicago":"Bett, Vincent K, Minerva S Trejo Arellano, and Beatriz Vicoso. “Chromatin Landscape Is Associated with Sex-Biased Expression and Drosophila-like Dosage Compensation of the Z Chromosome in Artemia Franciscana.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2025. <a href=\"https://doi.org/10.1093/molbev/msaf085\">https://doi.org/10.1093/molbev/msaf085</a>.","mla":"Bett, Vincent K., et al. “Chromatin Landscape Is Associated with Sex-Biased Expression and Drosophila-like Dosage Compensation of the Z Chromosome in Artemia Franciscana.” <i>Molecular Biology and Evolution</i>, vol. 42, no. 5, msaf085, Oxford University Press, 2025, doi:<a href=\"https://doi.org/10.1093/molbev/msaf085\">10.1093/molbev/msaf085</a>.","short":"V.K. Bett, M.S. Trejo Arellano, B. Vicoso, Molecular Biology and Evolution 42 (2025).","ista":"Bett VK, Trejo Arellano MS, Vicoso B. 2025. Chromatin landscape is associated with sex-biased expression and Drosophila-like dosage compensation of the Z chromosome in Artemia franciscana. Molecular Biology and Evolution. 42(5), msaf085.","ama":"Bett VK, Trejo Arellano MS, Vicoso B. Chromatin landscape is associated with sex-biased expression and Drosophila-like dosage compensation of the Z chromosome in Artemia franciscana. <i>Molecular Biology and Evolution</i>. 2025;42(5). doi:<a href=\"https://doi.org/10.1093/molbev/msaf085\">10.1093/molbev/msaf085</a>","apa":"Bett, V. K., Trejo Arellano, M. S., &#38; Vicoso, B. (2025). Chromatin landscape is associated with sex-biased expression and Drosophila-like dosage compensation of the Z chromosome in Artemia franciscana. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msaf085\">https://doi.org/10.1093/molbev/msaf085</a>"},"external_id":{"pmid":["40202086"],"isi":["001483460200001"]},"has_accepted_license":"1","month":"05","publication":"Molecular Biology and Evolution","acknowledged_ssus":[{"_id":"ScienComp"}],"date_updated":"2026-06-25T22:30:41Z","DOAJ_listed":"1","publication_status":"published","status":"public","doi":"10.1093/molbev/msaf085","ddc":["570"],"OA_type":"gold","oa_version":"Published Version","oa":1,"file":[{"file_name":"2025_MBE_Bett.pdf","file_id":"19756","success":1,"date_created":"2025-05-28T09:34:36Z","relation":"main_file","access_level":"open_access","checksum":"6c14b03f94b4aadf8869be2c4366d077","file_size":1282772,"date_updated":"2025-05-28T09:34:36Z","creator":"dernst","content_type":"application/pdf"}],"project":[{"grant_number":"PAT 8748323","name":"Sex chromosomes in evolution and development","_id":"8ed82125-16d5-11f0-9cad-fbcae312235b"},{"grant_number":"F8810","name":"The highjacking of meiosis for asexual reproduction","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396"}],"file_date_updated":"2025-05-28T09:34:36Z","volume":42,"day":"01","article_processing_charge":"Yes","isi":1,"article_type":"original","publisher":"Oxford University Press","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}],"acknowledgement":"We thank the Vicoso lab for their help in maintaining Artemia and for their valuable feedback and suggestions. We thank Marwan Elkrewi for his useful technical advice and discussions. We are also grateful to the Scientific Unit at ISTA Austria for computational resources and assistance. This work was supported by Austrian science fund (FWF) grants PAT8748323 and SFB F88-10 (as part of the SFB Meiosis consortium https://sfbmeiosis.org) to BV and Swedish Research Council (Vetenskapsrådet, grant number 2020-06424) to MSTA.","OA_place":"publisher","date_created":"2025-05-25T22:16:56Z","issue":"5","scopus_import":"1","intvolume":"        42","_id":"19735","article_number":"msaf085","pmid":1,"date_published":"2025-05-01T00:00:00Z","corr_author":"1","type":"journal_article","publication_identifier":{"eissn":["1537-1719"],"issn":["0737-4038"]},"title":"Chromatin landscape is associated with sex-biased expression and Drosophila-like dosage compensation of the Z chromosome in Artemia franciscana","related_material":{"record":[{"id":"20449","status":"public","relation":"dissertation_contains"},{"id":"20444","relation":"dissertation_contains","status":"deleted"}],"link":[{"relation":"software","url":"https://github.com/vkb25/Chromatin-landscape-in-Artemia-franciscana.git"}]},"author":[{"full_name":"Bett, Vincent K","last_name":"Bett","first_name":"Vincent K","id":"57854184-AAE0-11E9-8D04-98D6E5697425"},{"full_name":"Trejo Arellano, Minerva S","last_name":"Trejo Arellano","orcid":"0000-0002-1982-3475","first_name":"Minerva S","id":"2b681148-eed5-11eb-b81b-ae229e8620f8"},{"full_name":"Vicoso, Beatriz","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","last_name":"Vicoso"}],"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"department":[{"_id":"BeVi"},{"_id":"DaZi"}],"abstract":[{"lang":"eng","text":"The males and females of the brine shrimp Artemia franciscana are highly dimorphic, and this dimorphism is associated with substantial sex-biased gene expression in heads and gonads. How these sex-specific patterns of expression are regulated at the molecular level is unknown. A. franciscana also has differentiated ZW sex chromosomes, with complete dosage compensation, but the molecular mechanism through which compensation is achieved is unknown. Here, we conducted CUT&TAG assays targeting 7 post-translational histone modifications (H3K27me3, H3K9me2, H3K9me3, H3K36me3, H3K27ac, H3K4me3, and H4K16ac) in heads and gonads of A. franciscana, allowing us to divide the genome into 12 chromatin states. We further defined functional chromatin signatures for all genes, which were correlated with transcript level abundances. Differences in the occupancy of the profiled epigenetic marks between sexes were associated with differential gene expression between males and females. Finally, we found a significant enrichment of the permissive H4K16ac histone mark in the Z-specific region in both tissues of females but not males, supporting the role of this histone mark in mediating dosage compensation of the Z chromosome."}],"quality_controlled":"1"},{"isi":1,"publisher":"Oxford University Press","article_type":"original","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","intvolume":"        40","_id":"14613","article_number":"msad245","pmid":1,"date_published":"2023-12-01T00:00:00Z","language":[{"iso":"eng"}],"acknowledgement":"We thank the Vicoso lab for their assistance with specimen collection, and Tim Connallon for valuable comments and suggestions on earlier versions of the manuscript. Computational resources and support were provided by the Scientific Computing unit at the ISTA. This research was supported by grants from the Austrian Science Foundation to C.L.\r\n(FWF ESP 39), and to B.V. (FWF SFB F88-10).","issue":"12","date_created":"2023-11-27T16:14:37Z","scopus_import":"1","title":"The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome","related_material":{"link":[{"relation":"press_release","description":"News on ISTA webpage","url":"https://ista.ac.at/en/news/on-the-hunt/"}],"record":[{"relation":"research_data","status":"public","id":"14614"},{"relation":"dissertation_contains","status":"public","id":"19386"}]},"corr_author":"1","type":"journal_article","publication_identifier":{"eissn":["1537-1719"],"issn":["0737-4038"]},"keyword":["Genetics","Molecular Biology","Ecology","Evolution","Behavior and Systematics"],"abstract":[{"text":"Many insects carry an ancient X chromosome - the Drosophila Muller element F - that likely predates their origin. Interestingly, the X has undergone turnover in multiple fly species (Diptera) after being conserved for more than 450 MY. The long evolutionary distance between Diptera and other sequenced insect clades makes it difficult to infer what could have contributed to this sudden increase in rate of turnover. Here, we produce the first genome and transcriptome of a long overlooked sister-order to Diptera: Mecoptera. We compare the scorpionfly Panorpa cognata X-chromosome gene content, expression, and structure, to that of several dipteran species as well as more distantly-related insect orders (Orthoptera and Blattodea). We find high conservation of gene content between the mecopteran X and the dipteran Muller F element, as well as several shared biological features, such as the presence of dosage compensation and a low amount of genetic diversity, consistent with a low recombination rate. However, the two homologous X chromosomes differ strikingly in their size and number of genes they carry. Our results therefore support a common ancestry of the mecopteran and ancestral dipteran X chromosomes, and suggest that Muller element F shrank in size and gene content after the split of Diptera and Mecoptera, which may have contributed to its turnover in dipteran insects.","lang":"eng"}],"quality_controlled":"1","author":[{"full_name":"Lasne, Clementine","id":"02225f57-50d2-11eb-9ed8-8c92b9a34237","first_name":"Clementine","orcid":"0000-0002-1197-8616","last_name":"Lasne"},{"full_name":"Elkrewi, Marwan N","first_name":"Marwan N","orcid":"0000-0002-5328-7231","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","last_name":"Elkrewi"},{"last_name":"Toups","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9752-7380","first_name":"Melissa A","full_name":"Toups, Melissa A"},{"id":"02814589-eb8f-11eb-b029-a70074f3f18f","first_name":"Lorena Alexandra","orcid":"0000-0002-1253-6297","last_name":"Layana Franco","full_name":"Layana Franco, Lorena Alexandra"},{"last_name":"Macon","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","first_name":"Ariana","full_name":"Macon, Ariana"},{"first_name":"Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","full_name":"Vicoso, Beatriz"}],"department":[{"_id":"BeVi"}],"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","citation":{"apa":"Lasne, C., Elkrewi, M. N., Toups, M. A., Layana Franco, L. A., Macon, A., &#38; Vicoso, B. (2023). The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msad245\">https://doi.org/10.1093/molbev/msad245</a>","ama":"Lasne C, Elkrewi MN, Toups MA, Layana Franco LA, Macon A, Vicoso B. The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome. <i>Molecular Biology and Evolution</i>. 2023;40(12). doi:<a href=\"https://doi.org/10.1093/molbev/msad245\">10.1093/molbev/msad245</a>","short":"C. Lasne, M.N. Elkrewi, M.A. Toups, L.A. Layana Franco, A. Macon, B. Vicoso, Molecular Biology and Evolution 40 (2023).","mla":"Lasne, Clementine, et al. “The Scorpionfly (Panorpa Cognata) Genome Highlights Conserved and Derived Features of the Peculiar Dipteran X Chromosome.” <i>Molecular Biology and Evolution</i>, vol. 40, no. 12, msad245, Oxford University Press, 2023, doi:<a href=\"https://doi.org/10.1093/molbev/msad245\">10.1093/molbev/msad245</a>.","ista":"Lasne C, Elkrewi MN, Toups MA, Layana Franco LA, Macon A, Vicoso B. 2023. The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome. Molecular Biology and Evolution. 40(12), msad245.","chicago":"Lasne, Clementine, Marwan N Elkrewi, Melissa A Toups, Lorena Alexandra Layana Franco, Ariana Macon, and Beatriz Vicoso. “The Scorpionfly (Panorpa Cognata) Genome Highlights Conserved and Derived Features of the Peculiar Dipteran X Chromosome.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2023. <a href=\"https://doi.org/10.1093/molbev/msad245\">https://doi.org/10.1093/molbev/msad245</a>.","ieee":"C. Lasne, M. N. Elkrewi, M. A. Toups, L. A. Layana Franco, A. Macon, and B. Vicoso, “The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome,” <i>Molecular Biology and Evolution</i>, vol. 40, no. 12. Oxford University Press, 2023."},"year":"2023","external_id":{"isi":["001122489000003"],"pmid":["37988296"]},"publication":"Molecular Biology and Evolution","month":"12","acknowledged_ssus":[{"_id":"ScienComp"}],"status":"public","publication_status":"published","doi":"10.1093/molbev/msad245","ddc":["570"],"date_updated":"2026-06-25T22:30:28Z","file":[{"content_type":"application/pdf","file_size":8623505,"date_updated":"2024-01-02T11:39:38Z","creator":"dernst","relation":"main_file","access_level":"open_access","checksum":"47c1c72fb499f26ea52d216b242208c8","file_name":"2023_MolecularBioEvo_Lasne.pdf","file_id":"14727","success":1,"date_created":"2024-01-02T11:39:38Z"}],"file_date_updated":"2024-01-02T11:39:38Z","project":[{"name":"The highjacking of meiosis for asexual reproduction","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","grant_number":"F8810"},{"_id":"ebb230e0-77a9-11ec-83b8-87a37e0241d3","name":"Mechanisms and Evolution of Reproductive Plasticity","grant_number":"ESP39 49461"}],"volume":40,"day":"01","article_processing_charge":"Yes","oa_version":"Published Version","oa":1},{"doi":"10.1093/molbev/msab178","status":"public","publication_status":"published","ddc":["610"],"date_updated":"2026-06-25T22:30:28Z","file_date_updated":"2022-05-06T09:47:18Z","project":[{"name":"Sex chromosome evolution under male- and female- heterogamety","call_identifier":"FWF","_id":"250ED89C-B435-11E9-9278-68D0E5697425","grant_number":"P28842-B22"}],"file":[{"content_type":"application/pdf","date_updated":"2022-05-06T09:47:18Z","file_size":1008594,"creator":"dernst","relation":"main_file","checksum":"1b096702fb356d9c0eb88e1b3fcff5f8","access_level":"open_access","success":1,"file_id":"11352","file_name":"2021_MolecularBiolEvolution_Elkrewi.pdf","date_created":"2022-05-06T09:47:18Z"}],"article_processing_charge":"No","day":"19","volume":138,"oa_version":"Published Version","oa":1,"has_accepted_license":"1","external_id":{"pmid":["34146097"],"isi":["000741368600009"]},"citation":{"apa":"Elkrewi, M. N., Moldovan, M. A., Picard, M. A. L., &#38; Vicoso, B. (2021). Schistosome W-linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination. <i>Molecular Biology and Evolution</i>. Oxford University Press . <a href=\"https://doi.org/10.1093/molbev/msab178\">https://doi.org/10.1093/molbev/msab178</a>","ama":"Elkrewi MN, Moldovan MA, Picard MAL, Vicoso B. Schistosome W-linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination. <i>Molecular Biology and Evolution</i>. 2021;138(12):5345-5358. doi:<a href=\"https://doi.org/10.1093/molbev/msab178\">10.1093/molbev/msab178</a>","chicago":"Elkrewi, Marwan N, Mikhail A. Moldovan, Marion A L Picard, and Beatriz Vicoso. “Schistosome W-Linked Genes Inform Temporal Dynamics of Sex Chromosome Evolution and Suggest Candidate for Sex Determination.” <i>Molecular Biology and Evolution</i>. Oxford University Press , 2021. <a href=\"https://doi.org/10.1093/molbev/msab178\">https://doi.org/10.1093/molbev/msab178</a>.","mla":"Elkrewi, Marwan N., et al. “Schistosome W-Linked Genes Inform Temporal Dynamics of Sex Chromosome Evolution and Suggest Candidate for Sex Determination.” <i>Molecular Biology and Evolution</i>, vol. 138, no. 12, Oxford University Press , 2021, pp. 5345–58, doi:<a href=\"https://doi.org/10.1093/molbev/msab178\">10.1093/molbev/msab178</a>.","ista":"Elkrewi MN, Moldovan MA, Picard MAL, Vicoso B. 2021. Schistosome W-linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination. Molecular Biology and Evolution. 138(12), 5345–58.","short":"M.N. Elkrewi, M.A. Moldovan, M.A.L. Picard, B. Vicoso, Molecular Biology and Evolution 138 (2021) 5345–58.","ieee":"M. N. Elkrewi, M. A. Moldovan, M. A. L. Picard, and B. Vicoso, “Schistosome W-linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination,” <i>Molecular Biology and Evolution</i>, vol. 138, no. 12. Oxford University Press , pp. 5345–58, 2021."},"year":"2021","month":"06","publication":"Molecular Biology and Evolution","acknowledged_ssus":[{"_id":"ScienComp"}],"title":"Schistosome W-linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"19386"}]},"publication_identifier":{"issn":["0737-4038"],"eissn":["1537-1719"]},"corr_author":"1","type":"journal_article","keyword":["sex chromosomes","evolutionary strata","W-linked gene","sex determining gene","schistosome parasites"],"abstract":[{"lang":"eng","text":"Schistosomes, the human parasites responsible for snail fever, are female-heterogametic. Different parts of their ZW sex chromosomes have stopped recombining in distinct lineages, creating “evolutionary strata” of various ages. Although the Z-chromosome is well characterized at the genomic and molecular level, the W-chromosome has remained largely unstudied from an evolutionary perspective, as only a few W-linked genes have been detected outside of the model species Schistosoma mansoni. Here, we characterize the gene content and evolution of the W-chromosomes of S. mansoni and of the divergent species S. japonicum. We use a combined RNA/DNA k-mer based pipeline to assemble around 100 candidate W-specific transcripts in each of the species. About half of them map to known protein coding genes, the majority homologous to S. mansoni Z-linked genes. We perform an extended analysis of the evolutionary strata present in the two species (including characterizing a previously undetected young stratum in S. japonicum) to infer patterns of sequence and expression evolution of W-linked genes at different time points after recombination was lost. W-linked genes show evidence of degeneration, including high rates of protein evolution and reduced expression. Most are found in young lineage-specific strata, with only a few high expression ancestral W-genes remaining, consistent with the progressive erosion of nonrecombining regions. Among these, the splicing factor u2af2 stands out as a promising candidate for primary sex determination, opening new avenues for understanding the molecular basis of the reproductive biology of this group."}],"quality_controlled":"1","author":[{"id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","orcid":"0000-0002-5328-7231","first_name":"Marwan N","last_name":"Elkrewi","full_name":"Elkrewi, Marwan N"},{"last_name":"Moldovan","first_name":"Mikhail A.","orcid":"0000-0002-8876-6494","id":"c8bb7f32-3315-11ec-b58b-e5950e6c14a0","full_name":"Moldovan, Mikhail A."},{"full_name":"Picard, Marion A L","first_name":"Marion A L","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8101-2518","last_name":"Picard"},{"full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","last_name":"Vicoso"}],"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"department":[{"_id":"BeVi"}],"publisher":"Oxford University Press ","article_type":"original","isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"5345-58","intvolume":"       138","_id":"10167","date_published":"2021-06-19T00:00:00Z","pmid":1,"acknowledgement":"The authors thank IT support at IST Austria for providing an optimal environment for bioinformatic analyses. This work was supported by an Austrian Science Foundation FWF grant (Project P28842) to B.V.","language":[{"iso":"eng"}],"scopus_import":"1","date_created":"2021-10-21T07:49:12Z","issue":"12"},{"department":[{"_id":"BeVi"},{"_id":"NiBa"}],"author":[{"full_name":"Fraisse, Christelle","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075","first_name":"Christelle"},{"last_name":"Puixeu Sala","first_name":"Gemma","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8330-1754","full_name":"Puixeu Sala, Gemma"},{"last_name":"Vicoso","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz"}],"abstract":[{"lang":"eng","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."}],"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30590559"}],"type":"journal_article","publication_identifier":{"issn":["0737-4038"],"eissn":["1537-1719"]},"related_material":{"record":[{"status":"public","relation":"popular_science","id":"5757"}]},"title":"Pleiotropy modulates the efficacy of selection in drosophila melanogaster","date_created":"2019-03-10T22:59:19Z","issue":"3","scopus_import":"1","language":[{"iso":"eng"}],"pmid":1,"date_published":"2019-03-01T00:00:00Z","_id":"6089","intvolume":"        36","page":"500-515","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","isi":1,"publisher":"Oxford University Press","oa":1,"oa_version":"Submitted Version","volume":36,"day":"01","article_processing_charge":"No","project":[{"grant_number":"P28842-B22","call_identifier":"FWF","_id":"250ED89C-B435-11E9-9278-68D0E5697425","name":"Sex chromosome evolution under male- and female- heterogamety"}],"date_updated":"2025-04-15T08:18:38Z","status":"public","publication_status":"published","doi":"10.1093/molbev/msy246","publication":"Molecular biology and evolution","month":"03","citation":{"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>.","short":"C. Fraisse, G. Puixeu Sala, B. Vicoso, Molecular Biology and Evolution 36 (2019) 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>.","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.","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>","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>","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."},"year":"2019","external_id":{"isi":["000462585100006"],"pmid":["30590559"]}},{"publication":"Molecular Biology and Evolution","month":"08","external_id":{"pmid":["30169679"],"isi":["000452567200006"]},"citation":{"ieee":"A. Palmer, R. P. Chait, and R. Kishony, “Nonoptimal gene expression creates latent potential for antibiotic resistance,” <i>Molecular Biology and Evolution</i>, vol. 35, no. 11. Oxford University Press, pp. 2669–2684, 2018.","apa":"Palmer, A., Chait, R. P., &#38; Kishony, R. (2018). Nonoptimal gene expression creates latent potential for antibiotic resistance. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msy163\">https://doi.org/10.1093/molbev/msy163</a>","ama":"Palmer A, Chait RP, Kishony R. Nonoptimal gene expression creates latent potential for antibiotic resistance. <i>Molecular Biology and Evolution</i>. 2018;35(11):2669-2684. doi:<a href=\"https://doi.org/10.1093/molbev/msy163\">10.1093/molbev/msy163</a>","chicago":"Palmer, Adam, Remy P Chait, and Roy Kishony. “Nonoptimal Gene Expression Creates Latent Potential for Antibiotic Resistance.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2018. <a href=\"https://doi.org/10.1093/molbev/msy163\">https://doi.org/10.1093/molbev/msy163</a>.","short":"A. Palmer, R.P. Chait, R. Kishony, Molecular Biology and Evolution 35 (2018) 2669–2684.","ista":"Palmer A, Chait RP, Kishony R. 2018. Nonoptimal gene expression creates latent potential for antibiotic resistance. Molecular Biology and Evolution. 35(11), 2669–2684.","mla":"Palmer, Adam, et al. “Nonoptimal Gene Expression Creates Latent Potential for Antibiotic Resistance.” <i>Molecular Biology and Evolution</i>, vol. 35, no. 11, Oxford University Press, 2018, pp. 2669–84, doi:<a href=\"https://doi.org/10.1093/molbev/msy163\">10.1093/molbev/msy163</a>."},"year":"2018","oa_version":"Submitted Version","oa":1,"article_processing_charge":"No","day":"28","volume":35,"date_updated":"2023-10-17T11:51:06Z","doi":"10.1093/molbev/msy163","publication_status":"published","status":"public","language":[{"iso":"eng"}],"scopus_import":"1","date_created":"2018-12-11T11:44:11Z","issue":"11","page":"2669 - 2684","_id":"19","intvolume":"        35","pmid":1,"date_published":"2018-08-28T00:00:00Z","article_type":"original","publisher":"Oxford University Press","isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"8036","author":[{"full_name":"Palmer, Adam","first_name":"Adam","last_name":"Palmer"},{"last_name":"Chait","first_name":"Remy P","orcid":"0000-0003-0876-3187","id":"3464AE84-F248-11E8-B48F-1D18A9856A87","full_name":"Chait, Remy P"},{"last_name":"Kishony","first_name":"Roy","full_name":"Kishony, Roy"}],"department":[{"_id":"CaGu"},{"_id":"GaTk"}],"abstract":[{"text":"Bacteria regulate genes to survive antibiotic stress, but regulation can be far from perfect. When regulation is not optimal, mutations that change gene expression can contribute to antibiotic resistance. It is not systematically understood to what extent natural gene regulation is or is not optimal for distinct antibiotics, and how changes in expression of specific genes quantitatively affect antibiotic resistance. Here we discover a simple quantitative relation between fitness, gene expression, and antibiotic potency, which rationalizes our observation that a multitude of genes and even innate antibiotic defense mechanisms have expression that is critically nonoptimal under antibiotic treatment. First, we developed a pooled-strain drug-diffusion assay and screened Escherichia coli overexpression and knockout libraries, finding that resistance to a range of 31 antibiotics could result from changing expression of a large and functionally diverse set of genes, in a primarily but not exclusively drug-specific manner. Second, by synthetically controlling the expression of single-drug and multidrug resistance genes, we observed that their fitness-expression functions changed dramatically under antibiotic treatment in accordance with a log-sensitivity relation. Thus, because many genes are nonoptimally expressed under antibiotic treatment, many regulatory mutations can contribute to resistance by altering expression and by activating latent defenses.","lang":"eng"}],"quality_controlled":"1","publication_identifier":{"issn":["0737-4038"]},"type":"journal_article","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30169679","open_access":"1"}],"title":"Nonoptimal gene expression creates latent potential for antibiotic resistance"},{"quality_controlled":"1","abstract":[{"text":"While chromosome-wide dosage compensation of the X chromosome has been found in many species, studies in ZW clades have indicated that compensation of the Z is more localized and/or incomplete. In the ZW Lepidoptera, some species show complete compensation of the Z chromosome, while others lack full equalization, but what drives these inconsistencies is unclear. Here, we compare patterns of male and female gene expression on the Z chromosome of two closely related butterfly species, Papilio xuthus and Papilio machaon, and in multiple tissues of two moths species, Plodia interpunctella and Bombyx mori, which were previously found to differ in the extent to which they equalize Z-linked gene expression between the sexes. We find that, while some species and tissues seem to have incomplete dosage compensation, this is in fact due to the accumulation of male-biased genes and the depletion of female-biased genes on the Z chromosome. Once this is accounted for, the Z chromosome is fully compensated in all four species, through the up-regulation of Z expression in females and in some cases additional down-regulation in males. We further find that both sex-biased genes and Z-linked genes have increased rates of expression divergence in this clade, and that this can lead to fast shifts in patterns of gene expression even between closely related species. Taken together, these results show that the uneven distribution of sex-biased genes on sex chromosomes can confound conclusions about dosage compensation and that Z chromosome-wide dosage compensation is not only possible but ubiquitous among Lepidoptera.","lang":"eng"}],"author":[{"id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8871-4961","first_name":"Ann K","last_name":"Huylmans","full_name":"Huylmans, Ann K"},{"id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","first_name":"Ariana","last_name":"Macon","full_name":"Macon, Ariana"},{"full_name":"Vicoso, Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","orcid":"0000-0002-4579-8306","last_name":"Vicoso"}],"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"department":[{"_id":"BeVi"}],"title":"Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome","type":"journal_article","publication_identifier":{"issn":["0737-4038"]},"intvolume":"        34","_id":"945","page":"2637 - 2649","date_published":"2017-07-06T00:00:00Z","language":[{"iso":"eng"}],"issue":"10","date_created":"2018-12-11T11:49:20Z","scopus_import":"1","publist_id":"6472","isi":1,"publisher":"Oxford University Press","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","project":[{"grant_number":"P28842-B22","name":"Sex chromosome evolution under male- and female- heterogamety","call_identifier":"FWF","_id":"250ED89C-B435-11E9-9278-68D0E5697425"}],"file_date_updated":"2020-07-14T12:48:15Z","file":[{"relation":"main_file","access_level":"open_access","checksum":"009fd68043211d645ceb9d1de28274f2","file_name":"IST-2017-848-v1+1_2017_Vicoso_GlobalDosage.pdf","file_id":"4810","date_created":"2018-12-12T10:10:23Z","content_type":"application/pdf","date_updated":"2020-07-14T12:48:15Z","file_size":462863,"creator":"system"}],"volume":34,"pubrep_id":"848","day":"06","article_processing_charge":"Yes (in subscription journal)","oa_version":"Published Version","oa":1,"status":"public","publication_status":"published","doi":"10.1093/molbev/msx190","ddc":["570","576"],"date_updated":"2026-04-16T09:58:19Z","publication":"Molecular Biology and Evolution","month":"07","has_accepted_license":"1","year":"2017","citation":{"ama":"Huylmans AK, Macon A, Vicoso B. Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome. <i>Molecular Biology and Evolution</i>. 2017;34(10):2637-2649. doi:<a href=\"https://doi.org/10.1093/molbev/msx190\">10.1093/molbev/msx190</a>","apa":"Huylmans, A. K., Macon, A., &#38; Vicoso, B. (2017). Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msx190\">https://doi.org/10.1093/molbev/msx190</a>","short":"A.K. Huylmans, A. Macon, B. Vicoso, Molecular Biology and Evolution 34 (2017) 2637–2649.","mla":"Huylmans, Ann K., et al. “Global Dosage Compensation Is Ubiquitous in Lepidoptera, but Counteracted by the Masculinization of the Z Chromosome.” <i>Molecular Biology and Evolution</i>, vol. 34, no. 10, Oxford University Press, 2017, pp. 2637–49, doi:<a href=\"https://doi.org/10.1093/molbev/msx190\">10.1093/molbev/msx190</a>.","ista":"Huylmans AK, Macon A, Vicoso B. 2017. Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome. Molecular Biology and Evolution. 34(10), 2637–2649.","chicago":"Huylmans, Ann K, Ariana Macon, and Beatriz Vicoso. “Global Dosage Compensation Is Ubiquitous in Lepidoptera, but Counteracted by the Masculinization of the Z Chromosome.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2017. <a href=\"https://doi.org/10.1093/molbev/msx190\">https://doi.org/10.1093/molbev/msx190</a>.","ieee":"A. K. Huylmans, A. Macon, and B. Vicoso, “Global dosage compensation is ubiquitous in Lepidoptera, but counteracted by the masculinization of the Z chromosome,” <i>Molecular Biology and Evolution</i>, vol. 34, no. 10. Oxford University Press, pp. 2637–2649, 2017."},"external_id":{"isi":["000411814800016"]}},{"license":"https://creativecommons.org/licenses/by-nc/4.0/","type":"journal_article","publication_identifier":{"eissn":["1537-1719"],"issn":["0737-4038"]},"related_material":{"record":[{"status":"public","relation":"research_data","id":"9719"}]},"title":"Adaptation to parasites and costs of parasite resistance in mutator and nonmutator bacteria","tmp":{"short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"department":[{"_id":"CaGu"}],"author":[{"full_name":"Wielgoss, Sébastien","last_name":"Wielgoss","first_name":"Sébastien"},{"first_name":"Tobias","orcid":"0000-0001-5396-4346","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","last_name":"Bergmiller","full_name":"Bergmiller, Tobias"},{"last_name":"Bischofberger","first_name":"Anna M.","full_name":"Bischofberger, Anna M."},{"full_name":"Hall, Alex R.","last_name":"Hall","first_name":"Alex R."}],"quality_controlled":"1","abstract":[{"text":"Parasitism creates selection for resistance mechanisms in host populations and is hypothesized to promote increased host evolvability. However, the influence of these traits on host evolution when parasites are no longer present is unclear. We used experimental evolution and whole-genome sequencing of Escherichia coli to determine the effects of past and present exposure to parasitic viruses (phages) on the spread of mutator alleles, resistance, and bacterial competitive fitness. We found that mutator alleles spread rapidly during adaptation to any of four different phage species, and this pattern was even more pronounced with multiple phages present simultaneously. However, hypermutability did not detectably accelerate adaptation in the absence of phages and recovery of fitness costs associated with resistance. Several lineages evolved phage resistance through elevated mucoidy, and during subsequent evolution in phage-free conditions they rapidly reverted to nonmucoid, phage-susceptible phenotypes. Genome sequencing revealed that this phenotypic reversion was achieved by additional genetic changes rather than by genotypic reversion of the initial resistance mutations. Insertion sequence (IS) elements played a key role in both the acquisition of resistance and adaptation in the absence of parasites; unlike single nucleotide polymorphisms, IS insertions were not more frequent in mutator lineages. Our results provide a genetic explanation for rapid reversion of mucoidy, a phenotype observed in other bacterial species including human pathogens. Moreover, this demonstrates that the types of genetic change underlying adaptation to fitness costs, and consequently the impact of evolvability mechanisms such as increased point-mutation rates, depend critically on the mechanism of resistance.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"publisher":"Oxford University Press","article_type":"original","issue":"3","OA_place":"publisher","date_created":"2018-12-18T13:18:10Z","scopus_import":"1","language":[{"iso":"eng"}],"acknowledgement":"The authors thank three anonymous reviewers and the editor for helpful comments on the manuscript, as well as Dominique Schneider for feedback on an earlier draft, Jenna Gallie for lytic λ and Julien Capelle for T5 and T6. This work was supported by the Swiss National Science Foundation (PZ00P3_148255 to A.H.) and an EU Marie Curie PEOPLE Postdoctoral Fellowship for Career Development (FP7-PEOPLE-2012-IEF-331824 to S.W.).","date_published":"2016-03-01T00:00:00Z","pmid":1,"_id":"5749","intvolume":"        33","page":"770-782","DOAJ_listed":"1","date_updated":"2026-04-29T05:57:02Z","ddc":["576"],"status":"public","publication_status":"published","doi":"10.1093/molbev/msv270","oa":1,"OA_type":"gold","oa_version":"Published Version","volume":33,"day":"01","pubrep_id":"587","article_processing_charge":"No","file":[{"relation":"main_file","checksum":"47d9010690b6c5c17f2ac830cc63ac5c","access_level":"open_access","file_name":"2016_MolBiolEvol_Wielgoss.pdf","file_id":"5750","date_created":"2018-12-18T13:21:45Z","content_type":"application/pdf","date_updated":"2020-07-14T12:47:10Z","file_size":634037,"creator":"dernst"}],"file_date_updated":"2020-07-14T12:47:10Z","year":"2016","citation":{"ama":"Wielgoss S, Bergmiller T, Bischofberger AM, Hall AR. Adaptation to parasites and costs of parasite resistance in mutator and nonmutator bacteria. <i>Molecular Biology and Evolution</i>. 2016;33(3):770-782. doi:<a href=\"https://doi.org/10.1093/molbev/msv270\">10.1093/molbev/msv270</a>","apa":"Wielgoss, S., Bergmiller, T., Bischofberger, A. M., &#38; Hall, A. R. (2016). Adaptation to parasites and costs of parasite resistance in mutator and nonmutator bacteria. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msv270\">https://doi.org/10.1093/molbev/msv270</a>","mla":"Wielgoss, Sébastien, et al. “Adaptation to Parasites and Costs of Parasite Resistance in Mutator and Nonmutator Bacteria.” <i>Molecular Biology and Evolution</i>, vol. 33, no. 3, Oxford University Press, 2016, pp. 770–82, doi:<a href=\"https://doi.org/10.1093/molbev/msv270\">10.1093/molbev/msv270</a>.","ista":"Wielgoss S, Bergmiller T, Bischofberger AM, Hall AR. 2016. Adaptation to parasites and costs of parasite resistance in mutator and nonmutator bacteria. Molecular Biology and Evolution. 33(3), 770–782.","short":"S. Wielgoss, T. Bergmiller, A.M. Bischofberger, A.R. Hall, Molecular Biology and Evolution 33 (2016) 770–782.","chicago":"Wielgoss, Sébastien, Tobias Bergmiller, Anna M. Bischofberger, and Alex R. Hall. “Adaptation to Parasites and Costs of Parasite Resistance in Mutator and Nonmutator Bacteria.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2016. <a href=\"https://doi.org/10.1093/molbev/msv270\">https://doi.org/10.1093/molbev/msv270</a>.","ieee":"S. Wielgoss, T. Bergmiller, A. M. Bischofberger, and A. R. Hall, “Adaptation to parasites and costs of parasite resistance in mutator and nonmutator bacteria,” <i>Molecular Biology and Evolution</i>, vol. 33, no. 3. Oxford University Press, pp. 770–782, 2016."},"external_id":{"isi":["000371219500015"],"pmid":["26609077"]},"has_accepted_license":"1","publication":"Molecular Biology and Evolution","month":"03"},{"ddc":["570"],"doi":"10.1093/molbev/mst187","status":"public","publication_status":"published","date_updated":"2026-06-18T18:03:30Z","article_processing_charge":"No","day":"01","volume":31,"oa":1,"oa_version":"Published Version","OA_type":"free access","external_id":{"isi":["000329253200022"],"pmid":["24170494"]},"citation":{"ieee":"B. Hall, H. Acar, A. Nandipati, and M. Barlow, “Growth rates made easy,” <i>Molecular Biology and Evolution</i>, vol. 31, no. 1. Oxford University Press, pp. 232–238, 2014.","chicago":"Hall, Barry, Hande Acar, Anna Nandipati, and Miriam Barlow. “Growth Rates Made Easy.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2014. <a href=\"https://doi.org/10.1093/molbev/mst187\">https://doi.org/10.1093/molbev/mst187</a>.","short":"B. Hall, H. Acar, A. Nandipati, M. Barlow, Molecular Biology and Evolution 31 (2014) 232–238.","ista":"Hall B, Acar H, Nandipati A, Barlow M. 2014. Growth rates made easy. Molecular Biology and Evolution. 31(1), 232–238.","mla":"Hall, Barry, et al. “Growth Rates Made Easy.” <i>Molecular Biology and Evolution</i>, vol. 31, no. 1, Oxford University Press, 2014, pp. 232–38, doi:<a href=\"https://doi.org/10.1093/molbev/mst187\">10.1093/molbev/mst187</a>.","apa":"Hall, B., Acar, H., Nandipati, A., &#38; Barlow, M. (2014). Growth rates made easy. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/mst187\">https://doi.org/10.1093/molbev/mst187</a>","ama":"Hall B, Acar H, Nandipati A, Barlow M. Growth rates made easy. <i>Molecular Biology and Evolution</i>. 2014;31(1):232-238. doi:<a href=\"https://doi.org/10.1093/molbev/mst187\">10.1093/molbev/mst187</a>"},"year":"2014","publication":"Molecular Biology and Evolution","month":"01","title":"Growth rates made easy","main_file_link":[{"url":"https://doi.org/10.1093/molbev/mst187","open_access":"1"}],"publication_identifier":{"eissn":["1537-1719"],"issn":["0737-4038"]},"type":"journal_article","abstract":[{"lang":"eng","text":"In the 1960s-1980s, determination of bacterial growth rates was an important tool in microbial genetics, biochemistry, molecular biology, and microbial physiology. The exciting technical developments of the 1990s and the 2000s eclipsed that tool; as a result, many investigators today lack experience with growth rate measurements. Recently, investigators in a number of areas have started to use measurements of bacterial growth rates for a variety of purposes. Those measurements have been greatly facilitated by the availability of microwell plate readers that permit the simultaneous measurements on up to 384 different cultures. Only the exponential (logarithmic) portions of the resulting growth curves are useful for determining growth rates, and manual determination of that portion and calculation of growth rates can be tedious for high-throughput purposes. Here, we introduce the program GrowthRates that uses plate reader output files to automatically determine the exponential portion of the curve and to automatically calculate the growth rate, the maximum culture density, and the duration of the growth lag phase. GrowthRates is freely available for Macintosh, Windows, and Linux.We discuss the effects of culture volume, the classical bacterial growth curve, and the differences between determinations in rich media and minimal (mineral salts) media. This protocol covers calibration of the plate reader, growth of culture inocula for both rich and minimal media, and experimental setup. As a guide to reliability, we report typical day-to-day variation in growth rates and variation within experiments with respect to position of wells within the plates."}],"quality_controlled":"1","department":[{"_id":"JoBo"}],"author":[{"full_name":"Hall, Barry","last_name":"Hall","first_name":"Barry"},{"id":"2DDF136A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1986-9753","first_name":"Hande","last_name":"Acar","full_name":"Acar, Hande"},{"full_name":"Nandipati, Anna","last_name":"Nandipati","first_name":"Anna"},{"full_name":"Barlow, Miriam","first_name":"Miriam","last_name":"Barlow"}],"publist_id":"5193","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Oxford University Press","article_type":"original","isi":1,"date_published":"2014-01-01T00:00:00Z","pmid":1,"page":"232 - 238","intvolume":"        31","_id":"1902","scopus_import":"1","date_created":"2018-12-11T11:54:37Z","issue":"1","OA_place":"publisher","language":[{"iso":"eng"}]},{"external_id":{"pmid":["12082136 "]},"citation":{"apa":"Bollback, J. P. (2002). Bayesian model adequacy and choice in phylogenetics. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/oxfordjournals.molbev.a004175\">https://doi.org/10.1093/oxfordjournals.molbev.a004175</a>","ama":"Bollback JP. Bayesian model adequacy and choice in phylogenetics. <i>Molecular Biology and Evolution</i>. 2002;19(7):1171-1180. doi:<a href=\"https://doi.org/10.1093/oxfordjournals.molbev.a004175\">10.1093/oxfordjournals.molbev.a004175</a>","chicago":"Bollback, Jonathan P. “Bayesian Model Adequacy and Choice in Phylogenetics.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2002. <a href=\"https://doi.org/10.1093/oxfordjournals.molbev.a004175\">https://doi.org/10.1093/oxfordjournals.molbev.a004175</a>.","mla":"Bollback, Jonathan P. “Bayesian Model Adequacy and Choice in Phylogenetics.” <i>Molecular Biology and Evolution</i>, vol. 19, no. 7, Oxford University Press, 2002, pp. 1171–80, doi:<a href=\"https://doi.org/10.1093/oxfordjournals.molbev.a004175\">10.1093/oxfordjournals.molbev.a004175</a>.","ista":"Bollback JP. 2002. Bayesian model adequacy and choice in phylogenetics. Molecular Biology and Evolution. 19(7), 1171–80.","short":"J.P. Bollback, Molecular Biology and Evolution 19 (2002) 1171–80.","ieee":"J. P. Bollback, “Bayesian model adequacy and choice in phylogenetics,” <i>Molecular Biology and Evolution</i>, vol. 19, no. 7. Oxford University Press, pp. 1171–80, 2002."},"year":"2002","month":"03","publication":"Molecular Biology and Evolution","date_updated":"2023-06-06T09:18:18Z","doi":"10.1093/oxfordjournals.molbev.a004175","status":"public","publication_status":"published","oa_version":"None","day":"25","article_processing_charge":"No","volume":19,"article_type":"original","publisher":"Oxford University Press","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","extern":"1","publist_id":"1112","acknowledgement":"This work was supported by grants from the NSF to John Huelsenbeck (MCB-0075404 and DEB0075406), to whom I am grateful for his support throughout this project. Also, I would like to express my deep thanks to Andrea Betancourt, John Huelsenbeck, Kelly Dyer, Rasmus Nielsen, and Frederick Ronquist for taking the time to read early versions of the\r\nmanuscript. Each and every one of them provided invaluable comments, that ultimately made the manuscript better. John Huelsenbeck, Bret Larget, Rasmus Nielsen, Ken Karol, and Andrea Betancourt patiently listened to me drone on about this project, and offered insightful comments that benefited this work, and for this they have my deepest gratitude. And finally, I would like to thank two anonymous reviewers who gave critical attention to the manuscript and provided valuable comments.","language":[{"iso":"eng"}],"scopus_import":"1","issue":"7","date_created":"2018-12-11T12:08:24Z","page":"1171 - 80","_id":"4349","intvolume":"        19","pmid":1,"date_published":"2002-03-25T00:00:00Z","publication_identifier":{"issn":["0737-4038"]},"type":"journal_article","title":"Bayesian model adequacy and choice in phylogenetics","author":[{"id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4624-4612","first_name":"Jonathan P","last_name":"Bollback","full_name":"Bollback, Jonathan P"}],"quality_controlled":"1","abstract":[{"text":"Bayesian inference is becoming a common statistical approach to phylogenetic estimation because, among other reasons, it allows for rapid analysis of large data sets with complex evolutionary models. Conveniently, Bayesian phylogenetic methods use currently available stochastic models of sequence evolution. However, as with other model-based approaches, the results of Bayesian inference are conditional on the assumed model of evolution: inadequate models (models that poorly fit the data) may result in erroneous inferences. In this article, I present a Bayesian phylogenetic method that evaluates the adequacy of evolutionary models using posterior predictive distributions. By evaluating a model's posterior predictive performance, an adequate model can be selected for a Bayesian phylogenetic study. Although I present a single test statistic that assesses the overall (global) performance of a phylogenetic model, a variety of test statistics can be tailored to evaluate specific features (local performance) of evolutionary models to identify sources failure. The method presented here, unlike the likelihood-ratio test and parametric bootstrap, accounts for uncertainty in the phylogeny and model parameters.","lang":"eng"}]},{"month":"07","publication":"Molecular Biology and Evolution","citation":{"apa":"Dallas, J., Barton, N. H., &#38; Dover, G. (1988). Interracial rDNA variation in the grasshopper Podisma Pedestris. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/oxfordjournals.molbev.a040528\">https://doi.org/10.1093/oxfordjournals.molbev.a040528</a>","ama":"Dallas J, Barton NH, Dover G. Interracial rDNA variation in the grasshopper Podisma Pedestris. <i>Molecular Biology and Evolution</i>. 1988;5(6):660-674. doi:<a href=\"https://doi.org/10.1093/oxfordjournals.molbev.a040528\">10.1093/oxfordjournals.molbev.a040528</a>","chicago":"Dallas, John, Nicholas H Barton, and Gabriel Dover. “Interracial RDNA Variation in the Grasshopper Podisma Pedestris.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 1988. <a href=\"https://doi.org/10.1093/oxfordjournals.molbev.a040528\">https://doi.org/10.1093/oxfordjournals.molbev.a040528</a>.","ista":"Dallas J, Barton NH, Dover G. 1988. Interracial rDNA variation in the grasshopper Podisma Pedestris. Molecular Biology and Evolution. 5(6), 660–674.","mla":"Dallas, John, et al. “Interracial RDNA Variation in the Grasshopper Podisma Pedestris.” <i>Molecular Biology and Evolution</i>, vol. 5, no. 6, Oxford University Press, 1988, pp. 660–74, doi:<a href=\"https://doi.org/10.1093/oxfordjournals.molbev.a040528\">10.1093/oxfordjournals.molbev.a040528</a>.","short":"J. Dallas, N.H. Barton, G. Dover, Molecular Biology and Evolution 5 (1988) 660–674.","ieee":"J. Dallas, N. H. Barton, and G. Dover, “Interracial rDNA variation in the grasshopper Podisma Pedestris,” <i>Molecular Biology and Evolution</i>, vol. 5, no. 6. Oxford University Press, pp. 660–674, 1988."},"year":"1988","oa_version":"None","oa":1,"article_processing_charge":"No","day":"01","volume":5,"date_updated":"2022-02-08T13:20:51Z","doi":"10.1093/oxfordjournals.molbev.a040528","publication_status":"published","status":"public","acknowledgement":"We thank Dr. W. Kunz for providing the clones pLm6F4 and pLm4Bll and Dr. D. Glover for the clone pDm238. We thank Brian Curtis for his photographic assistance. ","language":[{"iso":"eng"}],"issue":"6","date_created":"2018-12-11T12:04:28Z","page":"660 - 674","intvolume":"         5","_id":"3655","date_published":"1988-07-01T00:00:00Z","article_type":"original","publisher":"Oxford University Press","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","extern":"1","publist_id":"2728","author":[{"full_name":"Dallas, John","first_name":"John","last_name":"Dallas"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","last_name":"Barton","full_name":"Barton, Nicholas H"},{"last_name":"Dover","first_name":"Gabriel","full_name":"Dover, Gabriel"}],"quality_controlled":"1","abstract":[{"lang":"eng","text":"The structural basis and distribution of variation in the ribosomal RNA multigene family ( rDNA) was studied in the X0 and neo-XY races of the Alpine grasshopper Podisma pedestris. Restriction-enzyme sites in the gene region of the rDNA repeat were identical in both races and homogeneous in the rDNA family. In contrast, sites for Hind111 and PvuII in the intergenic spacer (IGS) region showed racial divergence and variation within the rDNA family and within populations. A short insertion in the 28s gene region was present in a minority of repeats in both races. The distributions of four polymorphic IGS Hind111 fragments were surveyed at 43 locations in and around the hybrid zone. Two of these fragments appear to be distributed as clines, one of which is strongly associated with the neo-X chromosome. The other two fragments show considerable variation in both races and show negative association. It is proposed that the clinally distributed variants arise from processes of amplification and divergence of IGS sequence variants and that such \r\ndivergence may contribute to hybrid inviability. "}],"publication_identifier":{"eissn":["1537-1719"],"issn":["0737-4038"]},"type":"journal_article","main_file_link":[{"url":"https://academic.oup.com/mbe/article/5/6/660/1044340","open_access":"1"}],"title":"Interracial rDNA variation in the grasshopper Podisma Pedestris"}]