[{"ddc":["576"],"author":[{"id":"353FAC84-AE61-11E9-8BFC-00D3E5697425","last_name":"Mrnjavac","full_name":"Mrnjavac, Andrea","first_name":"Andrea"}],"article_processing_charge":"No","title":"Early stages of sex chromosome evolution","year":"2024","page":"181","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa_version":"Published Version","date_published":"2024-11-11T00:00:00Z","publisher":"Institute of Science and Technology Austria","OA_place":"publisher","has_accepted_license":"1","status":"public","corr_author":"1","month":"11","keyword":["Sex chromosomes","evolution","selection","sheltering"],"publication_identifier":{"issn":["2663-337X"]},"department":[{"_id":"GradSch"},{"_id":"BeVi"}],"doi":"10.15479/at:ista:18531","file":[{"creator":"amrnjava","date_created":"2024-11-13T12:15:28Z","file_size":26870629,"embargo_to":"open_access","file_id":"18551","relation":"source_file","checksum":"3e48b163c22114ef5d5371f758668289","access_level":"closed","date_updated":"2025-05-11T22:30:04Z","file_name":"AMrnjavac_thesis_library.docx","title":"Early stages of sex chromosome evolution","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"},{"checksum":"3ead60c1b678e7dcf018043aef3b5db2","access_level":"open_access","date_updated":"2025-05-11T22:30:04Z","file_name":"AMrnjavac_thesis_library.pdf","title":"Early stages of sex chromosome evolution","content_type":"application/pdf","creator":"amrnjava","embargo":"2025-05-11","date_created":"2024-11-13T12:15:54Z","file_size":4228766,"file_id":"18552","relation":"main_file"}],"degree_awarded":"PhD","date_created":"2024-11-11T08:40:45Z","publication_status":"published","supervisor":[{"orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","first_name":"Beatriz","full_name":"Vicoso, Beatriz"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"type":"dissertation","day":"11","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","abstract":[{"lang":"eng","text":"Sex chromosomes and autosomes exhibit very different evolutionary dynamics.\r\nThe Y chromosome usually degenerates, leaving many X-linked loci hemizygous in\r\nmales. Since recessive X-linked mutations are always exposed to selection in males,\r\nselection is more efficient on the X chromosome than on autosomes on recessive\r\nmutations, leading to faster adaptation on the X chromosome than other genomic\r\nregions, if beneficial mutations are on average recessive (known as the Faster-X\r\neffect). In the presence of the functional, but non-recombining gametolog on the Y (as\r\nis often the case in young non-recombining regions), recessive mutations are\r\nsheltered from selection on the X chromosome. We model this scenario and show that\r\nthe efficiency of selection is reduced on diploid X loci due to sheltering by the Y\r\nchromosome. Reduced efficiency of selection leads to slower adaptation and\r\nincreased accumulation of deleterious mutations (Slower-X effect). We extended this\r\nmodel to explore the effect of sex-specific selection on degeneration of sex\r\nchromosomes, showing theoretically that male-limited genes degenerate on the X\r\nchromosome and female-biased genes degenerate on the Y chromosome. This\r\nprediction depends on the effective population size and the mutation rate, explaining\r\nthe variety of sex chromosome degeneration patterns observed in nature.\r\nTo test for direct evidence of a Slower-X (or Slower-Z) effect, we analyzed the\r\nZW sex chromosomes of the flatworm Schistosoma japonicum, which have a very\r\nyoung non-recombining region with non-degenerated W. Diploid Z-linked genes have\r\nhigher ratios of non-synonymous to synonymous polymorphisms than autosomal\r\ngenes, supporting reduced efficiency of selection on the diploid Z region. These results\r\nprovide evidence of sheltering by the W chromosome, a mechanism that could\r\ncontribute to Z (X) chromosome degeneration, and illustrate contrasting evolutionary\r\npatterns in old and young sex chromosome regions. In addition, genes with sexspecific patterns of expression show opposite patterns of selection in the young\r\n(diploid) and old (hemizygous) Z, showing the complex manner in which sex-specific selection shapes the evolutionary patterns of sex chromosomes. "}],"oa":1,"language":[{"iso":"eng"}],"file_date_updated":"2025-05-11T22:30:04Z","OA_embargo":"6","alternative_title":["ISTA Thesis"],"_id":"18531","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"12521"},{"status":"public","relation":"part_of_dissertation","id":"18549"}]},"date_updated":"2026-04-07T13:22:45Z","citation":{"chicago":"Mrnjavac, Andrea. “Early Stages of Sex Chromosome Evolution.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18531\">https://doi.org/10.15479/at:ista:18531</a>.","short":"A. Mrnjavac, Early Stages of Sex Chromosome Evolution, Institute of Science and Technology Austria, 2024.","mla":"Mrnjavac, Andrea. <i>Early Stages of Sex Chromosome Evolution</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18531\">10.15479/at:ista:18531</a>.","ieee":"A. Mrnjavac, “Early stages of sex chromosome evolution,” Institute of Science and Technology Austria, 2024.","apa":"Mrnjavac, A. (2024). <i>Early stages of sex chromosome evolution</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18531\">https://doi.org/10.15479/at:ista:18531</a>","ama":"Mrnjavac A. Early stages of sex chromosome evolution. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18531\">10.15479/at:ista:18531</a>","ista":"Mrnjavac A. 2024. Early stages of sex chromosome evolution. Institute of Science and Technology Austria."},"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"CampIT"}]},{"day":"02","article_processing_charge":"No","title":"Strong amplifiers of natural selection","project":[{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"year":"2017","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","date_published":"2017-01-02T00:00:00Z","datarep_id":"51","doi":"10.15479/AT:ISTA:51","ddc":["519"],"department":[{"_id":"KrCh"}],"file":[{"content_type":"video/mp4","file_name":"IST-2017-51-v1+2_illustration.mp4","date_updated":"2020-07-14T12:47:02Z","access_level":"open_access","checksum":"b427dd46a30096a1911b245640c47af8","relation":"main_file","file_id":"5644","file_size":32987015,"date_created":"2018-12-12T13:05:18Z","creator":"system"}],"date_created":"2018-12-12T12:31:32Z","author":[{"id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas","first_name":"Andreas","last_name":"Pavlogiannis"},{"full_name":"Tkadlec, Josef","first_name":"Josef","last_name":"Tkadlec","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1097-9684"},{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Nowak , Martin","first_name":"Martin","last_name":"Nowak "}],"type":"research_data","month":"01","keyword":["natural selection"],"_id":"5559","related_material":{"record":[{"status":"public","relation":"research_paper","id":"5452"},{"relation":"research_paper","id":"5751","status":"public"}]},"citation":{"apa":"Pavlogiannis, A., Tkadlec, J., Chatterjee, K., &#38; Nowak , M. (2017). Strong amplifiers of natural selection. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:51\">https://doi.org/10.15479/AT:ISTA:51</a>","ama":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak  M. Strong amplifiers of natural selection. 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:51\">10.15479/AT:ISTA:51</a>","ista":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak  M. 2017. Strong amplifiers of natural selection, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:51\">10.15479/AT:ISTA:51</a>.","chicago":"Pavlogiannis, Andreas, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak . “Strong Amplifiers of Natural Selection.” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:51\">https://doi.org/10.15479/AT:ISTA:51</a>.","short":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M. Nowak , (2017).","mla":"Pavlogiannis, Andreas, et al. <i>Strong Amplifiers of Natural Selection</i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:51\">10.15479/AT:ISTA:51</a>.","ieee":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. Nowak , “Strong amplifiers of natural selection.” Institute of Science and Technology Austria, 2017."},"date_updated":"2025-04-15T08:12:19Z","ec_funded":1,"publisher":"Institute of Science and Technology Austria","abstract":[{"text":"Strong amplifiers of natural selection","lang":"eng"}],"file_date_updated":"2020-07-14T12:47:02Z","oa":1,"has_accepted_license":"1","status":"public"},{"date_created":"2018-12-12T12:31:30Z","author":[{"orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field","first_name":"David","full_name":"Field, David"},{"full_name":"Ellis, Thomas","first_name":"Thomas","last_name":"Ellis","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8511-0254"}],"tmp":{"short":"CC0 (1.0)","name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode"},"type":"research_data","datarep_id":"37","department":[{"_id":"NiBa"}],"ddc":["576"],"doi":"10.15479/AT:ISTA:37","file":[{"file_size":132808,"date_created":"2018-12-12T13:03:02Z","creator":"system","file_id":"5620","relation":"main_file","file_name":"IST-2016-37-v1+1_paternity_archive.zip","date_updated":"2020-07-14T12:47:01Z","access_level":"open_access","checksum":"4ae751b1fa4897fa216241f975a57313","content_type":"application/zip"}],"year":"2016","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2016-02-19T00:00:00Z","oa_version":"Published Version","day":"19","article_processing_charge":"No","title":"Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012","has_accepted_license":"1","status":"public","publisher":"Institute of Science and Technology Austria","license":"https://creativecommons.org/publicdomain/zero/1.0/","abstract":[{"text":"Genotypic, phenotypic and demographic data for 2128 wild snapdragons and 1127 open-pollinated progeny from a natural hybrid zone, collected as part of Tom Ellis' PhD thesis (submitted) February 2016).\r\n\r\nTissue samples were sent to LGC Genomics in Berlin for DNA extraction, and genotyping at 70 SNP markers by KASPR genotyping. 29 of these SNPs failed to amplify reliably, and have been removed from this dataset.\r\n\r\nOther data were retreived from an online database of this population at www.antspec.org.","lang":"eng"}],"contributor":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","contributor_type":"project_manager","first_name":"Nicholas H","last_name":"Barton"}],"file_date_updated":"2020-07-14T12:47:01Z","oa":1,"related_material":{"record":[{"id":"1398","relation":"part_of_dissertation","status":"public"}]},"date_updated":"2026-04-09T10:52:06Z","citation":{"apa":"Field, D., &#38; Ellis, T. (2016). Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:37\">https://doi.org/10.15479/AT:ISTA:37</a>","ama":"Field D, Ellis T. Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:37\">10.15479/AT:ISTA:37</a>","ista":"Field D, Ellis T. 2016. Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:37\">10.15479/AT:ISTA:37</a>.","chicago":"Field, David, and Thomas Ellis. “Inference of Mating Patterns among Wild Snapdragons in a Natural Hybrid Zone in 2012.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:37\">https://doi.org/10.15479/AT:ISTA:37</a>.","short":"D. Field, T. Ellis, (2016).","mla":"Field, David, and Thomas Ellis. <i>Inference of Mating Patterns among Wild Snapdragons in a Natural Hybrid Zone in 2012</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:37\">10.15479/AT:ISTA:37</a>.","ieee":"D. Field and T. Ellis, “Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012.” Institute of Science and Technology Austria, 2016."},"month":"02","keyword":["paternity assignment","pedigree","matting patterns","assortative mating","Antirrhinum majus","frequency-dependent selection","plant-pollinator interaction"],"_id":"5553"},{"author":[{"last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"type":"book_chapter","publication_status":"published","date_created":"2022-03-21T07:46:22Z","department":[{"_id":"NiBa"}],"doi":"10.1016/b978-0-12-384719-5.00031-9","date_published":"2013-01-01T00:00:00Z","oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2013","page":"508-515","title":"Differentiation","article_processing_charge":"No","day":"01","corr_author":"1","scopus_import":"1","status":"public","language":[{"iso":"eng"}],"publication":"Encyclopedia of Biodiversity","publisher":"Elsevier","publication_identifier":{"isbn":["978-0-12-384720-1"]},"quality_controlled":"1","citation":{"ieee":"N. H. Barton, “Differentiation,” in <i>Encyclopedia of Biodiversity</i>, 2nd ed., Elsevier, 2013, pp. 508–515.","mla":"Barton, Nicholas H. “Differentiation.” <i>Encyclopedia of Biodiversity</i>, 2nd ed., Elsevier, 2013, pp. 508–15, doi:<a href=\"https://doi.org/10.1016/b978-0-12-384719-5.00031-9\">10.1016/b978-0-12-384719-5.00031-9</a>.","short":"N.H. Barton, in:, Encyclopedia of Biodiversity, 2nd ed., Elsevier, 2013, pp. 508–515.","chicago":"Barton, Nicholas H. “Differentiation.” In <i>Encyclopedia of Biodiversity</i>, 2nd ed., 508–15. Elsevier, 2013. <a href=\"https://doi.org/10.1016/b978-0-12-384719-5.00031-9\">https://doi.org/10.1016/b978-0-12-384719-5.00031-9</a>.","ista":"Barton NH. 2013.Differentiation. In: Encyclopedia of Biodiversity. , 508–515.","ama":"Barton NH. Differentiation. In: <i>Encyclopedia of Biodiversity</i>. 2nd ed. Elsevier; 2013:508-515. doi:<a href=\"https://doi.org/10.1016/b978-0-12-384719-5.00031-9\">10.1016/b978-0-12-384719-5.00031-9</a>","apa":"Barton, N. H. (2013). Differentiation. In <i>Encyclopedia of Biodiversity</i> (2nd ed., pp. 508–515). Elsevier. <a href=\"https://doi.org/10.1016/b978-0-12-384719-5.00031-9\">https://doi.org/10.1016/b978-0-12-384719-5.00031-9</a>"},"date_updated":"2024-10-09T21:02:37Z","edition":"2","_id":"10899","keyword":["Adaptive landscape","Cline","Coalescent process","Gene flow","Hybrid zone","Local adaptation","Natural selection","Neutral theory","Population structure","Speciation"],"month":"01"},{"publication":"Journal of Theoretical Biology","publisher":"Elsevier","status":"public","intvolume":"       240","keyword":["Mutation","Selection","Synonymous site","Evolution","Genetic drift"],"month":"06","publication_identifier":{"issn":["1095-8541"]},"external_id":{"pmid":["16343547"]},"author":[{"full_name":"Kondrashov, Fyodor","first_name":"Fyodor","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694"},{"full_name":"Ogurtsov, Aleksey","first_name":"Aleksey","last_name":"Ogurtsov"},{"last_name":"Kondrashov","first_name":"Alexey","full_name":"Kondrashov, Alexey"}],"acknowledgement":"This research was supported in part by the Intramural Research Program of the NIH, National Library of Medicine.","title":"Selection in favor of nucleotides G and C diversifies evolution rates and levels of polymorphism at mammalian synonymous sites","article_processing_charge":"No","pmid":1,"volume":240,"date_published":"2006-06-21T00:00:00Z","oa_version":"None","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","year":"2006","page":"616 - 626","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"The impact of synonymous nucleotide substitutions on fitness in mammals remains controversial. Despite some indications of selective constraint, synonymous sites are often assumed to be neutral, and the rate of their evolution is used as a proxy for mutation rate. We subdivide all sites into four classes in terms of the mutable CpG context, nonCpG, postC, preG, and postCpreG, and compare four-fold synonymous sites and intron sites residing outside transposable elements. The distribution of the rate of evolution across all synonymous sites is trimodal. Rate of evolution at nonCpG synonymous sites, not preceded by C and not followed by G, is ∼10% below that at such intron sites. In contrast, rate of evolution at postCpreG synonymous sites is ∼30% above that at such intron sites. Finally, synonymous and intron postC and preG sites evolve at similar rates. The relationship between the levels of polymorphism at the corresponding synonymous and intron sites is very similar to that between their rates of evolution. Within every class, synonymous sites are occupied by G or C much more often than intron sites, whose nucleotide composition is consistent with neutral mutation-drift equilibrium. These patterns suggest that synonymous sites are under weak selection in favor of G and C, with the average coefficient s∼0.25/Ne∼10-5, where Ne is the effective population size. Such selection decelerates evolution and reduces variability at sites with symmetric mutation, but has the opposite effects at sites where the favored nucleotides are more mutable. The amino-acid composition of proteins dictates that many synonymous sites are CpGprone, which causes them, on average, to evolve faster and to be more polymorphic than intron sites. An average genotype carries ∼107 suboptimal nucleotides at synonymous sites, implying synergistic epistasis in selection against them."}],"scopus_import":"1","OA_type":"closed access","issue":"4","_id":"869","extern":"1","quality_controlled":"1","citation":{"ista":"Kondrashov F, Ogurtsov A, Kondrashov A. 2006. Selection in favor of nucleotides G and C diversifies evolution rates and levels of polymorphism at mammalian synonymous sites. Journal of Theoretical Biology. 240(4), 616–626.","ama":"Kondrashov F, Ogurtsov A, Kondrashov A. Selection in favor of nucleotides G and C diversifies evolution rates and levels of polymorphism at mammalian synonymous sites. <i>Journal of Theoretical Biology</i>. 2006;240(4):616-626. doi:<a href=\"https://doi.org/10.1016/j.jtbi.2005.10.020\">10.1016/j.jtbi.2005.10.020</a>","apa":"Kondrashov, F., Ogurtsov, A., &#38; Kondrashov, A. (2006). Selection in favor of nucleotides G and C diversifies evolution rates and levels of polymorphism at mammalian synonymous sites. <i>Journal of Theoretical Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jtbi.2005.10.020\">https://doi.org/10.1016/j.jtbi.2005.10.020</a>","ieee":"F. Kondrashov, A. Ogurtsov, and A. Kondrashov, “Selection in favor of nucleotides G and C diversifies evolution rates and levels of polymorphism at mammalian synonymous sites,” <i>Journal of Theoretical Biology</i>, vol. 240, no. 4. Elsevier, pp. 616–626, 2006.","mla":"Kondrashov, Fyodor, et al. “Selection in Favor of Nucleotides G and C Diversifies Evolution Rates and Levels of Polymorphism at Mammalian Synonymous Sites.” <i>Journal of Theoretical Biology</i>, vol. 240, no. 4, Elsevier, 2006, pp. 616–26, doi:<a href=\"https://doi.org/10.1016/j.jtbi.2005.10.020\">10.1016/j.jtbi.2005.10.020</a>.","short":"F. Kondrashov, A. Ogurtsov, A. Kondrashov, Journal of Theoretical Biology 240 (2006) 616–626.","chicago":"Kondrashov, Fyodor, Aleksey Ogurtsov, and Alexey Kondrashov. “Selection in Favor of Nucleotides G and C Diversifies Evolution Rates and Levels of Polymorphism at Mammalian Synonymous Sites.” <i>Journal of Theoretical Biology</i>. Elsevier, 2006. <a href=\"https://doi.org/10.1016/j.jtbi.2005.10.020\">https://doi.org/10.1016/j.jtbi.2005.10.020</a>."},"date_updated":"2026-05-08T10:18:03Z","publist_id":"6779","doi":"10.1016/j.jtbi.2005.10.020","type":"journal_article","date_created":"2018-12-11T11:48:56Z","publication_status":"published","day":"21","article_type":"original"}]