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Here, we used whole\u2010genome resequencing of wild Rocky Mountain bighorn sheep (<jats:italic>Ovis canadensis<\/jats:italic>) to &gt;50\u2010fold coverage to identify 2.8\u00a0million single nucleotide polymorphisms (<jats:styled-content style=\"fixed-case\">SNP<\/jats:styled-content>s) and genomic regions bearing signatures of directional selection (i.e. selective sweeps). A comparison of <jats:styled-content style=\"fixed-case\">SNP<\/jats:styled-content> diversity between the X chromosome and the autosomes indicated that bighorn males had a dramatically reduced long\u2010term effective population size compared to females. This probably reflects a long history of intense sexual selection mediated by male\u2013male competition for mates. Selective sweep scans based on heterozygosity and nucleotide diversity revealed evidence for a selective sweep shared across multiple populations at <jats:italic><jats:styled-content style=\"fixed-case\">RXFP<\/jats:styled-content>2<\/jats:italic>, a gene that strongly affects horn size in domestic ungulates. The massive horns carried by bighorn rams appear to have evolved in part via strong positive selection at <jats:italic><jats:styled-content style=\"fixed-case\">RXFP<\/jats:styled-content>2<\/jats:italic>. We identified evidence for selection within individual populations at genes affecting early body growth and cellular response to hypoxia; however, these must be interpreted more cautiously as genetic drift is strong within local populations and may have caused false positives. These results represent a rare example of strong genomic signatures of selection identified at genes with known function in wild populations of a nonmodel species. Our results also showcase the value of reference genome assemblies from agricultural or model species for studies of the genomic basis of adaptation in closely related wild taxa.<\/jats:p>","DOI":"10.1111\/mec.13415","type":"journal-article","created":{"date-parts":[[2015,10,10]],"date-time":"2015-10-10T13:57:45Z","timestamp":1444485465000},"page":"5616-5632","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":86,"title":["Whole\u2010genome resequencing uncovers molecular signatures of natural and sexual selection in wild bighorn sheep"],"prefix":"10.1111","volume":"24","author":[{"given":"Marty","family":"Kardos","sequence":"first","affiliation":[{"name":"Division of Biological Sciences University of Montana Missoula MT 59812 USA"},{"name":"Evolutionary Biology Centre Uppsala University SE\u201075236 Uppsala 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