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We characterized genetic diversity at an <jats:styled-content style=\"fixed-case\">MHC<\/jats:styled-content> class <jats:styled-content style=\"fixed-case\">II<\/jats:styled-content> locus (<jats:italic>DRB1<\/jats:italic>) in Gunnison's prairie dog (<jats:italic>C.\u00a0gunnisoni<\/jats:italic>) and quantified population genetic structure at the <jats:italic>DRB1<\/jats:italic> versus 12 microsatellite loci in three large Arizona colonies. Two colonies, Seligman (<jats:styled-content style=\"fixed-case\">SE<\/jats:styled-content>) and Espee Ranch (<jats:styled-content style=\"fixed-case\">ES<\/jats:styled-content>), have experienced multiple plague\u2010related die\u2010offs in recent years, whereas plague has never been documented at Aubrey Valley (<jats:styled-content style=\"fixed-case\">AV<\/jats:styled-content>). We found fairly low allelic diversity at the <jats:italic>DRB1<\/jats:italic> locus, with one allele (<jats:italic>DRB1<\/jats:italic>*01) at high frequency (0.67\u20130.87) in all colonies. Two other <jats:italic>DRB1<\/jats:italic> alleles appear to be trans\u2010species polymorphisms shared with the black\u2010tailed prairie dog (<jats:italic>C.\u00a0ludovicianus<\/jats:italic>), indicating that these alleles have been maintained across evolutionary time frames. Estimates of genetic differentiation were generally lower at the <jats:styled-content style=\"fixed-case\">MHC<\/jats:styled-content> locus (<jats:italic>F<\/jats:italic><jats:sub>ST<\/jats:sub>\u00a0=\u00a00.033) than at microsatellite markers (<jats:italic>F<\/jats:italic><jats:sub>ST<\/jats:sub>\u00a0=\u00a00.098). The reduced differentiation at <jats:italic>DRB1<\/jats:italic> may indicate that selection has been important for shaping variation at <jats:styled-content style=\"fixed-case\">MHC<\/jats:styled-content> loci, regardless of the presence or absence of plague in recent decades. However, genetic drift has probably also influenced the <jats:italic>DRB1<\/jats:italic> locus because its level of differentiation was not different from that of microsatellites in an <jats:italic>F<\/jats:italic><jats:sub>ST<\/jats:sub> outlier analysis. We then compared specific <jats:styled-content style=\"fixed-case\">MHC<\/jats:styled-content> alleles to plague survivorship in 60 <jats:italic>C.\u00a0gunnisoni<\/jats:italic> that had been experimentally infected with <jats:italic>Y.\u00a0pestis<\/jats:italic>. We found that survival was greater in individuals that carried at least one copy of the most common allele (<jats:italic>DRB1<\/jats:italic>*01) compared to those that did not (60% vs. 20%). Although the sample sizes of these two groups were unbalanced, this result suggests the possibility that this <jats:styled-content style=\"fixed-case\">MHC<\/jats:styled-content> class <jats:styled-content style=\"fixed-case\">II<\/jats:styled-content> locus, or a nearby linked gene, could play a role in plague survival.<\/jats:p>","DOI":"10.1002\/ece3.2077","type":"journal-article","created":{"date-parts":[[2016,3,19]],"date-time":"2016-03-19T02:10:49Z","timestamp":1458353449000},"page":"2624-2651","source":"Crossref","is-referenced-by-count":6,"title":["Genetic variation at the <scp>MHC <\/scp><i>DRB1<\/i> locus is similar across Gunnison's prairie dog (<i>Cynomys gunnisoni<\/i>) colonies regardless of plague history"],"prefix":"10.1002","volume":"6","author":[{"given":"Kacy R.","family":"Cobble","sequence":"first","affiliation":[{"name":"Center for Microbial Genetics and Genomics Northern Arizona University PO Box\u00a04073 Flagstaff Arizona 86011 USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Katy J.","family":"Califf","sequence":"additional","affiliation":[{"name":"Center for Microbial Genetics and Genomics Northern Arizona University PO Box\u00a04073 Flagstaff Arizona 86011 USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nathan E.","family":"Stone","sequence":"additional","affiliation":[{"name":"Center for Microbial Genetics and Genomics Northern Arizona University PO Box\u00a04073 Flagstaff Arizona 86011 USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Megan M.","family":"Shuey","sequence":"additional","affiliation":[{"name":"Center for Microbial Genetics and Genomics Northern Arizona University PO Box\u00a04073 Flagstaff Arizona 86011 USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dawn N.","family":"Birdsell","sequence":"additional","affiliation":[{"name":"Center for Microbial Genetics and Genomics Northern Arizona University PO Box\u00a04073 Flagstaff Arizona 86011 USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6854-2100","authenticated-orcid":false,"given":"Rebecca E.","family":"Colman","sequence":"additional","affiliation":[{"name":"Translational Genomics Research Institute North 3051\u00a0W. 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