Population Genetics of Ovis and Phylogenetics of Caprinae: A Comparison of Different Genetic Markers for Evaluation of Diversity at Multiple Taxonomic Levels

Driscoll, Catherine Colleen

Graduate Thesis Or Dissertation

Population Genetics of Ovis and Phylogenetics of Caprinae: A Comparison of Different Genetic Markers for Evaluation of Diversity at Multiple Taxonomic Levels Public Deposited

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Citeable URL: https://scholar.colorado.edu/concern/graduate_thesis_or_dissertations/zp38wc65b

Abstract

This research was initiated due to concern that one of the four Rocky Mountain National Park (RMNP) bighorn sheep (Ovis canadensis) herds (the Mummy) could be suffering from inbreeding depression following a documented pneumonia outbreak and die-off in 1994. Failure of this herd to recover led to a comprehensive population genetic analysis of five bighorn sheep herds (Big Thompson, Continental Divide, Mummy, Never Summer and St. Vrain) to address four main questions: 1) Using data from 13 microsatellite loci: How much genetic variation exists in non-coding DNA in each herd? 2) Using sequence data from two distinct regions of the maternally inherited mitochondrial genome (Cytochrome Oxidase I gene (COI) and D-Loop control region (DL)): To what extent are ewes a source of gene flow between herds? 3) Using sequence data from two regions of the Y-chromosome gene SRY (promoter (PRO) and complete gene coding region (ORF)): to what extent are rams a source of gene flow between herds? 4) Do these data support evidence of a recent and severe genetic bottleneck in any of these five herds such that inbreeding depression could be a significant factor in long-term viability? Our results support that all five herds have high levels of heterozygosity, low population substructure maintained by on-going gene flow, and no evidence of a recent genetic bottleneck. All data clearly refute the hypothesis that decreased genetic variation is a significant factor in the Mummy herd's failure to thrive and instead suggest that environmental factors should be investigated. Unfortunately, our analyses of Y-chromosome data showed the SRY sequences to be invariant among RMNP bighorn herds; however we realized these data would still be useful in a broader context and we therefore expanded analyses to include all genera within the subfamily Caprinae (Artiodactyla, Bovidae) and incorporated comparative data from the mitochondrial gene ND5. These data provide comprehensive and complementary phylogenetic analyses for which the more conserved Y-chromosome sequences generally showed better resolution of the most basal nodes, while the more variable mitochondrial sequences were usually better able to resolve relationships among recently diverged genera as well as between species within individual genera.

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