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Development and Application of Genomic Resources for Bighorn Sheep (Ovis canadensis)

  • Author / Creator
    Miller, Joshua Moses
  • Since the mid-2000’s there has been a major shift in molecular ecology to the use of genomic methodologies. These methods utilize genome-wide sampling of genetic variation and allow for consideration of questions that cannot be answered with a handful of microsatellite markers or a few gene sequences. However, the necessary resources for genomic analyses do not exist for many wild taxa. I developed such resources for the bighorn sheep (Ovis canadensis), and then applied these to several questions and analyses that can be conducted in the absence of a species-specific reference genome sequence. First, I used two parallel methodologies to rapidly discover genome-wide sets of single nucleotide polymorphisms (SNPs). Second, I used some of those loci as well as a large set of microsatellite markers to investigate how many loci and of what marker type would be needed to reflect genome-wide heterozygosity in two populations of bighorn sheep. This consideration is important for studies that wish to search for evidence of inbreeding depression in a population via heterozygosity fitness correlations (HFCs). Third, I performed a meta-analysis of 50 HFC studies to quantify the predicted magnitude of association between marker heterozygosity and inbreeding, and the number of markers that would have been needed to definitively detect such an association. Fourth, I conducted a genome wide association analysis to search for potential links between SNP variants and fitness related characteristics in a single population of bighorn sheep. I then checked the validity of the associations using an expanded set of individuals, and assessed if there have been changes in allele frequency over time. Finally, I constructed a draft whole genome sequence (WGS) from a single bighorn sheep via alignment to a domestic sheep genome as a reference. Together this work provides a robust set of genomic tools for research not only on bighorn sheep but other members of the genus Ovis, as well as guidance for those who wish to conduct HFC studies in any taxa.

  • Subjects / Keywords
  • Graduation date
    2015-11
  • Type of Item
    Thesis
  • Degree
    Doctor of Philosophy
  • DOI
    https://doi.org/10.7939/R33B5WD5P
  • License
    This thesis is made available by the University of Alberta Libraries with permission of the copyright owner solely for non-commercial purposes. This thesis, or any portion thereof, may not otherwise be copied or reproduced without the written consent of the copyright owner, except to the extent permitted by Canadian copyright law.
  • Language
    English
  • Institution
    University of Alberta
  • Degree level
    Doctoral
  • Department
    • Department of Biological Sciences
  • Specialization
    • Systematics and Evolution
  • Supervisor / co-supervisor and their department(s)
    • Coltman, David W (Biological Sciences)
  • Examining committee members and their departments
    • Davis, Corey S (Biological Science)
    • Stothard, Paul (Agricultural, Food and Nutritional Science)
    • Li, Changxi (Agricultural, Food and Nutritional Science)
    • Schwartz, Michael K. (United State Department of Agriculture Forest Service)