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


Other title
heterozygosity fitness correlation
Single nucleotide poltmorphism
Type of item
Degree grantor
University of Alberta
Author or creator
Miller, Joshua Moses
Supervisor and department
Coltman, David W (Biological Sciences)
Examining committee member and department
Stothard, Paul (Agricultural, Food and Nutritional Science)
Schwartz, Michael K. (United State Department of Agriculture Forest Service)
Li, Changxi (Agricultural, Food and Nutritional Science)
Davis, Corey S (Biological Science)
Department of Biological Sciences
Systematics and Evolution
Date accepted
Graduation date
Doctor of Philosophy
Degree level
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.
Permission is hereby granted to the University of Alberta Libraries to reproduce single copies of this thesis and to lend or sell such copies for private, scholarly or scientific research purposes only. The author reserves all other publication and other rights in association with the copyright in the thesis and, except as herein before provided, neither the thesis nor any substantial portion thereof may be printed or otherwise reproduced in any material form whatsoever without the author's prior written permission.
Citation for previous publication
Miller, Joshua M., Jocelyn Poissant, James W. Kijas, and D. W. Coltman. "A genome-wide set of SNPs detects population substructure and long range linkage disequilibrium in wild sheep." Molecular Ecology Resources 11, no. 2 (2011): 314-322Coltman, David W., John T. Hogg, and Joshua M. Miller. "Genomic Resources Notes accepted 1 April 2013–31 May 2013." Molecular Ecology Resources 13, no. 5 (2013): 965-965Miller, J. M., R. M. Malenfant, P. David, C. S. Davis, J. Poissant, J. T. Hogg, M. Festa-Bianchet, and D. W. Coltman. "Estimating genome-wide heterozygosity: effects of demographic history and marker type." Heredity 112, no. 3 (2013): 240-247Joshua M. Miller and David W. Coltman. "Assessment of identity disequilibrium and its relation to empirical heterozygosity fitness correlations: a meta‐analysis." Molecular Ecology 23, no. 8 (2014): 1899-1909Joshua M Miller, Stephen S Moore, Paul Stothard, Xiaoping Liao, and David W. Coltman. "Harnessing cross-species alignment to discover SNPs and generate a draft genome sequence of a bighorn sheep (Ovis canadensis)" BMC Genomics 16, no. 1 (2015): doi: 10.1186/s12864-015-1618-x

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