Midwest Fish & Wildlife Conference 2016

AUTHORS: John H. Powell*, Inland Fish and Wildlife Department Sault Ste. Marie Tribe of Chippewa Indians; Stephen J. Amish, Fish & Wildlife Genomics Group University of Montana; Gwilym D. Haynes, Department of Biological Sciences Simon Fraser University; Gordon Luikart, Fish & Wildlife Genomics Group University of Montana; Emily K. Latch, Department of Biological Sciences University of Wisconsin-Milwaukee

ABSTRACT: Mule deer Odocoileus hemionus are a highly variable species that occupies a wide range of habitats in large populations with high rates of gene flow. These traits make this species an excellent non-model system for testing hypotheses in population genomics and landscape genetics, two fields that emphasize increasing the resolution of population genetic studies both across a landscape and within a genome. However, no genomic resources exist for mule deer. Here we describe using a cattle Bos taurus reference genome to direct targeted re-sequencing of exons in seven mule deer, a technique that can be extended to other cervids and non-model organisms. This targeted re-sequencing yielded approximately 3.75 Mbp of sequence at a minimum 20X coverage in each individual. We identified 23,204 single nucleotide polymorphisms (SNPs) within this sequence, 91 of which have putatively fixed allele frequency differences between the two major evolutionary lineages of mule deer (mule deer and black-tailed deer). Our estimate of genetic divergence between these lineages remained consistent with what had been found using microsatellite loci. Although we did not detect a signature of natural selection at individual loci, we did find an over-representation of apoptotic process genes among loci with the highest 10% of the observed FST values between mule deer and black-tailed deer. We also detected an overrepresentation of gamete generation and amino acid transport genes among the subset of genes with loci exhibiting putative fixed allele frequency differences between these two lineages. Our targeted re-sequencing using exon capture techniques has identified loci that can be used in future studies investigating the genomic basis of adaptation and differentiation between the two evolutionary lineages of mule deer.