Data from: Candidate adaptive genes associated with lineage divergence: identifying SNPs via next-generation targeted resequencing in mule deer (Odocoileus hemionus)

Mule deer (Odocoileus hemionus) are an excellent nonmodel species for
empirically testing hypotheses in landscape and population genomics due to
their large population sizes (low genetic drift), relatively continuous
distribution, diversity of occupied habitats and phenotypic variation.
Because few genomic resources are currently available for this species, we
used exon data from a cattle (Bos taurus) reference genome to direct
targeted resequencing of 5935 genes in mule deer. We sequenced
approximately 3.75 Mbp at minimum 20X coverage in each of the seven mule
deer, identifying 23 204 single nucleotide polymorphisms (SNPs) within, or
adjacent to, 6886 exons in 3559 genes. We found 91 SNP loci (from 69
genes) with putatively fixed allele frequency differences between the two
major lineages of mule deer (mule deer and black-tailed deer), and our
estimate of mean genetic divergence (genome-wide FST = 0.123) between
these lineages was consistent with previous findings using microsatellite
loci. We detected an over-representation of gamete generation and amino
acid transport genes among the genes with SNPs exhibiting potentially
fixed allele frequency differences between lineages. This targeted
resequencing approach using exon capture techniques has identified a suite
of loci that can be used in future research to investigate the genomic
basis of adaptation and differentiation between black-tailed deer and mule
deer. This study also highlights techniques (and an exon capture array)
that will facilitate population genomic research in other cervids and
nonmodel organisms.