A panel of 96 SNPs to identify individuals and differentiate subspecies of elk (Cervus canadensis) for microfluidic and other genotyping platforms

The tule elk ( Cervus canadensis nannodes ) is endemic to California, USA, where it experienced an extreme genetic bottleneck in the 1870s. Two other subspecies of elk co-occur in California, Roosevelt ( C . c. roosevelti ) and Rocky Mountain ( C. c. nelsoni ) elk. These subspecies potentially interbreed in contact zones. For monitoring and genetic management of fragmented populations, markers are needed to differentiate both individuals and subspecies. Using Illumina HiSeq sequencing of 12 individuals, including four from each subspecies, we developed a suite of 96 SNP markers for a Fluidigm platform. This marker set enabled differentiation of individuals and subspecies with high confidence and will facilitate genetic monitoring of elk throughout their range.