GENETIC STRUCTURE OF ROCKY MOUNTAIN ELK FROM WIND CAVE NATIONAL PARK

Kaneesha Marie Hemmerling

doi:10.7273/000004555

Elk (Cervus canadensis) play an integral role in balancing ecosystems, have significant economic value, and hold cultural value across diverse groups. Diseases such as chronic wasting disease (CWD), a fatal prion disease of cervids, threaten elk populations. Improved understanding of elk genetics can contribute to disease management, may provide information integral for determining genetic trends and future directions, and may lead to identification of trait associated variants, opening the door to selection desirable for production or even disease resistance. To advance the field and provide a foundation for elk conservation genomics, sequencing and genotyping of elk is necessary. This study employed the first reported genotype-by-sequencing in elk. Single nucleotide polymorphism (SNPs) discovery was undertaken in 306 Rocky Mountain elk (Cervus canadensis nelsoni) from Wind Cave National Park (WICA), South Dakota, USA. Genetic diversity and population structure of WICA elk were analyzed as one single population and as three subpopulations, as designated by geospatial analysis in a previous study. Effective population size (Ne) was determined to range from 36-316 and tests identified 3,251 variants out of Hardy-Weinberg equilibrium. Pairwise differentiation (Fst) indicated little difference in the genetic structure between WICA subpopulations (Fst≈0.003), but principal component analysis showed weak population structure when analyzed as a total population. Analysis that included 38,583 alleles private to the subpopulations revealed distinct genetic structure by geographical location, confirming previous field observations. Measurements of observed heterozygosity indicated subpopulation A (Ho=0.645) and subpopulation B (Ho=0.658) had the higher heterozygosity compared to subpopulation C (Ho=0.60). All subpopulation heterozygosity’s were higher than the total population average (Ho=0.53). The genetic structure seen in these subpopulations is likely due to the design of the park fence. Low areas of the fence and elk dropdown gates at the western and southwestern boarder of the park allowed elk to freely cross near regions A and B, but not region C, until renovations completely enclosed the park after 2013. This recent enclosure, along with other park geographical features and efforts to reduce WICA elk population density, will require managers employ periodic genetic monitoring to ensure that genetically differentiated subpopulations do not lose standing genetic diversity.

GENETIC STRUCTURE OF ROCKY MOUNTAIN ELK FROM WIND CAVE NATIONAL PARK

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