LB 20-209 - Genome-wide analysis of intraspecific lineage distribution and diversification in American pika

Background/Question/Methods:

Reconstructing intraspecific phylogenetic relationships is important for understanding species evolutionary histories. Especially for those species that have persisted through multiple glacial periods, phylogenetic patterns can provide insight into the geographic, demographic, and environmental processes that have shaped genomic variation range wide, providing a basis for examining species responses to climate change. One species likely impacted by climate change is the American pika (Ochotona princeps), a thermally sensitive lagomorph found in talus slopes across western North America. Previous phylogenetic and demographic analyses of this species using mitochondrial DNA (mtDNA) markers provided evidence for five discrete genetic lineages distributed across several mountain ranges. These lineages are thought to have been maintained by range retraction and expansion along elevational gradients during glacial climate fluctuations. However, recent research on O. princeps and host-specific parasite co-diversification, as well as genetic analyses of admixture between lineages, suggest a more complex biogeographic history than previously thought. We examined 25,269 nuclear single-nucleotide polymorphisms (SNPs) from 37 populations across the species range to further investigate the distribution and number of distinct genetic lineages of O. princeps, as well as estimate patterns of lineage divergence, using a combination of phylogenetic analyses and demographic modeling.

Results/Conclusions:

Our results show evidence for six distinct genetic groups of American pika distributed range-wide (Casades, Sierra Nevada, Central Utah, Northern Rocky Mountain, Central Rocky Mountain, Southern Rocky Mountain). We found evidence for 6 reciprocally monophyletic lineages from species phylogenies that are concordant with patterns of inferred genetic structure. The recovered lineages largely mirror those detected in previous work using mtDNA, with evidence for an additional lineage (Central Rocky Mountain) composed of southern populations within the Northern Rocky Mountains lineage. We also detected evidence for admixture among the three Rocky Mountain lineages, which supports other recent findings. Through the use of nuclear DNA markers (SNPs), these results provide an additional perspective on the evolutionary history of the American pika, as well as a foundation for future studies to explore the role of climate in the lineage diversification of this species.