Genomic Variation, Population Structure, and Gene Flow across Asian Pikas

Asian pikas have one of the most complex systematics and evolutionary history. The Himalayas is an important habitat for Asian pikas as it hosts 23 - 25% of pikas global diversity and has provided the ancestral training ground for local adaptation to high altitudes. They are one of the most abundant species in the Himalayas and Qinghai Tibetan Plateau (QTP), however genetic studies to explore their population structure and evolution are limited. Here, we utilize a population genomics approach using ~28,000 genome-wide SNP markers obtained from restriction-site associated DNA sequencing in six species of Asian Pikas (Ochotona spp.) that are distributed across the Himalayas and neighboring high-altitude mountains. We examined intra- and inter-species genetic diversity, population structure, phylogenetic history and explored processes that shaped the current genetic diversity of Pikas across the Himalayas. We identified low nucleotide diversity and high inbreeding coefficient across all species which possibly indicated decreasing population size in these species. We also identified extensive evidence of gene flow (both historic and contemporary) across these species. Our findings indicate that inter-species gene flow is a key evolutionary process that has been countering the negative effect of low genetic diversity among Asian pikas.