LB 20-204 - A spatio-temporal investigation of neutral and adaptive variation of the American pika (Ochotona princeps) in Canadian Rocky Mountain National Parks

Background/Question/Methods:

The American pika (Ochotona princeps) is a small alpine mammal that is highly sensitive to environmental changes, and is therefore expected to be a useful sentinel species for detecting the biological consequences of climate change in alpine environments. Long-term monitoring is conducted on the Northern Rocky Mountains (NRM) genetic lineage in Banff, Kootenay, and Yoho National Parks (British Columbia and Alberta, Canada) to investigate population trends. However, it is currently unknown how these trends relate to changes in genetic diversity and patterns of connectivity among discrete habitat patches. As many genetic techniques require high-quality and quantity DNA from invasive sampling, genetic studies of wildlife may be time-consuming and resource-intensive. Genotyping-in-Thousands by sequencing (GT-seq) is a cost-effective targeted amplicon method capable of genotyping hundreds of single nucleotide polymorphisms (SNPs) across thousands of individuals simultaneously. Importantly, it allows for effective genotyping of minimally invasive samples (e.g. hair and feces), making GT-seq a valuable tool for wildlife monitoring in protected areas. To evaluate genetic patterns in American pika populations, we have designed a multi-purpose GT-seq panel capable of identifying/sexing individuals, estimating relatedness/inbreeding, reconstructing connectivity, and tracking adaptive variants across spatial and temporal scales for use with non-invasive fecal pellet samples and archival specimens.

Results/Conclusions:

Preliminary simulation and quality control analyses revealed that a single GT-seq panel spanning the entire range or multiple lineages of American pika was not tenable. Therefore, we designed the GT-seq panel to specifically target the NRM lineage. The design of the GT-seq panel includes 818 SNPs: 9 sex-associated SNPs, 700 putatively neutral SNPs informative about genetic diversity and population structure within and among groups, and 109 candidate SNPs putatively under natural selection. The latter group of adaptive variants included 49 SNPs demonstrating a significant association with altitude, 4 SNPs linked to genes found to be under positive selection, and 56 SNPs corresponding with genes reported in the literature to demonstrate an association with climate. The GT-seq panel will be used to assess neutral and adaptive variation of pikas in Canadian Rocky Mountain National Parks, and to compare population connectivity and the distribution of adaptive variants between historical and contemporary populations in select locations. Through both applications, we aim to improve our understanding of the ecological impacts of climate change in alpine environments.