Genomic variation in the American pika: signatures of geographic isolation and implications for conservation

Distributional responses by alpine taxa to repeated, glacial-interglacial cycles throughout the last two million years have significantly influenced the spatial genetic structure of populations. These effects have been exacerbated for the American pika (Ochotona princeps), a small alpine lagomorph constrained by thermal sensitivity and a limited dispersal capacity. As a species of conservation concern, long-term lack of gene flow has important consequences for landscape genetic structure and levels of diversity within populations. Here, we use reduced representation sequencing (ddRADseq) to provide a genome-wide perspective on patterns of genetic variation across pika populations representing distinct subspecies. To investigate how landscape and environmental features shape genetic variation, we collected genetic samples from distinct geographic regions as well as across finer spatial scales in two geographically proximate mountain ranges of eastern Nevada.

Methods
DNA was extracted from pika tissue samples representing 35 O. p. schisticeps, 21 O. p. saxitilis, and 115 O. p. princeps individuals (Fig. 1) using a Qiagen DNeasy Blood and Tissue Kit and quantified on a QIAxpert UV/VIS spectrophotometer (Qiagen, Inc., Valencia, CA, USA). Reduced representation libraries were prepared for Illumina sequencing following a genotyping-by-sequencing (GBS) protocol (Parchman et al. 2012) analogous to ddRADseq (Peterson et al. 2012).