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

Kelly B Klingler,Mary M Peacock,Thomas L Parchman,Joshua P Jahner,Chris Ray

doi:10.1186/s12862-020-01739-9

Abstract

BackgroundDistributional 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.ResultsOur genome-wide analyses corroborate range-wide, mitochondrial subspecific designations and reveal pronounced fine-scale population structure between the Ruby Mountains and East Humboldt Range of eastern Nevada. Populations in Nevada were characterized by low genetic diversity (π = 0.0006–0.0009; θW = 0.0005–0.0007) relative to populations in California (π = 0.0014–0.0019; θW = 0.0011–0.0017) and the Rocky Mountains (π = 0.0025–0.0027; θW = 0.0021–0.0024), indicating substantial genetic drift in these isolated populations. Tajima’s D was positive for all sites (D = 0.240–0.811), consistent with recent contraction in population sizes range-wide.ConclusionsSubstantial influences of geography, elevation and climate variables on genetic differentiation were also detected and may interact with the regional effects of anthropogenic climate change to force the loss of unique genetic lineages through continued population extirpations in the Great Basin and Sierra Nevada.

Highlights

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
Expanding the genetic characterization of population level genetic diversity will be necessary to define fully the genetic variation within pika lineages and how this diversity is partitioned across the landscape
The patterns of climate-associated, range-wide differentiation observed in this study, along with the significant role of geography at finer scales, reinforces the need to tease apart the specific climatic or non-climatic factors that can shape genetic variation across small to moderate spatial scales within each mountain system

Summary

Introduction

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. The American pika has become a canary-in-the-coalmine for the effects of anthropogenic climate change in montane habitats, as a result of extensive extirpations from warmer, lower elevation sites over the past two decades [13,14,15,16,17] This small lagomorph is found in the mountainous regions of western North America where it lives primarily on talus slopes above timberline [18]. Most species are found in Asia and Eastern Europe with one North American congener in Alaska and Canada, O. collaris [18, 21]

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