Genome-wide analysis reveals associations between climate and regional patterns of adaptive divergence and dispersal in American pikas.

Understanding the role of adaptation in species' responses to climate change is important for evaluating the evolutionary potential of populations and informing conservation efforts. Population genomics provides a useful approach for identifying putative signatures of selection and the underlying environmental factors or biological processes that may be involved. Here, we employed a population genomic approach within a space-for-time study design to investigate the genetic basis of local adaptation and reconstruct patterns of movement across rapidly changing environments in a thermally sensitive mammal, the American pika (Ochotona princeps). Using genotypic data at 49,074 single-nucleotide polymorphisms (SNPs), we analyzed patterns of genome-wide diversity, structure, and migration along three independent elevational transects located at the northern extent (Tweedsmuir South Provincial Park, British Columbia, Canada) and core (North Cascades National Park, Washington, USA) of the Cascades lineage. We identified 899 robust outlier SNPs within- and among-transects. Of those annotated to genes with known function, many were linked with cellular processes related to climate stress including ATP-binding, ATP citrate synthase activity, ATPase activity, hormone activity, metal ion-binding, and protein-binding. Moreover, we detected evidence for contrasting patterns of directional migration along transects across geographic regions that suggest an increased propensity for American pikas to disperse among lower elevation populations at higher latitudes where environments are generally cooler. Ultimately, our data indicate that fine-scale demographic patterns and adaptive processes may vary among populations of American pikas, providing an important context for evaluating biotic responses to climate change in this species and other alpine-adapted mammals.

Adaptive population divergence and directional gene flow across steep elevational gradients in a climate-sensitive mammal.

The ecological effects of climate change have been shown in most major taxonomic groups; however, the evolutionary consequences are less well-documented. Adaptation to new climatic conditions offers a potential long-term mechanism for species to maintain viability in rapidly changing environments, but mammalian examples remain scarce. The American pika (Ochotona princeps) has been impacted by recent climate-associated extirpations and range-wide reductions in population sizes, establishing it as a sentinel mammalian species for climate change. To investigate evidence for local adaptation and reconstruct patterns of genomic diversity and gene flow across rapidly changing environments, we used a space-for-time design and restriction site-associated DNA sequencing to genotype American pikas along two steep elevational gradients at 30,966 SNPs and employed independent outlier detection methods that scanned for genotype-environment associations. We identified 338 outlier SNPs detected by two separate analyses and/or replicated in both transects, several of which were annotated to genes involved in metabolic function and oxygen transport. Additionally, we found evidence of directional gene flow primarily downslope from high-elevation populations, along with reduced gene flow at outlier loci. If this trend continues, elevational range contractions in American pikas will likely be from local extirpation rather than upward movement of low-elevation individuals; this, in turn, could limit the potential for adaptation within this landscape. These findings are of particular relevance for future conservation and management of American pikas and other elevationally restricted, thermally sensitive species.

Individual-based analysis of hair corticosterone reveals factors influencing chronic stress in the American pika.

Glucocorticoids are often measured in wildlife to assess physiological responses to environmental or ecological stress. Hair, blood, saliva, or fecal samples are generally used depending on the timescale of the stress response being investigated and species-specific considerations. Here, we report the first use of hair samples to measure long-term corticosterone levels in the climate-sensitive American pika (Ochotona princeps). We validated an immunoassay-based measurement of corticosterone extracted from hair samples and compared corticosterone estimates obtained from plasma, hair, and fecal samples of nine pikas. To demonstrate an ecological application of this technique, we characterized physiological stress in 49 pikas sampled and released at eight sites along two elevational transects. Microclimate variation was measured at each site using both ambient and subsurface temperature sensors. We used an information theoretic approach to compare support for linear, mixed-effects models relating corticosterone estimates to microclimate, body size, and sex. Corticosterone was measured accurately in pika hair samples after correcting for the influence of sample mass on corticosterone extraction efficiency. Hair- and plasma-based estimates of corticosterone were weakly correlated. The best-supported model suggested that corticosterone was lower in larger, male pikas, and at locations with higher ambient temperatures in summer. Our results are consistent with a general negative relationship between body mass and glucocorticoid concentration observed across mammalian species, attributed to the higher mass-specific metabolic rates of smaller bodied animals. The higher corticosterone levels in female pikas likely reflected the physiological demands of reproduction, as observed in a wide array of mammalian species. Additionally, we establish the first direct physiological evidence for thermal stress in the American pika through nonlethal sampling of corticosterone. Interestingly, our data suggest evidence for cold stress likely induced during the summer molting period. This technique should provide a useful tool to researchers wishing to assess chronic stress in climate-sensitive mammals.

From promise to practice: pairing non-invasive sampling with genomics in conservation.

Conservation genomics has become an increasingly popular term, yet it remains unclear whether the non-invasive sampling that is essential for many conservation-related studies is compatible with the minimum requirements for harnessing next-generation sequencing technologies. Here, we evaluated the feasibility of using genotyping-by-sequencing of non-invasively collected hair samples to simultaneously identify and genotype single nucleotide polymorphisms (SNPs) in a climate-sensitive mammal, the American pika (Ochotona princeps). We identified and genotyped 3,803 high-confidence SNPs across eight sites distributed along two elevational transects using starting DNA amounts as low as 1 ng. Fifty-five outlier loci were detected as candidate gene regions under divergent selection, constituting potential targets for future validation. Genome-wide estimates of gene diversity significantly and positively correlated with elevation across both transects, with all low elevation sites exhibiting significant heterozygote deficit likely due to inbreeding. More broadly, our results highlight a range of issues that must be considered when pairing genomic data collection with non-invasive sampling, particularly related to field sampling protocols for minimizing exogenous DNA, data collection strategies and quality control steps for enhancing target organism yield, and analytical approaches for maximizing cost-effectiveness and information content of recovered genomic data.