Life on the edge-a changing genetic landscape within an iconic American pika metapopulation over the last half century

Declines and extirpations of American pika (Ochotona princeps) populations at historically occupied sites started being documented in the literature during the early 2000s. Commensurate with global climate change, many of these losses at peripheral and lower elevation sites have been associated with changes in ambient air temperature and precipitation regimes. Here, we report on a decline in available genetic resources for an iconic American pika metapopulation, located at the southwestern edge of the species distribution in the Bodie Hills of eastern California, USA. Composed of highly fragmented habitat created by hard rock mining, the ore dumps at this site were likely colonized by pikas around the end of the 19th century from nearby natural talus outcrops. Genetic data extracted from both contemporary samples and archived natural history collections allowed us to track population and patch-level genetic diversity for Bodie pikas across three distinct sampling points during the last half- century (1948-1949, 1988-1991, 2013-2015). Reductions in within-population allelic diversity and expected heterozygosity were observed across the full time period. More extensive sampling of extant patches during the 1988-1991 and 2013-2015 periods revealed an increase in population structure and a reduction in effective population size. Furthermore, census records from the last 51 years as well as archived museum samples collected in 1947 from a nearby pika population in the Wassuk range (Nevada, USA) provide further support of the increasing isolation and genetic coalescence occurring in this region. This study highlights the importance of museum samples and long-term monitoring in contextualizing our understanding of population viability.

Return of the pika: American pikas re-occupy long-extirpated, warm locations

American pikas (Ochotona princeps), small mammals related to rabbits, occur in mountainous regions of western North America, where they live in shattered‐rock habitats (talus). Aspects of their physiology and life history create situations that appear to put pikas at risk from warming climates. Some low‐elevation, warm sites that historically harbored pikas have become extirpated, and the assumption is that these will not be re‐colonized under current climate trends. Unexpectedly, in 2021, we found that pikas had re‐colonized two very warm, low‐elevation, dry sites in eastern California, USA, in the Bodie Mountains and Mono Craters. Resident pikas appear to have been absent at both sites for ≥10 years. These findings suggest that pikas, which are normally diurnally active, are able to overcome thermal dispersal barriers and re‐colonize long‐extirpated sites, perhaps by moving during cool nights. Our data also highlight the often unrecognized suitability of pika habitat in warm regions where the interiors of taluses can remain stably cool even when external air temperatures are hot.

Temporal vs. spatial variation in stress-associated metabolites within a population of climate-sensitive small mammals

Temporal variation in stress might signify changes in an animal's internal or external environment, while spatial variation in stress might signify variation in the quality of the habitats that individual animals experience. Habitat-induced variations in stress might be easiest to detect in highly territorial animals, and especially in species that do not take advantage of common strategies for modulating habitat-induced stress, such as migration (escape in space) or hibernation (escape in time). Spatial and temporal variation in response to potential stressors has received little study in wild animals, especially at scales appropriate for relating stress to specific habitat characteristics. Here, we use the American pika (Ochotona princeps), a territorial small mammal, to investigate stress response within and among territories. For individually territorial animals such as pikas, differences in habitat quality should lead to differences in stress exhibited by territory owners. We indexed stress using stress-associated hormone metabolites in feces collected non-invasively from pika territories every 2 weeks from June to September 2018. We hypothesized that differences in territory quality would lead to spatial differences in mean stress and that seasonal variation in physiology or the physical environment would lead to synchronous variation across territories through time. We used linear mixed-effects models to explore spatiotemporal variation in stress using fixed effects of day-of-year and broad habitat characteristics (elevation, aspect, site), as well as local variation in habitat characteristics hypothesized to affect territory quality for this saxicolous species (talus depth, clast size, available forage types). We found that temporal variation within territories was greater than spatial variation among territories, suggesting that shared seasonal stressors are more influential than differences in individual habitat quality. This approach could be used in other wildlife studies to refine our understanding of habitat quality and its effect on individual stress levels as a driver of population decline.

Conservation status of American pikas (Ochotona princeps)

The American pika (Ochotona princeps) is commonly perceived as a species that is at high risk of extinction due to climate change. The purpose of this review is two-fold: to evaluate the claim that climate change is threatening pikas with extinction, and to summarize the conservation status of the American pika. Most American pikas inhabit major cordilleras, such as the Rocky Mountain, Sierra Nevada, and Cascade ranges. Occupancy of potential pika habitat in these ranges is uniformly high and no discernible climate signal has been found that discriminates between the many occupied and relatively few unoccupied sites that have been recently surveyed. Pikas therefore are thriving across most of their range. The story differs in more marginal parts of the species range, primarily across the Great Basin, where a higher percentage of available habitat is unoccupied. A comprehensive review of Great Basin pikas revealed that occupied sites, sites of recent extirpation, and old sites, were regularly found within the same geographic and climatic space as extant sites, and suggested that pikas in the Great Basin tolerated a broader set of habitat and climatic conditions than previously understood. Studies of a small subset of extirpated sites in the Great Basin and in California found that climate variables (most notably measures of hot temperature) were associated more often with extirpated sites than occupied sites. Importantly, upward contraction of the lower elevation boundary also was found at some sites. However, models that incorporated variables other than climate (such as availability of upslope talus habitat) often were better predictors of site persistence. Many extirpations occurred on small habitat patches, which were subject to stochastic extinction, as informed by a long-term pika metapopulation study in Bodie, California. In addition, several sites may have been compromised by cattle grazing or other anthropogenic factors. In contrast, several low, hot sites (Bodie, Mono Craters, Craters of the Moon National Monument and Preserve, Lava Beds National Monument, Columbia River Gorge) retain active pika populations, demonstrating the adaptive capacity and resilience of pikas in response to adverse environmental conditions. Pikas cope with warm temperatures by retreating into cool interstices of their talus habitat and augment their restricted daytime foraging with nocturnal activity. Pikas exhibit significant flexibility in their foraging tactics and are highly selective in their choice of available vegetation. The trait that places pikas at greatest risk from climate change is their poor dispersal capability. Dispersal is more restricted in hotter environments, and isolated low-elevation sites that become extirpated are unlikely to be recolonized in a warming climate. The narrative that American pikas are going extinct appears to be an overreach. Pikas are doing well across most of their range, but there are limited, low-elevation losses that are likely to be permanent in what is currently marginal pika habitat. The resilience of pikas in the face of climate change, and their ability or inability to persist in marginal, hot environments, will continue to contribute to our understanding of the impact of climate change on individual species.

Identification of a contact zone and hybridization for two subspecies of the American pika (Ochotona princeps) within a single protected area

Genetic variation is the basis upon which natural selection acts to yield evolutionary change. In a rapidly changing environment, increasing genetic variation should increase evolutionary potential, particularly for small, isolated populations. However, the introduction of new alleles, either through natural or human-mediated processes, may have unpredictable consequences such as outbreeding depression. In this study, we identified a contact zone and limited gene flow between historically separated genetic lineages of American pikas (Ochotona princeps), representing the northern and southern Rocky Mountain subspecies, within Rocky Mountain National Park. The limited spatial extent of gene flow observed may be the result of geographic barriers to dispersal, selection against hybrid individuals, or both. Our fine-scale population genetic analysis suggests gene flow is limited but not completely obstructed by extreme topography such as glacial valleys, as well as streams including the Colorado River. The discovery of two subspecies within this single protected area has implications for monitoring and management, particularly in the light of recent analyses suggesting that the pikas in this park are vulnerable to fragmentation and local extinction under future projected climates. Future research should focus on the fitness consequences of introgression among distinct genetic lineages in this location and elsewhere, as well as within the context of genetic rescue as a conservation and management strategy for a climate sensitive species.