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 a highly fragmented habitat created by hard rock mining, the ore dumps at this site were likely colonized by pikas at 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, 1988-1991, 2013-2015). In addition to declines in within-population allelic diversity and expected heterozygosity, we observed an increase in population structure and a reduction in effective population size from more extensive sampling of extant patches during 1988-1991 and 2013-2015, respectively. Furthermore, census records from the last 50 years as well as archived museum samples collected in 1947 from a nearby pika population in the Wassuk range (NV, USA) provide further support for 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.

We  include two datasets. (1) Tissue samples were collected from live-trapped animals and museum specimens. We also collected fecal material. Genomic DNA was isolated from all samples and PCR amplified using 7 nuclear microsatellite loci. Alleles were generated using an ABI 3730 DNA sequencer. These genotype data were then analyzed using population genetic methods. (2) Annual pika census and occupancy data for 75-82 habitat patches from 1972-2022.

Census data was added for Version 2.