We sampled 187 adult or sub-adult Belding’s ground squirrels at 15 sites across California from Modoc County to the southern Sierra Nevada from 2003 to 2011, with the majority of samples obtained in 2010 and 2011. Ground squirrels were trapped in Sherman or Tomahawk Live Traps. Genetic samples were collected through an ear snip or from a liver biopsy during preparation of museum skins. DNA was extracted using standard methods and amplified using ten polymorphic microsatellite loci optimized from protocols developed based on other sciurid species. We tested for and, where necessary, adjusted for null alleles, as well as Hardy-Weinberg equilibrium, and linkage disequilibrium. To assign individuals to populations, we ran an analysis in STRUCTURE 2.3.4, first across the entire study area based on the 15 sampling sites. Initially we split state-wide samples into four major areas: Northern California, Tahoe area, Yosemite, and southern Sierras. Then these four subpopulations were iteratively run until samples grouped into a single genetic population (i.e., K = 1 had the strongest support based on the method by Evanno et al). Each run was replicated ten times with K set from 1 to 8 populations, with an initial burn-in of 10,000 iterations followed by 106 Markov chain Monte Carlo repetitions.
