Revisiting conservation units using multiple genomic methods for the endangered mountain yellow-legged frog species complex (Rana muscosa/sierrae)

Our study used two different sequencing strategies, amplicon-based sequencing and exome capture, to refine our understanding of the population genetics of these imperiled amphibians. We used buccal swabs, museum tissue samples, and archived skin swabs that to genotype frog populations across the range. By evaluating our two datasets and producing a combined dataset with complete geographic coverage, we document five major genetic clusters within this species complex. Notably, we found evidence supporting previous species boundaries within Kings Canyon National Park. Though we see evidence of genetic clustering, especially in the R. muscosa clade, we also found evidence of some admixture across cluster boundaries in the R. sierrae clade, suggesting a stepping-stone model of population structure. We also found that the southern R. muscosa cluster had large runs of homozygosity and the lowest overall heterozygosity of any of the clusters, aligning with previous reports of precipitous declines in this area. Overall, our results provide clarity on management units across the range of an endangered species and highlight the utility of genomic resolution and the importance of sampling design in conservation genetic studies.