Integrating genomics into the genetic management of the endangered mountain yellow-legged frog

Conservation breeding programs have long been an important management tool for species recovery. Recently, breeding programs have begun to integrate next generation sequencing data into pedigree-based management strategies designed to maximize retention of genetic diversity and minimize inbreeding. In 2005, an ex situ breeding program for two of the three extant, geographically separate populations of the endangered southern mountain yellow-legged frog (Rana muscosa) was established at the San Diego Zoo Wildlife Alliance. To provide improved breeding recommendations for the species, we conducted molecular population genetic assessments using double digest restriction site-associated DNA sequencing data. We first studied genetic diversity, population differentiation, and genetic structure of wild frogs to validate the status of management units in R. muscosa. Genetic diversity was relatively low (H_O = 0.166–0.245), population differentiation moderate (F_ST = 0.29), and patterns of genetic structure and admixture supported the evolutionary divergence of frogs by mountain ranges with limited gene flow. In the breeding program, relatedness estimates identified close relatives amongst the founders, and molecularly-derived kinship values were used to determine and rank suitable breeders to minimize population mean kinship. Ex situ management recommendations highlight the need for importing additional founders from the wild to enhance genetic diversity in the breeding program, as an effective source for genetic restoration. Alternatively, the use of advanced reproductive technologies to capture wild diversity without removal of individuals from the wild seem promising.