Integrating Genomics into the Genetic Management of the Endangered Mountain Yellow-Legged Frog

Abstract

Abstract 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. The San Diego Zoo Wildlife Alliance established an ex situ breeding program for the endangered southern mountain yellow-legged frog (Rana muscosa), including two separately populations from the San Jacinto and San Bernardino mountain ranges. In this study, we conducted molecular population genetic assessments using double digest restriction site-associated DNA sequencing data to provide improved breeding recommendations for the managed R. muscosa populations. We found that genetic diversity of ex situ populations was relatively low (HO = 0.166–0.245) and population differentiation moderate (FST = 0.29). Patterns of genetic structure of captive frogs supported the evolutionary divergence of individuals by mountain ranges in the wild, with limited gene flow. Relatedness estimates identified close relatives among the founders, and molecularly-derived kinship values were used to determine and rank suitable breeders to minimize population mean kinship. Management recommendations highlight the need for importing additional founders from the wild to enhance genetic diversity in the breeding program, as effective source for genetic restoration.