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

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 pedigreebased 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 (H O = 0.166-0.245) and population differentiation moderate (F ST = 0.29). Patterns of genetic structure of captive frogs supported the evolutionary divergence of individuals by mountain ranges in the wild, with limited gene ow. Relatedness estimates identi ed 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. et al. 2002). Applying molecular tools to species management may also help to characterize population structure to de ne management units and estimate effective population size, inbreeding, and genetic load (Allendorf and O'Brien 2010). These estimates then can be used to make informed decisions about breeding of ex situ populations, and translocation for genetic restoration in the wild (Wilder et al. 2020).Recently, conservation breeding programs have started to bene t from the use of next generation sequencing technologies and bioinformatics for designing management strategies (Ivy and Lacy 2012;