Integrating genomics and evolution into the conservation and breeding management of a Threatened Australian frog

Conservation Breeding Programs (CBPs) are an increasingly important tool for conserving biodiversity in a rapidly changing world, with genomic approaches playing a critical role in managing genetic diversity and minimising the risks of inbreeding and outbreeding depression. The Southern Stuttering Frog ( Mixophyes australis ) is a threatened ground-dwelling amphibian native to eastern Australia, which is currently the focus of a CBP designed to secure an insurance population and reintroduce the species to their historic range. As a newly described threatened species with a recently established CBP, M. australis provides an ideal case study for demonstrating how genomic data can inform and direct conservation management decisions. Here, we integrate genome-wide single nucleotide polymorphism (SNP) data from founders of the CBP alongside samples from wild populations to assess population structure, genetic diversity, and relatedness among individuals used in the CBP. Using evolutionary methods, we uncover patterns of gene flow and quantify differentiation between wild populations, identifying structuring between geographically distinct northern and southern populations of M. australis and translating these findings into management recommendations. We compare genetic diversity metrics, illustrating how these metrics can be used to assess populations genetic health and adaptive potential. Finally, we demonstrate how genomic data can characterise founder relatedness when pedigree data is unavailable and compare widely used relatedness estimators, providing managers with an informed framework for future mate-pairings. Overall, our study provides a foundation for the long-term genetic management of a threatened frog species, and highlights the value of evolution and genomics in conservation assessments