Assessing Genetic Diversity and Inbreeding Effects in an Endangered Amphibian: Effects of Ecological Restoration and Stochasticity

ABSTRACT The application of population genetic metrics to evaluate the health of a population after undergoing anthropogenic management and experiencing environmental stochasticity remains underexplored in amphibians. Several metrics can be used to measure loss of genetic diversity and decreased gene flow to determine population health, including heterozygosity, inbreeding, and structure. This study assessed the genetic health of the endangered frog, Rawlinsonia littlejohni using genetic metrics in a population exposed to human modifications (dam creation) and extreme climatic events (droughts followed by heavy rainfall). We detected strong population structuring, with two distinct sub‐populations located only 2.5 km apart but exhibiting limited gene flow. Genetic differentiation between these sub‐populations, determined by PCoA analysis, decreased after high rainfall in 2021, but returned during drought conditions in 2023, indicating that environmental conditions influence dispersal dynamics. The northern sub‐population, which includes both constructed ponds and natural creek pools, exhibited significantly higher heterozygosity and lower mean kinship. In contrast, the southern sub‐population, dominated by constructed ponds and lacking natural creek connectivity, showed reduced heterozygosity and a marked increase in inbreeding (0.003 in 2020 to 0.162 in 2023). These finding suggest that limited connectivity is constraining gene flow and contributing to reduced genetic health in the southern sub‐population. We propose that additional ponds spaced between sub‐populations may act as stepping‐stones to enhance connectivity and reduce inbreeding. However, our results reveal a key conservation trade‐off: constructed ponds support breeding and population persistence, while natural stream systems facilitate dispersal and genetic connectivity. These findings highlight that restoring long‐term population viability will require multiple, complementary management actions that balance breeding habitat provision with landscape connectivity.