A decade of genetic monitoring reveals increased inbreeding for the Endangered western leopard toad, Sclerophrys pantherina

Genetic diversity provides the capacity for species to evolve in response to environmental change, and its importance in assessing the status of species is well established. However, there is a paucity of genetic monitoring studies. The Endangered western leopard toad (Sclerophrys pantherina), endemic to South Africa, is a good candidate for genetic monitoring, due to its restricted distribution consisting of two disjunct populations (within the City of Cape Town (CoCT) and the Overstrand), with the CoCT population having experienced more drastic habitat alteration due to urbanisation, and presumably a large population decline. To establish a baseline for genetic monitoring, we examined the change in genetic diversity and structure within the CoCT population across two time periods (2008 and 2018) using 12 microsatellite markers. Despite monitoring occurring over only four generations, there is evidence of increased inbreeding and a shift in the genetic structure. These changes are likely due to previous, severe impacts on the population, with 91% of natural habitat lost in the study area. There is also evidence of at least three historical bottlenecks that are likely the initial cause of inbreeding, with extreme habitat loss in the twentieth century leading to the genetic changes detected within the last decade. Although declines in allelic richness were not detected, the inbreeding and change in genetic structure can be considered early warning signs of genetic erosion, even over a short monitoring interval. This provides a baseline for future monitoring, with the ultimate goal of tracking long-term trends to guide conservation actions.