Analysis of genetic diversity in Rose’s mountain toadlet (Capensibufo rosei) using novel microsatellite markers

Abstract On the Cape Peninsula, Capensibufo rosei is known from only two isolated breeding populations within Table Mountain National Park. Because of its declining state, there is an urgent need to understand the genetic diversity, population structure and patterns of movement of this species. To do this, 15 microsatellite primer pairs were designed, optimised and tested. Successful loci were screened for null alleles and genotyping errors and then analysed, specifically noting the number of alleles, allelic size range, observed and expected heterozygosities, deviations from Hardy–Weinberg equilibrium (HWE) and linkage disequilibria. Bottleneck tests and analyses of molecular variance (AMOVA) were also conducted to gain insight into each population’s structure. Eleven primer pairs produced unambiguous polymerase chain reactions (PCR) products and scoreable bands, which were found to be polymorphic across both breeding populations. Deviations from HWE were detected owing to the presence of null alleles and inbreeding. Significant bottleneck signatures were detected for both populations and the AMOVA revealed significant differentiation between the two populations, indicating genetic structure at the population level.