Characterisation of microsatellite markers in the Spotted Sand Lizard (Pedioplanis lineoocellata) shows low levels of inbreeding and moderate genetic diversity on a small spatial scale

Abstract

Population genetic methods can be useful for understanding spatial genetic patterns, gene flow and diversity. While genetic markers such as gene sequences are useful for understanding broad scale phylogeographic patterns, microsatellite markers allow for inferences within species and on smaller spatial scales. Such data can then be used to glean information on biological processes at the landscape level. Because portions of southern Africa are predicted to be heavily impacted by climatic changes forecast for the next century, a better understanding of the biota at the species level would be beneficial for advancing knowledge on the southern African system. Therefore, we characterised 11 microsatellite markers for an arid adapted lacertid lizard, Pedioplanis lineoocellata, in order to obtain a microsatellite library for future studies. Five of 11 loci were out of Hardy-Weinberg (H-W) equilibrium, showing a homozygote excess. Frequency-based analysis suggested this is due to the presence of null alleles. We further investigated this using a model-based Bayesian approach to simultaneously estimate inbreeding, null alleles and random amplification failures. In contrast to the frequency-based approach, this method indicated that both inbreeding and random amplification failures, not null alleles, are the most significant components of the model for nine of 11 loci. Overall, the inbreeding coefficient was low, but not zero, suggesting that low levels of inbreeding contribute to H-W deviations. Finally, we examined whether population bottlenecks could be a factor in deviations from H-W using multiple methods, but found no evidence to suggest that bottlenecks have played a role.