Esther Levy, W. Jason Kennington, Joseph L. Tomkins, Natasha R. LeBas

Species inhabiting ancient, geologically stable landscapes that have been impacted by agriculture and urbanisation are expected to have complex patterns of genetic subdivision due to the influence of both historical and contemporary gene flow. Here, we investigate genetic differences among populations of the granite outcrop-dwelling lizard Ctenophorus ornatus, a phenotypically variable species with a wide geographical distribution across the south-west of Western Australia. Phylogenetic analysis of mitochondrial DNA sequence data revealed two distinct evolutionary lineages that have been isolated for more than four million years within the C. ornatus complex. This evolutionary split is associated with a change in dorsal colouration of the lizards from deep brown or black to reddish-pink. In addition, analysis of microsatellite data revealed high levels of genetic structuring within each lineage, as well as strong isolation by distance at multiple spatial scales. Among the 50 outcrop populations' analysed, non-hierarchical Bayesian clustering analysis revealed the presence of 23 distinct genetic groups, with outcrop populations less than 4 km apart usually forming a single genetic group. When a hierarchical analysis was carried out, almost every outcrop was assigned to a different genetic group. Our results show there are multiple levels of genetic structuring in C. ornatus, reflecting the influence of both historical and contemporary evolutionary processes. They also highlight the need to recognise the presence of two evolutionarily distinct lineages when making conservation management decisions on this species.