Ain't no mountain high enough, ain't no valley low enough? Phylogeography of the rupicolous Cape girdled lizard (Cordylus cordylus) reveals a generalist pattern

In the present study we examined the phylogeography of the rupicolous Cape girdled lizard, Cordylus cordylus. Samples were collected from 63 localities across the species distribution range in the Eastern and Western Cape and Free State provinces of South Africa, yielding a total sample size of 207 specimens. Four partial DNA loci, two mitochondrial (16S rRNA and ND2) and two nuclear (PRLR and PTPN12), were sequenced. Bayesian inference, maximum likelihood and maximum parsimony methods were employed to test evolutionary relationships among populations, followed by population structure analyses, divergence time estimations and niche modelling. Our results confirm the species monophyly and revealed the presence of two distinct clades. Clade 1 comprised specimens from the western and southern portions of the Western Cape coast, while clade 2 comprised specimens from the southern and eastern Cape coast and adjacent interior of the Eastern and Western Cape and Free State provinces. An area of sympatry between the two clades was observed in the Breede river valley. The divergence time estimates revealed an Early Pliocene (4.31 Ma), Late Miocene (6.01 Ma) divergence for each of the two clades retrieved. Phylogeographic data suggest that clade 1 coalesced more recently (lower haplotypic and nucleotide diversity), when compared to clade 2. Furthermore, the niche modelling shows that C. cordylus occupies a wide range of unfavourable habitats, though slight niche differentiation was observed for each clade. The absence of marked phylogeographic patterning within clades is very uncharacteristic for a rupicolous vertebrate species. The ecological pliability and generalist nature of C. cordylus presumably contributed to the observed phylogeographic pattern and have facilitated the absence of within clade differentiation. Moreover, we suggest that microclimatic variables, rather than geographic barriers influence the genetic structuring of C. cordylus.