Tracking the impact of Pliocene/Pleistocene sea level and climatic oscillations on the cladogenesis of the Cape legless skink, Acontias meleagris species complex, in South Africa

AIM: To determine the geographical boundaries among cryptic lineages and examine the evolutionary drivers of cladogenesis within the Cape legless skink, Acontias meleagris species complex. LOCATION: Coastal plains and adjacent interior of the Eastern, Northern and Western Cape provinces of South Africa. METHODS: A total of 231 specimens from 55 localities were collected from the entire known distribution range of the A. meleagris complex. Partial sequence data were collected from two mitochondrial DNA loci, 16S rRNA and cytochrome c oxidase subunit I (COI), and one protein‐coding nuclear DNA locus, exophilin 5 (EXPH5). Phylogenetic, phylogeographical and population genetic analyses, together with divergence time estimation, were conducted on the DNA sequence data to examine evolutionary history and diversification within the species complex. RESULTS: Marked genetic structure was observed within the A. meleagris complex, and five clades were retrieved, most of which were statistically well supported. These five clades were also evident within the haplotypic analyses and were characterized by demographic stability. Cladogenesis was induced during the Pliocene/Pleistocene epochs, most likely as a result of oscillations in climate and sea level, and Neogene geomorphic phenomena. The Breede River Valley is an area of high genetic diversity and is likely to have served as a refugium. MAIN CONCLUSIONS: Lineage diversification and the current biogeographical patterning reflect the impact of sea level oscillations on historical coastal habitat availability. Fine‐scale differences between co‐distributed subterranean and supraterranean herpetofaunal taxa can be attributed to differences in life‐history traits amongst different habitat types. Historical evolutionary drivers within this subterranean species complex are inferred and discussed.