Unmasking evolutionary diversity among two closely related South African legless skink species (Acontinae: Acontias) using molecular data

We examined species boundaries among two phylogenetically closely related and morphologically similar South African fossorial legless skink species, Acontias breviceps and Acontias gracilicauda. Samples of these two species were collected throughout their distribution ranges and sequenced for three DNA loci (two mitochondrial loci, 16S rRNA and cytochrome b (Cyt b), plus the nuclear locus prolactin). Phylogenetic relationships were determined using maximum parsimony, Bayesian inference and maximum likelihood analyses of the combined DNA sequence data set. The total evidence topology retrieved two paraphyletic clades in both Acontias species with strong statistical support. The phylogenetic results revealed that A. breviceps specimens from the Eastern Cape Province were basal (Clade 1), while the Highveld specimens of A. breviceps from the Mpumalanga Province (Clade 2) were retrieved as sister to A. gracilicauda (Clade 1). In addition, the A. gracilicauda specimens from the interior of the Northern Cape Province (Clade 2) were found embedded within the A. occidentalis species complex. These clades were characterised by marked sequence divergence for the Cyt b locus. Furthermore, no maternal or nuclear haplotypes were shared between clades within both A. breviceps and A. gracilicauda, alluding to genetic and reproductive isolation. The results provide overwhelming evidence to assign A. breviceps from the Mpumalanga Highveld to a novel species. Further sampling is required to accurately delineate species boundaries within A. gracilicauda. The conservation implications of our results are briefly discussed.