Diversification of the African legless skinks in the subfamily Acontinae (Family Scincidae)

[Display omitted] •A large-scale study investigating the complex genetic structure, species boundaries, evolutionary relationships, and diversification among all the species in the subfamily Acontinae.•The subfamily Acontinae is an African group of legless skinks which consists of multiple species complexes.•This study resolved many long-standing phylogenetic enigmas and clarified many blurry species boundaries within the subfamily Acontinae in general and within its species complexes.•Lineage diversification is associated with Miocene climatic oscillations, epeirogenic uplift, expansion of open habitats, variable rainfall patterns, and the presence of the warm Agulhas Current since the early Miocene, as well as their co-effects.•Possible “ghost introgression” and interspecies gene flow was detected in the subfamily Acontinae. Cladogenic diversification is often explained by referring to climatic oscillations and geomorphic shifts that cause allopatric speciation. In this regard, southern Africa retains a high level of landscape heterogeneity in vegetation, geology, and rainfall patterns. The legless skink subfamily Acontinae occurs broadly across the southern African subcontinent and therefore provides an ideal model group for investigating biogeographic patterns associated with the region. A robust phylogenetic study of the Acontinae with comprehensive coverage and adequate sampling of each taxon has been lacking up until now, resulting in unresolved questions regarding the subfamily’s biogeography and evolution. In this study, we used multi-locus genetic markers (three mitochondrial and two nuclear) with comprehensive taxon coverage (all currently recognized Acontinae species) and adequate sampling (multiple specimens for most taxa) of each taxon to infer a phylogeny for the subfamily. The phylogeny retrieved four well-supported clades in Acontias and supported the monophyly of Typhlosaurus. Following the General Lineage Concept (GLC), many long-standing phylogenetic enigmas within Acontias occidentalis and the A. kgalagadi, A. lineatus and A. meleagris species complexes, and within Typhlosaurus were resolved. Our species delimitation analyses suggest the existence of hidden taxa in the A. occidentalis, A. cregoi and A. meleagris species groups, but also suggest that some currently recognized species in the A. lineatus and A. meleagris species groups, and within Typhlosaurus, should be synonymised. We also possibly encountered “ghost introgression” in A