Phylogenomic and demographic history of the Cape cliff lizard ( Hemicordylus capensis )

Hemicordylus capensis, the Cape cliff lizard, is endemic to South Africa and occurs across the entire range of the Cape Fold Mountains. Despite previously reported phenotypic variation among populations, the species’ population structure and evolutionary history remain poorly resolved. Here, we conducted population genomic and phylogenomic analyses using whole-genome resequencing data from 64 individuals representing 18 populations spanning the species’ entire distribution. We uncovered five major lineages whose genetic relationships broadly mirror geography and landscape connectivity. Demographic reconstructions reveal contrasting histories among clades, with evidence of expansion in the Cederberg lineage coinciding with higher inferred connectivity, whereas other lineages show stronger isolation and reduced genetic diversity. We also detect signatures of historical gene flow and mitonuclear discordance among several populations. Overall, our results provide a genomic and biogeographic framework for understanding diversification in H. capensis across the Cape Fold Mountains and for interpreting patterns of genetic and phenotypic variation across its range.