New insights from RADseq data on differentiation in the Hottentot golden mole species complex from South Africa Samantha Mynhardta,b, Nigel C. Bennettb,c and Paulette Bloomera,c a Molecular Ecology and Evolution Programme, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa b Department of Zoology and Entomology, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa c Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa *Corresponding author at: Molecular Ecology and Evolution Programme, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa. Email;
[email protected] Highlights • Our results support Amblysomus hottentotus meesteri as a distinct divergent lineage. • Central coastal A. h. pondoliae is divergent from southern A. h. pondoliae. • Central coastal A. h. pondoliae may be worthy of specific or subspecific status. • Mito-nuclear discordance found in a cryptic mtDNA lineage from Umtata. • These cryptic lineages may be in need of conservation attention. Abstract Golden moles (Family Chrysochloridae) are small subterranean mammals, endemic to sub- Saharan Africa, and many of the 21 species are listed as threatened on the IUCN Red List. Most species have highly restricted ranges; however two species, the Hottentot golden mole (Amblysomus hottentotus) and the Cape golden mole (Chrysochloris asiatica) have relatively wide ranges. We recently uncovered cryptic diversity within A. hottentotus, through a phylogeographic analysis of this taxon using two mitochondrial gene regions and a nuclear intron. To further investigate this cryptic diversity, we generated nuclear SNP data from across the genome of A.