The African Mole‐Rat Genus Cryptomys and Its Species: Distinct in Their Genes and Habitats

ABSTRACT The African mole‐rat genus Cryptomys comprises five morphologically cryptic lineages distributed across South Africa and in Zimbabwe, historically treated as subspecies of C. hottentotus ( C. h. hottentotus , C. h. mahali , C. h. natalensis , C. h. pretoriae and C. h. nimrodi ). Despite extensive ecological and physiological research, their taxonomic status and evolutionary relationships have remained unresolved because of limited genetic data. Here, we integrate mitochondrial and genome‐wide nuclear data, broad geographic sampling and environmental niche modelling to reassess species limits and diversification history within the genus. Our analyses recover five deeply divergent, reciprocally monophyletic and strongly supported evolutionary lineages corresponding to C. hottentotus , C. mahali , C. natalensis , C. pretoriae and C. nimrodi , which we interpret as distinct species despite limited gene flow in parapatry. Divergence dating indicates a Plio–Pleistocene origin of extant diversity, with an initial split between C. hottentotus and the remaining lineages at ~2.8 Ma (2.0–3.5 Ma). Short internal branches and discordance between mitochondrial and nuclear phylogenies suggest near‐polytomous split among C. mahali , C. nimrodi and the ancestor of C. natalensis + C. pretoriae , followed by the divergence of C. natalensis and C. pretoriae . Species distributions are largely parapatric and structured along environmental gradients, particularly precipitation and soil properties, rather than by strong physical barriers. Environmental niche models further reveal clear ecological differentiation with relatively limited interspecific overlap. Together, these results resolve long‐standing taxonomic uncertainty within Cryptomys and demonstrate that the genus comprises five independently evolving species shaped by rapid Pliocene–Pleistocene diversification and ecological divergence.