The Greater Maputaland-Pondoland-Albany (GMPA) region of southern Africa was recently
designated as a centre of vertebrate endemism. The phylogeography of the vertebrate taxa
occupying this region may provide insights into the evolution of faunal endemism in southeastern
Africa. Here we investigate the phylogeographic patterns of an understudied small
mammal species assemblage (Amblysomus) endemic to the GMPA, to test for cryptic diversity
within the genus, and to better understand diversification across the region.We sampled
specimens from 50 sites across the distributional range of Amblysomus, with
emphasis on the widespread A. hottentotus, to analyse geographic patterns of genetic
diversity using mitochondrial DNA (mtDNA) and nuclear intron data. Molecular dating was
used to elucidate the evolutionary and phylogeographic history of Amblysomus. Our phylogenetic
reconstructions show that A. hottentotus comprises several distinct lineages, or
evolutionarily significant units (ESUs), some with restricted geographic ranges and thus
worthy of conservation attention. Divergence of the major lineages dated to the early Pliocene,
with later radiations in the GMPA during the late-Pliocene to early-Pleistocene. Evolutionary
diversification within Amblysomus may have been driven by uplift of the Great
Escarpment c. 5–3 million years ago (Ma), habitat changes associated with intensification
of the east-west rainfall gradient across South Africa and the influence of subsequent global
climatic cycles. These drivers possibly facilitated geographic spread of ancestral lineages,
local adaptation and vicariant isolation. Our study adds to growing empirical evidence identifying
East and southern Africa as cradles of vertebrate diversity.
S1 Fig. Maximum Likelihood and Bayesian gene trees.
S2 Fig. Divergence dating tree with outgroups included.
S3 Fig. Population-level coalescent analyses.
S1 Table. Sample information for all Amblysomus samples used in this study.
S2 Table. Estimates of evolutionary divergence over sequence pairs between clades.