Abstract:
BACKGROUND: Intraspecific variation within the diverse southern African murine rodents has not been extensively
investigated, yet cryptic diversity is evident in several taxa studied to date. The Namaqua rock mouse, Micaelamys
namaquensis Smith, 1834 is a widespread endemic murine rodent from the subregion. Currently, a single species
with four subspecies is recognised, but in the past up to 16 subspecies were described. Thus, this species is a
good candidate for the investigation of patterns and processes of diversification in a diverse but under-studied
mammalian subfamily and geographic region. Here, we report genetic differentiation based on mitochondrial DNA
(mtDNA) cytochrome b (cyt b) sequences among samples collected over an extensive coverage of the species’
range.
RESULTS: Cytochrome b sequences of 360 widely sampled individuals identified 137 unique maternal alleles. Gene
tree and phylogeographic analyses of these alleles suggest the presence of at least eight lineages or haplogroups
(A-H), with varying degrees of intra-lineage diversity. This differentiation is in contrast with the most recent
taxonomic treatment based on cranial morphometrics which only recognised four subspecies. The mtDNA diversity
strongly supports earlier views that this taxon may represent a species complex. We further show statistical support
for the association of several of these lineages with particular vegetation biomes of southern Africa. The time to
the most recent common ancestor (TMRCA) dates to the Pliocene (~5 Mya) whereas coalescent-based divergence
time estimates between lineages vary between 813 Kya [0.22 - 1.36] and 4.06 Mya [1.21 - 4.47]. The major
diversification within lineages occurred during the Pleistocene. The identification of several regions of sympatry of
distinct lineages offers future opportunities for the elucidation of the underlying speciation processes in the
suggested species complex.
CONCLUSIONS: Similar to other African murine rodents, M. namaquensis radiated during the Pliocene and
Pleistocene coinciding with major periods of aridification and the expansion of savanna habitats. The suggested
species complex is represented by at least eight lineages of which the majority are confined to only one or a few
neighbouring biomes/bioregions. Contrasting intra-lineage phylogeographic patterns suggest differences in
adaptation and responses to Plio-Pleistocene climatic and vegetation changes. The role of ecological factors in
driving speciation in the group needs further investigation.
