Mammalian Biology, 91 (2018): 79-90
Despite the high degree of biological diversity in the Zambezian region, little information is available regarding the evolutionary history of its biota, and this is especially true for the fauna and flora of non-forested habitats. Here we use the most comprehensive multi-locus genetic dataset available to (1) reconstruct the phylogeny of spiny mice of the Acomys spinosissimus complex and to describe the spatial distribution of its genetic diversity; (2) to assess the level of reproductive isolation between genetic clades; (3) to analyse differences in climatic niche between potential species; and (4) to model their current and past distribution. The complex comprises four main genetic clades that correspond to four nominal species living in the east of the Zambezian region. Their distribution is delimited by important geographical divides including the Eastern Arc Mountains, Lake Malawi and the Zambezi River. Two species considered Tanzanian endemics, A. ngurui and A. muzei, are now known to be more widespread than previously thought and they have their centres of genetic diversity just north of the Zambezi. The first split between the extant members of the A. spinosissimus complex is estimated at 3 Mya. Most intraspecific diversification events are thought to have occurred in the Pleistocene, suggesting that climatic oscillations played an important role in their diversification. The climatic niches of parapatric taxa differ significantly; hence, local adaptations have likely played an important role in reproductive isolation. Species distribution modelling predicts a dramatic reduction of occurrence probability across the area during the last interglacial period, facilitating allopatric diversification of fragmented populations. Our results strongly suggest the combined role of Pleistocene climatic change, biogeographical barriers and local adaptation in forming current taxa diversity in east African savannah-like habitats. While such processes have frequently been observed in forest-living organisms (theory of allopatric diversification in forest refugia), similar mechanisms were likely also working in open ecosystems ("savannah refugia").