The phylogeography of the rodent genus Malacomys suggests multiple Afrotropical Pleistocene lowland forest refugia

Aim: This study aims to reconstruct the evolutionary history of the African rodent genus Malacomys and to identify factors driving diversification within this genus. Location: African tropical lowland forest. Methods: Analyses were based on sampling representatives from most of the known geographical range of the genus. We assessed genetic structure and historical biogeography using a combination of mitochondrial and nuclear markers. Morphological differences between lineages were analysed using a geometric morphometric approach. Results: Three species of Malacomys are recognized within the genus. Two are endemic to West Africa, and one is endemic to Central Africa. Our analyses reveal a strong phylogeographical structure with 13 lineages, most of them allopatric or parapatric. A complex biogeographical history, including dispersal-vicariance events, explains the current genetic structure of Malacomys. Discrete divergence events within the genus are dated to the mid-Pliocene (3.7 Ma, 95% range: 2.4-5.2 Ma) and the Pleistocene (less than 1.9 Ma, with most events less than 1 Ma). Morphological variation is partly congruent with genetic structure and may indicate local adaptations. Main conclusions: Climatic oscillations, which led to periodic fragmentation of the forest habitat, seem to be the major driver of diversification within this genus. Our results support the existence of multiple small, rather than a few large, forest refugia during glacial maxima. Rivers have played a significant role in shaping boundaries of several regional haplogroups, either by promoting diversification or by preventing secondary contact between previously isolated lineages.