Aim We investigate the Plio‐Pleistocene evolutionary history of one of the most abundant rodents in Afrotropical forests. Specifically, we ask how their diversification was influenced by climate change, topography and major rivers. Location Tropical Africa: Lower Guinea (including Cameroon volcanic line; CVL), Congolia, Albertine Rift (AR), Kenyan highlands (KH). Taxon Murine rodents of the Praomys jacksoni complex. Methods We used 849 genotyped individuals to describe the overall diversity and spatial genetic structure across a majority of their known distribution area. The combination of one mitochondrial and three nuclear markers was used to infer dated phylogenies using Bayesian and maximum likelihood approaches. Genetic structure was further assessed by multispecies coalescent species delimitation. Current and past distributions of particular taxa were predicted using environmental niche modelling. Results The complex is composed of five major genetic clades (proposed species). Two of them are restricted to specific habitat types (either montane forests of AR or wetlands in lowland forests along the Congo River), three others have wide geographic distributions and lower levels of ecological specialization. The earliest divergence is dated to the Plio‐Pleistocene boundary and is in accordance with the separation of AR forests and Guineo‐Congolian forests. Further diversification of the complex is associated with Pleistocene climate changes. Relatively stable refugia of suitable climatic conditions were identified in lowland Congolia (for two species currently distributed only in lowland forests) as well as in montane forests of CVL, AR, KH (playing the role of reservoirs of diversity). Large rivers, especially the Congo River, are important barriers to gene flow for most taxa, but probably were not the primary cause of differentiation. Main conclusions The evolutionary history of the complex was primarily affected by Pleistocene climate changes and diversification in forest refugia. There is little support for ecological parapatric speciation or the riverine barrier hypothesis.

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Several rodent genera radiated in Ethiopian highlands during Pleistocene, giving rise to species specialized to different elevation zones. The zonation is accompanied by vegetation change from savannahs or forests in lower elevations, through the mid-elevation belt of ericaceous shrublands to Afroalpine moorlands on the mountain tops. Such evolution on elevation gradient is expected to promote phenotypic adaptations and several genera are known to include highly distinctive high-elevation specialists. In this study, we systematically examined shape and size differentiation of skull and mandible in three genera, Lophuromys, Arvicanthis and Stenocephalemys, each including from six to eight species inhabiting different elevation zones on both sides of the Great Rift Valley. Employing computed tomography, three-dimensional virtual models, landmark-based geometric morphometrics and a powerful toolkit of partial least squares analysis, we demonstrated the elevation-related differentiation is a prominent feature of skull and mandible shape variation in all three genera. We identified the parts of skull and mandible which change most between the successive zones. These include, notably, orbits and insertion areas of masticatory muscles, which suggests adaptive shifts in visual perception and diet. We also showed that while the same parts are modified in all three genera, they are modified in different ways and to a different degree. The evidence for size differentiation was mixed despite the universal trend of larger size in higher elevations. Our study confirms the high-elevation specialists represent the most distinctive forms, which is especially true for the species from Bale and Arsi Mountains, East of the Great Rift Valley.