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BackgroundRodents of the genus Mus represent one of the most valuable biological models for biomedical and evolutionary research. Out of the four currently recognized subgenera, Nannomys (African pygmy mice, including the smallest rodents in the world) comprises the only original African lineage. Species of this subgenus became important models for the study of sex determination in mammals and they are also hosts of potentially dangerous pathogens. Nannomys ancestors colonized Africa from Asia at the end of Miocene and Eastern Africa should be considered as the place of their first radiation. In sharp contrast with this fact and despite the biological importance of Nannomys, the specimens from Eastern Africa were obviously under-represented in previous studies and the phylogenetic and distributional patterns were thus incomplete.ResultsWe performed comprehensive genetic analysis of 657 individuals of Nannomys collected at approximately 300 localities across the whole sub-Saharan Africa. Phylogenetic reconstructions based on mitochondrial (CYTB) and nuclear (IRBP) genes identified five species groups and three monotypic ancestral lineages. We provide evidence for important cryptic diversity and we defined and mapped the distribution of 27 molecular operational taxonomic units (MOTUs) that may correspond to presumable species. Biogeographical reconstructions based on data spanning all of Africa modified the previous evolutionary scenarios. First divergences occurred in Eastern African mountains soon after the colonization of the continent and the remnants of these old divergences still occur there, represented by long basal branches of M. (previously Muriculus) imberbis and two undescribed species from Ethiopia and Malawi. The radiation in drier lowland habitats associated with the decrease of body size is much younger, occurred mainly in a single lineage (called the minutoides group, and especially within the species M. minutoides), and was probably linked to aridification and climatic fluctuations in middle Pliocene/Pleistocene.ConclusionsWe discovered very high cryptic diversity in African pygmy mice making the genus Mus one of the richest genera of African mammals. Our taxon sampling allowed reliable phylogenetic and biogeographic reconstructions that (together with detailed distributional data of individual MOTUs) provide a solid basis for further evolutionary, ecological and epidemiological studies of this important group of rodents.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-014-0256-2) contains supplementary material, which is available to authorized users.

Aim Grammomys are mostly arboreal rodents occurring in forests, woodlands and thickets throughout sub‐Saharan Africa. We investigated whether the divergence events within the genus follow the existing evolutionary scenario for the development of African forests since the late Miocene. Location Sub‐Saharan African forests and woodlands. Methods We inferred the molecular phylogeny of Grammomys using Bayesian and maximum likelihood methods and DNA sequences of 351 specimens collected from across the distribution of the genus. We mapped the genetic diversity, estimated the divergence times by a relaxed clock model and compared evolution of the genus with forest history. Results Phylogenetic analysis confirms the monophyly of Grammomys and reveals five main Grammomys lineages with mainly parapatric distributions: (1) the poensis group in Guineo‐Congolese forests; (2) the selousi group with a distribution mainly in coastal forests of southern and eastern Africa; (3) the dolichurus group restricted to the easternmost part of South Africa; (4) the macmillani group in the northern part of eastern and Central Africa with one isolated species in Guinean forests; and (5) the surdaster group, widely distributed in eastern Africa south of the equator. Every group contains well supported sublineages suggesting the existence of undescribed species. The earliest split within the genus (groups 1 vs. 2–5) occurred in the late Miocene and coincides with the formation of the Rift Valley which resulted in the east–west division of the initially pan‐African forest. The subsequent separation between groups (2 vs. 3–5) also dates to the end of the Miocene and suggests the split between Grammomys from coastal to upland forests in eastern Africa followed by a single dispersal event into western Africa during the Pleistocene. Conclusions The evolutionary history of the genus Grammomys closely reflects the accepted scenario of major historical changes in the distribution of tropical African forests since the late Miocene.

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Aim Species living in East African montane forests have highly fragmented distributions. Plio-Pleistocene climatic cycles, however, may have allowed temporary contact between forest blocks, thereby allowing gene flow. Our aim was to reconstruct the colonization history of Praomys delectorum, a rodent species adapted to montane forests. We tested two alternative scenarios: (1) the occurrence of a series of vicariance events related to Quaternary climatic changes; and (2) colonization from a single origin through successive dispersal events. Location Montane forests of East Africa.Methods Analyses were based on large-scale sampling covering the complete range of the species distribution. We assessed genetic structure and historical demography using a combination of mitochondrial and nuclear markers. Morphological differences between allopatric populations were analysed using a geometric morphometric approach.Results Populations of P. delectorum are genetically differentiated along the north-south axis of the distribution range, consistent with postulated vicariance events. The oldest vicariance event, which separated the species into three main genetic groups, dates to the beginning of the Pleistocene. Further fragmentation within the three main lineages is consistent with successive vicariance events, probably linked to Pleistocene climatic cycles. Morphological variation between geographically structured populations may indicate local environmental adaptations. Main conclusionsThe most likely explanation for the strong genetic differentiation among fragmented populations is a series of vicariance events caused by periodic fragmentation of montane forests that resulted from climatic oscillations in the Pleistocene, rather than successive dispersal events. The recently proposed splitting of P. delectorum into three allopatric morphospecies only partly reflects the observed genetic structure.

Aim The rodent genus Gerbilliscus is widespread in savannas throughout sub-Saharan Africa. The eastern clade comprises four species with distributions centred in the Somali-Masai biogeographical region of East Africa. We investigated the genetic diversity of the group with a view to illuminating the historical (Plio-Pleistocene) processes that formed contemporary biota of the understudied Somali-Masai region.Location Somali-Masai savanna, East Africa. MethodsWe performed multilocus genetic analyses of 240 samples from 112 localities, combining genotyping of recently collected samples (N = 145), 454pyrosequencing of museum material (N = 34) and published sequences (N = 61). We used Bayesian and maximum likelihood approaches for phylogenetic reconstructions, and coalescent-based methods to delimit species. We also estimated divergence times and modelled recent and past distributions to reconstruct the major evolutionary influences in the Somali-Masai region during the Plio-Pleistocene.Results Genetic analyses provided evidence for six lineages, possibly corresponding to distinct species. The two main species groups (with two and four putative species, respectively) have overlapping distributions, but species within each group are distributed parapatrically. The origin of the eastern clade dates back to the Pliocene, while individual species diverged in the Pleistocene. The distribution of genetic diversity and ecological niche modelling point to the importance of the Rift Valley and the presence of unsuitable xeric habitats in the allopatric diversification of Gerbilliscus in the Somali-Masai savanna within the last 5 Myr.Conclusions This is the first detailed phylo(bio-)geographical study of animals with predominant distribution in the Somali-Masai region. It revealed currently underestimated diversity of eastern clade of Gerbilliscus and proposed a scenario of its evolution during Plio-Pleistocene. Conspicuous genetic structure of these taxa can be now used to test detailed phylogeographical hypotheses related to Plio-Pleistocene history of gerbils and, to some extent, also biota of Somali-Masai bioregion in general.

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