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Background  Rodents 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.    Results  We 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.    Conclusions  We 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 material  The online version of this article (doi:10.1186/s12862-014-0256-2) contains supplementary material, which is available to authorized users.

Pan-African phylogeny of Mus (subgenus Nannomys) reveals one of the most successful mammal radiations in Africa