Increased geographic sampling reveals considerable new genetic diversity in the morphologically conservative African Pygmy Mice (Genus Mus; Subgenus Nannomys)

African endemic pygmy mice (Genus Mus; sub-genus Nannomys) have considerable economic and public health significance, and some species exhibit novel sex determination systems, making accurate knowledge of their phylogenetics and distribution limits important. This phylogenetic study was based on the mitochondrial control region and cytochrome b gene, for which a substantial body of published data was available. Study specimens were sourced from eight previously unsampled or poorly sampled countries, and include samples morphologically identified as Mus bufo, M. indutus, M. callewaerti, M. triton and M. neavei. These analyses increase the known genetic diversity of Nannomys from 65 to 102 haplotypes; at least 5 unassigned haplotypes are distinguished by potentially species-level cytochrome b genetic distances. The monophyly of Nannomys is supported. Mus musculoides, M. callewaerti, M. indutus, M. bufo, M. haussa, M. mattheyi, M. baoulei and M. sorella are supported as discrete species. The range of M. indutus is extended to include Botswana. M. setulosus and M. minutoides appear to be species complexes. A south and east African M. minutoides clade was defined and includes 8 new haplotypes out of 15. M. setulosus sensu lato includes M. setulosus sensu stricto and a strongly-supported M. bufo clade. Two samples, morphologically identified as M. triton and M. neavei, fall within the M. minutoides clade.