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

Abstract

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.

Evolutionary history of the thicket rats (genus Grammomys) mirrors the evolution of African forests since late Miocene

“…Such distribution patterns have not been observed in previously studied forest specialists restricted to the EAM and SRM (e.g. Lawson, 2010;Tolley et al, 2011;Bryja et al, 2014b;Loader et al, 2014).…”

“…Genetic data obtained from fresh material were complemented by eight museum samples (mostly dry skins) (see Appendix S1) pyrosequenced on GS Junior using the CYTB mini-barcode protocol (Galan et al, 2012). This approach was used for samples from geographical areas that are difficult to access today or from the type localities of G. dryas and G. poensis (see more details in Bryja et al, 2014a).…”

“…However, it is unlikely that a single spatiotemporal scenario applies for all faunal components, as even species with presumably similar ecological requirements may have different responses to the same environmental changes (Carleton & Stanley, 2012). For example, phylogenetic reconstructions of the forest-dependent rodent Praomys delectorum revealed two distinct lineages corresponding to the Usambara Mts in the north and Nguru Mts in the south, which are separated by the wide savanna belt in northeastern Tanzania (Bryja et al, 2014b). However, both sides of this belt are inhabited by a single mitochondrial Grammomys lineage (su10; Fig.…”

Molecular phylogenetic analyses indicate paraphyly of the genusHybomys(Rodentia: Muridae): Taxonomic implications

“…badius , respectively. Molecular genetic analyses are increasingly used to delimit species, particularly in rodents (Baker & Bradley, ; Bryja et al., , ; Granjon & Montgelard, ; Taylor et al., ). In the following paragraphs, we discuss the status of rufocanus and eisentrauti based on our DNA sequence data, and data from the literature.…”

Genetic variation of the most abundant forest‐dwelling rodents in Central Africa (Praomys jacksoni complex): Evidence for Pleistocene refugia in both montane and lowland forests

“…All individuals were genotyped for the mitochondrial gene cytochrome b ( CYTB ), using the protocol of Bryja, Mikula, Šumbera et al. (). Selected specimens from each major mitochondrial clade (see Appendix S1) were also genotyped at three unlinked autosomal introns: ACPT , CARHSP , and GAD2 (see details in Demos et al., ).…”