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

Abstract

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.

Figure 1

Distribution of genotyped specimens and individual MOTUs. (a) Distribution of analyzed material of Nannomys in Africa. Blue dots indicate the geographical position of published sequences (downloaded from GenBank), red dots show the localities of newly sequenced individuals. Geographical distribution of (b) MOTUs of the triton group (circles) and three ancient monotypic lineages (rhombuses); (c) MOTUs of the setulosus group; (d) MOTUs of the baoulei (rhombuses) and the sorella (circles) groups; (e) MOTUs of the minutoides group (except M. minutoides); (f) phylogeographic structure of MOTU 27, i.e. M. minutoides. In Figures 1e identical symbol shapes represent monophyletic groups. In Figure 1f the clade abbreviations correspond to Figure 4. Question marks indicate doubtful records based on genotyping of old museum material (see [64]). For more information on analysed material see Additional file 1.

Figure 2

Inferred phylogenetic relationships within Nannomys . Maximum likelihood phylogenetic tree of Nannomys is based on the combined dataset of mitochondrial (CYTB) and nuclear (IRBP) genes. Black circles indicate the support by both ML (bootstrap values > 75%) and BI (posterior probabilities > 0.95) analyses; grey circles indicate nodes supported by only one analysis. MOTUs were identified by the combination of GMYC approach and distribution of genetic distances on CYTB. Only outgroups from the genus Mus are shown. GenBank accession numbers correspond to CYTB sequences, for IRBP numbers see Additional file 1. Abbreviations of countries: BE: Benin, BF: Burkina Faso, BOT: Botswana, BUR: Burundi, CAM: Cameroon, CAR: Central African Republic, CI: Côte d’Ivoire, CON: Congo, DRC: Democratic Republic of Congo, ETH: Ethiopia, GAB: Gabon, GUI: Guinea, KE: Kenya, MAL: Mali, MOZ: Mozambique, MW: Malawi, NIG: Niger, RWA: Rwanda, SA: South Africa, SEN: Senegal, TOG: Togo, TCH: Tchad, TZ: Tanzania, ZA: Zambia.

Figure 3

Reconstruction of divergence dates and ancestral distributions of MOTUs. (a) Phylogenetic relationships among 49 GMYC-species and definition of 27 MOTUs. The vertical line indicates the threshold where the speciation processes are replaced by coalescence. Black circles indicate strong support (>95%) for either speciation (left of the threshold) or intraspecific coalescence (right of the threshold). White circles indicate weak support (<95%) for these processes. The dating of divergences within Nannomys was assessed by BEAST using the previously estimated divergence times (see Additional file 2) as priors for calibration of relaxed molecular clock. (b) Reconstruction of ancestral distribution areas (blue – mountains in Eastern Africa, green – tropical forests of central and western Africa; red – open savannah-like habitats surrounding forests and mountains in sub-Saharan Africa. The different colours on pie charts indicate the probability of a particular state of the trait for each node. The analysis of ancestral traits was performed in BEAST (see text for more details).

Figure 4

Phylogeographical structure of Mus minutoides (MOTU 27). Haplotype network was constructed by the median-joining algorithm from 131 CYTB sequences (84 haplotypes) in the program Network. The circle size is proportional to haplotype frequency and the connecting lines are proportional to number of substitutions.