Diversity, distribution, and evolutionary history of the most studied African rodents, multimammate mice of the genusMastomys: An overview after a quarter of century of using DNA sequencing

Abstract

Despite the importance of rodents as agricultural pests and reservoirs of zoonoses, the taxonomy and evolutionary history of many groups is still not sufficiently understood. The genus Mastomys (multimammate mice or rats) comprises abundant and intensively studied rodents, widespread across sub‐Saharan Africa. Here, we used an extensive dataset of mitochondrial DNA markers comprising of nearly 2700 individual sequences from 30 African countries to update the information about the geographical distribution of their genetic diversity. In the next step, we sequenced complete mitogenomes, six nuclear markers, and produced anchored phylogenomic data (355 loci) and, for the first time, sufficiently resolved phylogenetic relationships among all extant Mastomys species and reconstructed their evolutionary history. The results suggest eight species of Mastomys occupying various non‐forested environments. Some species are very widespread (Mastomys natalensis, Mastomys kollmannspergeri, and Mastomys erythroleucus; for the latter we provide first records from Tanzania, thus significantly extending its distribution), while others have their distribution restricted to particular geographical areas (Mastomys coucha in South African region, Mastomys awashensis in Ethiopia, and Mastomys angolensis in Angola and southern DRC) or to particular habitat, that is, wetlands in western (Mastomys huberti) or southwestern (Mastomys shortridgei) Africa. The first split separating M. angolensis (with five pairs of mammae only) from remaining multimammate taxa occurred in mid‐Pliocene, but the most intensive radiation occurred in mid‐Pleistocene and was likely driven by the intensification of climate oscillations. The resolved phylogeny of Mastomys will facilitate their further use as model taxa, for example, in understanding proximate mechanisms of evolution of the multimammate phenotype.

MHC-I alleles mediate clearance and antibody response to the zoonotic Lassa virus in Mastomys rodent reservoirs

“…A similarly expansive allelic MHC-I repertoire has been reported for birds and bats with a particularly wide range [71,72]. The fact that M. natalensis and M. erythroleucus share 27 alleles implies trans-species polymorphism possibly maintained by balancing selection acting from a million years ago, when both taxa are estimated to have split from their common ancestor [73]. Furthermore, 12 of 16 positively selected sites are shared by M. natalensis and M. erythroleucus, which supports the idea that both species experience similar pathogen-mediated selection.…”

“…natalensis and M . erythroleucus share 27 alleles implies trans-species polymorphism possibly maintained by balancing selection acting from a million years ago, when both taxa are estimated to have split from their common ancestor [ 73 ]. Furthermore, 12 of 16 positively selected sites are shared by M .…”

Widespread human exposure to ledanteviruses in Uganda: A population study

“…Cytochrome B sequence barcoding for speciation of Mastomys was performed by aligning NGS sequencing reads to the optimal Mastomys mitochondrial reference sequences, with the optimal reference determined by blastn query of initial consensus sequence against the NCBI nucleotide database (MZ131552). The subsequent consensus was aligned with a panel of previously published reference sequences [ 62 ].…”

Widespread human exposure to ledanteviruses in Uganda – a population study

“…Cytochrome B sequence barcoding for speciation of Mastomys was performed by aligning NGS sequencing reads to the optimal Mastomys mitochondrial reference sequences, with the optimal reference determined by blastn query of initial consensus sequence against the NCBI nucleotide database (MZ131552). The subsequent consensus was aligned with a panel of previously published reference sequences (39).…”