The roles of rivers and Pleistocene refugia in shaping genetic diversity in Praomys misonnei in tropical Africa

Aim This study aims to elucidate the phylogeography of the murid rodent Praomys misonnei and to document whether or not rain forest refugia and rivers structure patterns of diversity within this species. Location Tropical Africa, from Ghana to Kenya. Methods Patterns of genetic structure and signatures of population history (cytochrome b gene) were assessed in a survey of 229 individuals from 54 localities. Using maximum likelihood, Bayesian, network and genetic structure analyses, we inferred intra-specific relationships and tested hypotheses for historical patterns of gene flow within P. misonnei. Results Our phylogenetic analyses reveal a strong phylogeographical structure. We identified four major geographical clades within P. misonnei: one clade in Ghana and Benin, a Nigerian clade, a West Central African clade and a Central and East African clade. Several subclades were identified within these four major clades. A signal of population expansion was detected in most clades or subclades. Coalescence within all of the major clades of P. misonnei occurred during the Middle Pleistocene and/or the beginning of Late Pleistocene. Main conclusions Our results suggest a role for both Pleistocene refugia and rivers in structuring genetic diversity in P. misonnei. This forest-dwelling rodent may have been isolated in a number of forest fragments during arid periods and expanded its range during wetter periods. Potential forest refugia may have been localized in Benin-Ghana, south-western Cameroon, southern Gabon, northern Gabon and eastern Democratic Republic of Congo-western Uganda. The Niger and/or the Cross Rivers, the Oubangui-Congo, Sanaga, Ogooue and/or Ivindo Rivers probably stopped the re-expansion of the species from relict areas.