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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. Tropical Africa, from Ghana to Kenya. 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. 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. 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. [ABSTRACT FROM AUTHOR]

Two sibling species of the rodent genus Praomys occur in West African forests: P. tullbergi and P. rostratus. By sampling across their geographical ranges (459 individuals from 77 localities), we test the hypothesis that climatic oscillations during the Quaternary made an impact on the observed pattern of cytochrome b sequence variation. We show that, although these two species have parapatric geographical distributions, their phylogeographical histories are dissimilar, which could be related to their distinct ecological requirements. Since the arid phases of the Pleistocene were characterized by isolated forest patches, and intervening wetter periods by forest expansion, these changes in forest cover may be the common mechanism responsible for the observed phylogeographical patterns in both of these species. For example, in both species, most clades had either allopatric or parapatric geographical distributions; however, genetic diversity was much lower in P. tullbergi than in P. rostratus. The genetic pattern of P. tullbergi fits the refuge hypothesis, indicating that a very small number of populations survived in distinct forest blocks during the arid phases, then expanded again with forest recovery. In contrast, a number of populations of P. rostratus appear to have survived during the dry periods in more fragmented forest habitats, with varying levels of gene flow between these patches depending on climatic conditions and forest extent. In addition, historical variations of the West African hydrographic network could also have contributed to the pattern of genetic differentiation observed in both species. [ABSTRACT FROM AUTHOR]