Phylogeography and molecular phylogenetics of East African rodents: Assessing the role of vicariance.

摘要

This study constitutes the first investigation into the effects of Plio-Pleistocene and Pleistocene climatic cycles and geologic activity on the phylogeographic structure of rodents distributed across the montane and lowland forests of east Africa. The speckled brush-furred rat, Lophuromys aquilus, is widely distributed throughout east and central Africa in moist, marshy and forest edge habitats. Mitochondrial DNA sequences from complete cytochrome b (1140 bp) and partial control region (365 bp) genes were collected from 201 individuals. Phylogenetic and Nested Clade analyses identified seven or eight phylogeographic regions that resulted from major vicariance events. Aridification during the Pleistocene separated the Northern Eastern Arc Mountains from the rest of montane East Africa around 0.9-1.2 MYBP and then separated all other montane areas from each other around 200,000-700,000 years ago.; Molecular phylogenies based on complete mitochondrial cytochrome b are assessed on a taxonomic sampling of the brush-furred mice, genus Lophuromys, including representatives of both subgenera ( Lophuromys and Kivumys). Maximum likelihood, maximum parsimony and Bayesian analyses produced similar topologies with subgenus Lophuromys representatives L. aquilus, L. ansorgei, L. rahmi, and L. sikapusi forming a monophyletic clade. Members of the subgenus Kivumys, L. woosnami and L. medicaudatus, form a monophyletic clade separate from the Lophuromys group. There is a high level of sequence divergence among the species examined in this study: intrageneric Kimura 2-parameter divergence levels range from 7.6% between rahmi and anasorgei to 17.6% between medicaudatus and sikapusi. Estimates of divergence time for these taxa suggest a separation between 4 and 5 MYBP for the two subgenera. Within each subgenus, divergence times suggest that much of the differentiation occurred between 1.5 and 4.0 MYBP.; The back-striped mice, Hybomys lunaris, are a group of rodents thought to be endemic to the montane forests of the Albertine Rift. Maximum parsimony, maximum likelihood and Bayesian Inference recovered a phylogeographic structure that questions this assumption. Two lowland forest populations cluster within the montane forest clade and suggest a pattern of historical gene flow and subsequent isolation. Additionally, the results of this analysis provide strong support for the recognition of at least two species of Hybomys from the Albertine Rift.; The phylogeographic structures recovered from east Africa rodent populations suggests that landscape alteration caused by cycles of climatic change, mountain uplift and volcanic activity during the Plio-Pleistocene has had a significant effect on the genetic diversity in this region. Taken collectively, our results suggest that aridification and geologic processes have had a profound effect on speciation in east and central Africa.