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.2013 Nov 1;8(11):e77815.
doi: 10.1371/journal.pone.0077815. eCollection 2013.

Mitochondrial and nuclear genes-based phylogeography of Arvicanthis niloticus (Murinae) and sub-Saharan open habitats pleistocene history

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Mitochondrial and nuclear genes-based phylogeography of Arvicanthis niloticus (Murinae) and sub-Saharan open habitats pleistocene history

Gauthier Dobigny et al. PLoS One..

Erratum in

  • PLoS One. 2013;8(12). doi:10.1371/annotation/a34daea8-8922-4eb0-8b4e-b0f9dbfd28ca

Abstract

A phylogeographic study was conducted on the Nile grass rat, Arvicanthis niloticus, a rodent species that is tightly associated with open grasslands from the Sudano-Sahelian regions. Using one mitochondrial (cytochrome b) and one nuclear (intron 7 of Beta Fibrinogen) gene, robust patterns were retrieved that clearly show that (i) the species originated in East Africa concomitantly with expanding grasslands some 2 Ma, and (ii) four parapatric and genetically well-defined lineages differentiated essentially from East to West following Pleistocene bioclimatic cycles. This strongly points towards allopatric genetic divergence within savannah refuges during humid episodes, then dispersal during arid ones; secondary contact zones would have then stabilized around geographic barriers, namely, Niger River and Lake Chad basins. Our results pertinently add to those obtained for several other African rodent as well as non-rodent species that inhabit forests, humid zones, savannahs and deserts, all studies that now allow one to depict a more comprehensive picture of the Pleistocene history of the continent south of the Sahara. In particular, although their precise location remains to be determined, at least three Pleistocene refuges are identified within the West and Central African savannah biome.

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Conflict of interest statement

Competing Interests:The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. Time-calibrated tree resulting from the partitioned Bayesian analysis of the combined dataset.
Age estimates correspond to the results of the BRC analysis using the fossil constraint with an exponential distribution. Labels on nodes correspond to the nodes listed in Table 2. Posterior probabilities (left) and bootstrap values (right) are also indicated for major nodes (values below<0.50 are not figured). On the bottom left (lower panel), a map is included to figure the localities of almost all sampledArvicanthis niloticus specimens (with the exception of the specimen from Ethiopia and the two specimens from Egypt). Additional information on mountain and hydrogeographic formations of interest is also provided. A red line is also used to figure the distribution limits of the two distinctA. niloticus cytotypes (ANI-1a and ANI-1b; see text for details). On the right side, the general origin ofArvicanthis niloticus specimens is represented using circles filled with colours corresponding to those used on the map. In addition, vertical sidebars highlight the three major lineages (A, B and C) and the four major clades within the lineage C (C-1, C-2, C-3 and C-4). On the bottom left again (upper panel), the simplified phylogenetic topology ofArvicanthis studied here is represented with corresponding geographic origin of extant lineages as well as of MRCA as inferred by the ancestral area optimization under Mesquite (see text for details).
Figure 2
Figure 2. Haplotype network and phylogenetic tree resulting from the analysis of the cytb dataset.
The haplotype network reconstruction takes into account missing data and gap so the inferred number of haplotype I higher than the one presented in Table 4. Red values on nodes indicate the inferred number of mutation steps between haplotypes or ancestral haplotypes (symbolized by a red node). The absence of value means that the number of steps is inferior to 10. The phylogenetic tree corresponds to the results of a Bayesian inference analysis (see text for details); posterior probabilities (PP) are indicated for major nodes (values below<0.50 are not figured). On the right side, the general origin ofArvicanthis niloticus specimens is figured using circles filled with different colours that directly refer to the map presented in Figure 1.
Figure 3
Figure 3. Haplotype network and phylogenetic tree resulting from the analysis of the Fib7 dataset.
The haplotype network reconstruction takes into account missing data and gaps, so that the inferred number of haplotypes is higher than the one presented in Table 4. Red values on nodes indicate the inferred number of mutation steps between haplotypes or ancestral haplotypes (symbolized by a red node). The absence of value means that the number of step is equal to 1. The phylogenetic tree corresponds to the results of a Bayesian inference analysis (see text for details); posterior probabilities (PP) are indicated for major nodes (values below<0.50 are not figured). On the right side, the general origin ofArvicanthis niloticus specimens is figured using circles filled with different colours that directly refer to the map presented in Figure 1.
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