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

Dobigny G, Tatard C, Gauthier P, Ba K, Duplantier JM, Granjon L, Kergoat GJ - PLoS ONE (2013)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: IRD, CBGP (IRD, Inra, CIRAD, Montpellier SupAgro), Campus de Baillarguet, Montferrier-sur-Lez, France ; Centre Régional Agrhymet, Rive Droite, Niamey, Niger.

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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Related in: MedlinePlus

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 of Arvicanthis niloticus specimens is figured using circles filled with different colours that directly refer to the map presented in Figure 1.
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pone-0077815-g003: 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 of Arvicanthis niloticus specimens is figured using circles filled with different colours that directly refer to the map presented in Figure 1.

Mentions: “CBGP”, “DM” and “MNHN” stand for Centre de Biologie pour la Gestion des Populations (Montpellier, France), Durban Natural Science Museum (Durban, South Africa) and Museum National d’Histoire Naturelle (Paris, France), respectively. Individuals’ labels corresponding to Figures 1 to 3 are also provided.


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

Dobigny G, Tatard C, Gauthier P, Ba K, Duplantier JM, Granjon L, Kergoat GJ - PLoS ONE (2013)

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 of Arvicanthis niloticus specimens is figured using circles filled with different colours that directly refer to the map presented in Figure 1.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3815218&req=5

pone-0077815-g003: 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 of Arvicanthis niloticus specimens is figured using circles filled with different colours that directly refer to the map presented in Figure 1.
Mentions: “CBGP”, “DM” and “MNHN” stand for Centre de Biologie pour la Gestion des Populations (Montpellier, France), Durban Natural Science Museum (Durban, South Africa) and Museum National d’Histoire Naturelle (Paris, France), respectively. Individuals’ labels corresponding to Figures 1 to 3 are also provided.

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: IRD, CBGP (IRD, Inra, CIRAD, Montpellier SupAgro), Campus de Baillarguet, Montferrier-sur-Lez, France ; Centre Régional Agrhymet, Rive Droite, Niamey, Niger.

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.

Show MeSH
Related in: MedlinePlus