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. 2014 Jun 6;9(6):e98499.
doi: 10.1371/journal.pone.0098499. eCollection 2014.

A Phylogeographic Survey of the Pygmy Mouse Mus Minutoides in South Africa: Taxonomic and Karyotypic Inference From Cytochrome B Sequences of Museum Specimens

Free PMC article

A Phylogeographic Survey of the Pygmy Mouse Mus Minutoides in South Africa: Taxonomic and Karyotypic Inference From Cytochrome B Sequences of Museum Specimens

Pascale Chevret et al. PLoS One. .
Free PMC article


The African pygmy mice (Mus, subgenus Nannomys) are a group of small-sized rodents that occur widely throughout sub-Saharan Africa. Chromosomal diversity within this group is extensive and numerous studies have shown the karyotype to be a useful taxonomic marker. This is pertinent to Mus minutoides populations in South Africa where two different cytotypes (2n = 34, 2n = 18) and a modification of the sex determination system (due to the presence of a Y chromosome in some females) have been recorded. This chromosomal diversity is mirrored by mitochondrial DNA sequences that unambiguously discriminate among the various pygmy mouse species and, importantly, the different M. minutoides cytotypes. However, the geographic delimitation and taxonomy of pygmy mice populations in South Africa is poorly understood. To address this, tissue samples of M. minutoides were taken and analysed from specimens housed in six South African museum collections. Partial cytochrome b sequences (400 pb) were successfully amplified from 44% of the 154 samples processed. Two species were identified: M. indutus and M. minutoides. The sequences of the M. indutus samples provided two unexpected features: i) nuclear copies of the cytochrome b gene were detected in many specimens, and ii) the range of this species was found to extend considerably further south than is presently understood. The phylogenetic analysis of the M. minutoides samples revealed two well-supported clades: a Southern clade which included the two chromosomal groups previously identified in South Africa, and an Eastern clade that extended from Eastern Africa into South Africa. Congruent molecular phylogenetic and chromosomal datasets permitted the tentative chromosomal assignments of museum specimens within the different clades as well as the correction of misidentified museum specimens.

Conflict of interest statement

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


Figure 1
Figure 1. A schematic showing the respective positions of the primers used in this study.
New primers defined specifically for use in the investigation are indicated in red.
Figure 2
Figure 2. Maximum likelihood phylogeny of the numt and mitochondrial cytb sequences of Mus indutus.
For each sample, the accession or collection number is indicated. The numbers in bold correspond to museum specimens; they are in red when two sets of sequences were obtained, in blue when only numt copies were sequenced and in orange when only mitochondrial copies were present. The three fresh tissue samples are in green. The number of clones selected for sequencing is shown. Boostrap supports above 50% are indicated.
Figure 3
Figure 3. Maximum likelihood tree using cytochrome b sequences of the studied samples and those available through GenBank for other specimens and species.
Each specimen is designated by its accession or museum number, and country of origin outside of South Africa. Diploid numbers refer to museum or published data. Bootstrap support and the posterior probability values are indicated for the main nodes. The symbol “–” Indicates nodes that were not supported. Colours refer to the different species or cytotypes identified in our study; the museum samples are in bold.
Figure 4
Figure 4. Geographic distribution of the samples. Orange = Mus indutus; Red = M. minutoides 2n = 18; Green = M. minutoides 2n = 34, Pink = M. minutoides 2n = 32, Blue = M. minutoides Eastern Clade.
The open squares refer to previously sampled localities in South Africa.

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    1. Chevret P, Veyrunes F, Britton-Davidian J (2005) Molecular phylogeny of the genus Mus (Rodentia: Murinae) based on mitochondrial and nuclear data. Biol J Linn Soc 84: 417–427.
    1. Veyrunes F, Britton-Davidian J, Robinson TJ, Calvet E, Denys C, et al. (2005) Molecular phylogeny of the African pygmy mice, subgenus Nannomys (Rodentia, Murinae, Mus): implications for chromosomal evolution. Mol Phylogenet Evol 36: 358–369. - PubMed
    1. Lamb J, Downs S, Eiseb S, John Taylor P (2014) Increased geographic sampling reveals considerable new genetic diversity in the morphologically conservative African Pygmy Mice (Genus Mus; Subgenus Nannomys). Mamm Biol - Zeitschrift für Säugetierkd 79: 24–35.
    1. Musser GG, Carleton MD (2005) Superfamily Muroidea. In: Wilson DE, Reeder DM, editors. Mammal Species of the World, Third Edition. Baltimore: Johns Hopkins University, 894–1531.
    1. Macholan M (2001) Multivariate Analysis of Morphometric Variation in Asian Mus and Sub-Saharan Nannomys (Rodentia: Muridae). Zool Anzeiger - A J Comp Zool 240: 7–14.

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Grant support

The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Funders: Ellerman Fellowship from the University of Stellenbosch ( to JBD and TJR; and ANR ( grant “SEXYMUS” (N° 10-JCJC-1605) to FV.