Assessment Of Three Mitochondrial Genes (16S, Cytb, CO1 ... - PubMed

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Abstract

The Praomyini tribe is one of the most diverse and abundant groups of Old World rodents. Several species are known to be involved in crop damage and in the epidemiology of several human and cattle diseases. Due to the existence of sibling species their identification is often problematic. Thus an easy, fast and accurate species identification tool is needed for non-systematicians to correctly identify Praomyini species. In this study we compare the usefulness of three genes (16S, Cytb, CO1) for identifying species of this tribe. A total of 426 specimens representing 40 species (sampled across their geographical range) were sequenced for the three genes. Nearly all of the species included in our study are monophyletic in the neighbour joining trees. The degree of intra-specific variability tends to be lower than the divergence between species, but no barcoding gap is detected. The success rate of the statistical methods of species identification is excellent (up to 99% or 100% for statistical supervised classification methods as the k-Nearest Neighbour or Random Forest). The 16S gene is 2.5 less variable than the Cytb and CO1 genes. As a result its discriminatory power is smaller. To sum up, our results suggest that using DNA markers for identifying species in the Praomyini tribe is a largely valid approach, and that the CO1 and Cytb genes are better DNA markers than the 16S gene. Our results confirm the usefulness of statistical methods such as the Random Forest and the 1-NN methods to assign a sequence to a species, even when the number of species is relatively large. Based on our NJ trees and the distribution of all intraspecific and interspecific pairwise nucleotide distances, we highlight the presence of several potentially new species within the Praomyini tribe that should be subject to corroboration assessments.

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Conflict of interest statement

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

Figures

Figure 1

Figure 1. Distribution of intraspecific (white bars)…

Figure 1. Distribution of intraspecific (white bars) and interspecific (black bars) divergences estimated from the…

Figure 1. Distribution of intraspecific (white bars) and interspecific (black bars) divergences estimated from the K2P distance for the genes 16S, Cytb and CO1 and for the first part of the Cytb gene. In several cases a non-null number of occurrences was observed, but this is not apparent on the histograms because of the scale. The symbol “*” indicates a non-null number of occurrences within species, and “+”a non-null number of occurrences between species.
Figure 2

Figure 2. 16S neighbour-joining tree of Praomyini…

Figure 2. 16S neighbour-joining tree of Praomyini (K2P distance), with bootstrap support (500 replicates).

To…

Figure 2. 16S neighbour-joining tree of Praomyini (K2P distance), with bootstrap support (500 replicates). To improve clarity, bootstrap support of each species is not indicated on the tree but is reported in Table 1. For species codes, see Table S1.
Figure 3

Figure 3. CO1 neighbour-joining tree of Praomyini…

Figure 3. CO1 neighbour-joining tree of Praomyini (K2P distance), with bootstrap support (500 replicates).

To…

Figure 3. CO1 neighbour-joining tree of Praomyini (K2P distance), with bootstrap support (500 replicates). To improve clarity bootstrap support of each species is not indicated on the tree but is reported in Table 1. For species codes (see Table S1).
Figure 4

Figure 4. Distributions of the cumulative errors…

Figure 4. Distributions of the cumulative errors among the 40 species of Praomyini tribe, calculated…

Figure 4. Distributions of the cumulative errors among the 40 species of Praomyini tribe, calculated from: (a) the CO1 gene; (b) the Cytb-part1 gene.
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References

    1. Lecompte E, Aplin K, Denys C, Catzeflis F, Chades M, et al. Phylogeny and biogeography of African Murinae based on mitochondrial and nuclear gene sequences, with a new tribal classification of the subfamily. BMC Evol Biol. 2008;8:199. - PMC - PubMed
    1. Nicolas V, Verheyen E, Verheyen W, Hulselmans J, Dillen M, et al. Systematics of African lowland rainforest Praomys (Rodentia, Muridae) based on molecular and craniometrical data. Zool J Linn Soc. 2005;145:539–553.
    1. Lecompte E, Denys C, Granjon L. Confrontation of morphological and molecular data: the Praomys group (Rodentia, Murinae) as a case of adaptive convergences and morphological stasis. Mol Phylogenet Evol. 2005;37:899–919. - PubMed
    1. Van der Straeten E, Lecompte E, Denys C. Praomys petteri: une nouvelle espèce de Muridae africains (Mammalia, Rodentia). Bonn Zool Beitr. 2003;50:329–345.
    1. Nicolas V, Quérouil S, Verheyen E, Verheyen W, Mboumba JF, et al. Mitochondrial phylogeny of African wood mice, genus Hylomyscus (Rodentia, Muridae): implications for their taxonomy and biogeography. Mol Phylogenet Evol. 2006;38:779–793. - PubMed
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