Assessment of Three Mitochondrial Genes (16S, Cytb, CO1) for Identifying Species in the Praomyini Tribe (Rodentia: Muridae)

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.

A new species of the rodent genus Hylomyscus from Angola, with a distributional summary of the H. anselli species group (Muridae: Murinae: Praomyini)

“…This total doubles the number recognized just 10 years ago (Musser & Carleton, 2005), and more species surely await description (e.g., see discussions or results in Carleton et al, 2006;Nicolas et al, 2010Nicolas et al, , 2012Bryja et al, 2012). This body of research accordingly portrays the Hylomyscus clade as a modest radiation in Sub-Saharan Africa, second to Praomys Thomas among the genera of Praomyini (sensu Lecompte et al, 2008).…”

Extensive cryptic diversity in the cosmopolitan sludge worm Limnodrilus hoffmeisteri (Clitellata, Naididae)

“…Single locus data are widely and conveniently used to estimate species boundaries in large samples of specimens of morphology-based taxa (Nicolas et al 2012;Lv et al 2014;Trebitz et al 2015). We tried to disentangle the mitochondrial diversity of the highly variable L. hoffmeisteri, by examining specimens from all continents of the northern hemisphere with ABGD and bGMYC.…”

Phylogenetic analysis of the king cobra, Ophiophagus hannah in Thailand based on mitochondrial DNA sequences

“…In this regard, molecular techniques have proven to be an effective tool for reliable species identification, phylogenetics, and biodiversity analysis, and may be the key to successful work in law enforcement and conservation of wildlife [17,18]. Phylogenetics and phylogeographic studies of snakes are rare and most have used mitochondrial genes, such as cytochrome c oxidase subunit 1 (CO1), cytochrome b (Cyt b), and NADH dehydrogenase subunit 4 (ND4) [9,19,20].…”