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Open Access Research article

Revisiting the taxonomy of the Rattini tribe: a phylogeny-based delimitation of species boundaries

Marie Pagès1*, Yannick Chaval1, Vincent Herbreteau23, Surachit Waengsothorn4, Jean-François Cosson1, Jean-Pierre Hugot5, Serge Morand67 and Johan Michaux18

Author Affiliations

1 INRA, UMR CBGP (INRA/IRD/Cirad/Montpellier SupAgro), Campus International de Baillarguet, CS 30016, 34988 Montferrier-sur-Lez cedex, France

2 Cemagref, Territories, Environment, Remote Sensing and Spatial Information Joint Research Unit (UMR TETIS), Maison de la Télédétection, 500 rue J-F Breton, 34093 Montpellier Cedex 5, France

3 Institut de Recherche pour le Développement (IRD), Research Unit UR178, Center for Vectors and Vector-borne Diseases (CVVD), Faculty of Sciences, Mahidol University, Bangkok 10400, Thailand

4 Thailand Institute of Scientific and Technological Research, Bangkok, Thailand

5 Muséum National d'Histoire Naturelle, Origine, Structure et Evolution de la Biodiversité, Paris, France

6 Institut des Sciences de l'Evolution, CNRS-UM2, Université Montpellier 2, 34095 Montpellier, France

7 UR AGIRs, CIRAD, Campus International de Baillarguet 34398 Montpellier, France

8 Laboratoire de génétique des microorganismes, Institut de Botanique, Université de Liège, 4000 Liège (Sart Tilman), Belgique

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BMC Evolutionary Biology 2010, 10:184  doi:10.1186/1471-2148-10-184

Published: 18 June 2010

Abstract

Background

Rodents are recognized as hosts for at least 60 zoonotic diseases and may represent a serious threat for human health. In the context of global environmental changes and increasing mobility of humans and animals, contacts between pathogens and potential animal hosts and vectors are modified, amplifying the risk of disease emergence. An accurate identification of each rodent at a specific level is needed in order to understand their implications in the transmission of diseases. Among the Muridae, the Rattini tribe encompasses 167 species inhabiting South East Asia, a hotspot of both biodiversity and emerging and re-emerging diseases. The region faces growing economical development that affects habitats, biodiversity and health. Rat species have been demonstrated as significant hosts of pathogens but are still difficult to recognize at a specific level using morphological criteria. DNA-barcoding methods appear as accurate tools for rat species identification but their use is hampered by the need of reliable identification of reference specimens. In this study, we explore and highlight the limits of the current taxonomy of the Rattini tribe.

Results

We used the DNA sequence information itself as the primary information source to establish group membership and estimate putative species boundaries. We sequenced two mitochondrial and one nuclear genes from 122 rat samples to perform phylogenetic reconstructions. The method of Pons and colleagues (2006) that determines, with no prior expectations, the locations of ancestral nodes defining putative species was then applied to our dataset. To give an appropriate name to each cluster recognized as a putative species, we reviewed information from the literature and obtained sequences from a museum holotype specimen following the ancient DNA criteria.

Conclusions

Using a recently developed methodology, this study succeeds in refining the taxonomy of one of the most difficult groups of mammals. Most of the species expected within the area were retrieved but new putative species limits were also indicated, in particular within Berylmys and Rattus genera, where future taxonomic studies should be directed. Our study lays the foundations to better investigate rodent-born diseases in South East Asia and illustrates the relevance of evolutionary studies for health and medical sciences.