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

M. Pagès (1) , Y. Chaval (1) , Vincent Herbreteau (2) , S. Waengsothorn (3) , J.F. Cosson (1) , J.P. Hugot (4) , S. Morand (5) , J. Michaux (6)

1 UMR CBGP - Centre de Biologie pour la Gestion des Populations
2 UMR TETIS - Territoires, Environnement, Télédétection et Information Spatiale
3 Thailand institute of scientific and technolocical research
4 OSEB - Origine, structure et évolution de la biodiversité
5 UMR ISEM - Institut des Sciences de l'Evolution de Montpellier
6 Université de Liège

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. DNAbarcoding 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. 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. 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.

Mots clés: MOLECULAR PHYLOGENY; MAXIMUM-LIKELIHOOD; ENDEMIC RODENTS; MIXED MODELS; NEW-GUINEA; MITOCHONDRIAL; NUCLEAR GENE-SEQUENCES; CYTOCHROME-B SEQUENCES; PHYLOGENETIQUE; GUINEE; RONGEUR; MALADIE HUMAINE; SANTE; ANCIENT DNA; EVOLUTIONARY RELATIONSHIPS

Domaines: Santé publique et épidémiologie

M. Pagès, Y. Chaval, Vincent Herbreteau, S. Waengsothorn, J.F. Cosson, et al.. Revisiting the taxonomy of the Rattini tribe: a phylogeny-based delimitation of species boundaries. BMC Evolutionary Biology, 2010, 10 (184), p. 1 - p. 27. ⟨10.1186/1471-2148-10-184⟩. ⟨hal-00521287⟩