When molecular phylogeny meets medical sciences: Taxonomic problems among rat species in Southeast Asia

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 to understand their implications in the transmission of diseases. Among 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 main hosts of pathogens but are still difficult to recognize at a specific level using morphological criteria. DNA-barcoding methods appear as the only tool for accurate rat species identifications but their usefulness is hampered by the need of reliable identifications of reference specimens. To provide a rigorous systematic framework for epidemiological surveys, we used DNA data to explore the limits of the current taxonomy of the Rattini tribe. Results: As morphological characters are often misleading, we decided to use 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 and applied the method developed by Pons and colleagues (2006) that determines with no a prior expectations, the locations of ancestral nodes defining putative species. To give an appropriate name to each cluster recognized as a valid species, we reviewed information from the literature and obtained sequences from a museum holotype specimen following all the ancient DNA criteria. One of the most striking results is that at least 6 putative species including a new cryptic one could exist among the Rattus rattus species group. Conclusions: Using a suitable methodology, this study succeeds in refining the taxonomy of one of the most difficult groups of mammals and lays the foundations to better investigate rodent-born diseases in South East Asia. Recognition of a new cryptic Rattus species in Southeast Asia could have serious implications for human health since each species is expected to have its own ecological traits and to carry its own set of diseases. To finish, first results based on independent nuclear DNA data (microsatellite loci) will be briefly exposed to demonstrate that defining species is not an easy task