Abstract
BackgroundRodents 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.ResultsWe 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.ConclusionsUsing 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.
Highlights
Rodents are recognized as hosts for at least 60 zoonotic diseases and may represent a serious threat for human health
The wide range of intra-specific morphological variation makes morphological criteria unsuitable for accurate rat species identification and has led to an over-description of species and to a confusing taxonomy, hampered by an overabundance of synonyms. It is true concerning the Rattus genus (e.g. 41 synonyms for R. norvegicus, 83 for R. rattus, etc. [16] and see [25]) that consists of a heterogeneous accumulation of species and of several monophyletic clusters that may or may not prove to be grouped in a single genus [16]. This polyphyletic pattern is highlighted by the six species groups proposed by Musser and Carleton [16] and a seventh assemblage containing unaffiliated species for which phylogenetic affinities are uncertain; some representatives will eventually be removed from the genus
Our phylogenetic analyses of Indochinese Rattini based on the combination of cytb, c oxydase I (COI) and the first exon of the interphotoreceptor retinoid binding protein (IRBP) genes is compatible with the revised taxonomy of Rattini divisions proposed by Musser and Carleton [16]
Summary
Rodents are recognized as hosts for at least 60 zoonotic diseases and may represent a serious threat for human health. As the Eurasian harvest mouse, Micromys was proven to belong to the Rattini tribe ([17,21]), the whole Micromys division should belong to the Rattini tribe if Musser and Carleton's assumption is right Some of these genera (i.e. Chiropodomys and Vandeleuria) were recently shown to be unaffiliated to Micromys according to molecular evidences [21], while putative representatives of the Rattini tribe (i.e. Tonkinomys daovantieni, Saxatilomys paulinae, Srilankamys sp., Hapalomys sp., Haeromys sp., Vernaya sp.) have not been investigated using molecular data and are currently considered as Murinae incertae sedis [17]. The wide range of intra-specific morphological variation makes morphological criteria unsuitable for accurate rat species identification and has led to an over-description of species and to a confusing taxonomy, hampered by an overabundance of synonyms It is true concerning the Rattus genus DNA-based methods, appear to be promising tools for easy and accurate rat species-specific identifications [26]
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