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

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.

Influence of microhabitat structure and disturbance on detection of native and non-native murids in logged and unlogged forests of northern Borneo

“…MtDNA sequencing of the Rattus species we refer to in this study confirmed that it was a member of the Rattus rattus species complex (sensu Aplin et al 2011, Pagès et al 2010), based on both cytochrome b and CO1 gene sequences (M. Pagès, pers. comm.).…”

Helminths in rodents from Wet Markets in Thailand

“…Also of interest is the study by Mohd Zain et al (2012) of R. norvegicus and R. rattus Linnaeus, 1758 (probably Rattus sp. according Pagès et al (2010)) in Kuala Lampur; how ever in this latter study collection sites were not characterized. Thus, in light of this lack of previous information, the aim of the present study was to fi ll the gaps in the knowledge of the role of rodents as reservoirs of zoonotic helminthiases in traditional wet markets in SEA.…”

“…To date, studies of rodents in wet markets in SEA are limited to just two studies. Firstly, fi ve wet markets were studied in Kuala Lumpur in insular Malaysia by Paramasvaran et al (2009), who detected 97 rodents belonging to three species: R. r. diardii, a taxon that, according Pagès et al (2010), should be considered as a Rattus sp. pending a defi nitive name, R. norvegicus Berkenhout, 1769 andR.…”

Progress on research on rodents and rodent-borne zoonoses in South-east Asia

“…Many of the results presented here are the outcome of the recent CERoPath project (Community Ecology of Rodents and their Pathogens in a South-east Asian changing environment), which aimed at better understanding the relationships between rodent-borne diseases, rodents and their habitats using intensive field work, molecular screening and geospatial analyses (Pagès et al 2010;Blasdell et al 2011;Herbreteau et al 2011;Dupuy et al 2012;Bordes et al 2013;Pumhom et al 2014Pumhom et al , 2015Cosson et al 2014;Jiyipong et al 2015).…”

“…Moreover, reliable species identification is hampered by our imprecise knowledge of South-east Asian rat taxonomy, the lack of clear species limits within some genera (e.g. Rattus, Maxomys, Niviventer) and problematic access to reference specimens Pagès et al 2010).…”