Abstract
Although mammals are a well-studied group of animals, making accurate field identification of small mammals is still complex because of morphological variation across developmental stages, color variation of pelages, and often damaged osteological and dental characteristics. In 2008, small mammals were collected for an epidemiological study of a spotted fever outbreak in Hainan, China. Ten species of small mammals were identified by morphological characters in the field, most using pelage color characters only. The study is extended here, in order to assess whether DNA barcoding would be suitable as an identification tool in these small mammals. Barcode clusters showed some incongruence with morphospecies, especially for some species of Rattus and Niviventer, so molecular delineation was carried out with an expanded dataset of combined cytochrome b (Cyt-b) and cytochrome c oxidase subunit I (COI) sequences. COI sequences were successfully amplified from 83% of collected mammals, but failed in all specimens of Suncus murinus, which were thus excluded in DNA barcoding analysis. Of note, ten molecular taxonomic units were found from samples of nine morphologically identified species. Accordingly, 11 species of small mammals were present in the investigated areas, including four Rattus species, three Niviventer species, Callosciurus erythraeus, Neohylomys hainanensis, Tupaia belangeri, and Suncus murinus. Based on the results of the phylogenetic and molecular delineation analyses, the systematic status of some rodent species should be redefined. R. rattus hainanicus and R. rattus sladeni are synonyms of R. andamanensis. R. losea from China and Southeast Asia comprises two independent species: R. losea and R. sakeratensis. Finally, the taxonomic status of three putative species of Niviventer should be further confirmed according to morphological, molecular and ecological characters.
Highlights
Rodents are important host animals for many zoonoses that threaten public health worldwide [1,2]
According to the morphological criteria we used, seven species belonged to three genera of Rodentia, two species belonged to two genera of Soricomorpha, and there was one species of Scandentia (Table 1)
The Neighbour Joining (NJ) tree of c oxidase subunit I (COI) sequence from Hainan showed that there were ten well supported lineages (Figure 2). Nine of these lineages corresponded to field identified species, but three specimens identified as N. confucianus were not clustered with other members of this species in the tree
Summary
Rodents are important host animals for many zoonoses that threaten public health worldwide [1,2]. Gaining accurate taxonomic information on host animals is important for surveillance and epidemiological investigation of rodent-borne diseases. Mammals rank amongst the most studied animal groups, with their taxonomy and species diversity well documented in the literature [4]. Field identification of many small mammal species remains difficult, in large part because of morphological variation through development, and color variation of pelages (mammalian coat) between individuals. Through analysis of internal morphology (e.g. skull and dentition) can definitive identification be made. Molecular data from one previous study suggests the frequent occurrence of cryptic mammal species that are overlooked when using morphological characters alone [5]. A standard molecular identification system is necessary as a complement to morphological methods, in order to reduce uncertainties in the identification of mammal species
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