Small Mammal Investigation in Spotted Fever Focus with DNA-Barcoding and Taxonomic Implications on Rodents Species from Hainan of China

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.

First report of Rickettsia felisin China

“…present in China [1]. We therefore used PCR to definitively identify R. felis in our study populations and provide further prevalence data.…”

“…Although tick-borne spotted fever group rickettsiae have been described in China [1], there is no information on the flea-borne emerging human pathogen Rickettsia felis . Described in 2001, R. felis appears to have the cat flea, Ctenocephalides felis felis , as its main vector and reservoir and can infect other arthropods (mosquitoes, ticks and mites) and mammals (rats, opossums, dogs, and cats).…”

DNA barcoding of Murinae (Rodentia: Muridae) and Arvicolinae (Rodentia: Cricetidae) distributed in China

“…; Lu et al . ). In addition, shortage of taxonomists, complex identification criteria and time‐consuming processes have sometimes made morphological methods impractical for accurate species authentication of rodents.…”

“…For example, Niviventer confucianus and N. fulvescens (Lunde et al 2009), and Leopoldamys edwardi and L. herberti (Balakirev et al 2013) have been misidentified even by experts. On the other hand, morphological divergence within many species is unusually wide Pag es et al 2010;Lu et al 2012). In addition, shortage of taxonomists, complex identification criteria and time-consuming processes have sometimes made morphological methods impractical for accurate species authentication of rodents.…”

Molecular identification of two gobi fishes of Bangladesh using cytochrome oxidase subunit I (CoI) gene sequences

“…This alternative method of PCR-based identification is more convenient and easier to perform than the taxonomic keys (Tiwary et al 2012, Ernieenor et al 2013. The approach can also provide genetic references to validate field identifications made by researchers with limited taxonomic background (Borisenko et al 2008, Lu et al 2012. Currently, the most commonly used barcode region for animals is a 50 bp segment of the mitochondrial gene cytochrome oxidase subunit (COI) called the 'Universal' or 'Folmer' region.…”