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

Abstract

Identification of rodents is very difficult mainly due to high similarities in morphology and controversial taxonomy. In this study, mitochondrial cytochrome oxidase subunit I (COI) was used as DNA barcode to identify the Murinae and Arvicolinae species distributed in China and to facilitate the systematics studies of Rodentia. In total, 242 sequences (31 species, 11 genera) from Murinae and 130 sequences (23 species, 6 genera) from Arvicolinae were investigated, of which 90 individuals were novel. Genetic distance, threshold method, tree-based method, online BLAST and BLOG were employed to analyse the data sets. There was no obvious barcode gap. The average K2P distance within species and genera was 2.10% and 12.61% in Murinae, and 2.86% and 11.80% in Arvicolinae, respectively. The optimal threshold was 5.62% for Murinae and 3.34% for Arvicolinae. All phylogenetic trees exhibited similar topology and could distinguish 90.32% of surveyed species in Murinae and 82.60% in Arvicolinae with high support values. BLAST analyses yielded similar results with identification success rates of 92.15% and 93.85% for Murinae and Arvicolinae, respectively. BLOG successfully authenticated 100% of detected species except Leopoldamys edwardsi based on the latest taxonomic revision. Our results support the species status of recently recognized Micromys erythrotis, Eothenomys tarquinius and E. hintoni and confirm the important roles of comprehensive taxonomy and accurate morphological identification in DNA barcoding studies. We believe that, when proper analytic methods are applied or combined, DNA barcoding could serve as an accurate and effective species identification approach for Murinae and Arvicolinae based on a proper taxonomic framework.

Field calibration of blowfly-derived DNA against traditional methods for assessing mammal diversity in tropical forests

“…For example, Rattus (under BIN BOLD:AAB2208) detected from blowfly-derived DNA, cage traps, and scat collection likely represents Rattus "sp. R3" (Pages et al 2010), a classic "dark taxon" (see Wilson et al 2014) whereby it has not yet been formally described and is likely to be reported as R. andamanensis, R. argentiventer, or R. tanezumi in studies relying on visual diagnosis (Robins et al 2007;Pages et al 2010;Latinne et al 2013;Li et al 2015). The BIN associated with this taxon comprises DNA barcode members under the traditional names Rattus tanezumi, Rattus tiomanicus, Rattus rattus, Rattus sp., and Rattus sp.…”

An endemic rat species complex is evidence of moderate environmental changes in the terrestrial biodiversity centre of China through the late Quaternary

“…We appended the new data generated in the present study to those used in our previous study and data from GenBank364041424388 and reconstructed a phylogenetic tree using CytB and the concatenated sequences of the four DNA fragments. The sequences were aligned with ClustalW89 as implemented in MEGA90.…”

Multilocus DNA barcoding – Species Identification with Multilocus Data

“…example, a success rate close to 100% were reported for Germany herpetofauna 48 (Hawlitschek et al 2016), more than 90% for Chinese rodents (Li et al 2015a), more 49 than 80% for freshwater fishes of the Congo basin ; Decru et al…”