Identifying Rattus species using mitochondrial DNA

Abstract

In recent years, research has shown that geographical variation in mitochondrial DNA of commensal rats provides a strong signal of human dispersal and migration. However, interpretation of genetic variation is complicated by the presence of multiple species of Rattus especially in Island Southeast Asia, by the occurrence of some of these Rattus sp. as subfossils in archaeological and natural sites, and by the difficulty of osteological identification of these remains. Amplification of DNA from ancient sources usually yields only small fragments (∼200 bp). We assessed whether we could identify Rattus sp. reliably with DNA barcoding using cytochrome oxidase I (COI) sequences, or tree‐based methods using D‐loop, cytochrome b and COI sequences. Species forming well‐differentiated clades in a molecular phylogeny were accurately identified by both methods, even when we used short DNA fragments. Identification was less accurate for paraphyletic and polyphyletic species. We suggest that taxonomic revisions that recognize cryptic or polytypic species will lead to even greater accuracy of DNA‐based identification methods.

Analysis of vkorc1 polymorphisms in Norway rats using the roof rat as outgroup

“…We followed the DNA barcoding protocol as described [25]. CO1 sequence information for R. rattus (EF186585), Norway rat (NC_001665), R. tanezumi (EF186623) and the mouse ( M. m. domesticus; NC_006914) were retrieved from GenBank.…”

Metal and metalloid contamination in roadside soil and wild rats around a Pb–Zn mine in Kabwe, Zambia

“…The university is very large and should be a non-contaminated area because there is little traffic on campus and it is located far from any industrial, agricultural or mining areas. Mitochondrial DNA sequencing suggested the rat species were Rattus rattus or Rattus tanezumi (Robins et al, 2007), and these species are closely related. Consequently, we treated our rat samples as coming from the same group.…”

DNA barcoding of 18 species of Bovidae

“…Previous DNA barcode studies led to large-scale barcoding campaigns for various animal groups, such as birds, fish, *Corresponding authors (email: zliang@panda.org.cn; zhangzhh@mail.sc.cninfo.net) and lepidopterans [11]. Although DNA barcoding is increasingly regarded as efficient, existing work on mammals has been limited to a few studies of primates and small mammals [1,6,8,12,13].…”