Genetic differentiation of geographic populations of Rattus tanezumi based on the mitochondrial Cytb gene

Abstract

Rattus tanezumiis a common domestic rat and host of the bubonic plague pathogen in China and Southeast Asia (SEA). The origin, genetic differentiation and dispersal ofR.tanezumihave received increasing attention from researchers. The population genetics ofR.tanezumibased on its mitochondrial cytochrome b gene have been studied to explain the origin, relationships and dispersal of populations. In this study, we captured a total of 229 rats; morphological and molecular biological identification cytochrome oxidase subunit I (COI) confirmed 131R.tanezumiindividuals collected from 6 provincial areas, and theirCytbgene sequences were analyzed. The results showed that the population in Mohan (MH), Yunnan, had the highest genetic diversity, while that in Ningde (ND), Fujian, had the lowest. Tajima’sDstatistic for all populations was negative and nonsignificant, indicating the possible expansion ofR.tanezumipopulations. Low gene flow occurred between the Zhangmu (ZM)R.tanezumipopulation and other populations, and the genetic differentiation among them was high. Furthermore, our analyses revealed the ZM lineage was the oldest lineage among the groups and diverged ~1.06 Mya, followed by the Luoyang (LY) lineages (~0.51 Mya) and Yunnan lineage (~0.33 Mya). In southeastern Yunnan, the Jinshuihe (JSH) and MH populations were more closely related to the populations in southeastern China (Fuzhou (FZ), ND, Quanzhou (QZ), Nanchang (NC)) and inland areas (Chongqing (CQ), LY) than to those in other areas of Yunnan (Jiegao (JG) and Qingshuihe (QSH)), indicating thatR.tanezumimay have spread from southeastern Yunnan to the interior of China. In summary,R.tanezumimay have originated in ZM and adjacent areas, spread to Yunnan, and then spread from the southeast of Yunnan inland or directly eastward from ZM to inland China.