Genomic analysis unveils mechanisms of northward invasion and signatures of plateau adaptation in the Asian house rat

Abstract

The Asian house rat (AHR), Rattus tanezumi, has recently invaded the northern half of China. The AHR is a highly adaptive rat species that has also successfully conquered the Qinghai-Tibet Plateau (QTP) and replaced the brown rat (BR), R. norvegicus, at the edge of the QTP. Here, we assembled a draft genome of the AHR and explored the mechanisms of its northward invasion and the genetic basis underlying plateau adaptation in this species. Population genomic analyses revealed that the northwardly invasive AHRs consisted of two independent and genetically distinct populations which might result from multiple independent primary invasion events. One invasive population exhibited reduced genetic diversity and distinct population structure compared with its source population, while the other displayed preserved genetic polymorphisms and little genetic differentiation from its source population. Genes involved in G-protein coupled receptors and carbohydrate metabolism may contribute to the local adaptation of northern AHRs. In particular, RTN4 was identified as a key gene for AHRs in the QTP that favours adaptation to high-altitude hypoxia. Coincidently, the physiological performance and transcriptome profiles of hypoxia-exposed rats both showed better hypoxia adaptation in AHRs than in BRs that failed to colonize the heart of the QTP, which may have facilitated the replacement of the BR population by the invading AHRs

Comparative phylogeography of two commensal rat species (Rattus tanezumi and Rattus norvegicus) in China: Insights from mitochondrial DNA, microsatellite, and 2b‐RAD data

“…The other 180 individuals belonging to R. tanezumi were distributed in 15 localities representing most areas of southern China and a part of northern China (Figure 2 ; Figures S1 and S2 ; Tables S1 and S4 ). The distribution patterns of the two species were consistent with previous records (Chen et al, 2021 ; Guo et al, 2019 ; Wang, 2003 ).…”

“…S2; Tables S1 and S4). The distribution patterns of the two species were consistent with previous records (Chen et al, 2021;Guo et al, 2019;Wang, 2003).…”

“…In addition, global warming is promoting the continued northward invasion of R. tanezumi in China, which contributes to the continuous increase of its Ne (Figure 6b). Both current results (Figure 2; Table S1) and previous studies (Chen et al, 2021;Zhang et al, 2000) indicated that R. tanezumi has established stable populations in Gansu (TS), Shanxi, Hebei, and Tianjin during recent decades.…”

“…It was believed that R. tanezumi originated in southeast Asian (Aplin et al, 2011 ; Chen et al, 2021 ; Guo et al, 2019 ). Based on mitochondrial DNA markers and several microsatellite loci, R. tanezumi immigrated into southeast coast of China by shipping transport and subsequently expanded to central China (Guo et al, 2019 ).…”

“…Based on microsatellite loci and mitochondrial DNA, R. tanezumi likely immigrated into China by shipping transportation over the sea and then expanded into Central China from coastal areas along the Yangtze River (Guo et al, 2019 ). Recent investigations with genome sequence data explored the possible genetic basis contributing to the northward invasion of R. tanezumi from southern China in recent decades, as well as the possible genetic basis favoring adaptation to high‐altitude hypoxia in Tibet (Chen et al, 2021 ). However, there are still key issues remaining to be solved, such as when R. tanezumi immigrated to China and the demographic history of this species.…”