Population genomics reveal rapid genetic differentiation in a recently invasive population of Rattus norvegicus

BACKGROUND: Invasive species bring a serious effect on local biodiversity, ecosystems, and even human health and safety. Although the genetic signatures of historical range expansions have been explored in an array of species, the genetic consequences of contemporary range expansions have received little attention, especially in mammal species. In this study, we used whole-genome sequencing to explore the rapid genetic change and introduction history of a newly invasive brown rat (Rattus norvegicus) population which invaded Xinjiang Province, China in the late 1970s. RESULTS: Bayesian clustering analysis, principal components analysis, and phylogenetic analysis all showed clear genetic differentiation between newly introduced and native rat populations. Reduced genetic diversity and high linkage disequilibrium suggested a severe population bottleneck in this colonization event. Results of TreeMix analyses revealed that the introduced rats were derived from an adjacent population in geographic region (Northwest China). Demographic analysis indicated that a severe bottleneck occurred in XJ population after the split off from the source population, and the divergence of XJ population might have started before the invasion of XJ. Moreover, we detected 42 protein-coding genes with allele frequency shifts throughout the genome for XJ rats and they were mainly associated with lipid metabolism and immunity, which could be seen as a prelude to future selection analyses in the novel environment of XJ. CONCLUSIONS: This study presents the first genomic evidence on genetic differentiation which developed rapidly, and deepens the understanding of invasion history and evolutionary processes of this newly introduced rat population. This would add to our understanding of how invasive species become established and aid strategies aimed at the management of this notorious pest that have spread around the world with humans. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12983-021-00387-z.