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

Yi Chen,Huajing Teng,Jianxu Zhang,Yaohua Zhang,Quansheng Liu,Chengmin Shi,Lei Zhao

doi:10.1186/s12983-021-00387-z

Abstract

BackgroundInvasive 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.ResultsBayesian 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.ConclusionsThis 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.

Highlights

Invasive species bring a serious effect on local biodiversity, ecosystems, and even human health and safety
After applying stringent quality control criteria, we identified a total of 11.3 million single nucleotide polymorphisms (SNPs) among all the individuals
Population structure and genetic relationships among rat populations To identify population structure and the genetic relationships of different rat populations, we performed a series of classical analyses including Bayesian clustering analysis by ADMIXTURE, principal components analysis (PCA), and phylogenetic assessments using wholegenome SNPs (Fig. 2)

Summary

Introduction

Invasive species bring a serious effect on local biodiversity, ecosystems, and even human health and safety. 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. Invasive species are a major threat for native biodiversity (such as species decline or extinction) and ecosystems [1, 2], and cause considerable annual damage to agriculture, property, human health and (2021) 18:6 population structure, demographic history, and molecular evolution of invasive populations [12,13,14,15]. Based on historical records, the brown rat was not observed in Xinjiang Province (XJ) until the late 1970s [25,26,27]. It has spread throughout XJ and there is a large population in the region [26, 28, 29]

Methods

Results

Discussion

Conclusion