Genomic differentiation and gene flow among Rattus species distributed in China and adjacent regions

The wild rat in the genus Rattus represents a group of rodents characterized by rapid lineage diversification but limited morphological variation. Within this genus, there are several commensal species with high invasive capacity, such as R. norvegicus and R. rattus, which pose a global threat. Investigating the mechanisms behind their adaptive evolution is of utmost importance. In this study, we conducted whole-genome sequencing on Rattus species distributed in China and adjacent regions to gain insights into genomic divergence and gene flow using assembled mitochondrion genome and high-quality SNPs. Despite their morphological similarity, our analyses have revealed significant genetic differentiation at the genomic level among Rattus species in China and adjacent regions. Specifically, subpopulation differentiation was observed in R. nitidus, R. norvegicus, and R. tanezumi, which may be related to habitat heterogeneity and long-distance migration. We hypothesize that as invasive rats expand their habitat, the diversification of ecological environments might lead to more environmentally adapted evolution, resulting in accelerated genetic differentiation between species. Furthermore, Dsuite and TreeMix analyses detected substantial introgression signals between different Rattus species, particularly evident in gene flow between R. norvegicus and R. tanezumi. Strong gene flow signals suggest frequent hybridization events between these species which might facilitate the acquisition of new environmental adaptability during expansion into new territories. This study provides a preliminary analysis for an in-depth exploration of rapid lineage diversification and adaptive introgression among Rattus, which can serve as a basis for further research.