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

The wild rats in the genus Rattus represent a group of murids characterized by rapid lineage diversification but limited morphological variation. Within this genus, there are several commensal species with high invasive capacity, such as Rattus 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 morphological study and whole‐genome sequencing on Rattus species distributed in China and adjacent regions to gain insights into morphological differentiation, as well as genomic divergence and gene flow using assembled mitochondrion genome and high‐quality single nucleotide polymorphisms. Despite their morphological similarity and large overlap in morphospace, our analyses revealed significant genetic differentiation at the genomic level among Rattus species in China and adjacent regions. Specifically, intraspecific differentiation was observed in R. nitidus, R. norvegicus, and R. tanezumi, which may be related to habitat heterogeneity and geographic isolation. We hypothesize that as invasive rats expand their habitat, the diversification of ecological environments might lead to more environmentally adapted evolution and accelerated genetic differentiation. Furthermore, Dsuite and TreeMix analyses detected substantial introgression among different Rattus species, particularly evident between R. norvegicus and R. tanezumi. Strong gene flow signals suggest frequent hybridization events among these species, which may facilitate the acquisition of new environmental adaptability during their expansion into new territories. This study provides a preliminary analysis that serves as a foundation for a more comprehensive investigation into the rapid lineage diversification and adaptive introgression among Rattus species.