Comparative genomics of widespread and narrow-ranged white-bellied rats in the Niviventer niviventer species complex sheds light on the success of invasive rodents

Widespread species that live in diversified environments have large population sizes and a high capacity for environmental tolerance and thus for range expansion. In contrast, narrow-ranged species are confined in restricted geographical areas and ecologically adjusted to narrow environmental conditions and consequently may have limited capacity to expand into a novel environment. However, it is not clear how genomic mechanisms underlie the differentiation in the closely related species that differ in their distribution ranges. The Niviventer niviventer species complex (NNSC), a group of the most abundant wild rats in Southeast Asia and China, provides an ideal system to investigate these questions, as this group includes widespread and narrow-ranged species that are phylogenetically closely related. In the present study, we combined ecological niche models with phylogenetic analysis suggesting that sister species cannot be both widespread and dominant in the same geographical region. Heterozygosity, linkage disequilibrium decay and Tajima's D analysis suggested that widespread species have higher genetic diversity than narrow-ranged species. Moreover, scanning ‘genomic islands of speciation’ revealed 13 genes in highly divergent regions that were shared by two widespread species, which distinguished them from the narrow-ranged species. In addition, functional annotation results suggested that these genes are involved in nervous system development and regulation. Adaptive evolution of these genes likely plays an important role in the speciation of these widespread species.