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

Widespread species that inhabit diverse environments possess large population sizes and exhibit a high capacity for environmental adaptation, thus enabling range expansion. In contrast, narrow-range species are confined to restricted geographical areas and are ecologically adapted to narrow environmental conditions, thus limiting their ability to expand into novel environments. However, the genomic mechanisms underlying the differentiation between closely related species with varying distribution ranges remain poorly understood. The Niviventer niviventer species complex (NNSC), consisting of highly abundant wild rats in Southeast Asia and China, offers an excellent opportunity to investigate these questions due to the presence of both widespread and narrow-range species that are phylogenetically closely related. In the present study, we combined ecological niche modeling with phylogenetic analysis, which suggested that sister species cannot be both widespread and dominant within the same geographical region. Moreover, by assessing heterozygosity, linkage disequilibrium decay, and Tajima's D analysis, we found that widespread species exhibited higher genetic diversity than narrow-range species. In addition, by exploring the "genomic islands of speciation", we identified 13 genes in highly divergent regions that were shared by the two widespread species, distinguishing them from their narrow-range counterparts. Functional annotation analysis indicated that these genes are involved in nervous system development and regulation. The adaptive evolution of these genes likely played an important role in the speciation of these widespread species.

Gene flow influences the genomic architecture of local adaptation in six riverine fish species.

Understanding how gene flow influences adaptive divergence is important for predicting adaptive responses. Theoretical studies suggest that when gene flow is high, clustering of adaptive genes in fewer genomic regions would protect adaptive alleles from recombination and thus be selected for, but few studies have tested it with empirical data. Here, we used restriction site-associated sequencing to generate genomic data for six fish species with contrasting life histories from six reaches of the Upper Mississippi River System, USA. We used four differentiation-based outlier tests and three genotype-environment association analyses to define neutral single nucleotide polymorphisms (SNPs) and outlier SNPs that were putatively under selection. We then examined the distribution of outlier SNPs along the genome and investigated whether these SNPs were found in genomic islands of differentiation and inversions. We found that gene flow varied among species, and outlier SNPs were clustered more tightly in species with higher gene flow. The two species with the highest overall FST (0.0303-0.0720) and therefore lowest gene flow showed little evidence of clusters of outlier SNPs, with outlier SNPs in these species spreading uniformly across the genome. In contrast, nearly all outlier SNPs in the species with the lowest FST (0.0003) were found in a single large putative inversion. Two other species with intermediate gene flow (FST  ~ 0.0025-0.0050) also showed clustered genomic architectures, with most islands of differentiation clustered on a few chromosomes. Our results provide important empirical evidence to support the hypothesis that increasingly clustered architecture of local adaptation is associated with high gene flow.

Genomic islands of differentiation in two songbird species reveal candidate genes for hybrid female sterility.

Hybrid sterility is a common first step in the evolution of postzygotic reproductive isolation. According to Haldane's Rule, it affects predominantly the heterogametic sex. While the genetic basis of hybrid male sterility in organisms with heterogametic males has been studied for decades, the genetic basis of hybrid female sterility in organisms with heterogametic females has received much less attention. We investigated the genetic basis of reproductive isolation in two closely related avian species, the common nightingale (Luscinia megarhynchos) and the thrush nightingale (L. luscinia), that hybridize in a secondary contact zone and produce viable hybrid progeny. In accordance with Haldane's Rule, hybrid females are sterile, while hybrid males are fertile, allowing gene flow to occur between the species. Using transcriptomic data from multiple individuals of both nightingale species, we identified genomic islands of high differentiation (FST ) and of high divergence (Dxy ), and we analysed gene content and patterns of molecular evolution within these islands. Interestingly, we found that these islands were enriched for genes related to female meiosis and metabolism. The islands of high differentiation and divergence were also characterized by higher levels of linkage disequilibrium than the rest of the genome in both species indicating that they might be situated in genomic regions of low recombination. This study provides one of the first insights into genetic basis of hybrid female sterility in organisms with heterogametic females.