Genome-wide patterns of differentiation and gene flow in the <i>Oligoryzomys flavescens</i> (Waterhouse, 1837) complex (Rodentia, Cricetidae): preliminary evidence from RAD-seq data

Abstract Genomic analyses combined with environmental data can help to elucidate evolutionary processes in closely related species. Here, we used a population genomics approach to assess whether speciation processes occurred with or without genetic exchange among three species of the Oligoryzomys flavescens complex. Using RAD-seq, we analyzed genetic diversity, signals of positive selection, genotype–environment associations, and population structure in O. flavescens sensu stricto (s.s.), O. fornesi, and O. f. occidentalis. We first estimated diversity metrics and population structure with 2008 genome-wide SNPs. Then, using Bayesian analyses, we identified 10 loci under putative positive selection and repeated the analyses only with this subset. Both datasets consistently showed that O. f. occidentalis had the highest nucleotide diversity and the greatest number of private alleles. This taxonomic entity was clearly distinct from the other two in all results, including PCA, phylogenetic trees, and Admixture analyses. In contrast, O. flavescens s.s. and O. fornesi exhibited lower differentiation levels. Redundancy analysis indicated that elevation and seasonal temperature were the main environmental variables explaining the observed genetic structure. Furthermore, we identified possible hybridization events in contact zones between O. flavescens s.s. and O. fornesi in Chaco and Corrientes provinces, and between O. f. occidentalis and O. flavescens s.s. in Córdoba province, Argentina. Our results suggest that speciation and diversification of these Neotropical rodents were shaped by interspecific gene flow in contact zones and divergent environmental pressures throughout the rest of their distribution ranges.