Prevalent Hybridisation Between Highly Divergent Iberian Chub Species Produces Contrasting Outcomes Across Different Geographic and Time Scales

Genomic data has revealed hybridisation is common in nature. Highly divergent allopatric species are often overlooked in our efforts to characterise the prevalence and consequences of hybridisation in natural systems, presumably because they are viewed as less likely to hybridise. Yet, such species are models to investigate later stages of the speciation continuum. Here, we study such a system-the Iberian chubs (Squalius spp.), a group of primary fish species with allopatric distributions across distinct environments and river catchments. Throughout their evolutionary history, the rivers inhabited by these species suffered quite dramatic changes, potentially allowing for multiple periods of isolation and secondary contact. To investigate if such a history left traces, we generated low-coverage whole-genome resequencing data for 125 individuals from eight Iberian chub species. Our results showed high levels of inter (0.44 ≤ F_ST ≤ 0.88) and intra-specific (0 ≤ F_ST ≤ 0.61) genetic differentiation. We uncovered four contrasting cases of potential hybridisation, spanning different geographical and time scales. First, we found evidence of ancient hybridisation on a species now inhabiting a whole river catchment. Second, we uncover recent hybridisation restricted to a localised stream, with introgression of nuclear and mitochondrial DNA. Third, we detected, at a regional scale, a case with nuclear introgression but no detectable mitochondrial DNA introgression. Finally, we uncover a case where two very distinct mitochondrial lineages persist at balanced frequencies in a putative hybrid population, despite no detectable nuclear introgression. Our findings suggest hybridisation and introgression led to assimilation or local exclusion of one or both parental species.