Data from: Contrasting interspecific hybridization patterns in two goby groups radiating in divergent freshwater habitats

Hybridization and introgression between closely related species significantly affect their evolutionary and ecological processes. Understanding of the ecological, environmental, and geographic conditions that promote their occurrence is imperative. It is hypothesized that species inhabiting geologically unstable habitats or with life-history constraints that prevent evasion from such environments, are more prone to interspecific hybridization, due to limited development of prezygotic isolation. To test this hypothesis, we conducted a comparative analysis of genome-wide hybridization patterns in two freshwater goby groups of <i>Gymnogobius</i>: the castaneus- and urotaenia-groups. Utilizing the newly determined draft genome of <i>G. isaza</i> and single nucleotide variants identified by RNA-seq, we first established the species phylogeny and then examined genetic signatures of interspecific hybridization in each group. The results revealed that all castaneus-group species, which primarily inhabit unstable habitats such as ponds, have undergone interspecific hybridization. Conversely, no species of the urotaenia-group showed clear evidence of hybridization over a period of more than one million years. These species inhabit an ancient lake (one species) or rivers (three amphidromous species), the latter possessing potential dispersal abilities in early life to evade geological disturbances. These ecology–geology relationships have remarkable implications for the intricate processes of adaptation and speciation.