Stable species boundaries despite ten million years of hybridization in tropical eels

Genomic evidence is increasingly underpinning that hybridization between
taxa is commonplace, challenging our views on the mechanisms that maintain
their boundaries. Here, we focus on seven catadromous eel species (genus
Anguilla), and use genome-wide sequence data from more than 450
individuals sampled across the tropical Indo-Pacific, morphological
information, and three newly assembled draft genomes to compare
contemporary patterns of hybridization with signatures of past gene flow
across a time-calibrated phylogeny. We show that the seven species have
remained distinct entities for up to 10 million years, despite a dynamic
scenario of incomplete isolation whereby the current frequencies of
hybridization across species pairs (over 5% of all individuals were either
F1 hybrids or backcrosses) contrast remarkably with patterns of past
introgression. Based on near-complete asymmetry in the directionality of
hybridization and decreasing frequencies of later-generation hybrids, we
identify cytonuclear incompatibilities and hybrid breakdown as two
powerful mechanisms that can support species cohesion even when
hybridization has been pervasive throughout the evolutionary history of
entire clades.