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.

A flow chart showing the steps used to generate files anguilla_hapl1.fa.gz, anguilla_hapl2.fa.gz, anguilla_aln1.tgz, anguilla_aln2.tgz, anguilla_var1.vcf.gz, anguilla_var2.vcf.gz, and anguilla_var3.vcf.gz is provided as Supplementary Figure 1 of the manuscript.

Files angmar.mapped.fq.gz, angmeg.mapped.fq.gz, and angobs.mapped.fq.gz were generated as described in section "Detecting past introgression" of the manuscript.

The file dotplots.tgz was generated as described in Supplementary Note 6.

Code used to generate and analyze the files of this repository can be found at https://github.com/mmatschiner/anguilla