THE HYBRID HISTORY OF ZEBRAFISH

Abstract

AbstractSince the description of the zebrafishDanio rerioin 1822, the identity of its closest living relative has been unclear. To address this problem, we sequenced the exomes of ten species in genusDanioand used them to infer relationships across the 25 chromosomes of the zebrafish genome. The majority of relationships withinDaniowere remarkably consistent across all chromosomes. Relationships of chromosome segments, however, depended systematically upon genomic location within zebrafish chromosomes. Regions near chromosome centers identifiedD. kyathitand/orD. aesculapiias the closest relative of zebrafish, while segments near chromosome ends supported onlyD. aesculapiias the zebrafish sister species. Genome-wide comparisons of derived character states revealed that danio relationships are inconsistent with a simple bifurcating species history and support an ancient hybrid origin of theD. reriolineage. We also found evidence of more recent gene flow limited to the high recombination ends of chromosomes and several megabases of chromosome 20 with a history distinct from the rest of the genome. The additional insight gained from incorporating genome structure into a phylogenomic study demonstrates the utility of such an approach for future studies in other taxa. The multiple genomic histories of species in the genusDaniohave important implications for comparative studies in these species and for our understanding of the hybrid evolutionary history of zebrafish.