The continuing impact of an ancient polyploidy on the genomes of teleosts

The ancestor of most teleost fishes underwent a whole-genome duplication event three hundred million years ago. Despite its antiquity, the effects of this event are evident both in the structure of teleost genomes and in how those genes still operate to drive form and function. I describe the inference of a set of shared syntenic regions that survive from the teleost genome duplication (TGD) using eight teleost genomes and the outgroup gar genome (which lacks the TGD). I phylogenetically modeled the resolution of the TGD via shared and independent gene losses, concluding that it was likely an allopolyploidy event due to the biased pattern of these gene losses. Duplicate genes surviving from this duplication in zebrafish are less likely to function in early embryo development than are genes that have returned to single copy. As a result, surviving ohnologs function later in development, and the pattern of which tissues these ohnologs are expressed in and their functions lend support to recent suggestions that the TGD was the source of a morphological innovation in the structure of the teleost retina. Surviving duplicates also appear less likely to be essential than singletons, despite the fact that their single-copy orthologs in mouse are no less essential than other genes. Nonetheless, the surviving duplicates occupy central positions in the zebrafish metabolic network.