Direct dating of fish gene duplications based on molecular clock was hampered by saturation of synonymous changes at the time scales considered, as well as by differences in evolutionary rates between mammals and fishes [ 1, 10- 13].
During the evolution of the lineages of the four fishes, gene duplications and losses occurred in each of these lineages.
Lysozyme g genes in fish species that diverged before the ancient fish-specific gene duplication do not have F in their name.
Our phylogenetic analysis reveals that both genes originated from a common ancestor by fish-specific gene duplication and represent the orthologs of the mammalian opg gene.
If subsequent phylogenetic surveys provided an indication for fish-specific gene duplication, additional BLAST searches were conducted to find more putative actinopterygian copies.
The ancient fish-specific gene duplication is incorporated into our proposed names for the lysozyme g genes, with the LygF1 genes being the paralog present in many species and the LygF2 being found in only a few (see Figure 1 and Additional files 1, 2, 11, and 13: Tables S1 and S2 and Figures S8 and S10).
There are at least four copies of genes under each of these branches in Tetraodon, but only one orthologous copy each has been identified in human genome, indicating fish specific gene duplications as observed earlier for trace amine receptors in zebrafish [ 20, 25].
This WGD explains the occurrence of many ray-finned fish-specific gene duplications [ 32, 33].
Furthermore, we show that among ray-finned fish, NASP has undergone gene duplication and two paralogs exist under different genomic G + C environments which suggests functional diversification of the two proteins.
Our molecular phylogenetic analyses of vertebrate Pgi genes showed that the Pgi-1 and Pgi-2 genes in teleost fishes resulted from a gene duplication event that occurred before the radiation of teleosts but after the separation of basal non-teleost ray-finned fishes.
This evolutionary pattern might suggest that the teleost fish scd experienced an ancient gene duplication event [ 12] or the genome duplication [ 6].
