Overview of nuclear genes used for the divergence time analysis.

The log-likelihood difference (ΔlogL) between the ML tree and the topology based on the generally accepted species phylogeny is shown with standard error. The topology of the ML tree is shown in newick format. The number of amino acid sites used for tree inference is shown for each gene, as well as their corresponding shape parameter α for gamma distribution. Abbreviations: aa, amino acid; ML, maximum likelihood tree; Dm, Drosophila melanogaster; Ds, Drosophila simulans; Ci, Ciona intestinalis; Cm, chimaeras; Sh, sharks; Ry, rays/skates; Fr, Takifugu rubripes; Ol, Oryzias latipes; Dr, Danio rerio; Hs, Homo sapiens; Md, Monodelphis domestica; Gg, Gallus gallus; Xt, Xenopus tropicalis.