Figure 2

BPs of the three trees for the datasets constructed by successively removing the 50 most rapidly evolving genes. The horizontal axis shows the number of genes removed from the whole dataset of 2,789 genes. The dataset was analyzed using the (a) concatenate model; the (b) separate model, in which a category contains 50 genes grouped according to their total branch length; and (c) the separate model, in which different parameters were provided to each gene. Each analysis was performed using nucleotide (GTR + Γ₈; the left-most column of panels), codon (+ Γ₄; the middle column of panels), and amino acid (JTT + Γ₈; the right-most column of panels) substitution models.