Phylogenetic tree and Ka/Ka ratio forCernunnos-XLF coding sequences. A. Phylogenetic tree and Ka/Ka ratio for Cernunnos-XLF mammalian coding sequences. Phylogenetic tree obtained by the free ratio codon model in PAML. The ancestral branches from Fig. 1A are indicated by italics. Branch labels mark the ω = Ka/Ks ratios for corresponding branches. For the human and chimpanzee branches we could not calculate the Ka/Ks ratio and instead we list the number of synonymous (S) and nonsynonymous (N) changes in square brackets. The boxes list selected tested hypotheses. The Ka/Ks rate is designated as ωH for the in the human lineage, ωC for the chimpanzee lineage, and ω0 for all other lineages. A single asterisk indicates P < 5%, χ21 = 3.84, double asterisk indicates P < 1%, χ21 = 6.63. The left box tests the hypotheses that the Ka/Ks ratio for the human lineage is the same as for the rest of the tree (rejected at P < 5%), and that both human and chimpanzee lineages have the same Ka/Ks ratio shared with other branches (rejected at P < 1%). The right box shows tests Ka/Ks ≤ 1 for the human lineage (not significant) and for both human and chimpanzee lineages (rejected at P < 5%). B. Amino acid residues for five critical positions changed between human and chimpanzee. The tree also includes orthologous positions from the orangutan Cernunnos-XLF protein. The figure shows conservation of the critical positions in macaque and orangutan, which represents the most likely ancestral state. Four human and one chimpanzee changes indicated in the figure represent the most parsimonious scenario of Cernunnos-XLF evolution.