Phylogenetic Trees and ω ratio for Complete <i>ASPM</i> and Three Selected Segments

<div><p>Trees and ω (Ka/Ka) ratios were computed using the ML method for codons implemented in PAML. Branch lengths represent ML distances for codons, i.e., using both synonymous and nonsynonymous nucleotide sites, and in all branches the ω ratio was set free to vary. All trees are drawn to the same scale. Branch labels mark the ω ratios for corresponding branches. Values in square brackets show ω for additional cDNA sequences whenever available. Default values and branch lengths were calculated from genomic copies. Selected tested hypotheses are listed. ω_H stands for the ω rate in the human lineage, ω_C in the chimpanzee lineage, ω_CH in the common human–chimpanzee ancestral lineage after the gorilla divergence, ω_G in the gorilla lineage, and ω₀ in all other branches. Single asterisks indicate <i>p</i> < 0.05, χ²₁ = 3.84; double asterisks indicate <i>p</i> < 0.01, χ²₁ = 6.63.</p> <p>(A) Phylogeny for the complete <i>ASPM</i> CDS. In addition to testing different ω values in the human lineage, we also tested the hypothesis that the complete gorilla–chimpanzee–human clade evolved at a constant rate, different from the rest of the tree (compared to the one-ratio model, boxed).</p> <p>(B) The <i>ASPM</i> phylogeny derived from a conserved segment from exon 5 to the beginning of the IQ domain (amino acids 676–1,266). The branch connecting the human and chimpanzee common ancestor with the gorilla–chimpanzee–human common ancestor had no substitutions, therefore the ω ratio could not be calculated.</p> <p>(C) IQ domain (amino acids 1,267–3,225). We also tested the hypothesis that the gorilla and human lineages evolved at the same ω rate, different from the rest of the tree (compared to the one-ratio model, boxed).</p> <p>(D) Phylogeny of eight primate sequences from a 1,215-amino-acid-long segment of exon 18 (amino acids 1,640–2,855). We also tested the hypothesis that the gorilla and human lineages evolved at the same ω rate, different from the rest of the tree (compared to the one-ratio model, boxed).</p>