Hoa→Thr flow in the three lineages of simians, sperm whale, and elephant, and hydrophobicity dependence.

Table gives the incoming (In) and outgoing (Out) AA numbers for the three AA groups of Hoa, Thr, and Rma (the remaining AAs except for Hoa and Thr), between the root and terminal sequences. For example, in the case A, the In and Out numbers denote the average site numbers of Thr residues which appeared and disappeared in the simian terminal sequences, respectively. These numbers were estimated in the two AA site domains, S<0.6 and S>0.6, of the local hydrophobic environment values (Methods and Materials). The flow denotes the differences of the AA numbers between In and Out, which become quite large in the high S-value domain of the AA sites. A, B and C represent the three cases of simians, sperm whale, and elephant, respectively. D gives the case of the real sequence of the tree shrew with a short branch from the root, to confirm that the estimation of the root sequence is not biased. The roots of the simians, the sperm whale and the elephant were defined as the most recent common ancestors of the tree shrew and primates, the sperm whale and hippopotamus, and the elephant and golden mole, respectively (Figure 1).