Text S1 - Positively Selected Sites in Cetacean Myoglobins Contribute to Protein Stability

Text S1 contains the following information: Table S1: Experimental and computed FoldX ΔΔG for a range of Mb mutations. The FoldX results (last two columns) are reported using two PDB structures: 1MBO and 1U7S. Figure S1: ΔΔG values predicted by FoldX versus experimental ΔΔGs (kcal/mol) for the validation set (pdb = 1MBO). Figure S2: ΔΔG values predicted by FoldX versus experimental ΔΔGs (kcal/mol) for the validation set (pdb = 1U7S). Table S2: FoldX calculations for all mutations in the Cetacean clade using PDB structure 1U7S. Mutations in the sites detected to be under positive selection are shown in grey. Table S3: The best nucleotide and amino acid substitution models fitted to the data. Table S4: Results of amino acid substitution models for the whale clade. Table S5: Results of nucleotide substitution models for the whale clade. Table S6: Likelihood ratio tests for site models when branch lengths are estimated for each model rather than taking the ML-estimated branch lengths from the M0 model. LRT values are shown for M7 vs. M8 and M8 vs. M8fix. Scheme S1: Alignment for sperm whale, pig, bovine, dog, sheep, horse and human myoglobin (Mb) sequences. Scheme S2: The most probable cetacean ancestor with the complete phylogenetic tree (Figure 1-B), primate-rodent truncated tree, and only the cetacean clade. Table S7: LRT values for M7 vs. M8 and M8 vs. M8fix for the gene tree of cetaceans rather than using the species tree. Table S8: Species name and accession number of Mb sequences used in this study. The end of Text S1 contains CODEML and NetPhos Output. (PDF)