A novel approach to the detection of unusual mitochondrial protein change suggests hypometabolism of ancestral simians: Supplemental Files

<p><strong>Supplementary Fig. S1</strong>: &theta;_evo calculated for each analyzed edge for specific OXPHOS complexes. Analyses were performed as in fig. 1F, except that SPCSs calculated from mtDNA-encoded protein positions in Complex I, Complex III, Complex IV, or Complex V were used to generate &theta;evo values.</p> <p><strong>Supplementary Fig. S2</strong>: Mammalian orders differ in their propensity for potentially efficacious mitochondrial protein substitutions within specific OXPHOS complexes (median calculations). Analysis was performed as in fig. 2A, except that &theta;_evo values were obtained by analysis of mtDNA-encoded Complex I, Complex III, Complex IV, or Complex V polypeptides.</p> <p><strong>Supplementary Fig. S3</strong>: Mammalian orders differ in their propensity for potentially efficacious mitochondrial protein substitutions within specific OXPHOS complexes (median confidence intervals). Analysis was performed as in (<em>A</em>) fig. 2B or (<em>B</em>) fig. 2C, except that &theta;_evo values were obtained by analysis of mtDNA-encoded Complex I, Complex III, Complex IV, or Complex V proteins.</p> <p><strong>Supplementary Fig. S4</strong>: Mammalian families differ in their propensity for potentially efficacious mitochondrial protein substitutions at specific OXPHOS complexes (median calculations). Analysis was performed as in fig. 3A, except that &theta;_evo values were obtained by analysis of mtDNA-encoded Complex I, Complex III, Complex IV, or Complex V subunits.</p> <p><strong>Supplementary Fig. S5</strong>: Mammalian families differ in their propensity for potentially efficacious mitochondrial protein substitutions at specific OXPHOS complexes (median confidence intervals ordered by lower 90% median confidence limit). Analysis was performed as in fig. 3B, except that &theta;_evo values were obtained by analysis of mtDNA-encoded Complex I, Complex III, Complex IV, or Complex V proteins.</p> <p><strong>Supplementary Fig. S6</strong>: Mammalian families differ in their propensity for potentially efficacious mitochondrial protein substitutions at specific OXPHOS complexes (median confidence intervals ordered by upper 90% median confidence limit). Analysis was performed as in fig. 3C, except that &theta;_evo values were obtained by analysis of mtDNA-encoded Complex I, Complex III, Complex IV, or Complex V polypeptides.</p> <p>---</p> <p><strong>Supplementary File 1</strong>: All predicted protein substitutions along all edges at positions containing less than 2% gaps across input and ancestral sequences are listed, along with associated taxonomy information, TSS, and branch length. All alignment positions refer to Bos taurus reference sequences.</p> <p><strong>Supplementary File 2</strong>: The TSS calculated for each mitochondrial protein alignment position. All alignment positions refer to Bos taurus reference sequences.</p> <p><strong>Supplementary File 3</strong>: SPCS and &theta;evo outputs are provided for analyses across all mitochondria-encoded positions, as well as for focused analyses of specific OXPHOS complexes and individual proteins.</p> <p><strong>Supplementary File 4</strong>: A GenBank flat file containing RefSeq entries for mammalian mtDNAs, as well as the entry for the reptile Anolis punctatus.</p> <p><strong>Supplementary File 5</strong>: A maximum likelihood inferred tree generated by a RAxML-NG analysis of concatenated and aligned protein coding sequences from mammalian and Anolis punctatusmtDNAs.</p> <p><strong>Supplementary File 6</strong>: Bootstrap replicates were generated from the alignment of concatenated protein coding sequences. Felsenstein&rsquo;s Bootstrap Proportions (Felsenstein 1985) were calculated and used to label the maximum likelihood inferred tree of mammalian mtDNAs.</p> <p><strong>Supplementary File 7</strong>: Bootstrap replicates were generated using concatenated mammalian mtDNA coding sequences. Transfer Bootstrap Expectations (Lemoine 2018) were calculated and used to label the maximum likelihood inferred tree of mammalian mtDNAs.</p> <p><strong>Supplementary File 8</strong>: PAGAN tree output produced using aligned amino acid sequences and the rooted maximum likelihood inferred tree as input.</p>