Supplemental files for manuscript entitled 'A novel approach to the detection of unusual mitochondrial protein change suggests hypometabolism of ancestral simians'

Supplemental files for the manuscript 'A novel approach to the detection of unusual mitochondrial protein change suggests hypometabolism of ancestral simians'. Supplemental File 1: All predicted protein substitutions along all edges at positions containing less than 2% gaps across input and ancestral sequences are listed, along with associated inferred taxonomy information, TSS, and branch length. All alignment positions refer to the Bos taurus reference sequences. Supplemental File 2: The TSS value calculated for each mitochondrial protein alignment position using the mammalian reference sequence dataset is provided. All alignment positions refer to the Bos taurus reference sequences. Supplemental File 3: SPCS and θevo outputs are provided for analyses across all mitochondria-encoded positions, as well as for focused analyses of specific OXPHOS complexes and individual proteins. Supplemental File 4: A GenBank flat file containing RefSeq entries for mammalian mtDNAs and the entry for the reptile Anolis punctatus. Supplemental File 5: A maximum likelihood inferred tree generated by RAxML-NG analysis of concatenated and aligned protein coding sequences from mammalian and Anolis punctatus mtDNAs. Supplemental File 6: Bootstrap replicates were generated from the alignment of concatenated protein coding sequences. Felsenstein’s Bootstrap Proportions (Felsenstein 1985) were calculated and used to label the maximum likelihood inferred tree of mammalian mtDNAs. Supplemental File 7: Bootstrap replicates were generated using concatenated mammalian mtDNA coding sequences. Transfer Bootstrap Expectations (Lemoine et al. 2018) were calculated and used to label the maximum likelihood inferred tree of mammalian mtDNAs. <br> Supplemental File 8: PAGAN tree output using aligned amino acid sequences and the rooted maximum likelihood inferred tree as input.本论文《检测异常线粒体蛋白变异的新方法提示类人猿祖先代谢减退》的补充材料如下： 补充文件1：列出了输入序列与祖先序列中缺失率低于2%的所有位点沿各分支的预测蛋白替换情况，同时附带相关的推断分类学信息、TSS以及分支长度。所有联配位点均以牛（Bos taurus）参考序列为参照基准。 补充文件2：提供了基于哺乳动物参考序列数据集计算得到的每个线粒体蛋白联配位点的TSS值。所有联配位点均以牛（Bos taurus）参考序列为参照基准。 补充文件3：提供了SPCS与θevo的分析输出结果，涵盖所有线粒体编码位点的全范围分析，以及针对特定氧化磷酸化（OXPHOS）复合物与单个蛋白的聚焦分析。 补充文件4：包含哺乳动物线粒体DNA（mtDNA）的参考序列（RefSeq）条目以及爬行动物斑点安乐蜥（Anolis punctatus）序列条目的GenBank平文件。 补充文件5：基于哺乳动物与斑点安乐蜥（Anolis punctatus）线粒体DNA的蛋白编码序列联配与拼接结果，通过RAxML-NG分析生成的最大似然法推断系统发育树。 补充文件6：基于拼接后的蛋白编码序列联配结果生成自举复制样本，计算得到费尔森斯坦自举比例（Felsenstein 1985），并以此标注哺乳动物线粒体DNA的最大似然法推断系统发育树。 补充文件7：基于拼接后的哺乳动物线粒体DNA编码序列联配结果生成自举复制样本，计算得到转移自举期望（Transfer Bootstrap Expectations，Lemoine et al. 2018），并以此标注哺乳动物线粒体DNA的最大似然法推断系统发育树。 补充文件8：以联配的氨基酸序列与已生根的最大似然法推断系统发育树作为输入，生成的PAGAN树输出结果。