Using parsimony, we analyzed codon usages across 12,337 species and 25,727 orthologous genes to rank specific genes and codons according to their phylogenetic signal. We examined each codon within each ortholog to determine the codon usage for each species. In total, 890,814 codons were parsimony informative. Next, we compared species that used a codon with species that did not use the codon. We assessed each codon's congruence with species relationships provided in the Open Tree of Life (OTL) and determined the statistical probability of observing these results by random chance. We determined that 25,771 codons had no parallelisms or reversals when mapped to the OTL. Codon usages from orthologous genes spanning many species were 1109× more likely to be congruent with species relationships in the OTL than would be expected by random chance. Using the OTL as a reference, we show that codon usage is phylogenetically conserved within orthologous genes in archaea, bacteria, plants, mammals, and other vertebrates. We also show how to use our provided framework to test different tree hypotheses by confirming the placement of turtles as sister taxa to archosaurs.

中文翻译：

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密码子的使用和厌恶在整个生命树上都得到了系统地保守。

使用简约性，我们分析了12,337个物种和25,727个直系同源基因的密码子使用，以根据其系统发生信号对特定基因和密码子进行排名。我们检查了每个直系同源物中的每个密码子，以确定每个物种的密码子使用情况。总共890,814个密码子具有简约信息。接下来，我们将使用密码子的物种与未使用密码子的物种进行了比较。我们用开放生命树（OTL）中提供的物种关系评估了每个密码子的一致性，并确定了通过随机机会观察到这些结果的统计概率。我们确定，当映射到OTL时，有25,771个密码子没有并行或逆转。来自OTL的直系同源基因的密码子用法与OTL中的物种关系相符的可能性比随机机会期望的高1109倍。使用OTL作为参考，我们表明在古细菌，细菌，植物，哺乳动物和其他脊椎动物的直系同源基因内，密码子使用在系统发育上是保守的。我们还展示了如何通过确认乌龟作为恐龙的姊妹类群的位置来使用我们提供的框架来测试不同的树假设。