Serine codon-usage bias in deep phylogenomics: pancrustacean relationships as a case study

Phylogenomic analyses of ancient relationships are usually performed using amino acid data, but it is unclear whether amino acids or nucleotides should be preferred. With the 2-fold aim of addressing this problem and clarifying pancrustacean relationships, we explored the signals in the 62 protein-coding genes carefully assembled by Regier et al. in 2010. With reference to the pancrustaceans, this data set infers a highly supported nucleotide tree that is substantially different to the corresponding, but poorly supported, amino acid one. We show that the discrepancy between the nucleotide-based and the amino acids-based trees is caused by substitutions within synonymous codon families (especially those of serine—TCN and AGY). We show that different arthropod lineages are differentially biased in their usage of serine, arginine, and leucine synonymous codons, and that the serine bias is correlated with the topology derived from the nucleotides, but not the amino acids. We suggest that a ...

针对古老演化关系的系统基因组学分析通常采用氨基酸序列数据开展，但学界尚未明确氨基酸与核苷酸两类数据何者更为适用。本研究旨在解决上述争议并阐明泛甲壳动物（Pancrustacea）的系统发育关系，为此我们对Regier等人2010年精心组装得到的62个蛋白质编码基因中的演化信号展开了探究。针对泛甲壳动物类群，本数据集通过核苷酸序列推断出一棵节点支持度极高的系统发育树，其拓扑结构与基于氨基酸序列得到的对应系统树差异显著，但后者的节点支持度较低。本研究表明，核苷酸与氨基酸两类系统树之间的拓扑差异，源于同义密码子家族（尤其是丝氨酸密码子家族TCN与AGY）内部的碱基替换事件。本研究还发现，不同节肢动物支系在丝氨酸、精氨酸与亮氨酸的同义密码子使用上存在显著偏好差异，且丝氨酸密码子的使用偏好与基于核苷酸序列推断的系统发育拓扑结构显著相关，但与基于氨基酸序列得到的拓扑结构无关。本研究提出，……