Serine Codon-Usage Bias in Deep Phylogenomics: Pancrustacean Relationships as a Case Study
Serine Codon-Usage Bias in Deep Phylogenomics: Pancrustacean Relationships as a Case Study
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DOI：
10.1093/sysbio/sys077
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发表时间：
2013-01-01
影响因子：
6.5
通讯作者：
Pisani, Davide
中科院分区：
文献类型：
--
作者：
Rota-Stabelli, Omar;Lartillot, Nicolas;Pisani, Davide
古代亲缘关系的系统遗传学分析通常使用氨基酸数据，但目前尚不清楚应该优先选择氨基酸还是核苷酸。为了解决这个问题和澄清泛甲壳动物之间的关系，我们探索了Regier等人精心组装的62个蛋白质编码基因中的信号。在2010年。参照盘壳类，这个数据集推断出一个高度支持的核苷酸树，它与相应的但支持较差的氨基酸树有很大不同。我们发现，基于核苷酸和基于氨基酸的树之间的差异是由同义密码子家族(特别是丝氨酸-TCN和AGY)内的替换引起的。我们发现不同的节肢动物在丝氨酸、精氨酸和亮氨酸同义密码子的使用上存在不同的偏向，并且丝氨酸偏向与来自核苷酸的拓扑相关，而与氨基酸无关。我们认为，平行的，部分成分驱动的，同义密码子的使用偏见影响核苷酸拓扑。由于丝氨酸密码子家族之间的替代可以通过苏氨酸或半胱氨酸中间体进行，氨基酸数据集也可能受到丝氨酸密码子使用偏向的影响。我们建议，代霍夫重新编码策略将部分改善这种偏见的影响。虽然氨基酸为泛甲目动物的关系提供了另一种假说，但无论是核苷酸还是氨基酸版本的数据集似乎都没有带来足够的真正的系统发育信息来有力地解决组内的关系，这些关系仍然应该被认为是未解决的。
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 parallel, partially compositionally driven, synonymous codon-usage bias affects the nucleotide topology. As substitutions between serine codon families can proceed through threonine or cysteine intermediates, amino acid data sets might also be affected by the serine codon-usage bias. We suggest that a Dayhoff recoding strategy would partially ameliorate the effects of such bias. Although amino acids provide an alternative hypothesis of pancrustacean relationships, neither the nucleotides nor the amino acids version of this data set seems to bring enough genuine phylogenetic information to robustly resolve the relationships within group, which should still be considered unresolved.