The Phylogenetic Informativeness of Nucleotide and Amino Acid Sequences for Reconstructing the Vertebrate Tree
The Phylogenetic Informativeness of Nucleotide and Amino Acid Sequences for Reconstructing the Vertebrate Tree
复制标题
DOI：
10.1007/s00239-008-9142-0
复制
发表时间：
2008-11-01
影响因子：
3.9
通讯作者：
Friedman, Robert
中科院分区：
文献类型：
--
作者：
Townsend, Jeffrey P.;Lopez-Giraldez, Francesc;Friedman, Robert
为了帮助未来的努力准确地重建脊椎动物树，将系统发育信息性的定量度量应用于一组11个基因的核苷酸和氨基酸序列。我们确定了直系同源物，并组装出已发表的化石释放时间，分类群已经对每个基因进行了测序。估计每个位点的分子进化速率以表征基因的分子进化模式并计算系统发育信息。快速发展的基因白蛋白在6000万年前到5亿年前产生的信息最高。相比之下，钙调蛋白产生的信息最低，大概是因为功能约束最小化氨基酸序列中的取代。基因C-MYC显示出中间信息的信息。细胞色素B的核苷酸序列在最近的时期显示出极高的效用，但在1亿年前之前的时间较低。在肉芽啮齿动物，早期胎盘哺乳动物，早期脊椎动物和早期后生动物的差异时期，我们对其效用进行了九个基因的效用，从而产生了与先前的研究相一致但更精确的结果。有趣的是，DNA序列在所有时间尺度上始终超过信息性中的氨基酸序列，但支持值充其量较高。对于由于收敛而不受严重系统发育冲突而不受强大系统发育冲突的时期，我们主张收集到DNA序列的三倍增加的额外功能，而不是诉诸于噪声较小但信息较少的氨基酸序列。
To aid in future efforts to accurately reconstruct the vertebrate tree, a quantitative measure of phylogenetic informativeness was applied to nucleotide and amino acid sequences for a set of 11 genes. We identified orthologues and assembled published fossil-calibrated divergence times between taxa that had been sequenced for each gene. Rates of molecular evolution for each site were estimated to characterize the molecular evolutionary pattern of genes and to calculate the phylogenetic informativeness. The fast-evolving gene albumin yielded the highest informativeness over the period from 60 million years ago to 500 million years ago. In contrast, calmodulin yielded the lowest informativeness, presumably because functional constraint minimized substitutions in the amino acid sequence. The gene c-myc showed an intermediate level of informativeness. The nucleotide sequence of cytochrome b showed extremely high utility for recent epochs, but low utility for times before 100 million years ago. We ranked nine other genes for their utility during the epochs of the divergence of the muroid rodents, early placental mammals, early vertebrates, and early metazoa, yielding results consistent with, but more precise than, previous studies. Interestingly, DNA sequence always exceeded amino acid sequence in informativeness over all time scales, yet support values were at best moderately higher. For epochs not subject to strong phylogenetic conflict due to convergence, we advocate gleaning the additional power of the threefold increase in number of characters that is present for DNA sequences over resorting to the less noisy but less informative amino acid sequences.