Calculation of evolutionary trees from sequence data.
Calculation of evolutionary trees from sequence data.
复制标题
根据序列数据计算进化树。
DOI：
10.1073/pnas.76.9.4516
复制
发表时间：
1979
影响因子：
11.1
通讯作者：
R. M. Mitchell
中科院分区：
文献类型：
--
作者：
L. Klotz;N. Komar;R. L. Blanken;R. M. Mitchell
进化树通常是通过利用仅使用差异矩阵的算法，对现今生物的蛋白质或核酸序列进行比较来计算的，其中差异矩阵是由来自生物的成对序列之间的序列差异构建而成。仅差异矩阵无法唯一确定现今生物祖先（树的根）的正确位置。此外，当不同序列以不同速率进化时，仅使用差异矩阵的方法往往无法给出正确的树枝状分支模式（拓扑结构）。只有在进化速率相等时，差异矩阵（当与所谓的矩阵方法一起使用时）才能准确得出正确的拓扑结构和根。在本文中，我们提出了一种从序列数据计算进化树的方法，该方法除了使用差异矩阵外，还使用了各种序列从其共同祖先开始的进化速率。通过分析证明，在理论上，对于序列进化速率不相等的情况，该方法能够唯一确定正确的拓扑结构和根。特别针对原核生物和真核生物的5S RNA序列以及铁氧化还原蛋白序列，讨论了如何估计该方法中要使用的祖先序列。
Evolutionary trees are usually calculated from comparisons of protein or nucleic acid sequences from present-day organisms by use of algorithms that use only the difference matrix, where the difference matrix is constructed from the sequence differences between pairs of sequences from the organisms. The difference matrix alone cannot define uniquely the correct position of the ancestor of the present-day organisms (root of the tree). Furthermore, methods using the difference matrix alone often fail to give the correct pattern of tree branching (topology) when the different sequences evolve at different rates. Only for equal rates of evolution can the difference matrix (when used with the so-called matrix method) yield exactly the correct topology and root. In this paper we present a method for calculating evolutionary trees from sequence data that uses, along with the difference matrix, the rate of evolution of the various sequences from their common ancestor. It is proven analytically that this method uniquely determines both the correct topology and root in theory for unequal rates of sequence evolution. How one would estimate an ancestral sequence to be used in the method is discussed in particular for the 5S RNA sequences from prokaryotes and eukaryotes and for ferredoxin sequences.