Plastid genome phylogeny and a model of amino acid substitution for proteins encoded by chloroplast DNA
Plastid genome phylogeny and a model of amino acid substitution for proteins encoded by chloroplast DNA
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DOI：
10.1007/s002399910038
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发表时间：
2000-04-01
影响因子：
3.9
通讯作者：
Hasegawa, M
中科院分区：
文献类型：
--
作者：
Adachi, J;Waddell, PJ;Hasegawa, M
基于蓝载藻（Cyanophora）、一种硅藻、一种红藻（红藻门植物）、一种裸藻以及五种陆地植物的质体基因组中编码的45种蛋白质的9957个氨基酸（AA）位点的最大似然（ML）系统发育树，就数据的若干特性进行了比较，包括位点间的速率变化以及个别物种中异常的氨基酸组成。当考虑到位点速率可变性时，来自氨基酸对数行列式（LogDet）距离的邻接树和最大似然分析被认为是一致的。在这些分析中确定了四棵可行的树，其中一棵是较优的，而有一棵几乎被统计标准所排除。在假定这四棵树中的每一棵的情况下，根据数据估计了氨基酸替代的一般可逆马尔可夫模型的转移概率矩阵。在所有情况下，硅藻和红藻作为姐妹分类群的树明显更受青睐。基于最优树的新的转移矩阵，称为cpREV，考虑了质体编码蛋白质中不同的替代模式，并且在未来使用此类数据进行最大似然推断时应该是有用的。还考虑了第二个速率矩阵，称为cpREV*，它基于来自不同树的速率矩阵的加权和。
Maximum likelihood (ML) phylogenies based on 9,957 amino acid (AA) sites of 45 proteins encoded in the plastid genomes of Cyanophora, a diatom, a rhodophyte (red algae), a euglenophyte, and five land plants are compared with respect to several properties of the data, including between-site rate variation and aberrant amino acid composition in individual species. Neighbor-joining trees from AA LogDet distances and ML analyses are seen to be congruent when site rate variability was taken into account. Four feasible trees are identified in these analyses, one of which is preferred, and one of which is almost excluded by statistical criteria. A transition probability matrix for the general reversible Markov model of amino acid substitutions is estimated from the data, assuming each of these four trees. In all cases, the tree with diatom and rhodophyte as sister taxa was clearly favored. The new transition matrix based on the best tree, called cpREV, takes into account distinct substitution patterns in plastid-encoded proteins and should be useful in future ML inferences using such data. A second rate matrix, called cpREV*, based on a weighted sum of rate matrices from different trees, is also considered.