Analysis on the reconstruction accuracy of the Fitch method for inferring ancestral states.
Analysis on the reconstruction accuracy of the Fitch method for inferring ancestral states.
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Fitch法推断祖先状态的重构精度分析
DOI：
10.1186/1471-2105-12-18
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发表时间：
2011-01-13
影响因子：
3
通讯作者：
Grünewald S
中科院分区：
文献类型：
--
作者：
Yang J;Li J;Dong L;Grünewald S
背景作为最广泛使用的简约的祖先重建方法之一，Fitch方法将树的所有分支上的假设替换总数降至最低，以解释字符的进化。由于这种方法的广泛应用，研究Fitch方法的重建精度已成为近年来的一项科学努力。然而，由于DNA序列具有4态序列的形式，而蛋白质序列甚至具有20个态，因此大多数研究局限于二态进化模型，而高态模型的研究还有待于进一步的研究。给出一个任意的系统发育树，首先提出一个递归系统来迭代地计算这两个精度。由于完全二叉树和梳状树是平衡进化树的两种极端拓扑结构，我们重点研究了这两种拓扑结构的重构精度，并分析了它们的渐近性质。然后，生成1000棵1024片叶子的圣诞树，并对其进行分析，以模拟真实的进化场景。众所周知，在双态模型下，较多的类群并不一定会增加重建精度。结论在一棵多叶的大树上，使用所有类群的重建精度有时会低于在N状态模型下使用一个叶子集的重建精度。对于完全二叉树，总是存在一个守恒概率的均衡区间[a，b]，其中极限模糊重构精度等于随机选取状态的概率。该值随状态数的增加而减小，且趋于收敛。当守恒概率大于b时，Fitch方法的重建精度迅速提高。在1000棵模拟圣诞树上的重建精度也表现出类似的行为。对于梳状树，当保存概率不小于时，使用所有类群的极限重建精度总是小于或等于使用最近的根到叶路径的重建精度。因此，当树形结构平衡且序列高度相似时，建议更多的类群用于祖先重建，而少数靠近根部的类群则建议相反。
BackgroundAs one of the most widely used parsimony methods for ancestral reconstruction, the Fitch method minimizes the total number of hypothetical substitutions along all branches of a tree to explain the evolution of a character. Due to the extensive usage of this method, it has become a scientific endeavor in recent years to study the reconstruction accuracies of the Fitch method. However, most studies are restricted to 2-state evolutionary models and a study for higher-state models is needed since DNA sequences take the format of 4-state series and protein sequences even have 20 states.ResultsIn this paper, the ambiguous and unambiguous reconstruction accuracy of the Fitch method are studied for N-state evolutionary models. Given an arbitrary phylogenetic tree, a recurrence system is first presented to calculate iteratively the two accuracies. As complete binary tree and comb-shaped tree are the two extremal evolutionary tree topologies according to balance, we focus on the reconstruction accuracies on these two topologies and analyze their asymptotic properties. Then, 1000 Yule trees with 1024 leaves are generated and analyzed to simulate real evolutionary scenarios. It is known that more taxa not necessarily increase the reconstruction accuracies under 2-state models. The result under N-state models is also tested.ConclusionsIn a large tree with many leaves, the reconstruction accuracies of using all taxa are sometimes less than those of using a leaf subset under N-state models. For complete binary trees, there always exists an equilibrium interval [a, b] of conservation probability, in which the limiting ambiguous reconstruction accuracy equals to the probability of randomly picking a state. The valuebdecreases with the increase of the number of states, and it seems to converge. When the conservation probability is greater thanb, the reconstruction accuracies of the Fitch method increase rapidly. The reconstruction accuracies on 1000 simulated Yule trees also exhibit similar behaviors. For comb-shaped trees, the limiting reconstruction accuracies of using all taxa are always less than or equal to those of using the nearest root-to-leaf path when the conservation probability is not less than. As a result, more taxa are suggested for ancestral reconstruction when the tree topology is balanced and the sequences are highly similar, and a few taxa close to the root are recommended otherwise.
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