Institute for Mathematics and Computer Science, Greifswald University, Walther-Rathenau-Str. 47, 17489, Greifswald, Germany.
Bull Math Biol. 2018 Apr;80(4):864-879. doi: 10.1007/s11538-018-0407-5. Epub 2018 Feb 23.
We examine a mathematical question concerning the reconstruction accuracy of the Fitch algorithm for reconstructing the ancestral sequence of the most recent common ancestor given a phylogenetic tree and sequence data for all taxa under consideration. In particular, for the symmetric four-state substitution model which is also known as Jukes-Cantor model, we answer affirmatively a conjecture of Li, Steel and Zhang which states that for any ultrametric phylogenetic tree and a symmetric model, the Fitch parsimony method using all terminal taxa is more accurate, or at least as accurate, for ancestral state reconstruction than using any particular terminal taxon or any particular pair of taxa. This conjecture had so far only been answered for two-state data by Fischer and Thatte. Here, we focus on answering the biologically more relevant case with four states, which corresponds to ancestral sequence reconstruction from DNA or RNA data.
我们研究了一个关于 Fitch 算法重建最接近共同祖先的祖先序列的准确性的数学问题，给定一个系统发育树和所有考虑的分类单元的序列数据。具体来说，对于对称的四状态替换模型（也称为 Jukes-Cantor 模型），我们肯定地回答了 Li、Steel 和 Zhang 的一个猜想，即对于任何超度量系统发育树和对称模型，使用所有末端分类单元的 Fitch 简约法在祖先状态重建方面比使用任何特定的末端分类单元或任何特定的分类单元对更准确，或者至少同样准确。这个猜想迄今为止只被 Fischer 和 Thatte 回答过针对二状态数据的情况。在这里，我们专注于回答更具生物学相关性的四状态情况，即从 DNA 或 RNA 数据重建祖先序列。
