Inference of molecular phylogenetic tree based on minimum complexity principle

在利用分子数据重建系统发生树的过程中，已有研究指出，用极大似然法等传统方法难以正确重建多分叉系统发生树。为了解决这一问题，我们一直致力于开发一种基于在归纳推理中广泛应用的最小复杂度原理的新的系统发育树重建方法。本文提出了“基于经验模型的复杂性”这一新的复杂性概念，并提出了“基于最小模型的复杂性”（minimum model-based complexity， MBC）标准来重建分子系统发育树。该方法通过与树的拓扑结构、分支长度和模型与似然函数测量的数据之间的适应度有关的三个术语来描述分子系统发育树的复杂性。通过计算机仿真，比较了该方法与最大似然法和赤池信息法（AIC）在估计有根和无根系统发育树方面的有效性。结果表明，与传统的极大似然方法或其改进方法相比，MBC方法具有良好的渐近性，当多分叉树作为树的备选拓扑时，且/或长DNA序列可以用于重建系统发育树（超过3000 bp），因为它避免了树模型相对于现有物种DNA序列可获得的信息量过大的复杂性。因此，该方法可广泛用于具有任意多功能的系统发育树的重建。

In reconstruction of phylogenetic trees from molecular data, it has been pointed oat that multifurcate phylogenetic trees are difficult to be correctly reconstructed by the conventional methods like maximum likelihood method. In order to resolve this problem, we have been engaged in developing a new phylogenetic tree reconstruction method based on the minimum complexity principle widely used in the inductive inference. In this study, we defined a new concept of complexity, which we call "empirical model-based complexity" and proposed "minimum model-based complexity(MBC)" criterion for reconstructing molecular phylogenetic tree. This method describes the complexity of molecular phylogenetic tree by three terms which are related to the tree topology, the branch length and fitness between the model and data measured by likelihood function.The Computer simulation is used to investigate the efficiency of this method in estimating rooted and unrooted phylogenetic tree in comparison with those of maximum likelihood method and Akaike information method(AIC). The results suggest that the MBC method has a good asymptotic property compared with traditional maximum likelihood method or its modification, AIC method in the case that the multifurcate tree is considered as a candidate topology of the tree and/or long DNA sequences could be used in reconstructing phylogenetic tree (over 3000-bp), because it avoids excess-complexity of the tree model in relation to the amount of the information available from DNA sequences of current species. Therefore it could be generally used for reconstruction of phylogenetic tree having arbitrary multifurcations.