Recoding amino acids to a reduced alphabet may increase or decrease phylogenetic accuracy

Common molecular phylogenetic characteristics such as long branches and compositional heterogeneity can be problematic for phylogenetic reconstruction when using amino acid data. Recoding alignments to reduced alphabets before phylogenetic analysis has often been used both to explore and potentially decrease the effect of such problems. We tested the effectiveness of this strategy on topological accuracy using simulated data on four-taxon trees. We simulated alignments in phylogenetically challenging ways to test the phylogenetic accuracy of analyses using various recoding strategies together with commonly-used homogeneous models. We tested three recoding methods based on amino acid exchangeability, and another recoding method based on lowering the compositional heterogeneity among alignment sequences as measured by the Chi-squared statistic. Our simulation results show that on trees with long branches where sequences approach saturation, accuracy was not greatly affected by exchangeabi...

使用氨基酸数据进行系统发育重建时，诸如长支（long branches）与组成异质性（compositional heterogeneity）这类常见的分子系统发育特征，往往会给分析带来干扰。在开展系统发育分析前，将序列比对重编码为缩减字母表（reduced alphabets）的策略，常被用于探究并潜在缓解此类问题的影响。本研究基于四分类群树（four-taxon trees）的模拟数据，检验了该策略对拓扑结构准确性（topological accuracy）的提升效果。我们通过系统发育层面的挑战性模拟场景生成比对序列，以测试多种重编码策略结合常用均一化模型（homogeneous models）时的系统发育分析准确性。本次检验共涵盖三种基于氨基酸可交换性（amino acid exchangeability）的重编码方法，以及另一种基于卡方统计量（Chi-squared statistic）、旨在降低比对序列间组成异质性的重编码方法。模拟结果显示，在序列趋近进化饱和的长支树拓扑结构中，可交换性相关的重编码策略并未对分析准确性造成显著影响……