The selection of the best-fitting substitution model of molecular evolution is a traditional step for phylogenetic inferences, including ancestral sequence reconstruction (ASR). However, a few recent studies suggested that applying this procedure does not affect the accuracy of phylogenetic tree reconstruction. Here, we revisited this debate topic by analyzing the influence of selection among substitution models of protein evolution, with focus on exchangeability matrices, on the accuracy of ASR using simulated and real data. We found that the selected best-fitting substitution model produces the most accurate ancestral sequences, especially if the data present large genetic diversity. Indeed, ancestral sequences reconstructed under substitution models with similar exchangeability matrices were similar, suggesting that if the selected best-fitting model cannot be used for the reconstruction, applying a model similar to the selected one is preferred. We conclude that selecting among substitution models of protein evolution is recommended for reconstructing accurate ancestral sequences.
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机译：选择分子进化的最佳拟合替换模型是系统发育推断的传统步骤，包括祖先序列重建 （ASR）。然而，最近的一些研究表明，应用此过程不会影响系统发育树重建的准确性。在这里，我们通过分析蛋白质进化的替代模型中的选择影响来重新审视这个辩论话题，重点是可交换性矩阵，使用模拟和真实数据对 ASR 的准确性。我们发现，选定的最佳拟合替换模型产生了最准确的祖先序列，特别是当数据呈现较大的遗传多样性时。事实上，在具有相似可交换性矩阵的替换模型下重建的祖先序列是相似的，这表明如果所选的最佳拟合模型不能用于重建，则首选应用与所选模型相似的模型。我们得出结论，建议在蛋白质进化的替换模型中进行选择，以重建准确的祖先序列。
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