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Phylogenetic Tree Reconstruction Accuracy and Model Fit when Proportions of Variable Sites Change across the Tree

机译：可变位点的比例在树上变化时系统发育树的重建精度和模型拟合

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摘要

Commonly used phylogenetic models assume a homogeneous process through time in all parts of the tree. However, it is known that these models can be too simplistic as they do not account for nonhomogeneous lineage-specific properties. In particular, it is now widely recognized that as constraints on sequences evolve, the proportion and positions of variable sites can vary between lineages causing heterotachy. The extent to which this model misspecification affects tree reconstruction is still unknown. Here, we evaluate the effect of changes in the proportions and positions of variable sites on model fit and tree estimation. We consider 5 current models of nucleotide sequence evolution in a Bayesian Markov chain Monte Carlo framework as well as maximum parsimony (MP). We show that for a tree with 4 lineages where 2 nonsister taxa undergo a change in the proportion of variable sites tree reconstruction under the best-fitting model, which is chosen using a relative test, often results in the wrong tree. In this case, we found that an absolute test of model fit is a better predictor of tree estimation accuracy. We also found further evidence that MP is not immune to heterotachy. In addition, we show that increased sampling of taxa that have undergone a change in proportion and positions of variable sites is critical for accurate tree reconstruction.
机译：常用的系统发育模型在树的所有部分中均假设时间上存在同质过程。但是，众所周知，这些模型可能过于简单，因为它们没有考虑非均匀谱系特定的属性。特别是，现已广泛认识到，随着序列限制的发展，可变位点的比例和位置在谱系之间​​可能会发生变化，从而导致异源杂交。该模型错误指定影响树重构的程度仍然未知。在这里，我们评估了可变位点的比例和位置变化对模型拟合和树估计的影响。我们考虑了贝叶斯马尔可夫链蒙特卡洛框架以及最大简约性（MP）中核苷酸序列进化的5个当前模型。我们显示，对于具有4个谱系的树，其中2个非姊妹类群在使用相对测试选择的最佳拟合模型下，可变位点树重构的比例发生变化，通常会导致错误的树。在这种情况下，我们发现模型拟合的绝对检验可以更好地预测树估计的准确性。我们还发现进一步的证据表明MP不能免疫异源性。此外，我们显示，经历了可变位置的比例和位置变化的分类单元的增加采样对于准确的树木重建至关重要。

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