Data from: Variation across mitochondrial gene trees provides evidence for systematic error: how much gene tree variation is biological?

The use of large genomic datasets in phylogenetics has highlighted extensive topological variation across genes. Much of this discordance is assumed to result from biological processes. However, variation among gene trees can also be a consequence of systematic error driven by poor model fit, and the relative importance of biological versus methodological factors in explaining gene tree variation is a major unresolved question. Using mitochondrial genomes to control for biological causes of gene tree variation, we estimate the extent of gene tree discordance driven by systematic error and employ posterior prediction to highlight the role of model fit in producing this discordance. We find that the amount of discordance among mitochondrial gene trees is similar to the amount of discordance found in other studies that assume only biological causes of variation. This similarity suggests that the role of systematic error in generating gene tree variation is underappreciated and critical evaluation of fit between assumed models and the data used for inference is important for the resolution of unresolved phylogenetic questions.

在系统发育学（phylogenetics）研究中应用大型基因组数据集时，已揭示不同基因间存在广泛的拓扑结构变异。这类基因树冲突通常被归因于生物学过程。然而，基因树之间的变异也可能源于模型适配不佳所引发的系统误差，而生物学因素与方法学因素在解释基因树变异时的相对重要性，仍是一个尚未解决的核心科学问题。本研究以线粒体基因组（mitochondrial genomes）为研究载体，控制基因树变异的生物学成因，以此估算由系统误差驱动的基因树冲突程度，并通过后验预测（posterior prediction）分析模型适配性对该冲突的影响。研究发现，线粒体基因树间的冲突程度与其他仅假设变异由生物学过程导致的同类研究中观测到的冲突程度相近。这一相似性表明，系统误差在基因树变异产生过程中的作用被严重低估，同时也说明，对统计推断所用模型与数据间的适配性开展严谨评估，对于解决尚未明确的系统发育学问题至关重要。