Data from: Distinguishing between convergent evolution and violation of the molecular clock for three taxa

We give a non-technical introduction to convergence-divergence models, a new modeling approach for phylogenetic data that allows for the usual divergence of lineages after lineage-splitting but also allows for taxa to converge, i.e. become more similar over time. By examining the $3$-taxon case in some detail we illustrate that phylogeneticists have been ``spoiled'' in the sense of not having to think about the structural parameters in their models by virtue of the strong assumption that evolution is tree-like. We show that there are not always good statistical reasons to prefer the usual class of tree-like models over more general convergence-divergence models. Specifically we show many $3$-taxon data sets can be equally well explained by supposing violation of the molecular clock due to change in the rate of evolution along different edges, or by keeping the assumption of a constant rate of evolution but instead assuming that evolution is not a purely divergent process. Given the abundance of evidence that evolution is not strictly tree-like, our discussion is an illustration that as phylogeneticists we need to think clearly about the structural form of the models we use. For cases with four taxa we show that there will be far greater ability to distinguish models with convergence from non-clock-like tree models.本文首先为趋同-趋异模型（convergence-divergence models）提供一篇非技术性导论——这类面向系统发育数据的新型建模范式，既支持谱系分裂后谱系的常规趋异过程，也允许分类单元（taxon）发生趋同，即随时间推移彼此相似度逐步提升。通过对三分类单元（3-taxon）场景展开细致剖析，我们阐明了系统发育研究者实则已被"惯坏"：由于"演化呈树状"这一强假设，他们无需考量自身模型中的结构参数。我们证明，相较于更具普适性的趋同-趋异模型，常规树状模型并非总能凭借充分的统计学依据获得青睐。具体而言，我们发现大量三分类单元数据集可通过两种路径得到同等程度的合理解释：其一，假设演化沿不同分支的速率存在差异，从而违背分子钟（molecular clock）假设；其二，保留演化速率恒定的前提，但假定演化并非单纯的趋异过程。鉴于已有大量证据表明演化并非严格遵循树状路径，本次讨论旨在说明：作为系统发育研究者，我们应当清晰审视自身所采用模型的结构形式。针对四分类单元场景，我们证明，相较于非分子钟树状模型，我们具备更强的能力区分包含趋同过程的模型与违背分子钟的树状模型。