Data from: Testing for independence between evolutionary processes

Evolutionary events co-occurring along phylogenetic trees usually point to complex adaptive phenomena, sometimes implicating epistasis. While a number of methods have been developed to account for co-occurrences of events on the same internal or external branch of an evolutionary tree, there is a need to account for the larger diversity of possible relative positions of events in a tree. Here we propose a method to quantify to what extent two or more evolutionary events are associated on a phylogenetic tree. The method is applicable to any discrete character, like substitutions within a coding sequence or gains/losses of a biological function. Our method uses a general approach to statistically test for significant associations between events along the tree, which encompasses both events coordinated in the same branch, and events chronologically ordered in different branches. We address this problem from the statistical viewpoint by a linear algebra representation of the localisation of the evolutionary events on the tree. We compute the full probability distribution of the number of paired events occurring in the same branch or in different branches of the tree, under a null model of independence. The strengths and weaknesses of the method are assessed via simulations; we then apply the method to explore the loss of cell motility in intracellular pathogens.

沿系统发育树（phylogenetic tree）共同发生的演化事件通常指向复杂的适应性现象，有时会涉及上位性（epistasis）。尽管已有诸多方法可处理演化树同一内部或外部分支上的事件共发生情况，但现有方法仍需覆盖演化树中事件相对位置的更多样可能情形。本研究提出一种方法，可量化两个或多个演化事件在系统发育树上的关联程度。该方法适用于任意离散性状，例如编码序列内的碱基替换，或是某一生物学功能的获得与丢失。我们的方法采用通用分析框架，可对演化树上事件间的显著关联开展统计学检验，该框架既涵盖同一分支上协同发生的事件，也包含不同分支上按时间先后顺序排布的事件。本研究从统计学视角出发，通过线性代数对演化事件在系统发育树上的定位进行表征，以此解决该问题。在独立零假设模型下，我们计算了同一分支或不同分支上发生的成对事件数量的完整概率分布。我们通过模拟实验评估了该方法的优缺点；随后将该方法应用于胞内病原体细胞运动能力丢失的相关研究中。