Interspecific interactions, including host-symbiont associations, can profoundly affect the evolution of the interacting species. Given the phylogenies of host and symbiont clades and knowledge of which host species interact with which symbiont, two questions are often asked: “Do closely related hosts interact with closely related symbionts?” and “Do host and symbiont phylogenies mirror one another?”. These questions are intertwined and can even collapse under specific situations, such that they are often confused one with the other. However, in most situations, a positive answer to the first question, hereafter referred to as “cophylogenetic signal”, does not imply a close match between the host and symbiont phylogenies. It suggests only that past evolutionary history has contributed to shaping present-day interactions, which can arise, for example, through present-day trait matching, or from a single ancient vicariance event that increases the probability that closely related species overlap geographically. A positive answer to the second, referred to as “phylogenetic congruence”, is more restrictive as it suggests a close match between the two phylogenies, which may happen, for example, if symbiont diversification tracks host diversification or if the diversifications of the two clades were subject to the same succession of vicariance events. Here we apply a set of methods (ParaFit, PACo, and eMPRess), which significance is often interpreted as evidence for phylogenetic congruence, to simulations under three biologically realistic scenarios of trait matching, a single ancient vicariance event, and phylogenetic tracking with frequent cospeciation events. The latter is the only scenario that generates phylogenetic congruence, whereas the first two generate a cophylogenetic signal in the absence of phylogenetic congruence. We find that tests of global-fit methods (ParaFit and PACo) are significant under the three scenarios, whereas tests of event-based methods (eMPRess) are only significant under the scenario of phylogenetic tracking. Therefore, significant results from global-fit methods should be interpreted in terms of cophylogenetic signal and not phylogenetic congruence; such significant results can arise under scenarios when hosts and symbionts had independent evolutionary histories. Conversely, significant results from event-based methods suggest a strong form of dependency between hosts and symbionts evolutionary histories. Clarifying the patterns detected by different cophylogenetic methods is key to understanding how interspecific interactions shape and are shaped by evolution.

中文翻译：

---

区分共系统发育信号和系统发育一致性阐明了进化历史和物种相互作用之间的相互作用


种间相互作用，包括宿主-共生体关联，可以深刻影响相互作用物种的进化。考虑到宿主和共生体进化枝的系统发育以及哪些宿主物种与哪些共生体相互作用的知识，经常会问两个问题：“密切相关的宿主是否与密切相关的共生体相互作用？”和“宿主和共生体的系统发育是否相互镜像？”。这些问题相互交织，甚至在特定情况下会崩溃，以致常常将它们相互混淆。然而，在大多数情况下，对第一个问题（以下称为“共系统发育信号”）的肯定回答并不意味着宿主和共生体系统发育之间的紧密匹配。它仅表明过去的进化历史有助于塑造当今的相互作用，例如，这种相互作用可以通过当今的性状匹配而产生，或者来自单个古代的变异事件，该事件增加了密切相关的物种在地理上重叠的可能性。对第二个问题的肯定答案，即“系统发育一致性”，更具限制性，因为它表明两个系统发育之间存在密切匹配，例如，如果共生体多样化跟踪宿主多样化，或者如果两个进化枝的多样化，则可能会发生这种情况受到同样一系列的替代事件的影响。在这里，我们应用一组方法（ParaFit、PACo 和 eMPRess）（其重要性通常被解释为系统发育一致性的证据）来模拟性状匹配、单个古代变异事件和频繁共种的系统发育跟踪三种生物学现实场景下的模拟事件。 后者是产生系统发育一致性的唯一情况，而前两种情况在缺乏系统发育一致性的情况下产生共系统发育信号。我们发现全局拟合方法（ParaFit 和 PACo）的测试在这三种情况下都很重要，而基于事件的方法（eMPRess）的测试仅在系统发育跟踪的情况下才有意义。因此，全局拟合方法的显着结果应根据共系统发育信号而不是系统发育一致性来解释；当宿主和共生体具有独立的进化历史时，就会出现如此重要的结果。相反，基于事件的方法的显着结果表明宿主和共生体进化历史之间存在很强的依赖性。阐明不同共系统发育方法检测到的模式是理解种间相互作用如何形成以及进化如何形成的关键。