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), whose significance is often interpreted as evidence for phylogenetic congruence, to simulations under 3 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 2 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 3 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：

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区分系统发育信号与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-共生体结合，可以深刻影响相互作用物种的进化。考虑到宿主和共生体分支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？这些问题是相互交织的，甚至在特定情况下可能会崩溃，以至于它们经常相互混淆。然而，在大多数情况下，对第一个问题的肯定回答，以下简称“共生信号”，并不意味着宿主和共生系统发育之间非常匹配。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，通过当今的特征匹配，或者来自增加密切相关物种在地理上重叠的可能性的单个古代替代事件。对第二个的肯定回答，称为“系统发育一致性”，则更具限制性，因为它表明两个系统发育之间非常匹配，例如，如果共生体多样化跟踪宿主多样化，或者如果两个分支的多样化受到相同的替代事件序列的影响，则可能会发生这种情况。在这里，我们应用了一组方法 （ParaFit、PACo 和 eMPRess），其重要性通常被解释为系统发育一致性的证据，用于 3 种生物学上现实的情景下的模拟，即性状匹配、单个古老的替代事件和具有频繁共物种识别事件的系统发育跟踪。 后者是唯一产生系统发育一致性的情况，而前 2 种情况在没有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） 的检验在 3 种情景下是有意义的，而基于事件的方法 （eMPRess） 的检验仅在系统发育跟踪的情景下才有意义。因此，全局拟合方法的重要结果应根据系统发育信号而不是系统发育一致性来解释;在宿主和共生体具有独立进化历史的情况下，可能会出现如此重要的结果。相反，基于事件的方法的重要结果表明宿主和共生体进化历史之间存在很强的依赖性。阐明不同系统发育方法检测到的模式是理解种间相互作用如何塑造和被进化塑造的关键。