Myriad branches in the tree of life are intertwined through ecological relationships. Biologists have long hypothesized that intimate symbioses between lineages can influence diversification patterns to the extent that it leaves a topological imprint on the phylogenetic trees of interacting clades. Over the past few decades, cophylogenetic methods development has provided a toolkit for identifying such histories of codiversification, yet it is often difficult to determine which tools best suit the task at hand. In this review, we organize currently available cophylogenetic methods into three categories—pattern-based statistics, event-scoring methods, and more recently developed generative model–based methods—and discuss their assumptions and appropriateness for different types of cophylogenetic questions. We classify cophylogenetic systems based on their biological properties to provide a framework for empiricists investigating the macroevolution of symbioses. In addition, we provide recommendations for the next generation of cophylogenetic models that we hope will facilitate further methods development.

中文翻译：

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解开生态相互作用进化史的共系统发生方法

生命之树的无数分支通过生态关系交织在一起。生物学家长期以来一直假设，谱系之间的密切共生可以影响多样化模式，从而在相互作用的进化枝的系统发育树上留下拓扑印记。在过去的几十年里，共系统发育方法的发展为识别这种共多样化的历史提供了一个工具包，但通常很难确定哪些工具最适合当前的任务。在这篇综述中，我们将当前可用的共系统发生方法分为三类——基于模式的统计、事件评分方法和最近开发的基于生成模型的方法——并讨论它们的假设和对不同类型共系统发生问题的适用性。我们根据共生系统的生物学特性对其进行分类，为经验主义者研究共生的宏观进化提供一个框架。此外，我们还为下一代共系统发育模型提供了建议，我们希望这些模型能够促进进一步的方法开发。