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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. 

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