Abstract:

Background & Aims: Coevolution is widely recognized as a fundamental driver of Earth’s biodiversity. Understanding coevolutionary processes is crucial for deciphering the evolutionary dynamics of species interactions and community assembly. Cophylogenetic analysis is a key tool for inferring the outcomes of coevolutionary processes in interspecies interactions and interaction networks. This review aims to systematically summarize methods and recent advances in cophylogenetic analysis and to provide insights into their applications for studying coevolutionary processes. 

Progress: We first introduce the conceptual foundations of coevolution and its significance in biodiversity research. We then present a detailed overview of cophylogenetic analysis methods. For pairwise interactions, we describe and compare global-fit and event-based methods, highlighting their principles, strengths, limitations, and applications. For complex multi-species interactions, we discuss phylogenetic cascade approaches and network-based approaches. We then review key applications of cophylogenetic analysis in studying antagonistic, competitive, and mutualistic interactions. Finally, we outline how cophylogenetic analysis has been used to investigate community assembly processes. 

Perspectives: Advancing cophylogenetic methods is crucial for improving our understanding of coevolutionary patterns. Key challenges include the lack of direct links between phylogenetic congruence and true coevolutionary processes, as well as limitations in accuracy assessment. Recent frameworks, such as cophylospace, enhance explanatory power by incorporating interaction network structures. Simulation tools, combined with machine learning approaches, show promise for evaluating and improving accuracy assessments. Future research should integrate reticulate phylogenies, phylogenetic dating, and quantitative measures of interaction into cophylogenetic inference. Furthermore, a more universal and adaptable framework could be developed through integration with multidisciplinary technologies such as artificial intelligence. These advancements will deepen our understanding of coevolutionary processes across ecological scales and contexts.

Key words: coevolution, cophylogenetic analysis, interspecific interactions, global-fit methods, event-based methods, macroevolution