Distinguishing cophylogenetic signal from phylogenetic congruence clarifies the interplay between evolutionary history and species interactions

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 ..., , , This Dryad data contains the Supplementary Information of the manuscript entitled \"Distinguishing cophylogenetic signal from phylogenetic congruence clarifies the interplay between evolutionary history and species interactions\" by Benoît Perez-Lamarque and Hélène Morlon published in Systematic Biology. ## Data and scripts included: The document \"Supplementary_data_cophylo.pdf\" contains the Supplementary Box (1), the Supplementary Methods (1), the Supplementary Tables (1-6), the Supplementary Figures (1-5) and the Supplementary References. It also contains the 3 scripts for reproducing all analyses: \- \"script_cophylogenetic_signal.R\": the script to reproduce the simulations, run global-fit approaches, and plot the figures \- \"functions_parafit_paco.R\": ParaFit and PACo functions that implement the \"null model 2\" (see [https://doi.org/10.1111/mec.16681](https://doi.org/10.1111/mec.16681) for more details) \- \"script_run_eMPRess.sh\": the script for automatically running eMPRess ...种间相互作用（包括宿主-共生体关联）可深刻影响相互作用物种的演化历程。若已知宿主与共生体支系的系统发育关系，且明确哪些宿主物种与哪些共生体物种存在相互作用，学界常围绕两个核心问题展开探讨：“亲缘关系相近的宿主是否会与亲缘关系相近的共生体发生相互作用？”以及“宿主与共生体的系统发育树是否彼此镜像对应？”。这两个问题彼此交织，在特定情境下甚至会趋于等价，因此常被混淆。然而在多数情形下，对第一个问题给出肯定答案（下文称之为共系统发育信号（cophylogenetic signal）），并不意味着宿主与共生体的系统发育树高度匹配。它仅表明过往的演化历史参与塑造了当前的相互作用模式，这种模式可通过当前的性状匹配，或是单次古老的地理隔离事件（该事件会提升亲缘关系相近的物种……）等途径形成。 本Dryad数据集包含贝诺瓦·佩雷斯-拉马尔克（Benoît Perez-Lamarque）与埃莱娜·莫尔隆（Hélène Morlon）发表于《Systematic Biology》的论文《区分共系统发育信号与系统发育一致性以阐明演化历史与物种相互作用的相互关系》的补充信息。 ## 包含的数据集与脚本 文件“Supplementary_data_cophylo.pdf”涵盖了补充框（1）、补充方法（1）、补充表格（1-6）、补充图（1-5）以及补充参考文献。 此外还包含可复现全部分析的3份脚本： - “script_cophylogenetic_signal.R”：用于复现模拟实验、运行全局拟合方法并绘制图表的脚本 - “functions_parafit_paco.R”：实现“零模型2”的ParaFit与PACo函数（详细说明请参见https://doi.org/10.1111/mec.16681） - “script_run_eMPRess.sh”：用于自动运行eMPRess的脚本