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 ...