DOI: 10.5061/dryad.7wm37pvzn
title: Distinguishing cophylogenetic signal from phylogenetic congruence clarifies the interplay between evolutionary history and species interactions

description: 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 overlap geographically. A positive answer to the second, referred
 to as “phylogenetic congruence”, is more restrictive as it suggests a
 close match between the two phylogenies, which may happen, for example, if
 symbiont diversification tracks host diversification or if the
 diversifications of the two clades were subject to the same succession of
 vicariance events. Here we apply a set of methods (ParaFit, PACo, and
 eMPRess), which significance is often interpreted as evidence for
 phylogenetic congruence, to simulations under three biologically realistic
 scenarios of trait matching, a single ancient vicariance event, and
 phylogenetic tracking. The latter is the only scenario that generates
 phylogenetic congruence, whereas the first two generate a cophylogenetic
 signal in the absence of phylogenetic congruence. We find that tests of
 global-fit methods (ParaFit and PACo) are significant under the three
 scenarios, whereas tests of event-based methods (eMPRess) are only
 significant under the scenario of phylogenetic tracking. Therefore,
 significant results from global-fit methods should be interpreted in terms
 of cophylogenetic signal and not phylogenetic congruence; such significant
 results can arise under scenarios when hosts and symbionts had independent
 evolutionary histories. Conversely, significant results from event-based
 methods suggest a strong form of dependency between hosts and symbionts
 evolutionary histories. Clarifying the patterns detected by different
 cophylogenetic methods is key to understanding how interspecific
 interactions shape and are shaped by evolution.
description: 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 with the command line on our simulations.
 All the codes for generating the simulations and performing the analyses
 are also available through the following link:\
 [https://github.com/BPerezLamarque/Scripts/tree/master/Cophylogenetic_signal](https://github.com/BPerezLamarque/Scripts/tree/master/Cophylogenetic_signal). Contact: [benoit.perez.lamarque@gmail.com](mailto:benoit.perez.lamarque@gmail.com)