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paco: implementing Procrustean Approach to Cophylogeny in R
Author(s) -
Hutchinson Matthew C.,
Cagua E. Fernando,
Balbuena Juan A.,
Stouffer Daniel B.,
Poisot Timothée
Publication year - 2017
Publication title -
methods in ecology and evolution
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.425
H-Index - 105
ISSN - 2041-210X
DOI - 10.1111/2041-210x.12736
Subject(s) - phylogenetic tree , congruence (geometry) , extant taxon , systematics , taxon , biogeography , concordance , ecology , biology , evolutionary biology , taxonomy (biology) , psychology , social psychology , biochemistry , bioinformatics , gene
Summary The concordance of evolutionary histories and extant species interactions provides a useful metric for addressing questions of how the structure of ecological communities is influenced by macro‐evolutionary processes. We introduce paco (v0.3.1), an R package to perform Procrustean Approach to Cophylogeny. This method assesses the phylogenetic congruence, or evolutionary dependence, of two groups of interacting species using both ecological interaction networks and their phylogenetic history. We demonstrate the functionality of paco through its application to empirical host‐parasite and plant‐pollinator communities. Although the package is intended to assess the phylogenetic congruence between groups of interacting species, the method is also directly applicable to other scenarios that may show phylogenetic congruence including historical biogeography, molecular systematics, and cultural evolution.