DOI: 10.5061/dryad.q6s1f
title: Data from: Rumbling orchids: how to assess divergent evolution between chloroplast endosymbionts and the nuclear host

description: Phylogenetic relationships inferred from multilocus organellar and nuclear
 DNA data are often difficult to resolve because of evolutionary conflicts
 among gene trees. However, conflicting or “outlier” associations (i.e.,
 linked pairs of “operational terminal units” in two phylogenies) among
 these data sets often provide valuable information on evolutionary
 processes such as chloroplast capture following hybridization, incomplete
 lineage sorting, and horizontal gene transfer. Statistical tools that to
 date have been used in cophylogenetic studies only also have the potential
 to test for the degree of topological congruence between organellar and
 nuclear data sets and reliably detect outlier associations. Two
 distance-based methods, namely ParaFit and Procrustean Approach to
 Cophylogeny (PACo), were used in conjunction to detect those outliers
 contributing to conflicting phylogenies independently derived from
 chloroplast and nuclear sequence data. We explored their efficiency of
 retrieving outlier associations, and the impact of input data (unit branch
 length and additive trees) between data sets, by using several simulation
 approaches. To test their performance using real data sets, we
 additionally inferred the phylogenetic relationships within Neotropical
 Catasetinae (Epidendroideae, Orchidaceae), which is a suitable group to
 investigate phylogenetic incongruence because of hybridization processes
 between some of its constituent species. A comparison between trees
 derived from chloroplast and nuclear sequence data reflected strong,
 well-supported incongruence within Catasetum, Cycnoches, and Mormodes. As
 a result, outliers among chloroplast and nuclear data sets, and in
 experimental simulations, were successfully detected by PACo when using
 patristic distance matrices obtained from phylograms, but not from unit
 branch length trees. The performance of ParaFit was overall inferior
 compared to PACo, using either phylograms or unit branch lengths as input
 data. Because workflows for applying cophylogenetic analyses are not
 standardized yet, we provide a pipeline for executing PACo and ParaFit as
 well as displaying outlier associations in plots and trees by using the
 software R. The pipeline renders a method to identify outliers with high
 reliability and to assess the combinability of the independently derived
 data sets by means of statistical analyses.
description: Concatenated alignment
 of nuclear and chloroplast loci of CatasetinaeCatasetinae_NR_CP_Syst_Biol_submit_v7_NX.nexConsensus chloroplast tree of SatyriumConsensus tree derived from Bayesian inferenceSatyrium_infile.nex.con_cp.treConsensus nuclear tree of SatyriumConsensus tree derived from Bayesian inferenceSatyrium_infile.nex.con_n.treSet of chloroplast posterior probability trees of Satyrium20000 posterior probability trees of Satyrium derived from Bayesian inference and chloroplast dataSatyrium_infile.nex.run1_cp.tSet of nuclear posterior probability trees of Satyrium20000 posterior probability trees of Satyrium derived from Bayesian inference and nuclear dataSatyrium_infile.nex.run1_n.tPACo-ParaFit script for outlier detection in phylogeniesDetailed R script for outlier detection in phylogenies using PACo and ParaFitRumbling_orchids_Script_03_vsubmit_SystBiol_SB.R