DOI: 10.5061/dryad.067qg
title: Data from: Among-character rate variation distributions in phylogenetic analysis of discrete morphological characters

description: Likelihood-based methods are commonplace in phylogenetic systematics.
 Although much effort has been directed toward likelihood-based models for
 molecular data, comparatively less work has addressed models for discrete
 morphological character data. Among-character rate variation may confound
 phylogenetic analysis, but there have been few analyses of the magnitude
 and distribution of rate heterogeneity among discrete morphological
 characters. Using seventy-six data sets covering a range of plants,
 invertebrate, and vertebrate animals, we used a modified version of
 MrBayes to test equal, gamma-distributed and lognormally-distributed
 models of among-character rate variation, integrating across phylogenetic
 uncertainty using Bayesian model selection. We found that in approximately
 80% of data sets, unequal-rates models outperformed equal-rates models,
 especially among larger data sets. Moreover, although most data sets were
 equivocal, more data sets favored the lognormal rate distribution relative
 to the gamma rate distribution, lending some support for more complex
 character correlations than in molecular data. Parsimony estimation of the
 underlying rate distributions in several data sets suggests that the
 lognormal distribution is preferred when there are many slowly evolving
 characters and fewer quickly evolving characters. The commonly adopted
 four rate category discrete approximation used for molecular data was
 found to be sufficient to approximate a gamma rate distribution with
 discrete characters. However, among the two data sets tested that favored
 a lognormal rate distribution, the continuous distribution was better
 approximated with at least eight discrete rate categories. Although the
 effect of rate model on the estimation of topology was difficult to assess
 across all data sets, it appeared relatively minor between the
 unequal-rates models for the one data set examined carefully. As in
 molecular analyses, we argue that researchers should test and adopt the
 most appropriate model of rate variation for the data set in question. As
 discrete characters are increasingly used in more sophisticated
 likelihood-based phylogenetic analyses, it is important that these studies
 be built on the most appropriate and carefully selected underlying models
 of evolution.
description: HarrisonLarsson_AmongCharacterRatesThis archive contains supporting materials for Harrison and Larsson (201X) Among-Character Rate Variation Distributions in Phylogenetic Analysis of Discrete Morphological Characters. SuppTable1.xlsx: Supplementary Table 1. List of data sets and TreeBase Accession Numbers SuppTable2.xlsx: Supplementary Table 2. Results of the main Bayesian analysis for ACRV model selection SupplementaryReferences.docx: Full references for the studies included in Supp. Table 1. MainAnalysis_MBControlFiles: MB Control files for the main analysis described in the text. NumberofRateCategoriesAnalysis_MBControlFiles: MB control files for the discrete rate category analysis. In the preceding two folders, all control files are indexed by Tree Base Accession number and by among-character rate variation model (and prior type). RScripts: folder containing R scripts (further explanation inside the .R files) 1. CombineLogExtractMCMC.R: script to process the output of MrBayes stepping-stone analysis to extract the initial MCMC portion (i.e. from the posterior) and summarize the posterior of these samples using MrBayes. 2. mb_to_beast_trees.sh: short BASH shell script to convert MrBayes formatted trees to BEAST-readable tree (used by #1, above). 3. PAUPOutputProcessor.R: R script to call PAUP* 4b10 (using Wine on Linux) and calculate per character change counts automatically given a data block (in special R format, please see the script file for details) and tree 4. PAUPLogProcessor.R: Simpler version of #3 to extract change counts from PAUP* log text file (but not call PAUP* directly). 5. S2128.rDa: the S2128 (TreeBaseID) data set in the correct R format for #3 6. S2128_Example.tree: a tree corresponding to the S2128 data set to test #3Link to modified source code for MrBayes 3.2.2-r512-SVNSource Code for MrBayes 3.2.2-r512-SVN. (http://mrbayes.sourceforge.net/) modified to include the lognormal model of Among-character Rate Variation. Distributed under the GPL license, with full credit to the developers of MrBayes. Please consult the README file in the archive.