DOI: 10.5061/dryad.dt732vc
title: Data from: Estimating correlated rates of trait evolution with uncertainty

description: Correlated evolution among traits, which can happen due to genetic
 constraints, ontogeny, and selection, can have an important impact on the
 trajectory of phenotypic evolution. For example, shifts in the pattern of
 evolutionary integration may allow the exploration of novel regions of the
 morphospace by lineages. Here we use phylogenetic trees to study the pace
 of evolution of several traits and their pattern of evolutionary
 correlation across clades and over time. We use regimes mapped to the
 branches of the phylogeny to test for shifts in evolutionary integration
 while incorporating the uncertainty related to trait evolution and
 ancestral regimes with joint estimation of all parameters of the model
 using Bayesian Markov chain Monte Carlo. We implemented the use of summary
 statistics to test for regime shifts based on a series of attributes of
 the model that can be directly relevant to biological hypotheses. In
 addition, we extend Felsenstein's pruning algorithm to the case of
 multivariate Brownian motion models with multiple rate regimes. We
 performed extensive simulations to explore the performance of the method
 under a series of scenarios. Finally, we provide two test cases; the
 evolution of a novel buccal morphology in fishes of the family
 Centrarchidae and a shift in the trajectory of evolution of traits during
 the radiation of anole lizards to and from the Caribbean islands.
description: 25_species_3_traitsSimulated data for simulation study. Please check README file inside the zip file.50_species_3_traitsSimulated data for simulation study. Please check README file inside the zip file.100_species_3_traitsSimulated data for simulation study. Please check README file inside the zip file.200_species_3_traitsSimulated data for simulation study. Please check README file inside the zip file.200_species_6_traitsSimulated data for simulation study. Please check README file inside the zip file.400_species_6_traitsSimulated data for simulation study. Please check README file inside the zip file.500_species_6_traitsSimulated data for simulation study. Please check README file inside the zip file.1000_species_6_traitsSimulated data for simulation study. Please check README file inside the zip file.anoles_MCMC_resultsA R Statistical Environment data file in the 'RData' format. Contains the posterior distribution for 4 independent MCMC chains estimated for the Anolis clade. See main text for more details. Also see files 'Caetano_Harmon_2018_Empirical_analyses.pdf' and 'Caetano_Harmon_2018_Empirical_analyses.Rmd' for more information.centrarchidae_MCMC_resultsA R Statistical Environment data file in the 'RData' format. Contains the posterior distribution for 4 independent MCMC chains estimated for the Centrarchidae empirical example. See main text for more details. Also see files 'Caetano_Harmon_2018_Empirical_analyses.pdf' and 'Caetano_Harmon_2018_Empirical_analyses.Rmd' for more information.Caetano_Harmon_2018_Empirical_analysesMarkdown pdf with the empirical analyses.Caetano_Harmon_2018_Empirical_analysesMarkdown 'rmd' with the empirical analyses. Created using RStudio.Caetano_Harmon_2018_Simulation_studyMarkdown 'pdf' with the code and functions used to analyze the simulated datasets.Caetano_Harmon_2018_Simulation_studyMarkdown 'rmd' with the code and functions used to analyze the simulated datasets.Caetano_Harmon_2018_pruning_exampleMarkdown 'pdf' with a detailed step-by-step commented code showing how to compute the new extension for the pruning algorithm applied to the case of multiple regimes of evolutionary rate matrices fitted to the tree.Caetano_Harmon_2018_pruning_exampleMarkdown 'rmd' with a detailed step-by-step commented code showing how to compute the new extension for the pruning algorithm applied to the case of multiple regimes of evolutionary rate matrices fitted to the tree.Supplementary Tables and FiguresOnline Supplementary Tables and Figures.Supplementary_Tables_and_Figures.pdf