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.
25_species_3_traits
Simulated data for simulation study. Please check README file inside the zip file.
50_species_3_traits
Simulated data for simulation study. Please check README file inside the zip file.
100_species_3_traits
Simulated data for simulation study. Please check README file inside the zip file.
200_species_3_traits
Simulated data for simulation study. Please check README file inside the zip file.
200_species_6_traits
Simulated data for simulation study. Please check README file inside the zip file.
400_species_6_traits
Simulated data for simulation study. Please check README file inside the zip file.
500_species_6_traits
Simulated data for simulation study. Please check README file inside the zip file.
1000_species_6_traits
Simulated data for simulation study. Please check README file inside the zip file.
anoles_MCMC_results
A 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_results
A 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_analyses
Markdown pdf with the empirical analyses.
Caetano_Harmon_2018_Empirical_analyses
Markdown 'rmd' with the empirical analyses. Created using RStudio.
Caetano_Harmon_2018_Simulation_study
Markdown 'pdf' with the code and functions used to analyze the simulated datasets.
Caetano_Harmon_2018_Simulation_study
Markdown 'rmd' with the code and functions used to analyze the simulated datasets.
Caetano_Harmon_2018_pruning_example
Markdown '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_example
Markdown '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 Figures
Online Supplementary Tables and Figures.
Supplementary_Tables_and_Figures.pdf