10.5061/DRYAD.DT732VC
Caetano, Daniel S.
University of Idaho
Harmon, Luke J.
University of Idaho
Data from: Estimating correlated rates of trait evolution with uncertainty
Dryad
dataset
2018
Modularity
Centrarchidae
evolutionary integration
pruning algorithm
Anolis
National Science Foundation
https://ror.org/021nxhr62
DEB-1208912
2018-10-13T01:12:37Z
2018-10-13T01:12:37Z
en
https://doi.org/10.1093/sysbio/syy067
213721408 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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_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