Data for: Correlated evolution of categorical characters under a simple model
Data files
Nov 27, 2024 version files 1.52 MB
-
README.md
3.64 KB
-
suppmat.tar.gz
1.51 MB
Abstract
I describe a simple model for quantifying the strength of association between two categorical characters evolving on a phylogenetic tree. The model can be used to estimate a correlation statistic that asks whether or not the two characters tend to change at the same time (positive correlation) or at different times (no correlation). This is different than asking if changes in one character are associated with a particular state in another character, which has been the focus of most prior tests for phylogenetic correlation in categorical characters. Analyses of simulated data indicate that positive correlations can be accurately estimated over a range of different tree sizes and phylogenetic signals.
README: Data for: Correlated evolution of categorical characters under a simple model
https://doi.org/10.5061/dryad.866t1g217
Description of the data and file structure
Data and codes for fitting and testing the correlated Mk model
Files and variables
File: suppmat.tar.gz
Description: A gzip compressed archive with the following contents:
The data-empirical
directory contains the squamate dental-diet dataset from 10.1038/s41467-021-26285-w:
41467_2021_26285_MOESM4_ESM.txt
Newick string formatted squamate reptile phylogeny for species with dental-diet data.41467_2021_26285_MOESM6_ESM.csv
CSV delimited file with dental-diet states for species in the phylogeny. Each row contains the dental-diet state combination for a single species. The file contains the following relevant headers:species
Latin binomial of the speciestooth.complexity
Dental state of the species. One of 1Unicuspid, 2Bicuspid, 3Tricuspid, or 4Multicuspiddiet
Diet state of the species. One of Insectivorous, Carnivorous, Omnivorous, or Herbivorous
CITATION
Reference for the squamate phylogeny and dental-diet dataset.
The data-simulated
directory contains the code for generating simulated datasets under the correlated Mk model:
simulate.R
R script for simulating data under the correlated and independent Mk modelssimulate-results.csv
CSV delimited file with output fromsimulate.R
. Each row contains the results of analyzing a single simulation that was generated under the correlated Mk model. The file contains the following headers:rx
the true rate of change in character X onlyry
the true rate of change in character Y onlyrxy
the true rate of simultaneous change in X and Ycorr
the true evolutionary correlation between X and Yrx.hat, ry.hat, rxy.hat, corr.hat
values estimated for the above quantities under the correlated Mk modelrx0.hat, ry0.hat
values estimated forrx
andry
under the independent Mk modelLR
the likelihood ratio statistic comparing the fit of the correlated Mk model to the independent Mk modelkx, ky
the number of character states in X and Y, respectivelytree.index, tree.size
the index and size of the phylogeny used in the simulation, respectively
simulate-results-uncorrelated.csv
As for above except that the simulations were generated under the independent Mk model.squamates_Title_Science2024_ultrametric_constrained.tre
Newick string formatted squamate reptile phylogeny used to generate the simulation phylogenies.CITATION
Reference for the squamate phylogeny.
The figs
directory contains the R scripts for generating the figures that appear in the publication.
The mkcor_1.0.tar.gz
archive is the mkcor R package version implementing the correlated Mk model that was used in the publication. The R package is also available from github.com/blueraleigh/mkcor.
The README
file contains instructions for installing the R package.
Access information
Other publicly accessible locations of the data:
- github.com/blueraleigh/mkcor for the mkcor R package.
Data was derived from the following sources:
- 10.1038/s41467-021-26285-w for the squamate dental-diet dataset.
- 10.1126/science.adh2449 for the squamate phylogeny used in the simulations.