Data for: Correlated evolution of categorical characters under a simple model

Published Nov 27, 2024 on Dryad. https://doi.org/10.5061/dryad.866t1g217

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.

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 species
- tooth.complexity Dental state of the species. One of 1Unicuspid, 2Bicuspid, 3Tricuspid, or 4Multicuspid
- diet 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 models
simulate-results.csv CSV delimited file with output from simulate.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 only
- ry the true rate of change in character Y only
- rxy the true rate of simultaneous change in X and Y
- corr the true evolutionary correlation between X and Y
- rx.hat, ry.hat, rxy.hat, corr.hat values estimated for the above quantities under the correlated Mk model
- rx0.hat, ry0.hat values estimated for rx and ry under the independent Mk model
- LR the likelihood ratio statistic comparing the fit of the correlated Mk model to the independent Mk model
- kx, ky the number of character states in X and Y, respectively
- tree.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.