Evaluating the accuracy of methods for detecting correlated rates of molecular and morphological evolution

Determining the link between genomic and phenotypic change is a fundamental goal in evolutionary biology. Insights into this link can be gained by using a phylogenetic approach to test for correlations between rates of molecular and morphological evolution. However, there has been persistent uncertainty about the relationship between these rates, partly because conflicting results have been obtained using various methods that have not been examined in detail. We carried out a simulation study to evaluate the performance of five statistical methods for detecting correlated rates of evolution. Our simulations explored the evolution of molecular sequences and morphological characters under a range of conditions. Of the methods tested, Bayesian relaxed-clock estimation of branch rates was able to detect correlated rates of evolution correctly in the largest number of cases. This was followed by correlations of root-to-tip distances, Bayesian model selection, independent sister-pairs contras..., , ,
[https://doi.org/10.5061/dryad.7wm37pw01](https://doi.org/10.5061/dryad.7wm37pw01)

## Description of the data and file structure

Supplementary data and text for \"Evaluating the Accuracy of Methods for Detecting Correlated Rates of Molecular and Morphological Evolution\".

Please refer to \"Supplementary_Files_Directory.pdf\" for a detailed guide of the folder structure.

## Code/Software

We used RStudio (version 4.0.0) to execute the scripts listed under \"Generate Phylograms\" in the R Scripts for methods folder. This requires the use of R packages NELSI (version 0.21); ape (version 5.7.1); phangorn (version 2.11.1); geiger (version 2.0.7); and phylotools (version 0.2.2). This script required a chronogram to generate the molecular and morphological synthetic data sets used in this study. The R script generates a morphological and molecular tree file (phylogram), and a morphological character matrix for 20 replicates. A molecular sequence alignment was then be generated in Seq-Gen (versi...