Complex models of sequence evolution improve fit, but not gene tree discordance, for tetrapod mitogenomes

Variation in gene tree estimates is widely observed in empirical phylogenomic data and is often assumed to be the result of biological processes. However, a recent study using tetrapod mitochondrial genomes to control for biological sources of variation due to their haploid, uniparentally inherited, and non-recombining nature found that levels of discordance among mitochondrial gene trees were comparable to those found in studies that assume only biological sources of variation. Additionally, they found that several of the models of sequence evolution chosen to infer gene trees were doing an inadequate job of fitting the sequence data. These results indicated that significant amounts of gene tree discordance in empirical data may be due to poor fit of sequence evolution models and that more complex and biologically realistic models may be needed. To test how the fit of sequence evolution models relates to gene tree discordance, we analyzed the same mitochondrial datasets as the previous..., , , # Complex models of sequence evolution improve fit, but not gene tree discordance, for tetrapod mitogenomes

[https://doi.org/10.5061/dryad.rr4xgxdgd](https://doi.org/10.5061/dryad.rr4xgxdgd)

This repository contains supplementary material for the associated manuscript, as well as all datasets used (folder: alignments), and example scripts for each analysis. The datasets provided were used in Bayesian MCMC, Stepping-Stone Marginal Likelihood Estimation, Non-Linear Dimensionality Reduction, and Bipartition-Covariance analysis.

## Description of the data and file structure

The example RevBayes scripts provided can be used for both MCMC, as well as stepping-stone analyses. Non-linear Dimensionality Reduction and Bipartition-Covariance analysis were performed in CloudForest, and tutorials for each can be found on the CloudForest website.

## Code/Software

All example scripts provided are for RevBayes, and additional details on setting up and running these analyses can be found on the Re...