DOI: 10.5061/dryad.k3j9kd582
title: Phylogenetic accuracy under non-stationary and non-homogeneous conditions: A simulation study

description: Phylogenetic inference typically assumes that the data have evolved under
 Stationary, Reversible, and Homogeneous (SRH) conditions. Many empirical
 and simulation studies have shown that assuming SRH conditions can lead to
 significant errors in phylogenetic inference when the data violate these
 assumptions. Yet, many simulation studies focused on extreme non-SRH
 conditions that represent worst-case scenarios and not the average
 empirical dataset. In this study, we simulate datasets under
 various degrees of non-SRH conditions using empirically derived
 parameters to mimic real data and examine the effects
 of incorrectly assuming SRH conditions on inferring phylogenies.
 Our results show that maximum likelihood inference is generally
 quite robust to a wide range of SRH model violations but is
 inaccurate under extreme convergent evolution.
description: # Phylogenetic accuracy under non-stationary and non-homogeneous
 conditions: A simulation study #### Overview This repository contains
 simulation outputs and supplementary materials used in the study
 investigating the robustness of maximum-likelihood phylogenetic inference
 under violations of stationarity, reversibility, and homogeneity (SRH)
 assumptions. The data include simulated sequence alignments generated
 under two alternative evolutionary simulation schemes, as well as
 supplementary figures and tables referenced in the manuscript. Dataset
 DOI: [10.5061/dryad.k3j9kd582](10.5061/dryad.k3j9kd582) #### Description
 of the data and file structure ### `simulation_alignments.zip` This
 archive contains all simulated sequence alignments and associated metadata
 used in the analyses. **Contents:** * Simulated nucleotide alignments
 generated under: * the *inheritance scheme*, in which substitution
 processes evolve along the tree * The *two-matrix scheme*, in which two
 monophyletic clades evolve under an alternative substitution process *
 Alignments were simulated under varying parameter settings (e.g., number
 of sites, inheritance weights, Δ(Q) values), as described in the Methods
 section of the associated manuscript. * File and directory names encode
 simulation conditions (e.g., scheme type, number of sites, parameter
 values). These alignments were used as input for maximum-likelihood
 phylogenetic inference and subsequent evaluation of topological and
 branch-length estimation error. #### Reproducibility All scripts used to
 generate simulations, perform analyses, and produce figures are available
 on GitHub:
 [https://github.com/suhanaser/empiricalGTRdist](https://github.com/suhanaser/empiricalGTRdist) The combination of the scripts (GitHub), simulated alignments (this Dryad repository), and the Appendix allows full reproduction of the analyses reported in the paper. #### Licensing All data in this repository are released under the **CC0 Public Domain Dedication**, allowing unrestricted reuse, modification, and redistribution. #### Contact For questions regarding the data or analyses, please contact the corresponding author via the associated publication.