DOI: 10.5061/dryad.m1n6m0m
title: The implications of lineage-specific rates for divergence time estimation

description: Rate variation adds considerable complexity to divergence time estimation
 in molecular phylogenies. Here, we evaluate the impact of lineage-specific
 rates—which we define as among-branch-rate-variation that acts
 consistently across the entire genome. We compare its impact to residual
 rates—defined as among-branch-rate-variation that shows a different
 pattern of rate variation at each sampled locus, and gene-specific
 rates—defined as variation in the average rate across all branches at each
 sampled locus. We show that lineage-specific rates lead to erroneous
 divergence time estimates, regardless of how many loci are sampled.
 Further, we show that stronger lineage-specific rates lead to increasing
 error. This contrasts to residual rates and gene-specific rates, where
 sampling more loci significantly reduces error. If divergence times are
 inferred in a Bayesian framework, we highlight that error caused by
 lineage-specific rates significantly reduces the probability that the 95%
 highest posterior density includes the correct value, and leads to
 sensitivity to the prior. Use of a more complex rate prior—which has
 recently been proposed to model rate variation more accurately—does not
 affect these conclusions. Finally, we show that the scale of
 lineage-specific rates used in our simulation experiments is comparable to
 that of an empirical data set for the angiosperm genus Ipomoea. Taken
 together, our findings demonstrate that lineage-specific rates cause error
 in divergence time estimates, and that this error is not overcome by
 analyzing genomic scale multilocus data sets.
description: ALT_inference_loop Rev bayes script for divergence time accounting for gene-specific rates   ALT_simple_heterogeneity_script Rev bayes script for divergence time accounting for gene-specific rates   ALT_simulation_study_version_five Python script for simulation   ALT_three_taxon_tree Three taxon start tree   COMP_dirichlet_heterogeneity revbayes script for inferring divergence time with dirichlet rate prior   COMP_inference_loop revbayes script for integrating multiple inference scripts for prior comparison experiment   COMP_inference_loop_dirichlet revbayes script for integrating several inference scripts   COMP_simulation_loop r script for integration simulation scripts   COMP_simulation_study_version_five python script for integrating entire experiment   COMP_standard_simple_heterogeneity_script simple heterogeneity script for prior comparison   DOU_heterogeneity_script_rate_prior_variance_doubled rev bayes heterogeneity script UCLN sd doubled   DOU_inference_loop revbayes loop for integration inference scripts   DOU_simple_clock_script stript clock script for heterogeneity doubled   DOU_simple_heterogeneity_script UCLN with sd fixed for lineage specific rates simulated as doubled   DOU_simulation_loop simulation loop, r script, lineage-specific rates doubled   DOU_simulation_study_version_five python script for integrating entire experiment with lineage specific rates doubled   QUAD_heterogeneity_script_rate_prior_variance_doubled UCLN relaxed clock script with sd quadrupled   QUAD_inference_loop revbayes loop for integrating inference   QUAD_simple_clock_script strict clock script with sequences simulated with heterogeneity quadrupled   QUAD_simple_heterogeneity_script   QUAD_simulation_loop simulatie sequences with lineage specific rates quadrupled   QUAD_simulation_study_version_five python script for integrating experiment with heterogeneity quadrupled   SUMM_inference_loop revbayes inference lop to integrate inference in summary experiment   SUMM_simple_clock_script strict clock script for summary experiment   SUMM_simple_heterogeneity_script UCLN relaxed clock script for summary experiment   SUMM_simulation_loop simulate sequences for summary experiment   SUMM_simulation_study_version_five python script for summary experiment   READ_ME Instructions for simulation experiments   SISTER_GROUP_COMPARISON_OF_TREE Sister group comparison script for estimation of lineage specific rates   Python_shell_for_eight_taxon_simulation Script to integrate analyses for eight taxon trees simulation_study_version_five.py simulate_tree simulate eight taxon trees   simulate_sequences simulate sequences for eight taxon trees   inference_loop overall inference script for eight taxon trees   simple_clock_script inference script for eight taxon trees with a strict clock   simple_heterogeneity_script inference script for eight taxon trees relaxed clock     <strong>Supplementary Appendix, Tables, Figure.docx</strong>