DOI: 10.5061/dryad.cc2fqz6d1
title: Data from: Phylogeny inference under time-decaying migration and varying information content

description: Postspeciation gene flow is widespread across the Tree of Life but is
 ignored as a cause of gene tree discordance under the standard
 multispecies coalescent. Failure to account for migration can lead to the
 misestimation of effective population sizes, divergence times, and
 topology. Isolation-with-migration and multispecies
 coalescent-with-introgression models accommodate migration but involve
 additional parameters that limit their computational viability with even
 moderate sized molecular datasets. Problematically, very large datasets
 may be required for reliable parameter estimation under these models. This
 study evaluates IM-based phylogeny inference using simulated and empirical
 datasets with a focus on incorporating gradually time-decaying migration,
 reflecting realistic expectations of reduced gene flow among more
 divergent lineages. We compare the performance of DENIM (an IM model) and
 StarBeast3 (an MSC model) using sequences simulated with continuous
 low-level migration and no migration on a ten-taxon ultrametric tree. Our
 results reveal that DENIM significantly improves phylogenetic accuracy in
 the presence of incomplete lineage and low-level, time-decaying migration,
 providing robust estimates with fewer loci and without requiring a
 predefined topology. Both DENIM and StarBeast3 benefit from rapidly
 decaying migration, but DENIM is more accurate and demonstrates faster
 convergence per generation across all migration scenarios despite its
 higher parameter complexity. Varying locus length and number had limited
 detectable effects on phylogenetic accuracy, although increasing sequence
 length improves convergence considerably. Empirical validation with
 autosomal sequences from the Anopheles gambiae group of African mosquitoes
 demonstrates confirms DENIM’s efficiency in inferring migration, and
 delivering node height and topology estimates consistent with previous
 studies. This study affirms DENIM as a robust method for mitigating
 migration-induced distortions in the species tree while offering enhanced
 computational efficiency.
description: # Data from: Phylogeny inference under time-decaying migration and varying
 information content
 [https://doi.org/10.5061/dryad.cc2fqz6d1](https://doi.org/10.5061/dryad.cc2fqz6d1) Input and output files for the simulated and empirical data for DENIM and StarBeast3 with supporting Figure S1 and Tables S1 and S2. ## Description of the data and file structure Empirical data: the folder "Anopheles_data.zip" contains all the DENIM and StarBeast3 analyses for the *Anopheles gambiae* sequence data. Simulated data: folders beginning with "1_" to "7_" contain the simulated data results. Folders "8_Locus-length-number-combs-not-included_filepart*" are the input and output data files for simulated locus length and number combinations that failed to reach convergence after several weeks of computation. Read-me.txt: a text file providing more detailed information about the folder structure and file contents. **Version changes:** 20 Sept. 2024: Added DENIM and StarBeast3 analyses for the simulated data with no migration. Also replaced an earlier empirical dataset with analyses for the *Anopheles gambiae* group of African mosquitoes, whose recent divergence times make the dataset more appropriate to our study. The XML files for the *Anopheles* analyses are available at the Zenodo link provided below. All changes are updated in the Read-me.txt file provided. ## Sharing/Access information Additional copyright-protected supporting files for the *A. gambiae* group are provided on Zenodo: 10.5281/zenodo.13771614   ## Code/Software Annotated R scripts for the empirical and simulated data are in the folder "R-scripts.zip".