DOI: 10.5061/dryad.68qt629
title: Data from: The relative importance of modeling site pattern heterogeneity versus partition-wise heterotachy in phylogenomic inference

description: Large taxa-rich genome-scale data sets are often necessary for resolving
 ancient phylogenetic relationships. But accurate phylogenetic inference
 requires that they are analyzed with realistic models that account for the
 heterogeneity in substitution patterns amongst the sites, genes and
 lineages. Two kinds of adjustments are frequently used: models that
 account for heterogeneity in amino acid frequencies at sites in proteins,
 and partitioned models that accommodate the heterogeneity in rates (branch
 lengths) among different proteins in different lineages (protein-wise
 heterotachy). Although partitioned and site-heterogeneous models are both
 widely used in isolation, their relative importance to the inference of
 correct phylogenies has not been carefully evaluated. We conducted several
 empirical analyses and a large set of simulations to compare the relative
 performances of partitioned models, site-heterogeneous models and combined
 partitioned site heterogeneous models. In general, site-homogeneous models
 (partitioned or not) performed worse than site heterogeneous, except in
 simulations with extreme protein-wise heterotachy. Furthermore,
 simulations using empirically-derived realistic parameter settings showed
 a marked long-branch attraction (LBA) problem for analyses employing
 protein-wise partitioning even when the generating model included
 partitioning. This LBA problem results from a small sample bias compounded
 over many single protein alignments. In some cases, this problem was
 ameliorated by clustering similarly-evolving proteins together into larger
 partitions using the PartitionFinder method. Similar results were obtained
 under simulations with larger numbers of taxa or heterogeneity in
 simulating topologies over genes. For an empirical Microsporidia test data
 set, all but one tested site-heterogeneous models (with or without
 partitioning) obtain the correct Microsporidia+Fungi grouping, whereas
 site-homogenous models (with or without partitioning) did not. The single
 exception was the fully partitioned site-heterogeneous analysis that
 succumbed to the compounded small sample LBA bias. In general unless
 protein-wise heterotachy effects are extreme, it is more important to
 model site-heterogeneity than protein-wise heterotachy in phylogenomic
 analyses. Complete protein-wise partitioning should be avoided as it can
 lead to a serious LBA bias. In cases of extreme protein-wise heterotachy,
 approaches that cluster similarly-evolving proteins together and coupled
 with site-heterogeneous models work well for phylogenetic estimation.
description: breviate.22taxa.datThis is one of the two empirical datasets discussed in the paper. It is a 22-taxa protein sequence alignment extracted from the original 68-taxa Breviate data set (Brown et al. Proc. Biol. Sci. 280:20131755, 2013). The file also includes a partition file for each of the concatenated proteins.simu.UBL.originalBL.1xsites100 sets of concatenated alignments were simulated under LG+F+G+UBL for 121 proteins under the original 4-taxon trees and for the same numbers of sites for each protein. The partition file is also included.simu.UBL.internalBL10timeshortened.1xsites100 sets of concatenated alignments were simulated under LG+F+G+UBL for 121 proteins under the 4-taxon trees whose internal branches were shorten by 10x and for the same numbers of sites for each protein. The partition file is also included.simu.UBL.internalBL10timeshortened.2xsites100 sets of concatenated alignments were simulated under LG+F+G+UBL for 121 proteins under the 4-taxon trees whose internal branches were shorten by 10x and for twice numbers of sites for each protein. The partition file is also included.USYB-2018-158.SupplementaryMaterialsC20UBL.simu.concate121pro.35taxon.bl5x.phy.tarThis file is for the section "35-taxon Tree Simulations with Empirically-derived Parameters" in the main text. The simulated data (100 sets of concatenated alignments) are included. Also included are the 121 35-taxon generating trees from the individual microsporidia datasets trimmed to 35 taxa. The script for simulating the alignments and a C program used to increase the branches to Microsporidia and to Pyrococcus by 5 fold are included.simupmsfUBLforILS.tarThis data is for the section "Four-taxon Tree Simulations with Empirically-derived Parameters and Gene Tree Heterogeneity" in the main text. The data are simulated under PMSF+UBL. The simulated alignments (100 sets) and the generating trees (97 MF trees, 12 MA trees and 12 other trees) are included. The internal branch of the trees are 10 times shortened.