DOI: 10.5061/dryad.7785h
title: Data from: The effects of model choice and mitigating bias on the ribosomal tree of life

description: Deep-level relationships within Bacteria, Archaea, and Eukarya as well as
 the relationships of these three domains to each other require resolution.
 The ribosomal machinery, universal to all cellular life, represents a
 protein repertoire resistant to horizontal gene transfer, which provides a
 largely congruent signal necessary for reconstructing a tree suitable as a
 backbone for life’s reticulate history. Here, we generate a ribosomal tree
 of life from a robust taxonomic sampling of Bacteria, Archaea, and Eukarya
 to elucidate deep-level intra-domain and inter-domain relationships. Lack
 of phylogenetic information and systematic errors caused by inadequate
 models (that cannot account for substitution rate or compositional
 heterogeneities) or improper model selection compound conflicting
 phylogenetic signals from HGT and/or paralogy. Thus, we tested several
 models of varying sophistication on three different datasets, performed
 removal of fast-evolving or long-branched Archaea and Eukarya, and
 employed three different strategies to remove compositional heterogeneity
 to examine their effects on the topological outcome. Our results support a
 two-domain topology for the tree of life, where Eukarya emerges from
 within Archaea as sister to a Korarchaeota/Thaumarchaeota (KT) or
 Crenarchaeota/KT clade for all models under all or at least one of the
 strategies employed. Taxonomic manipulation allows single-matrix and
 certain mixture models to vacillate between two-domain and three-domain
 phylogenies. We find that models vary in their ability to resolve
 different areas of the tree of life, which does not necessarily correlate
 with model complexity. For example, both single-matrix and some mixture
 models recover monophyletic Crenarchaeota and Euryarchaeota archaeal
 phyla. In contrast, the most sophisticated model recovers a paraphyletic
 Euryarchaeota but detects two large clades that comprise the Bacteria,
 which were recovered separately but never together in the other models.
 Overall, models recovered consistent topologies despite dataset
 modifications due to the removal of compositional bias, which reflects
 either ineffective bias reduction or robust datasets that allow models to
 overcome reconstruction artifacts. We recommend a comparative approach for
 evolutionary models to identify model weaknesses as well as consensus
 relationships.
description: aeb1
 phylogeniesThe Aeb1 phylogenies
 include representatives of all major phyla/supergroups for the three
 domains of life (when available). Archaea, Eukarya, and Bacteria protein
 sequences were aligned at once (no profile alignment) and protein
 alignments were trimmed individually and then concatenated into a
 supermatrix (resulting in 13432 positions). Aeb1 contains no “Archezoan”
 sequences (polyphyletic group of long branched eukaryotes such as Giardia,
 Trichomonas, Microsporidia, and Entamoeba) but has some fast evolving
 eukaryotes, including Euglenozoa. Methods of inference included maximum
 likelihood as implemented in RAxML, PhyML-4X (Le et al., 2012), and
 PhyML-Structure (Le and Gascuel, 2010) or Bayesian inference as
 implemented in PhyloBayes v. 3.3 or 3.3e (Lartillot et al.,
 2009).aeb1.alltrees.treeaeb2 phylogeniesAeb2 includes members of Bacteria, Archaea, and Eukarya. Methods of tree inference included maximum likelihood as implemented in RAxML, PhyML-4X (Le et al., 2012), and PhyML-Structure (Le and Gascuel, 2010) or Bayesian inference as implemented in PhyloBayes v. 3.3 or 3.3e (Lartillot et al., 2009). Aeb2 includes “Archezoan” (polyphyletic group of long branched eukaryotes such as Giardia, Trichomonas, Microsporidia, and Entamoeba) sequences; the subset “aeb2 Arch+” refers to the presence of Archezoa without Korarchaeota and Thaumarchaeota and the subset, “aeb2 KT+” refers to the presence of Korarchaeota and Thaumarchaeota without Archezoa. Aeb2 Arch+ and KT+ attempt to mitigate long-branch attraction (LBA) artifacts due to substitution rate saturation and allow us to assess the influence of taxonomic sampling on phylogenetic outcome. Gap removal occurred after the creation of the supermatrix (resulting in 13929 positions for aeb2 Arch+ and 13941 positions for aeb2 KT+).aeb2.alltrees.treeaeb3 phylogeniesMethods of inference included maximum likelihood as implemented in RAxML, PhyML-4X (Le et al., 2012), and PhyML-Structure (Le and Gascuel, 2010) or Bayesian inference as implemented in PhyloBayes v. 3.3 or 3.3e (Lartillot et al., 2009). Aeb3 comprises representatives from each phylum/supergroup with no sequences from Archezoa or Euglenozoa and trimming performed after the construction of the supermatrix (resulting in 17876 positions). The removal of the fast-evolving Euglenozoa represents an attempt to further mitigate LBA artifacts. To examine the effects of missing data and specifically test how missing data influences the relationship between Archaea and Eukarya, ribosomal proteins shared by Archaea and Eukarya were deleted from some archaeal taxa.aeb3.alltrees.treeaeb1 alignmentaeb1 alignment in fasta formataeb1.fasaeb2 Arch+ alignmentaeb2_Arch.fasaeb2 KT+ alignmentaeb2_KT.fasaeb3 alignmentAeb3 comprises representatives from each phylum/supergroup with no sequences from Archezoa or Euglenozoa and trimming performed after the construction of the supermatrix (resulting in 17876 positions). The removal of the fast-evolving Euglenozoa represents an attempt to further mitigate LBA artifacts. To examine the effects of missing data and specifically test how missing data influences the relationship between Archaea and Eukarya, ribosomal proteins shared by Archaea and Eukarya were deleted from some archaeal taxa.aeb3.fas