DOI: 10.5061/dryad.hq4gc
title: Data from: Ancient horizontal gene transfer and the last common ancestors

description: Background: The genomic history of prokaryotic organismal lineages is
 marked by extensive non-vertical inheritance of genes, with horizontal
 gene transfer (HGT) between many groups of organisms at all taxonomic
 levels. These HGT events have played an essential role in the origin and
 distribution of biological innovations. Analyses of ancient gene families
 show that HGT existed in the distant past, even at the time of the
 organismal last universal common ancestor (LUCA). Most gene transfers
 originated in lineages that have since gone extinct. Therefore, one cannot
 assume that the last common ancestors of each gene were all present in the
 same cell representing the cellular ancestor of all extant life. Results:
 An ancient population of organisms existing as part of a diverse ecosystem
 at the time of LUCA would likely be sharing genetic material between
 lineages. If these other lineages persisted for some time, HGT with the
 descendants of LUCA could have continued into the bacterial and archaeal
 lineages. Phylogenetic analyses of aminoacyl-tRNA synthetase protein
 families support the hypothesis that the molecular common ancestors of the
 most ancient gene families did not all coincide in space and time. This is
 most apparent in the evolutionary histories of seryl-tRNA synthetase and
 threonyl-tRNA synthetase protein families, each containing highly
 divergent “rare” forms, as well as the sparse phylogenetic distributions
 of pyrrolysyl-tRNA synthetase, and the bacterial heterodimeric form of
 glycyl-tRNA synthetase. These topologies and phyletic distributions are
 consistent with horizontal transfers from ancient, likely extinct branches
 of the tree of life. Conclusions: Of all the organisms that may have
 existed at the time of LUCA, by definition only one lineage is survived by
 known progeny; however, this lineage retains a genomic record of
 heterogeneous genetic origins. The evolutionary histories of
 aminoacyl-tRNA synthetases (aaRS) are especially informative in detecting
 this signal, as they are intimately associated with some of the earliest
 biochemical processes to evolve, have undergone several ancient HGT
 events, and contain many sites with low substitution rates allowing deep
 phylogenetic reconstruction. We conclude that some aaRS families contain
 groups that diverge before LUCA. We propose that these ancient gene
 variants be described by the term “hypnologs”, reflecting their ancient,
 reticulate origin from a time in life history that has been all but
 erased.
description: Phylogenetic tree of
 PylRS reconstructed using PhyloBayes3.3Phylogenetic
 reconstruction of PylRS sequences from the full FASTA alignment, using
 PhyloBayes3.3 with C60 fixed CAT site profiles.File1_PylRS_PB.treePhylogenetic tree of SerRS/ThrRS using GUIDANCE decomposed alignment, reconstructed using PhyloBayes3.3Phylogenetic reconstruction of SerRS/ThrRS sequences from the GUIDANCE decomposed FASTA alignment (Additional File 3) using PhyloBayes3.3 with C60 fixed CAT site profiles.File2_SerThrRS_GUIDANCEDecomposed_C60_LG.con.treGUIDANCE decomposed alignment of SerRS/ThrRSDecomposed alignment of sites identified by GUIDANCE as being well-aligned between and within SerRS and ThrRS paralogs (see methods).File3_Aligned_SerRS_ThrRS_GUIDANCE_Decomposed.fastaPhylogenetic tree of GlyRS homodimer using GUIDANCE alignment, reconstructed using PhyloBayes3.3Phylogenetic reconstruction of GlyRS homodimer sequences from the GUIDANCE FASTA alignment (Additional File 10) using PhyloBayes3.3 with C60 fixed CAT site profiles.File4_GlyRS_Homodimer_GUIDANCE_noOut_C60_LG.con.trePhylogenetic tree of GlyRS heterodimer using GUIDANCE alignment, reconstructed using PhyloBayes3.3Phylogenetic reconstruction of GlyRS heterodimer sequences from the GUIDANCE FASTA alignment (Additional File 11) using PhyloBayes3.3 with C60 fixed CAT site profiles.File5_GlyRS_Heterodimer_GUIDANCE_noOut_PB_C60_LG.con.treeAligned SerRS and ThrRS sequencesMUSCLE-aligned rare and common forms of SerRS and ThrRS protein sequences sampled across 3 Domains of life.File6_Aligned_SerRS_ThrRS.fastaAligned GlyRS homodimer sequencesMUSCLE-aligned of GlyRS homodimer subunit protein sequences sampled across 3 Domains of life, including other aaRS outgroupsFile7_Aligned_GlyRS_homodimer.fastaGlyRS heterodimer subunit sequencesConcatenation of MUSCLE-aligned GlyRS heterodimer subunit protein sequences sampled across bacterial taxa, including other aaRS outgroups.File8_Aligned_GlyRS_heterodimer.fastaAligned PylRS sequencesMUSCLE-aligned C-terminal region homologous to C-terminal subunit in bacteria, including other aaRS outgroups.File9_Aligned_PylRS_Cterm.fastaGUIDANCE selected sites of GlyRS homodimer alignmentSites from Additional File 7 identified by GUIDANCE as being well-aligned, with single-taxon insertions removed.File10_Aligned_GUIDANCE_GlyRS_homodimer.fastaGUIDANCE selected sites of GlyRS heterodimer alignmentSites from Additional File 8 identified by GUIDANCE as being well-aligned, with single-taxon insertions removed.File11_Aligned_GUIDANCE_GlyRS_heterodimer.fastaMaximum-likelihood (ML) tree of known PylRS homologsTree in Figure 1Tree1_PylRS_Arc_Bac_Cterm.phy.reduced_phyml_tree.txtML tree showing the common and rare types of SerRS and ThrRSTree in Figure 2Tree2_Oct22014_ProfileSer1Thr2_ProfileCommon1Rare2_muscle.phy_phyml_tree.txtML tree of the GlyRS homodimer subunitTree in Figure 3Tree3_Oct22014_Gly_ABE_homodimer_withOutgrpSerPro_muscle.phy_phyml_tree.txtPhylogenetic analyses of the GlyRS heterodimer subunitsTree in Figure 4Tree4_Sept26_Gly_concatAlphaBeta_Bact_pherrsOutgrp_muscle.phy_phyml_tree.txt