DOI: 10.5061/dryad.068d0d0
title: Data from: Deep mitochondrial origin outside the sampled alphaproteobacteria

description: Mitochondria are ATP-generating organelles whose endosymbiotic origin has
 been a key event in the evolution of eukaryotic cells. Despite
 overwhelming phylogenetic evidence for an alphaproteobacterial ancestry,
 efforts to pinpoint the closest relatives among the sampled
 alphaproteobacteria have been conflicting, complicating detailed
 inferences about the identity and nature of the mitochondrial ancestor.
 While most studies support that mitochondria evolved from an ancestor
 related to Rickettsiales, an order that includes several host-associated
 pathogenic and endosymbiotic lineages, others suggest that mitochondria
 evolved from a free-living group. Here we re-evaluate the phylogenetic
 placement of mitochondria. We employ genome-resolved binning of oceanic
 metagenome datasets and increase the genomic sampling of
 Alphaproteobacteria with twelve novel divergent clades, and one novel
 clade representing a sister group to all Alphaproteobacteria. Subsequent
 phylogenomic analyses that specifically address long branch attraction and
 compositional bias artefacts suggest that mitochondria did not evolve from
 Rickettsiales or any other currently recognized alphaproteobacterial
 lineage. Rather, our analyses indicate that mitochondria evolved from a
 proteobacterial lineage that branched off prior to the divergence of all
 sampled alphaproteobacteria. In light of this new result, previous
 hypotheses on the nature of the mitochondrial ancestor should be
 re-evaluated.
description: AtlanticOcean_100m_contigs.faComplete assembly of the Moca1 metagenome (SRA accession: SRP081826). Metagenome was derived from Atlantic Ocean sampled at 100m depth. See the associated publication for technical details.AtlanticOcean_776m_contigs.faComplete assembly of the Moca2 metagenome (SRA accession: SRP081826). Metagenome was derived from Atlantic Ocean sampled at 776m depth. See the associated publication for technical details.AtlanticOcean_2745m_contigs.faComplete assembly of the Moca3 metagenome (SRA accession: SRP081826). Metagenome was derived from Atlantic Ocean sampled at 2745m depth. See the associated publication for technical details.AtlanticOcean_5002m_contigs.faComplete assembly of the Moca4 metagenome (SRA accession: SRP081826). Metagenome was derived from Atlantic Ocean sampled at 5002m depth. See the associated publication for technical details.PacificOcean_115m_contigs.fastaComplete assembly of the Tara Oceans metagenome (SRA accession: ERR594304). Metagenome was derived from Pacific Ocean sampled at 115m depth. See the associated publication for technical details.PacificOcean_5m_contigs.faComplete assembly of the Tara Oceans metagenome (SRA accession: ERR594339). Metagenome was derived from Pacific Ocean sampled at 5m depth. See the associated publication for technical details.PacificOcean_140m_contigs.faComplete assembly of the Tara Oceans metagenome (SRA accession: ERR599156). Metagenome was derived from Pacific Ocean sampled at 140m depth. See the associated publication for technical details.alphaproteobacteria_untreated.alnConcatenated supermatrix alignment of 72 genes conserved among alphaproteobacteria. See associated publication for technical details on how this alignment was prepared.alphaproteobacteria_stationarytrimmed.alnStationary trimmed, concatenated supermatrix alignment of 72 genes conserved among alphaproteobacteria. See associated publication for technical details on how this alignment was prepared.alphaproteobacteria_SR4recoded.alnSR4 recoded, concatenated supermatrix alignment of 72 genes conserved among alphaproteobacteria. See associated publication for technical details on how this alignment was prepared.alphaproteobacteria_mitochondria_untreated.alnConcatenated supermatrix alignment of 24 genes conserved among alphaproteobacteria and mitochondrial genomes. See associated publication for technical details on how this alignment was prepared.alphaproteobacteria_mitochondria_stationarytrimmed.alnStationary-trimmed, concatenated supermatrix alignment of 24 genes conserved among alphaproteobacteria and mitochondrial genomes. See associated publication for technical details on how this alignment was prepared.alphaproteobacteria_mitochondria_SR4recoded.alnSR4 recoded, concatenated supermatrix alignment of 24 genes conserved among alphaproteobacteria and mitochondrial genomes. See associated publication for technical details on how this alignment was prepared.alphamito38.concat.untreated.alnConcatenated supermatrix alignment of 38 genes conserved among alphaproteobacteria and mitochondrial genomes. See associated publication for technical details on how this alignment was prepared.alphamito38.concat.stattrim.alnStationary-trimmed, concatenated supermatrix alignment of 38 genes conserved among alphaproteobacteria and mitochondrial genomes. See associated publication for technical details on how this alignment was prepared.nuclearEncoded29_concat_Composite.untreated.alnConcatenated supermatrix alignment of 29 genes conserved among alphaproteobacteria and mitochondrial genes encoded on nuclear eukaryotic genomes. See associated publication for technical details on how this alignment was prepared.nuclearEncoded29_concat_Composite.stattrim.alnStationary-trimmed, concatenated supermatrix alignment of 29 genes conserved among alphaproteobacteria and mitochondrial genes encoded on nuclear eukaryotic genomes. See associated publication for technical details on how this alignment was prepared.alphamito24.otherMitoTaxa.concat.untreated.alnConcatenated supermatrix alignment of 24 genes conserved among alphaproteobacteria and mitochondrial genomes. Here, a more diverse set of mitochondria has been selected. See associated publication for technical details on how this alignment was prepared.alphamito24.otherMitoTaxa.concat.stattrim.alnStationary-trimmed, concatenated supermatrix alignment of 24 genes conserved among alphaproteobacteria and mitochondrial genomes. Here, a more diverse set of mitochondria has been selected. See associated publication for technical details on how this alignment was prepared.alphamito24.concat.NoOutgroups.untreated.alnConcatenated supermatrix alignment of 24 genes conserved among alphaproteobacteria and mitochondrial genomes. Here, the outgroups MarineProteo1, Magnetococcales, Beta- and Gammaproteobacteria have been removed. See associated publication for technical details on how this alignment was prepared.alphamito24.concat.NoOutgroups.stattrim.alnStationary-trimmed, concatenated supermatrix alignment of 24 genes conserved among alphaproteobacteria and mitochondrial genomes. Here, the outgroups MarineProteo1, Magnetococcales, Beta- and Gammaproteobacteria have been removed. See associated publication for technical details on how this alignment was prepared.