Phylogenetic analyses with systematic taxon sampling show that mitochondria branch within Alphaproteobacteria

  title={Phylogenetic analyses with systematic taxon sampling show that mitochondria branch within Alphaproteobacteria},
  author={Luice Fan and Dingfeng Wu and Vadim V. Goremykin and Jing Xiao and Yanbing Xu and Sriram G. Garg and Chuanlun Zhang and William F. Martin and Ruixin Zhu},
  journal={Nature Ecology \& Evolution},
Though it is well accepted that mitochondria originated from an alphaproteobacteria-like ancestor, the phylogenetic relationship of the mitochondrial endosymbiont to extant Alphaproteobacteria is yet unresolved. The focus of much debate is whether the affinity between mitochondria and fast-evolving alphaproteobacterial lineages reflects true homology or artefacts. Approaches such as site exclusion have been claimed to mitigate compositional heterogeneity between taxa, but this comes at the cost… 

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A site-and-branch-heterogeneous model on an expanded dataset favor mitochondria as sister to known Alphaproteobacteria

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Anomalous Phylogenetic Behavior of Ribosomal Proteins in Metagenome-Assembled Asgard Archaea.

It is shown that universal proteins including ribosomal proteins of asgard archaeal MAGs fail to meet the basic phylogenetic criterion fulfilled by genome sequences of cultured archaea investigated to date: These proteins do not share common evolutionary histories to the same extent as pure culture genomes do, pointing to a chimeric nature of as Gard archaealing MAGs.

New Alphaproteobacteria Thrive in the Depths of the Ocean with Oxygen Gradient

This work analyzed the classification of Alphaproteobacteria lineages that are most common in marine environments, using integrated approaches of phylogenomics and functional profiling of metabolic features that define their aerobic metabolism, and characterized the new ‘oxycline’ clade.

Ancestral State Reconstructions Trace Mitochondria But Not Phagocytosis to the Last Eukaryotic Common Ancestor

It is indicated that both phagocytosis and phagotrophy arose subsequent to the origin of mitochondria, consistent with findings from comparative physiology and, like wings in animals, these traits are useful but neither ancestral nor homologous across groups.

A spectrum of verticality across genes

Lateral gene transfer (LGT) has impacted prokaryotic genome evolution, yet the extent to which LGT compromises vertical evolution across individual genes and individual phyla is unknown, as are the

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Deep mitochondrial origin outside the sampled alphaproteobacteria

It is suggested that mitochondria evolved from a proteobacterial lineage that branched off before the divergence of all sampled alphaproteobacteria and previous hypotheses on the nature of the mitochondrial ancestor should be re-evaluated.

An integrated phylogenomic approach toward pinpointing the origin of mitochondria

The results suggest that mitochondria most likely originated from a Rickettsiales endosymbiont already residing in the host, but not from the distantly related free-living Pelagibacter and Rhodospirillales.

Phylogenomic evidence for a common ancestor of mitochondria and the SAR11 clade

The evidence supports a common origin of mitochondria and SAR11 as a sister group to the Rickettsiales, and the simplest explanation is that mitochondria evolved from a planktonic marine alphaproteobacterial lineage that participated in multiple inter-specific cell colonization events, in some cases yielding parasitic relationships, but in at least one case producing a symbiosis that characterizes modern eukaryotic life.

A Phylometagenomic Exploration of Oceanic Alphaproteobacteria Reveals Mitochondrial Relatives Unrelated to the SAR11 Clade

The results allude to the existence of an alphaproteobacterial clade in the oxygen-rich surface waters of the oceans that represents the closest free-living relative to mitochondria identified thus far, and underscore the importance of expanding the taxonomic diversity in phylogenetic analyses beyond that represented by cultivated bacteria to study the origin of mitochondria.

Genome phylogenies indicate a meaningful alpha-proteobacterial phylogeny and support a grouping of the mitochondria with the Rickettsiales.

There is some evidence of horizontal gene transfer within the alpha-proteobacteria, but it appears to be restricted to a minority of genes most of whom can be categorized as operational, which means that placement of the mitochondrion should not be excessively hampered by interspecies gene transfer.

Rooting the eukaryotic tree with mitochondrial and bacterial proteins.

A new approach to the rooting of the eukaryotic tree is applied by using a subset of genomic information with more recent evolutionary origin-mitochondrial sequences, whose closest relatives are α-Proteobacteria.

The SAR11 Group of Alpha-Proteobacteria Is Not Related to the Origin of Mitochondria

Preliminary phylogenetic analyses support that SAR11 group is not the sistergroup of the Rickettsiales+mitochondria clade and confirm that the position of this group in the alpha-proteobacterial tree is strongly affected by tree reconstruction artefacts due to compositional bias.

Bacterial genome chimaerism and the origin of mitochondria.

The results support the idea that notable bacterial genome chimaerism has occurred en route to the formation of mitochondria.

A genome phylogeny for mitochondria among alpha-proteobacteria and a predominantly eubacterial ancestry of yeast nuclear genes.

It is indicated that at the levels of overall amino acid sequence identity and gene content, yeast shares a sister-group relationship with eubacteria, not with archaebacteria, in contrast to the current phylogenetic paradigm based on ribosomal RNA.

Mitochondrial evolution.

  • M. Gray
  • Biology
    Cold Spring Harbor perspectives in biology
  • 2012
New data continue to reshape views regarding mitochondrial evolution, particularly raising the question of whether the mitochondrion originated after the eukaryotic cell arose, as assumed in the classical endosymbiont hypothesis, or whether this organelle had its beginning at the same time as the cell containing it.