ReviewPhilosophical transactions of the Royal Society of London. Series B, Biological sciences2009
Genome beginnings: rooting the tree of life.
Review in Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
40 citing papers in PubMed.
- Universal paralogs provide a window into evolution before the last universal common ancestor.Cell genomics · 2026Review
- Tracing the Origin and Evolution of the Secondary Structure of RNA.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Permeability selection of biologically relevant membranes matches the stereochemistry of life on Earth.PLoS biology · 2025Article
- ATP synthase evolution on a cross-braced dated tree of life.Nature communications · 2023Article
- Evolving Perspective on the Origin and Diversification of Cellular Life and the Virosphere.Genome biology and evolution · 2022Review
- Reconciling Asgardarchaeota Phylogenetic Proximity to Eukaryotes and Planctomycetes Cellular Features in the Evolution of Life.Molecular biology and evolution · 2021Article
- Multidomain ribosomal protein trees and the planctobacterial origin of neomura (eukaryotes, archaebacteria).Protoplasma · 2020Review
- Descent of Bacteria and Eukarya From an Archaeal Root of Life.Evolutionary bioinformatics online · 2020Article
- Phylogenomics provides robust support for a two-domains tree of life.Nature ecology & evolution · 2020Article
- Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea.Nature communications · 2019Article
- Identification of a basal system for unwinding a bacterial chromosome origin.The EMBO journal · 2019Article
- Investigating the Origins of Membrane Phospholipid Biosynthesis Genes Using Outgroup-Free Rooting.Genome biology and evolution · 2019Article
- Genome size evolution in the Archaea.Emerging topics in life sciences · 2018Article
- Rooting Phylogenies and the Tree of Life While Minimizing Ad Hoc and Auxiliary Assumptions.Evolutionary bioinformatics online · 2018Review
- The Rhizome of Lokiarchaeota Illustrates the Mosaicity of Archaeal Genomes.Genome biology and evolution · 2017Article
- Characterization of Reconstructed Ancestral Proteins Suggests a Change in Temperature of the Ancient Biosphere.Life (Basel, Switzerland) · 2017Review
- Integrative modeling of gene and genome evolution roots the archaeal tree of life.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Sporulation, bacterial cell envelopes and the origin of life.Nature reviews. Microbiology · 2016Review
- New substitution models for rooting phylogenetic trees.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2015Article
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
A rooted tree of life provides a framework to answer central questions about the evolution of life. Here we review progress on rooting the tree of life and introduce a new root of life obtained through the analysis of indels, insertions and deletions, found within paralogous gene sets. Through the analysis of indels in eight paralogous gene sets, the root is localized to the branch between the clade consisting of the Actinobacteria and the double-membrane (Gram-negative) prokaryotes and one consisting of the archaebacteria and the firmicutes. This root provides a new perspective on the habitats of early life, including the evolution of methanogenesis, membranes and hyperthermophily, and the speciation of major prokaryotic taxa. Our analyses exclude methanogenesis as a primitive metabolism, in contrast to previous findings. They parsimoniously imply that the ether archaebacterial lipids are not primitive and that the cenancestral prokaryotic population consisted of organisms enclosed by a single, ester-linked lipid membrane, covered by a peptidoglycan layer. These results explain the similarities previously noted by others between the lipid synthesis pathways in eubacteria and archaebacteria. The new root also implies that the last common ancestor was not hyperthermophilic, although moderate thermophily cannot be excluded.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.