ArticleeLife2022
An estimate of the deepest branches of the tree of life from ancient vertically evolving genes.
Article in eLife, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers.
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54 citing papers in PubMed, 90 citations in OpenAlex.
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- Unbinned contigs expand known diversity in the global microbiome.Nature microbiology · 2026Article
- Gram-negative-staining Bacillaceae with thick cell wall and monoderm architecture uncover evolutionary diversity and challenge Gram-based classification.Communications biology · 2026Article
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- The selfish ribosome.PLoS biology · 2026Article
- Coevolution of RNase P and the ribosome.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Molecular clock dating using complex mixture models: applied to ancient symbionts.Molecular biology and evolution · 2026Article
- Recent Microbial Evolutionary Insights From Metagenomics.Genome biology and evolution · 2026Review
- The selfish ribosome.ArXiv · 2026Article
- Microbial Evolution and Systematics: Archaea and Bacteria.Progress in molecular and subcellular biology · 2026Review
- The Thermococcales as a model system: historical perspectives and emerging tools.Journal of bacteriology · 2025Review
- Dating the Bacterial Tree of Life Based on Ancient Symbiosis.Systematic biology · 2025Article
- Species Tree Branch Length Estimation despite Incomplete Lineage Sorting, Duplication, and Loss.Genome biology and evolution · 2025Article
- Molecular phylogeny and taxonomic notes on Premna (Lamiaceae) in Thailand.Scientific reports · 2025Article
- Phylogenomic Analyses Reveal that Panguiarchaeum Is a Clade of Genome-Reduced Asgard Archaea Within the Njordarchaeia.Molecular biology and evolution · 2025Article
- The emergence of metabolisms through Earth history and implications for biospheric evolution.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Article
- DPANN Archaea and CPR Bacteria: insights into early cellular evolution?Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Review
- Piecing Together the History of Protein Folds From a Fragmented Evolutionary Record.Genome biology and evolution · 2025Article
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Authors and funding
9 authors at 4 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Core gene phylogenies provide a window into early evolution, but different gene sets and analytical methods have yielded substantially different views of the tree of life. Trees inferred from a small set of universal core genes have typically supported a long branch separating the archaeal and bacterial domains. By contrast, recent analyses of a broader set of non-ribosomal genes have suggested that Archaea may be less divergent from Bacteria, and that estimates of inter-domain distance are inflated due to accelerated evolution of ribosomal proteins along the inter-domain branch. Resolving this debate is key to determining the diversity of the archaeal and bacterial domains, the shape of the tree of life, and our understanding of the early course of cellular evolution. Here, we investigate the evolutionary history of the marker genes key to the debate. We show that estimates of a reduced Archaea-Bacteria (AB) branch length result from inter-domain gene transfers and hidden paralogy in the expanded marker gene set. By contrast, analysis of a broad range of manually curated marker gene datasets from an evenly sampled set of 700 Archaea and Bacteria reveals that current methods likely underestimate the AB branch length due to substitutional saturation and poor model fit; that the best-performing phylogenetic markers tend to support longer inter-domain branch lengths; and that the AB branch lengths of ribosomal and non-ribosomal marker genes are statistically indistinguishable. Furthermore, our phylogeny inferred from the 27 highest-ranked marker genes recovers a clade of DPANN at the base of the Archaea and places the bacterial Candidate Phyla Radiation (CPR) within Bacteria as the sister group to the Chloroflexota.
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