ArticleMolecular biology and evolution2021
Phylogenetic Signal, Congruence, and Uncertainty across Bacteria and Archaea.
Article in Molecular biology and evolution, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 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
49 citing papers in PubMed.
- Phylogenetic reconciliation supports a methanogenic ancestor of the Archaea and a derived origin for host-associated lineages.Nature communications · 2026Article
- Evolutionary trajectory of microbial sulfur oxidation pathways recapitulates Earth's oxygenation history.Nature communications · 2026Article
- Abiotic sources of fixed nitrogen sustained early ecosystems for several hundred million years after the origin of life.Science advances · 2026Article
- Two-hourly resolved microbial and viral dynamics in the subtropical Daya Bay.Scientific data · 2026Article
- Prevalence and Evolutionary Implications of Genome Rearrangements in Bacteria.Genome biology and evolution · 2026Article
- Reconstruction of 2,965 Microbial Genomes from Mangrove Sediments across Guangxi, China.Scientific data · 2025Article
- Identification of a deep-branching lineage of algae using environmental plastid genomes.Nature communications · 2025Article
- Augmenting microbial phylogenomic signal with tailored marker gene sets.Nature communications · 2025Article
- Rapid Radiations Outweigh Reticulations During the Evolution of a 750-Million-Year-Old Lineage of Cyanobacteria.Molecular biology and evolution · 2025Article
- The evolution of the tree of life.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
- Review
- Ancient Host-Virus Gene Transfer Hints at a Diverse Pre-LECA Virosphere.Journal of molecular evolution · 2025Article
- Towards a unifying phylogenomic framework for tailed phages.PLoS genetics · 2025Article
- A New Method for Constructing High-Resolution Phylogenomic Topologies Using Core Gene-Associated MNP Markers: A Case Study From Agaricus bisporus.Microbial biotechnology · 2025Article
- Multi-sample long-read nanopore sequencing of Agabus bipustulatus (Coleoptera: Dytiscidae: Agabinae) mitogenome produces effectively reliable data for downstream analyses.Journal of insect science (Online) · 2025Article
- Microbial ecology of serpentinite-hosted ecosystems.The ISME journal · 2025Review
- Dynamic quinone repertoire accompanied the diversification of energy metabolism in Pseudomonadota.The ISME journal · 2025Article
- Essential nucleic acid omics: a theoretical foundation for early-stage users.Frontiers in bioinformatics · 2025Review
- The Last Universal Common Ancestor of Ribosome-Encoding Organisms: Portrait of LUCA.Journal of molecular evolution · 2024Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Reconstruction of the Tree of Life is a central goal in biology. Although numerous novel phyla of bacteria and archaea have recently been discovered, inconsistent phylogenetic relationships are routinely reported, and many inter-phylum and inter-domain evolutionary relationships remain unclear. Here, we benchmark different marker genes often used in constructing multidomain phylogenetic trees of bacteria and archaea and present a set of marker genes that perform best for multidomain trees constructed from concatenated alignments. We use recently-developed Tree Certainty metrics to assess the confidence of our results and to obviate the complications of traditional bootstrap-based metrics. Given the vastly disparate number of genomes available for different phyla of bacteria and archaea, we also assessed the impact of taxon sampling on multidomain tree construction. Our results demonstrate that biases between the representation of different taxonomic groups can dramatically impact the topology of resulting trees. Inspection of our highest-quality tree supports the division of most bacteria into Terrabacteria and Gracilicutes, with Thermatogota and Synergistota branching earlier from these superphyla. This tree also supports the inclusion of the Patescibacteria within the Terrabacteria as a sister group to the Chloroflexota instead of as a basal-branching lineage. For the Archaea, our tree supports three monophyletic lineages (DPANN, Euryarchaeota, and TACK/Asgard), although we note the basal placement of the DPANN may still represent an artifact caused by biased sequence composition. Our findings provide a robust and standardized framework for multidomain phylogenetic reconstruction that can be used to evaluate inter-phylum relationships and assess uncertainty in conflicting topologies of the Tree of Life.
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.