ArticleGenome biology and evolution2014
Archaeal "dark matter" and the origin of eukaryotes.
Article in Genome biology and evolution, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 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
54 citing papers in PubMed, 96 citations in OpenAlex.
- The archaeal roots of eukaryotic life.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- The evolution of the tree of life.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Article
- Review
- Endosymbioses Have Shaped the Evolution of Biological Diversity and Complexity Time and Time Again.Genome biology and evolution · 2024Review
- Microbial Diversity and Open Questions about the Deep Tree of Life.Genome biology and evolution · 2024Article
- Review
- Genomic Signatures of Mitonuclear Coevolution in Mammals.Molecular biology and evolution · 2022Article
- SpeciesRax: A Tool for Maximum Likelihood Species Tree Inference from Gene Family Trees under Duplication, Transfer, and Loss.Molecular biology and evolution · 2022Article
- A divide-and-conquer phylogenomic approach based on character supermatrices resolves early steps in the evolution of the Archaea.BMC ecology and evolution · 2022Article
- Article
- Embryo-Like Features in Developing Bacillus subtilis Biofilms.Molecular biology and evolution · 2021Article
- Cultivation of Dominant Freshwater Bacterioplankton Lineages Using a High-Throughput Dilution-to-Extinction Culturing Approach Over a 1-Year Period.Frontiers in microbiology · 2021Article
- High-throughput cultivation based on dilution-to-extinction with catalase supplementation and a case study of cultivating acI bacteria from Lake Soyang.Journal of microbiology (Seoul, Korea) · 2020Article
- Undinarchaeota illuminate DPANN phylogeny and the impact of gene transfer on archaeal evolution.Nature communications · 2020Article
- Multidomain ribosomal protein trees and the planctobacterial origin of neomura (eukaryotes, archaebacteria).Protoplasma · 2020Review
- Phylogenomics provides robust support for a two-domains tree of life.Nature ecology & evolution · 2020Article
- Energy metabolism in anaerobic eukaryotes and Earth's late oxygenation.Free radical biology & medicine · 2019Review
- Human microbial ecology and the rising new medicine.Annals of translational medicine · 2019Review
- Chromatin Evolution-Key Innovations Underpinning Morphological Complexity.Frontiers in plant science · 2019Review
- The last universal common ancestor between ancient Earth chemistry and the onset of genetics.PLoS genetics · 2018Review
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 at 1 institution in 1 country.
Funding
Abstract
Current hypotheses about the history of cellular life are mainly based on analyses of cultivated organisms, but these represent only a small fraction of extant biodiversity. The sequencing of new environmental lineages therefore provides an opportunity to test, revise, or reject existing ideas about the tree of life and the origin of eukaryotes. According to the textbook three domains hypothesis, the eukaryotes emerge as the sister group to a monophyletic Archaea. However, recent analyses incorporating better phylogenetic models and an improved sampling of the archaeal domain have generally supported the competing eocyte hypothesis, in which core genes of eukaryotic cells originated from within the Archaea, with important implications for eukaryogenesis. Given this trend, it was surprising that a recent analysis incorporating new genomes from uncultivated Archaea recovered a strongly supported three domains tree. Here, we show that this result was due in part to the use of a poorly fitting phylogenetic model and also to the inclusion by an automated pipeline of genes of putative bacterial origin rather than nucleocytosolic versions for some of the eukaryotes analyzed. When these issues were resolved, analyses including the new archaeal lineages placed core eukaryotic genes within the Archaea. These results are consistent with a number of recent studies in which improved archaeal sampling and better phylogenetic models agree in supporting the eocyte tree over the three domains hypothesis.
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.