Evidence map›Paper›PMID 31792218›Full record

ArticleNature communications2019

Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea.

Qiyun Zhu, Uyen Mai, Wayne Pfeiffer, Stefan Janssen, Francesco Asnicar, Jon G Sanders, Pedro Belda-Ferre, Gabriel A Al-Ghalith, Evguenia Kopylova, Daniel McDonald and 20 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature communications, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 211 papers.

0numbers the graph read from it
0cells of the map it votes in
211citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

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.

2 · The registry

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.

3 · Its place in the literature

Who cites it

211 citing papers in PubMed.

  1. Trial
  2. Trial
  3. Observational
  4. Article
  5. Review
  6. Article
  7. Genome microbiology at 20 years: who we are and where we are going.DNA research : an international journal for rapid publication of reports on genes and genomes · 2026
    Article
  8. Article
  9. Article
  10. Article
  11. Review
  12. Article
  13. Article
  14. Article
  15. Article
  16. Article
  17. The Phylogenetic Structure ofBulletin of mathematical biology · 2026
    Article
  18. Article
  19. Article
  20. Article

151 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

30 authors.

Qiyun ZhuDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0002-3568-6271
Uyen MaiDepartment of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.
Wayne PfeifferSan Diego Supercomputer Center, University of California San Diego, La Jolla, CA, USA.
Stefan JanssenDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0003-0955-0589
Francesco AsnicarDepartment CIBIO, University of Trento, Trento, Italy.ORCID http://orcid.org/0000-0003-3732-1468
Jon G SandersDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0001-6077-4014
Pedro Belda-FerreDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0001-6532-1161
Gabriel A Al-GhalithDepartment of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA.ORCID http://orcid.org/0000-0002-6953-6319
Evguenia KopylovaDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.
Daniel McDonaldDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.
Tomasz KosciolekDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0002-9915-7387
John B YinDepartment of Electrical and Computer Engineering, University of California San Diego, La Jolla, CA, USA.
Shi HuangDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.
Nimaichand SalamState Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.
Jian-Yu JiaoState Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.
Zijun WuDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.
Zhenjiang Z XuDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.
Kalen CantrellDepartment of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA.
Yimeng YangDepartment of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA.ORCID http://orcid.org/0000-0003-4819-1005
Erfan SayyariDepartment of Electrical and Computer Engineering, University of California San Diego, La Jolla, CA, USA.
Maryam RabieeDepartment of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.
James T MortonDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA.
Sheila PodellScripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0001-7073-5190
Dan KnightsDepartment of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA.
Wen-Jun LiState Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.ORCID http://orcid.org/0000-0002-1233-736X
Curtis HuttenhowerDepartment of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA.ORCID http://orcid.org/0000-0002-1110-0096
Nicola SegataDepartment CIBIO, University of Trento, Trento, Italy.ORCID http://orcid.org/0000-0002-1583-5794
Larry SmarrDepartment of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.
Siavash MirarabMalopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.ORCID http://orcid.org/0000-0001-5410-1518
Rob KnightDepartment of Pediatrics, University of California San Diego, La Jolla, CA, USA. robknight@ucsd.edu.ORCID http://orcid.org/0000-0002-0975-9019

Funding

STRUCTURAL NEUROIMAGING COREP30MH062512 · NIMH · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI DAVID J MOORE · 2001 to 2026
$50.4M
NIMH NIH HHS P30 MH062512
6 · The paper itself

Abstract

Rapid growth of genome data provides opportunities for updating microbial evolutionary relationships, but this is challenged by the discordant evolution of individual genes. Here we build a reference phylogeny of 10,575 evenly-sampled bacterial and archaeal genomes, based on a comprehensive set of 381 markers, using multiple strategies. Our trees indicate remarkably closer evolutionary proximity between Archaea and Bacteria than previous estimates that were limited to fewer "core" genes, such as the ribosomal proteins. The robustness of the results was tested with respect to several variables, including taxon and site sampling, amino acid substitution heterogeneity and saturation, non-vertical evolution, and the impact of exclusion of candidate phyla radiation (CPR) taxa. Our results provide an updated view of domain-level relationships.

Indexed as

Evolution, MolecularGenome, ArchaealGenome, BacterialPhylogenyArchaeaBacteria

Identifiers

PMID31792218
PMCPMC6889312

What OpenQuestion holds

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LicenceCC BY
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Registered trials

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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.