Cited by 286Genomics and Phylogenetic StudiesMicrobial Community Ecology and PhysiologyProtist diversity and phylogeny

Mapping the Tree of Life: Progress and Prospects

Open access
Pace, Norman R.·2009·Microbiology and Molecular Biology Reviews

Abstract

The intent of this article is to provide a critical assessment of our current understanding of life's phylogenetic diversity. Phylogenetic comparison of gene sequences is a natural way to identify microorganisms and can also be used to infer the course of evolution. Three decades of molecular phylogenetic studies with various molecular markers have provided the outlines of a universal tree of life (ToL), the three-domain pattern of archaea, bacteria, and eucarya. The sequence-based perspective on microbial identification additionally opened the way to the identification of environmental microbes without the requirement for culture, particularly through analysis of rRNA gene sequences. Environmental rRNA sequences, which now far outnumber those from cultivars, expand our knowledge of the extent of microbial diversity and contribute increasingly heavily to the emerging ToL. Although the three-domain structure of the ToL is established, the deep phylogenetic structure of each of the domains remains murky and sometimes controversial. Obstacles to accurate inference of deep phylogenetic relationships are both systematic, in molecular phylogenetic calculations, and practical, due to a paucity of sequence representation for many groups of organisms.

Integrity signals

Registry

Crossref · 10.1128/mmbr.00033-09

Cites

82 of 82 references verified0 citation errors · 0 not checkable

Statistics

Recomputing p-values needs the paper’s full text.

Claims the paper makes

We couldn’t retrieve this paper’s full text, so its claims and self-check weren’t run. The registry and citation checks still apply.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • The slow evolution of the ssu rRNA gene makes it an excellent choice when comparing diverse species but less useful at differentiating close relatives.

    “The slow evolution of the ssu rRNA gene makes it an excellent choice when comparing diverse species but less useful at differentiating close relatives (Pace, 2009).”

    From The Astrobiology Primer v2.0 (2016) · cites this paper as Pace, 2009

Cites

Flagged first, then by citations

Cited by

Sorted by citations

Authors
Pace, N. R.
Affiliations
University of Colorado Boulder (US)
Corresponding author
Pace, Norman R.
Venue
Microbiology and Molecular Biology Reviews
Published
2009-12
Volume
73
Issue
4
Pages
565-576
ISSN
  • 1092-2172 (ISSN-L)
  • 1098-5557
OpenAlex
W2139469924
Cited by
286
References
82
Citations by year
2026: 3 · 2025: 11 · 2024: 9 · 2023: 8 · 2022: 4 · 2021: 7 · 2020: 10 · 2019: 16 · 2018: 41 · 2017: 17 · 2016: 19 · 2015: 20 · 2014: 22 · 2013: 35 · 2012: 28
FWCI
1.61
Type
journal article
Language
en
Open access
Locations
  • Microbiology and Molecular Biology Reviews (publishedVersion)
  • PubMed Central (publishedVersion)
  • PubMed (publishedVersion)
Funders
  • Alfred P. Sloan Foundation
  • National Institutes of Health
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protist diversity and phylogeny
Keywords
tree of life, phylogenetic diversity, three-domain system, archaea, bacteria, Eukarya, rRNA gene sequences, environmental microorganisms, unculturable microorganisms, microbial identification, deep phylogenetic relationships, molecular phylogeny, microbial diversity
MeSH terms
Animals, Archaea, Bacteria, Humans, Phylogeny, RNA, Ribosomal, Genetic Variation, Genome, Biodiversity, Eukaryota

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review