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

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Mapping the Tree of Life: Progress and Prospects

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

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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.

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Authors: Pace, N. R.
Affiliations: University of Colorado Boulder (US)
Corresponding author: Pace, Norman R.
ORCID: Pace, Norman R.
Venue: Microbiology and Molecular Biology Reviews
Publisher: American Society for Microbiology
Published: 2009-12
Volume: 73
Issue: 4
Pages: 565-576
ISSN: 1092-2172 (ISSN-L)
1098-5557
DOI: 10.1128/mmbr.00033-09
PMC: PMC2786576
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: green
www.ncbi.nlm.nih.gov
Licence: journals.asm.org/non-commercial-tdm-license (tdm)
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 › Agricultural and Biological Sciences › Ecology, Evolution, Behavior and Systematics › 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

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