Cited by 152Genomics and Phylogenetic StudiesProtist diversity and phylogenyEvolution and Genetic Dynamics

Horizontal gene transfer: essentiality and evolvability in prokaryotes, and roles in evolutionary transitions

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Koonin, Eugene V.·2016·F1000Research

Abstract

The wide spread of gene exchange and loss in the prokaryotic world has prompted the concept of ‘lateral genomics’ to the point of an outright denial of the relevance of phylogenetic trees for evolution. However, the pronounced coherence congruence of the topologies of numerous gene trees, particularly those for (nearly) universal genes, translates into the notion of a statistical tree of life (STOL), which reflects a central trend of vertical evolution. The STOL can be employed as a framework for reconstruction of the evolutionary processes in the prokaryotic world. Quantitatively, however, horizontal gene transfer (HGT) dominates microbial evolution, with the rate of gene gain and loss being comparable to the rate of point mutations and much greater than the duplication rate. Theoretical models of evolution suggest that HGT is essential for the survival of microbial populations that otherwise deteriorate due to the Muller’s ratchet effect. Apparently, at least some bacteria and archaea evolved dedicated vehicles for gene transfer that evolved from selfish elements such as plasmids and viruses. Recent phylogenomic analyses suggest that episodes of massive HGT were pivotal for the emergence of major groups of organisms such as multiple archaeal phyla as well as eukaryotes. Similar analyses appear to indicate that, in addition to donating hundreds of genes to the emerging eukaryotic lineage, mitochondrial endosymbiosis severely curtailed HGT. These results shed new light on the routes of evolutionary transitions, but caution is due given the inherent uncertainty of deep phylogenies.

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  • The 16S rRNA tree represents the evolutionary history of this particular marker gene and may or may not be reflective of the phylogenetic history of microorganisms.

    “Third, at its best, the 16S rRNA tree represents the evolutionary history of this particular marker gene and may or may not be reflective of the phylogenetic history of microorganisms, which is known to be shaped by both vertical and horizontal components of evolution (Koonin 2016) with different protein families displaying independent histories.”

    From The Emergence of Life (2019) · cites this paper as Koonin 2016

    In “Pervasive horizontal gene transfer in microbial evolution and the statistical tree of life” (page not provided), Koonin says a 16S rRNA tree cannot be considered an accurate representation of organismal evolution, and that individual gene trees often differ. But the same section says trees of nearly universal genes share a substantial signal with other gene trees and can represent the central trend of microbial genome evolution. Thus, describing the 16S tree as, at best, only the history of that marker understates the source’s conclusion. (LLM, conf=0.87)

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Authors
Koonin, E. V.
Affiliations
National Institutes of Health (US)
Corresponding author
Koonin, Eugene V.
Venue
F1000Research
Published
2016-07-25
Volume
5
Pages
1805
ISSN
2046-1402 (ISSN-L)
OpenAlex
W2479258543
Cited by
152
References
87
Citations by year
2026: 7 · 2025: 11 · 2024: 10 · 2023: 10 · 2022: 12 · 2021: 15 · 2020: 15 · 2019: 21 · 2018: 23 · 2017: 25 · 2016: 3
FWCI
2.17
Type
journal article
Language
en
Open access
Locations
  • F1000Research (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
  • U.S. Department of Health and Human Services
  • U.S. National Library of Medicine
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protist diversity and phylogeny
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
Keywords
horizontal gene transfer, prokaryotic evolution, Muller's ratchet, plasmids, bacteriophages, eukaryotic origin, mitochondrial endosymbiosis, evolutionary transitions, gene gain and loss

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