Horizontal gene transfer constrains the timing of methanogen evolution

Wolfe, Joanna M.; Fournier, Gregory P.

doi:10.1038/s41559-018-0513-7

Cited by 160Origins and Evolution of LifeProtist diversity and phylogenyPaleontology and Stratigraphy of Fossils

Horizontal gene transfer constrains the timing of methanogen evolution

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Wolfe, Joanna M., Fournier, Gregory P.·2018·Nature Ecology & Evolution

DOI 10.1038/s41559-018-0513-7

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Abstract

Microbial methanogenesis may have been a major component of Earth's carbon cycle during the Archaean eon, generating a methane greenhouse that increased global temperatures enough for a liquid hydrosphere, despite the Sun's lower luminosity at the time. Evaluation of potential solutions to the 'faint young Sun' hypothesis by determining the age of microbial methanogenesis has been limited by ambiguous geochemical evidence and the absence of a diagnostic fossil record. To overcome these challenges, we use a temporal constraint: a horizontal gene transfer event from within archaeal methanogens to the ancestor of Cyanobacteria, one of the few microbial clades with recognized crown-group fossils. Results of molecular clock analyses calibrated by this horizontal-gene-transfer-propagated constraint show methanogens diverging within Euryarchaeota no later than 3.51 billion years ago, with methanogenesis itself probably evolving earlier. This timing provides independent support for scenarios wherein microbial methane production was important in maintaining temperatures on the early Earth.

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The Archean lower atmosphere is unlikely to have been H2-rich given the antiquity of methanogens.
“The Archean lower atmosphere is unlikely to have been H2-rich given the antiquity of methanogens (23, 51, 197), some of which convert H2 into methane through a net reaction”
From The Archean atmosphere (2020) · cites this paper as [23]
The Discussion (page unavailable) estimates that methanogens emerged by the early Archaean, supporting their antiquity. The paper does not assess whether the Archaean lower atmosphere was H2-rich or conclude that methanogens made it unlikely to be H2-rich. (LLM, conf=0.86)
Experimental — accuracy not yet measured
An origin of life during ~4.3 to 4.0 Ga ago is consistent with phylogenetic inferences.
“An origin of life during the period ~4.3 to 4.0 Ga ago is consistent with phylogenetic inferences [e.g., (23)].”
From The Archean atmosphere (2020) · cites this paper as [23]
The Discussion (page unavailable) estimates the Euryarchaeota ancestor at 4.17 Ga ± 228 Myr and methanogens at 3.94 Ga ± 228 Myr, broadly consistent with life existing around the proposed period. These are dates for particular microbial lineages, however, not a phylogenetic estimate of when life originated. (LLM, conf=0.82)
Experimental — accuracy not yet measured
Some methanogens convert H2 into methane.
“The Archean lower atmosphere is unlikely to have been H2-rich given the antiquity of methanogens (23, 51, 197), some of which convert H2 into methane through a net reaction”
From The Archean atmosphere (2020) · cites this paper as [23]
The Introduction describes methanogens as methane-producing microbes, and the Discussion dates their emergence to the early Archaean. Neither passage says that some methanogens use H2 to produce methane, so the specific conversion attributed to this source is unsupported. (LLM, conf=0.82)
Experimental — accuracy not yet measured
Phylogenetically, methanogens date back to >3.5 Ga ago.
“Phylogenetically, methanogens date back to >3.5 Ga ago (23).”
From The Archean atmosphere (2020) · cites this paper as [23]

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Authors: Wolfe, J. M., & Fournier, G. P.
Affiliations: Massachusetts Institute of Technology (US)
Corresponding author: Wolfe, Joanna M.
ORCID: Wolfe, Joanna M.
Fournier, Gregory P.
Venue: Nature Ecology & Evolution
Publisher: Springer Science and Business Media LLC
Published: 2018-04-02
Volume: 2
Issue: 5
Pages: 897-903
ISSN: 2397-334X (ISSN-L)
DOI: 10.1038/s41559-018-0513-7
OpenAlex: W2794637696
Cited by: 160
References: 62
Citations by year: 2026: 18 · 2025: 22 · 2024: 18 · 2023: 16 · 2022: 28 · 2021: 18 · 2020: 12 · 2019: 10 · 2018: 16
FWCI: 7.55
Type: journal article
Language: en
Open access: bronze
doi.org
Licence: www.springernature.com/gp/researchers/text-and-data-mining (tdm)
www.springernature.com/gp/researchers/text-and-data-mining (vor)
Locations: Nature Ecology & Evolution (publishedVersion)
PubMed (publishedVersion)
DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc)
Funders: National Science Foundation (1615426)
Massachusetts Green High Performance Computing Center
Topics: Physical Sciences › Physics and Astronomy › Astronomy and Astrophysics › Origins and Evolution of Life
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protist diversity and phylogeny
Physical Sciences › Earth and Planetary Sciences › Paleontology › Paleontology and Stratigraphy of Fossils
Keywords: horizontal gene transfer, methanogenesis, methanogenic archaea, archaea, cyanobacteria, molecular clock, divergence time estimation, Euryarchaeota, molecular phylogeny
MeSH terms: Cyanobacteria, Biological Evolution, Methane, Phylogeny, Temperature, Evolution, Planetary, Euryarchaeota, Gene Transfer, Horizontal

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Horizontal gene transfer constrains the timing of methanogen evolution

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