Integrated genomic and fossil evidence illuminates life’s early evolution and eukaryote origin
Open accessAbstract
Establishing a unified timescale for the early evolution of Earth and life is challenging and mired in controversy because of the paucity of fossil evidence, the difficulty of interpreting it and dispute over the deepest branching relationships in the tree of life. Surprisingly, it remains perhaps the only episode in the history of life where literal interpretations of the fossil record hold sway, revised with every new discovery and reinterpretation. We derive a timescale of life, combining a reappraisal of the fossil material with new molecular clock analyses. We find the last universal common ancestor of cellular life to have predated the end of late heavy bombardment (>3.9 billion years ago (Ga)). The crown clades of the two primary divisions of life, Eubacteria and Archaebacteria, emerged much later (<3.4 Ga), relegating the oldest fossil evidence for life to their stem lineages. The Great Oxidation Event significantly predates the origin of modern Cyanobacteria, indicating that oxygenic photosynthesis evolved within the cyanobacterial stem lineage. Modern eukaryotes do not constitute a primary lineage of life and emerged late in Earth's history (<1.84 Ga), falsifying the hypothesis that the Great Oxidation Event facilitated their radiation. The symbiotic origin of mitochondria at 2.053-1.21 Ga reflects a late origin of the total-group Alphaproteobacteria to which the free living ancestor of mitochondria belonged.
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The age of LUCA is sensitive to the root calibration used.
“This is consistent with previous work suggesting that the age of LUCA is sensitive to the root calibration used19,21,27,95,96.”
From ATP synthase evolution on a cross-braced dated tree of life (2023) · cites this paper as [27]
The Results state that a 4.52 Ga maximum was applied to the root, and the Abstract says calibrations are necessary for an absolute timescale. But the paper does not show how LUCA’s estimated age changes under different root calibrations; the calibration strategies it did compare produced robust results (Results). (LLM, conf=0.78)
Experimental — accuracy not yet measuredThe LECA estimate from the species tree analysis falls within published molecular clock estimates, placing LECA within a broad interval of approximately 1-2.4 Ga.
“The LECA estimate (1.93–1.84 Ga, 95% highest posterior density) from our species tree analysis falls within published molecular clock estimates, placing LECA within a broad interval ~1–2.4 Ga25–27,97–99 (Fig. 5A, C, Supplementary Fig. 16, Supplementary Data 10).”
From ATP synthase evolution on a cross-braced dated tree of life (2023) · cites this paper as [27]
Molecular clock estimates place the last common ancestor of extant eukaryotes between ~1.87 and 1.68 Ga.
“consistent with molecular clock estimates that place the last common ancestor of extant eukaryotes between ∼1.87 and 1.68 Ga (Parfrey et al., 2011; Betts et al., 2018).”
From Oxygenation, Life, and the Planetary System during Earth's Middle History: An Overview (2021) · cites this paper as Betts et al., 2018
Molecular clocks suggest an origin of life prior to the late heavy bombardment >3.9 Ga.
“First, the earliest undisputed fossil evidence places life on Earth prior to 3.35 Ga [3] and molecular clocks suggest an origin prior to the late heavy bombardment >3.9 Ga [4].”
From The Future of Origin of Life Research: Bridging Decades-Old Divisions (2020) · cites this paper as [4]
Integrating fossil data with molecular evolutionary clocks has solidified evidence for the age of LUCA at >3.9 Ga.
“Integrating fossil data with molecular evolutionary clocks has solidified evidence for the age of LUCA at >3.9 Ga [4].”
From The Future of Origin of Life Research: Bridging Decades-Old Divisions (2020) · cites this paper as [4]
Computational models allow testing hypotheses unattainable in a laboratory alone, including chemical conditions, timescales, or other routine perturbations to the model.
“Computational models allow us to test hypotheses unattainable in a laboratory alone, be it chemical conditions [22], timescales [4] or other routine perturbations to the model.”
From The Future of Origin of Life Research: Bridging Decades-Old Divisions (2020) · cites this paper as [4]
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“…the first observable, datable, probable eukaryotic remains occur at *1.7 to 1.6 Ga (Knoll and Nowak, 2017; Javaux and Lepot, 2018)—consistent with molecular clock estimates that place the last common ancestor of extant eukaryotes between *1.87 and 1.68 Ga (Parfrey et al., 2011; Betts et al., 2018).”
BackgroundInfluentialA one-billion-year-old multicellular chlorophyte
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- Authors
- Betts, H. C., Puttick, M. N., Clark, J. W., Williams, T. A., Donoghue, P. C. J., & Pisani, D.
- Affiliations
- University of Bristol (GB)
- Corresponding author
- Pisani, Davide
- ORCID
- Venue
- Nature Ecology & Evolution
- Published
- 2018-08-20
- Volume
- 2
- Issue
- 10
- Pages
- 1556-1562
- ISSN
- 2397-334X (ISSN-L)
- PMC
- PMC6152910
- OpenAlex
- W2886949501
- Cited by
- 437
- References
- 75
- Citations by year
- 2026: 38 · 2025: 42 · 2024: 65 · 2023: 60 · 2022: 53 · 2021: 62 · 2020: 66 · 2019: 44 · 2018: 7
- FWCI
- 23.98
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- Locations
- Nature Ecology & Evolution (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Bristol Research (University of Bristol) (acceptedVersion, other-oa)
- Pure (University of Bath) (submittedVersion, other-oa)
- Funders
- Biotechnology and Biological Sciences Research Council (1563670, BB/N000919/1)
- Natural Environment Research Council (NE/P013678/1, NE/N003438/1, NE/P00251X/1, 1671097)
- 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 › Evolution and Paleontology Studies
- Keywords
- early evolution of life, eukaryotic origin, molecular clock, fossil record, last universal common ancestor, Late Heavy Bombardment, archaea, eubacteria, Great Oxidation Event, cyanobacteria, oxygenic photosynthesis, mitochondrial origin, Alphaproteobacteria, tree of life
- MeSH terms
- Archaea, Bacteria, Biological Evolution, Fossils, Genome, 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 ›
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