On the Age of Eukaryotes: Evaluating Evidence from Fossils and Molecular Clocks
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Our understanding of the phylogenetic relationships among eukaryotic lineages has improved dramatically over the few past decades thanks to the development of sophisticated phylogenetic methods and models of evolution, in combination with the increasing availability of sequence data for a variety of eukaryotic lineages. Concurrently, efforts have been made to infer the age of major evolutionary events along the tree of eukaryotes using fossil-calibrated molecular clock-based methods. Here, we review the progress and pitfalls in estimating the age of the last eukaryotic common ancestor (LECA) and major lineages. After reviewing previous attempts to date deep eukaryote divergences, we present the results of a Bayesian relaxed-molecular clock analysis of a large dataset (159 proteins, 85 taxa) using 19 fossil calibrations. We show that for major eukaryote groups estimated dates of divergence, as well as their credible intervals, are heavily influenced by the relaxed molecular clock models and methods used, and by the nature and treatment of fossil calibrations. Whereas the estimated age of LECA varied widely, ranging from 1007 (943-1102) Ma to 1898 (1655-2094) Ma, all analyses suggested that the eukaryotic supergroups subsequently diverged rapidly (i.e., within 300 Ma of LECA). The extreme variability of these and previously published analyses preclude definitive conclusions regarding the age of major eukaryote clades at this time. As more reliable fossil data on eukaryotes from the Proterozoic become available and improvements are made in relaxed molecular clock modeling, we may be able to date the age of extant eukaryotes more precisely.
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The 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 [26]
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Background
- Authors
- Eme, L., Sharpe, S. C., Brown, M. W., & Roger, A. J.
- Affiliations
- Dalhousie University (CA)
- Venue
- Cold Spring Harbor Perspectives in Biology
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2014-08-01
- Volume
- 6
- Issue
- 8
- Pages
- a016139-a016139
- ISSN
- 1943-0264 (ISSN-L)
- PMC
- PMC4107988
- OpenAlex
- W2056820963
- Cited by
- 287
- References
- 28
- Citations by year
- 2026: 11 · 2025: 15 · 2024: 29 · 2023: 34 · 2022: 21 · 2021: 36 · 2020: 22 · 2019: 22 · 2018: 28 · 2017: 21 · 2016: 25 · 2015: 18 · 2014: 5
- Type
- posted content
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Cold Spring Harbor Perspectives in Biology (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Compute Canada
- Government of Ontario
- Tula Foundation
- University of Toronto
- Killam Trusts
- Natural Sciences and Engineering Research Council of Canada
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protist diversity and phylogeny
- Physical Sciences › Earth and Planetary Sciences › Paleontology › Evolution and Paleontology Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- eukaryotic origin, last eukaryotic common ancestor, fossil calibration, relaxed molecular clock, Bayesian phylogenetics, eukaryotic supergroups
- MeSH terms
- Bayes Theorem, Classification, Fossils, Models, Genetic, Phylogeny, Likelihood Functions, Genetic Speciation, Eukaryota
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