A late origin of the extant eukaryotic diversity: divergence time estimates using rare genomic changes
Open accessAbstract
Background: Accurate estimation of the divergence time of the extant eukaryotes is a fundamentally important but extremely difficult problem owing primarily to gross violations of the molecular clock at long evolutionary distances and the lack of appropriate calibration points close to the date of interest. These difficulties are intrinsic to the dating of ancient divergence events and are reflected in the large discrepancies between estimates obtained with different approaches. Estimates of the age of Last Eukaryotic Common Ancestor (LECA) vary approximately twofold, from ~1,100 million years ago (Mya) to ~2,300 Mya. Results: We applied the genome-wide analysis of rare genomic changes associated with conserved amino acids (RGC_CAs) and used several independent techniques to obtain date estimates for the divergence of the major lineages of eukaryotes with calibration intervals for insects, land plants and vertebrates. The results suggest an early divergence of monocot and dicot plants, approximately 340 Mya, raising the possibility of plant-insect coevolution. The divergence of bilaterian animal phyla is estimated at ~400-700 Mya, a range of dates that is consistent with cladogenesis immediately preceding the Cambrian explosion. The origin of opisthokonts (the supergroup of eukaryotes that includes metazoa and fungi) is estimated at ~700-1,000 Mya, and the age of LECA at ~1,000-1,300 Mya. We separately analyzed the red algal calibration interval which is based on single fossil. This analysis produced time estimates that were systematically older compared to the other estimates. Nevertheless, the majority of the estimates for the age of the LECA using the red algal data fell within the 1,200-1,400 Mya interval. Conclusion: The inference of a "young LECA" is compatible with the latest of previously estimated dates and has substantial biological implications. If these estimates are valid, the approximately 1 to 1.4 billion years of evolution of eukaryotes that is open to comparative-genomic study probably was preceded by hundreds of millions years of evolution that might have included extinct diversity inaccessible to comparative approaches. Reviewers: This article was reviewed by William Martin, Herve Philippe (nominated by I. King Jordan), and Romain Derelle.
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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 [98]
The Discussion (page unavailable) says the paper's LECA estimate of about 1.1–1.2 Ga agrees with previous relaxed molecular-clock estimates. It does not establish a published interval of approximately 1–2.4 Ga; instead, it says its estimate is clearly inconsistent with an older molecular-clock estimate of about 2.5 Ga. The citing authors' 1.93–1.84 Ga species-tree estimate is their own result, not this paper's. (LLM, conf=0.84)
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- Authors
- Chernikova, D., Motamedi, S., Csürös, M., Koonin, E. V., & Rogozin, I. B.
- Affiliations
- National Institutes of Health (US)
- Université de Montréal (CA)
- Corresponding author
- Koonin, Eugene V
- Venue
- Biology Direct
- Published
- 2011-05-19
- Volume
- 6
- Issue
- 1
- Pages
- 26-26
- ISSN
- 1745-6150 (ISSN-L)
- PMC
- PMC3125394
- OpenAlex
- W2067593790
- Cited by
- 72
- References
- 112
- Citations by year
- 2026: 1 · 2025: 5 · 2024: 4 · 2023: 7 · 2022: 6 · 2021: 5 · 2020: 7 · 2019: 1 · 2018: 3 · 2017: 5 · 2016: 4 · 2015: 2 · 2014: 9 · 2013: 4 · 2012: 8
- FWCI
- 2.86
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by
- Locations
- Biology Direct (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- Funders
- U.S. Department of Health and Human Services
- National Institute for Health and Care Research
- National Institutes of Health
- U.S. National Library of Medicine
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protist diversity and phylogeny
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Earth and Planetary Sciences › Paleontology › Evolution and Paleontology Studies
- Keywords
- last eukaryotic common ancestor, conserved residues, molecular clock, plant-insect coevolution, Cambrian explosion, eukaryotic origin
- MeSH terms
- Amino Acid Sequence, Biological Evolution, Fossils, Molecular Sequence Data, Phylogeny, Sequence Alignment, Genome, Conserved Sequence, Evolution, Molecular, Amino Acid Substitution, Genetic Speciation, Eukaryota
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