The DOI matches its Crossref record; 49 of the 50 references it cites were found in a registry or an index.
A molecular timescale of eukaryote evolution and the rise of complex multicellular life
Open accessAbstract
BACKGROUND: The pattern and timing of the rise in complex multicellular life during Earth's history has not been established. Great disparity persists between the pattern suggested by the fossil record and that estimated by molecular clocks, especially for plants, animals, fungi, and the deepest branches of the eukaryote tree. Here, we used all available protein sequence data and molecular clock methods to place constraints on the increase in complexity through time. RESULTS: Our phylogenetic analyses revealed that (i) animals are more closely related to fungi than to plants, (ii) red algae are closer to plants than to animals or fungi, (iii) choanoflagellates are closer to animals than to fungi or plants, (iv) diplomonads, euglenozoans, and alveolates each are basal to plants+animals+fungi, and (v) diplomonads are basal to other eukaryotes (including alveolates and euglenozoans). Divergence times were estimated from global and local clock methods using 20-188 proteins per node, with data treated separately (multigene) and concatenated (supergene). Different time estimation methods yielded similar results (within 5%): vertebrate-arthropod (964 million years ago, Ma), Cnidaria-Bilateria (1,298 Ma), Porifera-Eumetozoa (1,351 Ma), Pyrenomycetes-Plectomycetes (551 Ma), Candida-Saccharomyces (723 Ma), Hemiascomycetes-filamentous Ascomycota (982 Ma), Basidiomycota-Ascomycota (968 Ma), Mucorales-Basidiomycota (947 Ma), Fungi-Animalia (1,513 Ma), mosses-vascular plants (707 Ma), Chlorophyta-Tracheophyta (968 Ma), Rhodophyta-Chlorophyta+Embryophyta (1,428 Ma), Plantae-Animalia (1,609 Ma), Alveolata-plants+animals+fungi (1,973 Ma), Euglenozoa-plants+animals+fungi (1,961 Ma), and Giardia-plants+animals+fungi (2,309 Ma). By extrapolation, mitochondria arose approximately 2300-1800 Ma and plastids arose 1600-1500 Ma. Estimates of the maximum number of cell types of common ancestors, combined with divergence times, showed an increase from two cell types at 2500 Ma to approximately 10 types at 1500 Ma and 50 cell types at approximately 1000 Ma. CONCLUSIONS: The results suggest that oxygen levels in the environment, and the ability of eukaryotes to extract energy from oxygen, as well as produce oxygen, were key factors in the rise of complex multicellular life. Mitochondria and organisms with more than 2-3 cell types appeared soon after the initial increase in oxygen levels at 2300 Ma. The addition of plastids at 1500 Ma, allowing eukaryotes to produce oxygen, preceded the major rise in complexity.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The cited source says what the claim attributes to it.
In the citing paper
“Indeed, there is a long history of attempts to estimate the timing of animal diversification [40], yielding ages for crown Metazoa that range between 1,298 Ma [41] and 615 Ma [42].”
From Uncertainty in the Timing of Origin of Animals and the Limits of Precision in Molecular Timescales (2015) · cites this paper as [41]
The cited source says what the claim attributes to it.
In the citing paper
“The effects this variation could have on molecular clocks, together with frequent disagreement between the ages estimated by way of the fossil record and molecular clocks—especially for the most ancient lineages (Hedges et al., 2004; Donoghue and Benton, 2007)—mean that it may not be possible to produce molecular clocks that can constrain the uncertainty enough to provide any useful information.”
From The Astrobiology Primer v2.0 (2016) · cites this paper as Hedges et al., 2004
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Thompson, J. D., Higgins, D. G., & Gibson, T. J. (1994) · Nucleic Acids Research · doi:10.1093/nar/22.22.4673 · Cited by 64,617 · cited 1×
“Sequences were aligned [ 36 ] and regions of ambiguous alignment were removed when necessary.”
PAML: a program package for phylogenetic analysis by maximum likelihood
Yang, Z. (1997) · Computer applications in the biosciences · doi:10.1093/bioinformatics/13.5.555 · Cited by 5,377 · cited 4×
“Gene-specific and supergene gamma shape parameters (α) were calculated [40] and used for distance and time estimation [45].”
InfluentialMOLECULAR BIOLOGY AND EVOLUTION
(2021) · WORLD SCIENTIFIC eBooks · doi:10.1142/9789811250378_0003 · Cited by 4,434
Quartet Puzzling: A Quartet Maximum-Likelihood Method for Reconstructing Tree Topologies
Strimmer, K., & von Haeseler, A. (1996) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a025664 · Cited by 2,531 · cited 1×
“These concatenated datasets were analyzed using maximum likelihood (JTT + gamma model, quartet puzzling with 1000 steps) [38], minimum evolution (Neighbor-joining, Poisson + gamma model, 2000 bootstraps, complete deletion) [37], and Bayesian Inference (JTT + gamma model, 50,000 generations, 4 chains with starting temp…”
Sanderson, M. J. (2002) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a003974 · Cited by 1,977 · cited 8×
“The SGLPL method was performed in R8S version 1.6 [48] with maximum likelihood branch lengths calculated under a PC+gamma model [40].”
InfluentialA molecular timescale for vertebrate evolution
Kumar, S., & Hedges, S. B. (1998) · Nature · doi:10.1038/31927 · Cited by 1,936 · cited 7×
“Because the coefficient of variation of time estimates is large for small numbers of genes [14], we used a minimum of 20 genes for each divergence.”
InfluentialSelf-citationSanderson, M. J. (2003) · Bioinformatics · doi:10.1093/bioinformatics/19.2.301 · Cited by 1,906 · cited 1×
“6 [48] with maximum likelihood branch lengths calculated under a PC+gamma model [40].”
Molecular Evidence for the Early Colonization of Land by Fungi and Plants
Heckman, D. S., Geiser, D. M., Eidell, B. R., Stauffer, R. L., Kardos, N. L., & Hedges, S. B. (2001) · Science · doi:10.1126/science.1061457 · Cited by 1,020 · cited 2×
“We chose eighteen divergences among major lineages of eukaryotes, including some analyzed previously [24].”
Self-citationVolcanic gases, black smokers, and the great oxidation event
Holland, H. D. (2002) · Geochimica et Cosmochimica Acta · doi:10.1016/s0016-7037(02)00950-x · Cited by 920 · cited 1×
“Organisms with more than 2–3 cell types (the maximum in prokaryotes) appeared relatively early (~2000 Ma), soon after the surface environment became oxygenated at 2300 Ma (Great Oxidation Event; [34]).”
Phylogenetic test of the molecular clock and linearized trees.
Takezaki, N., Rzhetsky, A., & Nei, M. (1995) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040259 · Cited by 826 · cited 1×
“All proteins were tested for rate constancy [45, 46 ]; those rejected at the 5% significance level were excluded from timing analyses.”
Research works printed but not linked: 5
- Huelsenbeck J, Ronquist F: MrBayes Version 3.0. 2003, Uppsala, Sweden, Evolutionary Biology Centre, Uppsala University
- Kumar S: Phyltest: a program for testing phylogenetic hypotheses, ed. 2.0. Institute of Molecular Evolutionary Genetics. 1996, University Park, PA, Pennsylvania State University
- Felsenstein J: PHYLIP version 3.6. 2002, Seattle, Department of Genetics, University of Washington
- Margulis L, Corliss JO, Melkonian M, Chapman DJ: Handbook of Protoctista. 1990, Boston, Massachusetts, Jones and Bartlett, 914-
- Maddison WP, Maddison DR: MacClade. 1992, Sunderland, MA, Sinauer Associates
Cited by
Sorted by citations
Items 501–578 of 578
Evolution of Metazoa and Fungi
Redecker, D. (2006) · Science · doi:10.1126/science.312.5770.53c · Cited by 1
Du rôle de l’oxygène dans l’évolution
Baudouin‐Cornu, P., & Thomas, D. (2007) · médecine/sciences · doi:10.1051/medsci/2007233255 · Cited by 1
Mitochondrial Evolution : Turning Bugs into Features
Karlberg, O. (2004) · KTH Publication Database DiVA (KTH Royal Institute of Technology) · Cited by 1
Almazán-García, C. (2005) · SHAREOK (University of Oklahoma; Oklahoma State University; Central Oklahoma University) · Cited by 1
Matryoshka RNA virus 1: a novel RNA virus associated with Plasmodium parasites in human malariaPreprint
Charon, J., Grigg, M. J., Eden, J., Piera, K. A., William, T., Rose, K. A., Davenport, M. P., Anstey, N. M., & Holmes, E. C. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/624403 · Cited by 1
Evolution of Specialization in Dynamic FluidsPreprint
Uppal, G., & Vural, D. C. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/735589 · Cited by 1
Tracking evolutionary trends towards increasing complexity: a case study in CyanobacteriaPreprint
Moyá, A., Oliver, J. L. T., Verdú, M., Delaye, L., Arnau, V., Bernaola‐Galván, P., de la Fuente, R., Dı́az-Villanueva, W., Gómez‐Martín, C., González, F. M., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.01.29.924464 · Cited by 1
Rensing, S. A., Lang, D., & Zimmer, A. D. (2017) · Annual Plant Reviews online · doi:10.1002/9781119312994.apr0386 · Cited by 1
Miwa, S., Müller, F. L., & Beckman, K. B. (2008) · Humana Press eBooks · doi:10.1007/978-1-59745-420-9_1 · Cited by 1
Aspergilli, More Than Just Fungi: Shaping the Last Decades of Model Systems
Degola, F. (2021) · Elsevier eBooks · doi:10.1016/b978-0-12-819990-9.00033-0 · Cited by 1
Approches génomiques de l’interaction Ostreococcus tauri-Prasinovirus
Thomy, J. (2022) · theses.fr (ABES) · doi:10.70675/e2e1fe35zee48z405az8011zbee5052321d4 · Cited by 1
Comparative analyses of adaptive phenomena in eukaryotic systems
Bush, S. J. (2014) · The University of Bath Online Publications Store (The University of Bath)
Rogers, A. R. (2013) · Elsevier eBooks · doi:10.1016/b978-0-08-095975-7.01206-7
Genomic Contributions to Understanding the Evolution of Red Algal Plastids and Pigment Biosynthesis
Neilan, B. A., Murray, S. A., & Chen, M. (2010) · Cellular origin and life in extreme habitats · doi:10.1007/978-90-481-3795-4_14
Phylogenetics and Evolution of Virulence in the Kingdom Fungi
Garcia-Solache, M. A., & Casadevall, A. (2012) · Wiley eBooks · doi:10.1002/9781118308165.ch4
Bioinformatics of Seven-Transmembrane Receptors in Plant Genomes
Moriyama, E. N., & Opiyo, S. O. (2009) · Signaling and communication in plants · doi:10.1007/978-3-642-03524-1_13
Cell individuality in adhesin expression of Candida glabrata
Halliwell, S. (2012) · Nottingham ePrints (University of Nottingham)
Characterization of protein import channel-forming proteins in chloroplasts
Kovács-Bogdán, E. (2011) · doi:10.5282/edoc.13319
Construction of a long hairpin RNA for knockdown of endogenous gene in budding yeast
Andersson, A. (2012) · Lund University Publications Student Papers (Lund University)
Les datations moléculaires de la génomique
Douzery, E., Delsuc, F., & Philippe, H. (2006)
Lateral Gene Transfer and the Evolution of Photosynthesis in Eukaryotes
Slamovits, C. H., & Reyes‐Prieto, A. (2013) · Springer eBooks · doi:10.1007/978-1-4614-7780-8_2
Genomic signatures of neurodegeneration and the evolution of mammalian brain.
Castillo-Morales, A. (2015) · The University of Bath Online Publications Store (The University of Bath)
Deciphering the genome of Desulfovibrio gigas: the role of the hydrogenases
Morais‐Silva, F. O. (2013)
THE PROTISTAN ORIGINS OF MULTICELLUARITY: TIMING AND EVOLUTION OF CELL ADHESION MOLECULES
Sharpe, S. C. (2015) · DalSpace (Dalhousie University)
Oxygen Signaling in Physiological and Pathological Angiogenesis
Henze, A., & Mazzone, M. (2015) · Springer eBooks · doi:10.1007/978-1-4939-2907-8_14
Pollari, M. (2008) · UTUPub (University of Turku)
DINÂMICA EVOLUTIVA DE DNAS REPETITIVOS COM ÊNFASE EM ESPÉCIES DA TRIBO PHANAEINI
Filho, J. D. M. (2013)
Spontaneous Emergence of Hierarchy in Biological Systems
He, J. (2010) · Rice Research Repository (Rice University)
The MicroRNA Repertoire of Symbiodinium, the Dinoflagellate Symbiont of Reef-Building Corals
Baumgarten, S. (2013) · King Abdullah University of Science and Technology Repository (King Abdullah University of Science and Technology) · doi:10.25781/kaust-a79nq
EDIACARAN RANGEOMORPHS IN THE MISTAKEN POINT BIOTA, NEWFOUNDLAND
Flude, L. I. (2009) · QSpace (Queen's University Library)
Oxygen Sensing in Lymnaea: from Behaviour to Central Pattern Generators
Janes, T. A. (2016) · Libraries and Cultural Resources (University of Calgary) · doi:10.5072/prism/27243
Mikkelsen, K. (2011) · NORA - Norwegian Open Research Archives
The Evolving Knowledge of Nutrition
Pond, W. G., Nichols, B. L., & Brown, D. L. (2009) · doi:10.1201/9781420077544-9
Bacteria and Eukaryotes Evolution
Ciancio, A. (2016) · Springer eBooks · doi:10.1007/978-94-024-0884-3_2
Article Convergent Evolution of Receptors for Protein Import into Mitochondria
Perry, A., Hulett, J. M., Likić, V. A., Lithgow, T. J., & Gooley, P. R. (2006)
Ewolucja systemów obrony antyoksydacyjnej
Wojtyla, Ł., & Garnczarska, M. (2016)
A Thesis on Life, the Universe and Almost Everything
Stevenson, D. S. (2017) · Astronomers' universe · doi:10.1007/978-3-319-52911-0_9
Persistent oscillations in the Aplysia bag cell network
Keplinger, K. (2017) · UWSpace (University of Waterloo)
Host-adapted lactobacilli: evolution, molecular mechanisms and functional applications
Duar, R. M. (2017) · ERA: Education and Research Archive (University of Alberta) · doi:10.7939/r3dn40915
A Brief Story of Success: The Manifestation of Knowledge and the Hydra of Ignorance
Glattfelder, J. B. (2019) · The frontiers collection · doi:10.1007/978-3-030-03633-1_8
Variation in protein coding genes identifies information flow as a contributor to animal complexityPreprint
Dean, J., Cardoso, D. L., & Sharpe, C. R. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/679456
The Origin and Early Evolution of Life
Stevenson, D. S. (2019) · Springer eBooks · doi:10.1007/978-3-030-25550-3_6
The Niche, Its Hypervolume and the Entropy of Existence
Stevenson, D. S. (2019) · Springer eBooks · doi:10.1007/978-3-030-25550-3_7
The Role of Two-Component and Small RNA Regulatory Systems in Pseudomonas aeruginosa Biofilms
Taylor, P. (2019) · uO Research (University of Ottawa) · doi:10.20381/ruor-23857
真核生物の高次分類体系の改訂―Adl et al. (2019)について―
裕規, 矢., & 島野, 智. (2020) · doi:10.19004/taxa.48.0_71
Investigation of early assembly of OXPHOS complexes during mitochondrial translation
Wang, C. (2020) · eDiss (Georg-August-Universität Göttingen) · doi:10.53846/goediss-8330
Chernogor, L. I., Елисейкина, М. Г., Petrushin, I. S., Chernogor, E. A., Khanaev, I. V., & Беликов, С. И. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.12.13.472427
Gagniuc, P. A. (2021) · Wiley eBooks · doi:10.1002/9781119698005.ch1
Gagniuc, P. A. (2021) · Wiley eBooks · doi:10.1002/9781119698005.ref
Oh, A. (2022) · Genetics and Molecular Research · doi:10.4238/gmr18996
Larsen, T. J., Queller, D. C., & Strassmann, J. E. (2018) · Elsevier eBooks · doi:10.1016/b978-0-12-809633-8.90165-1
Hongo, J. A. (2015) · doi:10.47749/t/unicamp.2015.962103
A genomic and phylogenetic perspective on endosymbiosis and algal origin
Yoon, H. S., Hackett, J. D., & Bhattacharya, D. (2008) · Springer eBooks · doi:10.1007/978-1-4020-5670-3_31 · Cited by 1
(2014) · Elsevier eBooks · doi:10.1016/b978-0-12-387731-4.00024-4
The Evolving Knowledge of Nutrition
Quezada‐Calvillo, R., & Nichols, B. L. (2009) · CRC Press eBooks · doi:10.1201/9781420077544.ch2
Huang, M. F., Robbins, K. R., Li, Y., Umanzor, S., Marty-Rivera, M., Bailey, D. L., Aydlett, M., Schmutz, J., Grimwood, J., Yarish, C., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.08.01.502376
Golden section hypothesis of macroevolution: unification of metabolic scaling and Fibonacci sequencePreprint
Yang, X., & Wang, L. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.09.19.508476
(2012) · Royal Society of Chemistry eBooks · doi:10.1039/9781849731614-00018
Endothelial Cell Reactions to Oxygen: Implications for Cancer
de Oliveira, R. L., & Mazzone, M. (2014) · Springer eBooks · doi:10.1007/978-2-8178-0466-8_12
Vitte, C., & Negre, N. N. (2025) · Wiley eBooks · doi:10.1002/9781394372683.ch4
Unique genes in plants : features, evolution and promoters
Giménez, D. S. A. (2008) · theses.fr (ABES) · doi:10.70675/45167e6ezf661z478eza6cezfa60e00dc1a9
Larsen, T. J., Queller, D. C., & Strassmann, J. E. (2026) · Elsevier eBooks · doi:10.1016/b978-0-443-29068-8.00152-5
Towards an atlas of green microalgae (Chlorophyta) in the ocean
Tragin, M. (2017) · theses.fr (ABES) · doi:10.70675/46f6a7baz4925z44cdz8b67z200b0fbb00f1
Impact phénotypique des réarrangements chromosomiques et évolution des génomes de levures
Fleiss, A. (2018) · theses.fr (ABES) · doi:10.70675/ef380bd2z14d5z4771za3e2z82b040f5da53
Chimie des océans au Paléoprotérozoïque
Thibon, F. (2019) · theses.fr (ABES) · doi:10.70675/b46ca998z0032z4822za964z77924518955c
Déniel, M. (2020) · theses.fr (ABES) · doi:10.70675/2a206eb3ze747z43b3z8a3eze797ccb544ef
Ashrafyan, L. А. (2026) · Academy for Practical Oncology · doi:10.63769/3033-9073-2026-1-2-62-69
7. Ancient Fossil Record and Early Evolution (ca. 3.8 to 0.5 Ga)
López‐García, P., Moreira, D., Douzery, E., Forterre, P., van Zuilen, M. A., Claeys, P., & Prieur, D. (2006) · Earth Moon and Planets · doi:10.1007/s11038-006-9091-9
Moczydłowska, M., & Willman, S. (2026) · Fossils and strata · doi:10.18261/9788294167562-2026-01
Tang, S., Luo, J., Zhang, X., Chen, Z., & Tian, D. (2026) · Scientia Horticulturae · doi:10.1016/j.scienta.2026.115178
Ma, X., Li, Y., Yang, Z., Zhao, Y., & Zhong, B. (2026) · PLANT PHYSIOLOGY · doi:10.1093/plphys/kiag738
Panigrahi, M., Rajawat, D., Upadhyay, A., Kamalakannan, D., Ranjith, G., Rath, P. K., Verma, S. K., & Nayak, S. S. (2026) · International Journal of Molecular Sciences · doi:10.3390/ijms27198921
“As a consequence of the absence of protective histones coupled with limited DNA repair mechanisms, the mtDNA exhibits higher mutation rates than nDNA [16].”
Strategies for increasing the applicability of biological network inference
Maier, E. J. (2015) · Open Scholarship Institutional Repository (Washington University in St. Louis) · doi:10.7936/k79c6vk2
(2006) · ANU Open Research (Australian National University) · Cited by 47
Metadata
- Authors
- Hedges, S. B., Blair, J. E., Venturi, M. L., & Shoe, J. L.
- Affiliations
- Pennsylvania State University (US)
- Corresponding author
- Hedges, S Blair
- Venue
- BMC Evolutionary Biology
- Published
- 2004-01-28
- Volume
- 4
- Issue
- 1
- Pages
- 2-2
- ISSN
- 1471-2148 (ISSN-L)
- PMC
- PMC341452
- OpenAlex
- W2166647921
- Cited by
- 578
- References
- 50
- Citations by year
- 2026: 10 · 2025: 8 · 2024: 12 · 2023: 15 · 2022: 23 · 2021: 19 · 2020: 22 · 2019: 23 · 2018: 17 · 2017: 33 · 2016: 22 · 2015: 27 · 2014: 31 · 2013: 37 · 2012: 33
- FWCI
- 14.80
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- BMC Evolutionary Biology (publishedVersion)
- PubMed Central (publishedVersion, other-oa)
- PubMed (publishedVersion)
- TUScholarShare (Temple University) (submittedVersion)
- Funders
- National Science Foundation (NNA04CC06A, 0112670, NCC2-1057)
- National Aeronautics and Space Administration (NNA04CC06A)
- Topics
- Life Sciences › Agricultural and Biological Sciences › Ecology, Evolution, Behavior and Systematics › 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 evolution, molecular clock, divergence time estimation, red algae, choanoflagellates, diplomonads, alveolates, mitochondrial origin, plastid origin, endosymbiosis
- MeSH terms
- Rhodophyta, Animals, Eukaryotic Cells, Fungi, Phylogeny, Plants, Proteins, Time Factors, Genetic Variation, Vertebrates, Evolution, Molecular
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 ›
Are you an author, or do you see a problem with this page? Request a review
