The origin and evolution of model organisms

Hedges, S. Blair

doi:10.1038/nrg929

Cited by 806Protist diversity and phylogenyGenomics and Phylogenetic StudiesEvolution and Genetic Dynamics

The origin and evolution of model organisms

Hedges, S. Blair·2002·Nature Reviews Genetics

DOI 10.1038/nrg929

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Abstract

The phylogeny and timescale of life are becoming better understood as the analysis of genomic data from model organisms continues to grow. As a result, discoveries are being made about the early history of life and the origin and development of complex multicellular life. This emerging comparative framework and the emphasis on historical patterns is helping to bridge barriers among organism-based research communities.

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The protostome/deuterostome divergence estimate is much lower than most previously published estimates but close to recent estimates.
“This value is much lower than most of the previously published ones (12, 17, 46) but is close to recent estimates (22, 23)”
From The timing of eukaryotic evolution: Does a relaxed molecular clock reconcile proteins and fossils? (2004) · cites this paper as [12]
Molecular estimates of divergence times are generally much more ancient than suggested by the fossil record.
“Molecular estimates of divergence times are, however, controversial and are generally much more ancient than suggested by the fossil record.”
From The timing of eukaryotic evolution: Does a relaxed molecular clock reconcile proteins and fossils? (2004) · cites this paper as [12]
The molecular time scale for the major eukaryotic clades is on average 1.5 times more recent than the one based on a global clock.
“Our molecular time scale for the major eukaryotic clades is on average 1.5 times more recent than the one based on a global clock (12).”
From The timing of eukaryotic evolution: Does a relaxed molecular clock reconcile proteins and fossils? (2004) · cites this paper as [12]
Previous molecular datings yielded molecular ages always more ancient than paleontological ones, but often to a large extent.
“Previous molecular datings yielded molecular ages always more ancient than paleontological ones, but often to a large extent (12, 15, 20, 46).”
From The timing of eukaryotic evolution: Does a relaxed molecular clock reconcile proteins and fossils? (2004) · cites this paper as [12]
The major eukaryotic kingdoms originated much more recently than previously thought but did not seem to have been affected by the postulated global glaciations ("snowball Earth" hypothesis) between 750 and 600 Mya.
“The major eukaryotic kingdoms therefore originated much more recently than previously thought (12) but did not seem to have been affected by the postulated global glaciations (“snowball Earth” hypothesis) between 750 and 600 Mya (56).”
From The timing of eukaryotic evolution: Does a relaxed molecular clock reconcile proteins and fossils? (2004) · cites this paper as [12]

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Eubacterial phylogeny based on translational apparatus proteins
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Discoidal Impressions and Trace-Like Fossils More Than 1200 Million Years Old
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Fossil Evidence for a Late Cretaceous Origin of “Hoofed” Mammals
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The Comparison of β-Thymosin Homologues Among Metazoa Supports an Arthropod-Nematode Clade
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Vertebrate Genomes Compared
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Molecular Estimates of Primate Divergences and new Hypotheses for Primate Dispersal and the Origin of Modern Humans*
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Bacterial molecular phylogeny using supertree approach.
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Phylogeny of 33 ribosomal and six other proteins encoded in an ancient gene cluster that is conserved across prokaryotic genomes: influence of excluding poorly alignable sites from analysis.
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Hominid revelations from Chad
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Early Evolution of the Bilateria
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Retortamonad Flagellates are Closely Related to Diplomonads—Implications for the History of Mitochondrial Function in Eukaryote Evolution
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Accounting for Evolutionary Rate Variation among Sequence Sites Consistently Changes Universal Phylogenies Deduced from rRNA and Protein-Coding Genes
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Chaperonin 60 Phylogeny Provides Further Evidence for Secondary Loss of Mitochondria Among Putative Early-Branching Eukaryotes
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Determining the Relative Rates of Change for Prokaryotic and Eukaryotic Proteins with Anciently Duplicated Paralogs
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Untitled work
Collins, A. G. (2000) · doi:10.1666/0094-8373(2000)026

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Application of Phylogenetic Networks in Evolutionary Studies
Huson, D. H., & Bryant, D. (2005) · Molecular Biology and Evolution · doi:10.1093/molbev/msj030 · Cited by 8,751 · see citing works
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Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution
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Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype
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The Aging Brain
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The timing of eukaryotic evolution: Does a relaxed molecular clock reconcile proteins and fossils?
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A molecular timescale of eukaryote evolution and the rise of complex multicellular life
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“ancestor some 300–900 million years ago [1,2], and, in terms of coding sequences, their genomes are approximately as divergent as”
Background
Genome modelling and design across all domains of life with Evo 2
Brixi, G., Durrant, M. G., Ku, J., Naghipourfar, M., Poli, M., Sun, G., Brockman, G., Chang, D., Fanton, A., Gonzalez, G. A., et al. (2026) · Nature · doi:10.1038/s41586-026-10176-5 · Cited by 431 · see citing works
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Topics in current genetics
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Comparative genomics supports a deep evolutionary origin for the large, four-module transcriptional mediator complex
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The genome sequence of the model ascomycete fungus Podospora anserina
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Molecular evolution of the reactive oxygen-generating NADPH oxidase (Nox/Duox) family of enzymes
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Evolution of the Aging Brain Transcriptome and Synaptic Regulation
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Contrasting Modes of Diversification in the Aux/IAA and ARF Gene Families
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The origin of eukaryotes: a reappraisal
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Analysis of evolution of exon-intron structure of eukaryotic genes
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Origin and Diversity of Plant Receptor-Like Kinases
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Evolutionary Dynamics of Prokaryotic Transcriptional Regulatory Networks
Babu, M. M., Teichmann, S. A., & Aravind, L. (2006) · Journal of Molecular Biology · doi:10.1016/j.jmb.2006.02.019 · Cited by 265 · see citing works
A General Definition and Nomenclature for Alternative Splicing Events
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Alternative splicing and RNA selection pressure — evolutionary consequences for eukaryotic genomes
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Genomic clocks and evolutionary timescales
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Evolution of alternative transcriptional circuits with identical logic
Tsong, A. E., Tuch, B. B., Li, H., & Johnson, A. D. (2006) · Nature · doi:10.1038/nature05099 · Cited by 255 · see citing works
Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution
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Evolution of a Combinatorial Transcriptional Circuit
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Coelomata and Not Ecdysozoa: Evidence From Genome-Wide Phylogenetic AnalysisPreprint
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Comparative genomics: genome-wide analysis in metazoan eukaryotes
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CodingQuarry: highly accurate hidden Markov model gene prediction in fungal genomes using RNA-seq transcripts
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Preferential Attachment in the Protein Network Evolution
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Comparison of the genomes of human and mouse lays the foundation of genome zoology
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More genes underwent positive selection in chimpanzee evolution than in human evolution
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Stepwise evolution of the centriole-assembly pathway
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Origin and evolution of the atmospheres of early Venus, Earth and Mars
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Authors: Hedges, S. B.
Affiliations: Pennsylvania State University (US)
Corresponding author: Hedges, S. Blair
ORCID: Hedges, S. Blair
Venue: Nature Reviews Genetics
Publisher: Springer Science and Business Media LLC
Published: 2002-11
Volume: 3
Issue: 11
Pages: 838-849
ISSN: 1471-0056 (ISSN-L)
1471-0064
DOI: 10.1038/nrg929
OpenAlex: W2118025286
Semantic Scholar: 862571824f8482780d0884d28274f54a62ec611f
Cited by: 806
References: 124
Citations by year: 2026: 10 · 2025: 17 · 2024: 22 · 2023: 27 · 2022: 27 · 2021: 21 · 2020: 18 · 2019: 19 · 2018: 30 · 2017: 29 · 2016: 27 · 2015: 23 · 2014: 38 · 2013: 25 · 2012: 30
FWCI: 3.13
Type: journal article
Language: en
Open access: closed
Licence: www.springer.com/tdm (tdm)
Locations: Nature Reviews Genetics (publishedVersion)
PubMed (publishedVersion)
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
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
Keywords: model organisms, origin of multicellularity, phylogeny, comparative genomics
MeSH terms: Animals, Archaea, Bacteria, Chronology as Topic, Biological Evolution, Fungi, Humans, Models, Biological, Phylogeny, Plants, Eukaryota

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