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Cited by 1,234Genomics and Phylogenetic StudiesEvolution and Paleontology StudiesPlant Diversity and Evolution

TimeTree: A public knowledge-base of divergence times among organisms

Open access
Hedges, S. Blair, Dudley, Joel, Kumar, Sudhir·2006·Bioinformatics
DOI 10.1093/bioinformatics/btl505
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Abstract

Summary: Biologists and other scientists routinely need to know times of divergence between species and to construct phylogenies calibrated to time (timetrees). Published studies reporting time estimates from molecular data have been increasing rapidly, but the data have been largely inaccessible to the greater community of scientists because of their complexity. TimeTree brings these data together in a consistent format and uses a hierarchical structure, corresponding to the tree of life, to maximize their utility. Results are presented and summarized, allowing users to quickly determine the range and robustness of time estimates and the degree of consensus from the published literature. Availability: TimeTree is available at Contact: sbh1@psu.edu

AI snapshot

Written from the paper’s full text.

TL;DR

TimeTree is a web-based public knowledge-base that aggregates published molecular divergence-time estimates into a consistent format organized by a hierarchical tree of life. Version 1.0 covers tetrapods only, drawing on 70 studies and 1102 divergence times.

Key findings

  • TimeTree v1.0 is limited in taxonomic scope to tetrapods (amphibians, reptiles, mammals and birds) and includes 70 studies and 1102 divergence times.
  • The database uses a hierarchical structure based on NCBI's Taxonomy Browser, which at the time contained approximately 225 000 taxa, so any query between two species whose divergence pertains to the same node returns the same results (e.g. mongoose–raccoon yields the same estimates as cat–dog).
  • Results are presented in tabular form grouped by study, with details including divergence time (millions of years ago), number of genes, gene type (nuclear/organellar), data type (nucleotide/amino acid), specific taxa compared, and the source table or figure within the article; confidence limits and standard errors appear on hover.
  • Time estimates are summarized on the Results page with means and weighted means shown for all data and partitions, letting users assess the range, robustness and degree of consensus across the published literature.

Methods

  • Design: a web-accessible database and query interface built to consolidate published molecular-clock time estimates, with two query forms — divergence of two taxa, and all time estimates from a particular author.
  • Data: published studies reporting time estimates from molecular data; v1.0 contains 70 studies and 1102 divergence times for tetrapods, with additional tetrapod data being added from community submissions and literature searches.
  • Analysis/implementation: taxon queries are resolved via an NCBI synonym list (translating common names) or phonetic encoding; the two most-inclusive groups containing the queried taxa are identified and all taxa in one group are compared with all taxa in the other to find published times for that split. Taxon names link to NCBI Taxonomy Browser entries and author names link to PubMed records.

Limitations

  • Stated: v1.0 is limited in taxonomic scope to tetrapods; future versions are planned to expand to all of life and to add enhanced tree-based graphics (timetrees and timelines), fossil times, user-submission of data, and community-based quality control via an already-established TimeTree Consortium.
  • Evident from the text: the guide tree depends on NCBI's Taxonomy Browser and will need updating as that resource is revised; the paper reports no quantitative validation or benchmarking of the aggregated estimates, and no usage or accuracy statistics are given.

Model-written summary. Check it against the paper before relying on it.

Integrity signals

Registry

Crossref · 10.1093/bioinformatics/btl505

Cites

10 of 10 references verified0 citation errors · 0 not checkable

Statistics

Nothing to recompute.

Claims the paper makes

0 of 4 cited sources checked · 0 supported · 0 flagged

  • Findingnone given

    TimeTree v1.0 is limited in taxonomic scope to tetrapods (amphibians, reptiles, mammals and birds).

    “This first version (v1.0) of TimeTree is limited in taxonomic scope to tetrapods (amphibians, reptiles, mammals and birds).”
    Quote in the paperNot a substantial claim
  • Interpretationreasoning

    A query of mongoose (Feliformia) and raccoon (Caniformia) will yield exactly the same results as a cat-dog query because their divergence pertains to the same node.

    “a query of mongoose (Feliformia) and raccoon (Caniformia) will yield exactly the same results because their divergence pertains to the same node.”
    Quote in the paperNot a substantial claim
  • Interpretationreasoning

    The hierarchical approach of TimeTree ensures that any query between any two species in the two most-inclusive groups defining a node will yield results if there are any data bearing on the node.

    “The advantage of this hierarchical approach is that any query between any two species in the two most-inclusive groups defining a node will yield results if there are any data bearing on the node.”
    Quote in the paperSubstantial claim
  • Classified as probably not a substantial claim. 6
  • May combine two claims. 7

  • Classified as probably not a substantial claim.

    Findingreasoning

    TimeTree presents and summarizes results, allowing users to quickly determine the range and robustness of time estimates and the degree of consensus from the published literature.

    “Results are presented and summarized, allowing users to quickly determine the range and robustness of time estimates and the degree of consensus from the published literature.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingnone given

    TimeTree brings time estimates together in a consistent format and uses a hierarchical structure, corresponding to the tree of life, to maximize their utility.

    “TimeTree brings these data together in a consistent format and uses a hierarchical structure, corresponding to the tree of life, to maximize their utility.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing), S4 (based).

    Findingnone given

    All current time estimates of the Feliformia-Caniformia divergence are derived from cat-dog sequence comparisons.

    “For example, all current time estimates of the Feliformia-Caniformia divergence are derived from cat-dog sequence comparisons”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Findingnone given

    The results of a taxon-query are presented in tabular form and list all published studies and time estimates bearing on that species divergence.

    “The results of a taxon-query (Fig. 3) are presented in tabular form and list all published studies and time estimates bearing on that species divergence.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Findingown data

    Time estimates are summarized on the Results page, with the means and weighted means shown for all data and partitions.

    “Time estimates are summarized on the Results page, with the means and weighted means shown for all data and partitions (Fig. 3b).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    TimeTree v1.0 includes 70 studies and 1102 divergence times.

    “It includes 70 studies and 1102-divergence times.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S2 (checkable).

    Premisenone given

    Time estimates from molecular data have been largely inaccessible to the greater community of scientists because of their complexity.

    “the data have been largely inaccessible to the greater community of scientists because of their complexity”
    Quote in the paperNot a substantial claim
    • Rests on an assumption: Most time estimates are not included in abstracts that are searchable on the web, but instead are usually buried in the text in a variety of formats (including trees) that are often difficult to assimilate and compare among studies.

  • May combine two claims.

    Premisecitation

    Published studies reporting time estimates from molecular data have been increasing rapidly, now numbering in the hundreds.

    “Published studies reporting time estimates from molecular data have been increasing rapidly”
    • Also stated in: § Abstract · plain
      “Publications involving molecular clocks, now numbering in the hundreds, are appearing more frequently (Kumar, 2005).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites Kumar, 2005

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    The increase in molecular clock publications has been driven in large part by the rapid increase in sequence data and by the development of methods that accommodate rate variation in estimating divergence times and their confidence intervals.

    “In large part, this has been driven by the rapid increase in sequence data that have become available in recent years, as well as the development of methods that accommodate rate variation in estimating divergence times and their confidence intervals (Drummond et al., 2006;Kumar et al., 2005;Sanderson, 1997;Thorne et al., 1998).”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites Drummond et al., 2006 source

      Not checked in the free run.

    • cites Kumar et al., 2005

      Not checked in the free run.

    • cites Sanderson, 1997 source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisenone given

    The guide tree used by TimeTree is based on NCBI's Taxonomy Browser, which currently contains approximately 225 000 taxa.

    “The guide tree used is based on NCBI's Taxonomy Browser, which currently contains approximately 225 000 taxa.”
    Quote in the paperNot a substantial claim
10 of 10

  • The paper relies on this without support.

    There are now thousands of individual published time estimates among organisms and species.

    “the global result is that there are now thousands of individual published time estimates among organisms and species.”

  • The paper relies on this without support.

    Scientists often need to know times of divergence to calculate rates of change, to search for connections with Earth history and to construct timetrees, among other reasons.

    “Scientists often need to know times of divergence to calculate rates of change, to search for connections with Earth history and to construct timetrees, among other reasons.”

  • The paper relies on this without support.

    Scientists need to know the range of time estimates and whether or not there is a consensus among studies.

    “They also need to know the range of time estimates and whether or not there is a consensus among studies.”

  • The paper relies on this without support.

    Most time estimates are not included in abstracts that are searchable on the web, but instead are usually buried in the text in a variety of formats (including trees) that are often difficult to assimilate and compare among studies.

    “Most time estimates are not included in abstracts that are searchable on the web, but instead are usually buried in the text in a variety of formats (including trees) that are often difficult to assimilate and compare among studies.”
4 of 4

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Related

Authors
Hedges, S. B., Dudley, J., & Kumar, S.
Affiliations
  • Pennsylvania State University (US)
  • Arizona State University (US)
Corresponding author
Hedges, S. Blair
ORCID
Venue
Bioinformatics
Publisher
Oxford University Press (OUP)
Published
2006-10-04
Volume
22
Issue
23
Pages
2971-2972
ISSN
  • 1367-4803 (ISSN-L)
  • 1367-4811
DOI
10.1093/bioinformatics/btl505
OpenAlex
W2153452535
Semantic Scholar
d2167c06eaa23893331ab0ae062e57ce22b89e29
Cited by
1,234
References
10
Citations by year
2026: 25 · 2025: 45 · 2024: 56 · 2023: 52 · 2022: 73 · 2021: 88 · 2020: 56 · 2019: 72 · 2018: 85 · 2017: 81 · 2016: 90 · 2015: 120 · 2014: 120 · 2013: 83 · 2012: 68
FWCI
2.99
Type
journal article
Language
en
Open access
Locations
  • Bioinformatics (publishedVersion)
  • PubMed (publishedVersion)
Funders
  • National Science Foundation
  • National Aeronautics and Space Administration
  • NASA Astrobiology Institute
  • National Institutes of Health
  • National Human Genome Research Institute (R01HG002096)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Physical Sciences › Earth and Planetary Sciences › Paleontology › Evolution and Paleontology Studies
  • Life Sciences › Agricultural and Biological Sciences › Ecology, Evolution, Behavior and Systematics › Plant Diversity and Evolution
Keywords
divergence time, timetree, divergence time estimation, phylogenetic calibration, knowledge base, tree of life
MeSH terms
Database Management Systems, Biological Evolution, Genetics, Population, Phylogeny, User-Computer Interface, Genetic Variation, Databases, Factual, Information Storage and Retrieval, Evolution, Molecular, Knowledge Bases

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