Cited by 530Chromosomal and Genetic VariationsGenome Rearrangement AlgorithmsGenomics and Phylogenetic Studies

Extensive genomic duplication during early chordate evolution

McLysaght, Aoife, Hokamp, Karsten, Wolfe, Kenneth H.·2002·Nature Genetics

Abstract

Opinions on the hypothesis that ancient genome duplications contributed to the vertebrate genome range from strong skepticism to strong credence. Previous studies concentrated on small numbers of gene families or chromosomal regions that might not have been representative of the whole genome, or used subjective methods to identify paralogous genes and regions. Here we report a systematic and objective analysis of the draft human genome sequence to identify paralogous chromosomal regions (paralogons) formed during chordate evolution and to estimate the ages of duplicate genes. We found that the human genome contains many more paralogons than would be expected by chance. Molecular clock analysis of all protein families in humans that have orthologs in the fly and nematode indicated that a burst of gene duplication activity took place in the period 350 650 Myr ago and that many of the duplicate genes formed at this time are located within paralogons. Our results support the contention that many of the gene families in vertebrates were formed or expanded by large-scale DNA duplications in an early chordate. Considering the incompleteness of the sequence data and the antiquity of the event, the results are compatible with at least one round of polyploidy.

Integrity signals

Registry

Crossref · 10.1038/ng884

Cites

32 of 32 references verified0 citation errors · 0 not checkable

Statistics

Recomputing p-values needs the paper’s full text.

Claims the paper makes

This paper’s full text isn’t openly available, so its claims and self-check weren’t run. The registry and citation checks still apply.

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 estimate of 23,300 genes in the sea urchin is similar to estimates for vertebrates, despite two whole-genome duplications believed to have occurred in the chordate lineage after divergence from echinoderms.

    “Our estimate of 23,300 genes is similar to estimates for vertebrates, despite the fact that two whole-genome duplications are believed to have occurred in the chordate lineage after divergence from the lineage leading to the echinoderms (25)(26)(27).”

Cites

Flagged first, then by citations

Cited by

Sorted by citations

Authors
McLysaght, A., Hokamp, K., & Wolfe, K. H.
Affiliations
Trinity College Dublin (IE)
Corresponding author
Wolfe, Kenneth H.
Venue
Nature Genetics
Published
2002-05-28
Volume
31
Issue
2
Pages
200-204
ISSN
  • 1061-4036 (ISSN-L)
  • 1546-1718
OpenAlex
W2011889195
Cited by
530
References
32
Citations by year
2026: 4 · 2025: 5 · 2024: 7 · 2023: 9 · 2022: 5 · 2021: 19 · 2020: 11 · 2019: 13 · 2018: 6 · 2017: 10 · 2016: 18 · 2015: 17 · 2014: 23 · 2013: 21 · 2012: 20
FWCI
64.82
Type
journal article
Language
en
Open access
closed
Locations
  • Nature Genetics (publishedVersion)
  • PubMed (publishedVersion)
Funders
  • Health Research Board
  • Science Foundation Ireland
  • Trinity College Dublin
Topics
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genome Rearrangement Algorithms
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Keywords
whole-genome duplication, chordate evolution, vertebrate genome evolution, gene family expansion, molecular clock, polyploidy, human genome
MeSH terms
Animals, Chordata, Nonvertebrate, Drosophila melanogaster, Humans, Polyploidy, Genome, Human, Genome, Caenorhabditis elegans, Evolution, Molecular, Gene Duplication

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