Evidence map›Paper›PMID 24402279›Full record

ArticleNature2014

Elephant shark genome provides unique insights into gnathostome evolution.

Byrappa Venkatesh, Alison P Lee, Vydianathan Ravi, Ashish K Maurya, Michelle M Lian, Jeremy B Swann, Yuko Ohta, Martin F Flajnik, Yoichi Sutoh, Masanori Kasahara and 23 more

Erratum issuedOpen access · bronzeAbstract read
In one paragraph

Article in Nature, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 340 papers.

0numbers the graph read from it
0cells of the map it votes in
340citing papers in PubMed
113.2field-weighted citation impact, top 1% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

340 citing papers in PubMed, 718 citations in OpenAlex.

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  7. Silver chimaera genome highlights lineage-specific sex chromosome and opsin gene evolution in holocephalans.DNA research : an international journal for rapid publication of reports on genes and genomes · 2026
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  14. Review
  15. Teeth outside the jaw: Evolution and development of the toothed head clasper in chimaeras.Proceedings of the National Academy of Sciences of the United States of America · 2025
    Article
  16. Article
  17. Article
  18. Article
  19. Article
  20. Functions of secretory calcium-binding phosphoproteins in dental mineralization.Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research · 2025
    Review

280 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

33 authors at 11 institutions in 6 countries.

Byrappa Venkatesh1] Comparative Genomics Laboratory, Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673 [2] Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228.
Alison P LeeComparative Genomics Laboratory, Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673.
Vydianathan RaviComparative Genomics Laboratory, Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673.
Ashish K MauryaDevelopmental and Biomedical Genetics Laboratory, Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673.
Michelle M LianComparative Genomics Laboratory, Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673.
Jeremy B SwannDepartment of Developmental Immunology, Max-Planck-Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108 Freiburg, Germany.
Yuko OhtaDepartment of Microbiology and Immunology, University of Maryland, Baltimore, Maryland 21201, USA.
Martin F FlajnikDepartment of Microbiology and Immunology, University of Maryland, Baltimore, Maryland 21201, USA.
Yoichi SutohDepartment of Pathology, Hokkaido University Graduate School of Medicine, Sapporo 060-8638, Japan.
Masanori KasaharaDepartment of Pathology, Hokkaido University Graduate School of Medicine, Sapporo 060-8638, Japan.
Shawn HoonMolecular Engineering Laboratory, Biomedical Sciences Institutes, A*STAR, Biopolis, Singapore 138673.
Vamshidhar GanguMolecular Engineering Laboratory, Biomedical Sciences Institutes, A*STAR, Biopolis, Singapore 138673.
Scott W RoyDepartment of Biology, San Francisco State University, San Francisco, California 94132, USA.
Manuel IrimiaBanting and Best Department of Medical Research and Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada.
Vladimir KorzhFish Developmental Biology Laboratory, Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673.
Igor KondrychynFish Developmental Biology Laboratory, Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673.
Zhi Wei LimComparative Genomics Laboratory, Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673.
Boon-Hui TayComparative Genomics Laboratory, Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673.
Sumanty TohariComparative Genomics Laboratory, Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673.
Kiat Whye KongMolecular Engineering Laboratory, Biomedical Sciences Institutes, A*STAR, Biopolis, Singapore 138673.
Shufen HoMolecular Engineering Laboratory, Biomedical Sciences Institutes, A*STAR, Biopolis, Singapore 138673.
Belen Lorente-Galdos1] Institut de Biologia Evolutiva (UPF-CSIC), PRBB, 08003 Barcelona, Spain [2] Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Catalonia, Spain.
Javier Quilez1] Institut de Biologia Evolutiva (UPF-CSIC), PRBB, 08003 Barcelona, Spain [2] Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Catalonia, Spain.
Tomas Marques-Bonet1] Institut de Biologia Evolutiva (UPF-CSIC), PRBB, 08003 Barcelona, Spain [2] Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Catalonia, Spain.
Brian J RaneyCenter for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz, Santa Cruz, California 95064, USA.
Philip W InghamDevelopmental and Biomedical Genetics Laboratory, Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673.
Alice TayComparative Genomics Laboratory, Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673.
LaDeana W HillierThe Genome Institute at Washington University, St Louis, Missouri 63108, USA.
Patrick MinxThe Genome Institute at Washington University, St Louis, Missouri 63108, USA.
Thomas BoehmDepartment of Developmental Immunology, Max-Planck-Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108 Freiburg, Germany.
Richard K WilsonThe Genome Institute at Washington University, St Louis, Missouri 63108, USA.
Sydney BrennerComparative Genomics Laboratory, Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673.
Wesley C WarrenThe Genome Institute at Washington University, St Louis, Missouri 63108, USA.
Institute of Molecular and Cell Biology · SGAgency for Science, Technology and Research · SGWashington University in St. Louis · USInstitut de Biologia Evolutiva · ESHokkaido University · JPMax Planck Institute of Immunobiology and Epigenetics · DEUniversity of Maryland, Baltimore · USNational University of Singapore · SGSan Francisco State University · USUniversity of California, Santa Cruz · USUniversity of Toronto · CA

Funding

Large Scale Genome SequencingU54HG003079 · NHGRI · WASHINGTON UNIVERSITY · PI DUTCHER, SUSAN K · 2004 to 2016
$445.7M
The UCSC Genome BrowserU41HG002371 · NHGRI · UNIVERSITY OF CALIFORNIA SANTA CRUZ · PI KENT, WILLIAM JAMES · 2012 to 2021
$36.6M
EVOLUTION OF THE MAJOR HISTOCOMPATIBILITY COMPLEXR01RR006603 · NCRR · UNIVERSITY OF MIAMI SCHOOL OF MEDICINE · PI FLAJNIK, MARTIN F · 1991 to 2011
$3.4M
ONTOGENY AND PHYLOGENY OF THE MHCR01AI027877 · NIAID · UNIVERSITY OF MIAMI SCHOOL OF MEDICINE · PI FLAJNIK, MARTIN F · 1995 to 2009
$3.2M
Evolution of Adaptive ImmunityR01OD010549 · OD · UNIVERSITY OF MARYLAND BALTIMORE · PI FLAJNIK, MARTIN F · 2013 to 2017
$1.7M
ONTOGENY AND PHYLOGENY OF THE MHCR29AI027877 · NIAID · UNIVERSITY OF MIAMI SCHOOL OF MEDICINE · PI FLAJNIK, MARTIN F. · 1989 to 1993
–
NCRR NIH HHS R01 RR006603NCRR NIH HHS RR006603NHGRI NIH HHS U41 HG002371NHGRI NIH HHS U54 HG003079NIAID NIH HHS AI27877NIAID NIH HHS R01 AI027877NIH HHS R01 OD010549
6 · The paper itself

Abstract

The emergence of jawed vertebrates (gnathostomes) from jawless vertebrates was accompanied by major morphological and physiological innovations, such as hinged jaws, paired fins and immunoglobulin-based adaptive immunity. Gnathostomes subsequently diverged into two groups, the cartilaginous fishes and the bony vertebrates. Here we report the whole-genome analysis of a cartilaginous fish, the elephant shark (Callorhinchus milii). We find that the C. milii genome is the slowest evolving of all known vertebrates, including the 'living fossil' coelacanth, and features extensive synteny conservation with tetrapod genomes, making it a good model for comparative analyses of gnathostome genomes. Our functional studies suggest that the lack of genes encoding secreted calcium-binding phosphoproteins in cartilaginous fishes explains the absence of bone in their endoskeleton. Furthermore, the adaptive immune system of cartilaginous fishes is unusual: it lacks the canonical CD4 co-receptor and most transcription factors, cytokines and cytokine receptors related to the CD4 lineage, despite the presence of polymorphic major histocompatibility complex class II molecules. It thus presents a new model for understanding the origin of adaptive immunity.

Indexed as

Evolution, MolecularAnimalsCalciumCell LineageFish ProteinsGene DeletionGenomeGenomicsImmunity, CellularMolecular Sequence AnnotationMolecular Sequence DataOsteogenesisPhosphoproteinsPhylogenyProtein Structure, TertiarySharksCalciumFish ProteinsPhosphoproteins

Identifiers

PMID24402279
PMCPMC3964593
OpenAlexW2061041720

What OpenQuestion holds

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LicenceCC BY-NC-SA
Read underepoch 390

Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.