Moderate nucleotide diversity in the Atlantic herring is associated with a low mutation rate

  1. Chungang Feng
  2. Mats Pettersson
  3. Sangeet Lamichhaney
  4. Carl-Johan Rubin
  5. Nima Rafati
  6. Michele Casini
  7. Arild Folkvord
  8. Leif Andersson  Is a corresponding author
  1. Uppsala University, Sweden
  2. Swedish University of Agricultural Sciences, Sweden
  3. University of Bergen, Norway

Abstract

The Atlantic herring is one of the most abundant vertebrates on earth but its nucleotide diversity is moderate (π=0.3%), only three-fold higher than in human. Here, we present a pedigree-based estimation of the mutation rate in this species. Based on whole-genome sequencing of four parents and 12 offspring, the estimated mutation rate is 2.0 x 10-9 per base per generation. We observed a high degree of parental mosaicism indicating that a large fraction of these de novo mutations occurred during early germ cell development. The estimated mutation rate - the lowest among vertebrates analyzed to date - partially explains the discrepancy between the rather low nucleotide diversity in herring and its huge census population size. But a species like the herring will never reach its expected nucleotide diversity because of fluctuations in population size over the millions of years it takes to build up high nucleotide diversity.

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Article and author information

Author details

  1. Chungang Feng

    Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
    Competing interests
    The authors declare that no competing interests exist.
  2. Mats Pettersson

    Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
    Competing interests
    The authors declare that no competing interests exist.
  3. Sangeet Lamichhaney

    Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
    Competing interests
    The authors declare that no competing interests exist.
  4. Carl-Johan Rubin

    Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
    Competing interests
    The authors declare that no competing interests exist.
  5. Nima Rafati

    Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
    Competing interests
    The authors declare that no competing interests exist.
  6. Michele Casini

    Department of Aquatic Resources, Swedish University of Agricultural Sciences, Lysekil, Sweden
    Competing interests
    The authors declare that no competing interests exist.
  7. Arild Folkvord

    Department of Biology, University of Bergen, Bergen, Norway
    Competing interests
    The authors declare that no competing interests exist.
  8. Leif Andersson

    Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
    For correspondence
    leif.andersson@imbim.uu.se
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-4085-6968

Funding

European Research Council (Bateson)

  • Leif Andersson

Norwegian Research Council (254774)

  • Arild Folkvord
  • Leif Andersson

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Molly Przeworski, Columbia University, United States

Publication history

  1. Received: December 4, 2016
  2. Accepted: June 28, 2017
  3. Accepted Manuscript published: June 30, 2017 (version 1)
  4. Version of Record published: July 24, 2017 (version 2)

Copyright

© 2017, Feng et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Chungang Feng
  2. Mats Pettersson
  3. Sangeet Lamichhaney
  4. Carl-Johan Rubin
  5. Nima Rafati
  6. Michele Casini
  7. Arild Folkvord
  8. Leif Andersson
(2017)
Moderate nucleotide diversity in the Atlantic herring is associated with a low mutation rate
eLife 6:e23907.
https://doi.org/10.7554/eLife.23907

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