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

Abstract
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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.

Data availability

The following data sets were generated

(2016) Moderate nucleotide diversity in the Atlantic herring is associated with a low mutation rate
Publicly available at NCBI BioProject (accession no: PRJNA356817).

http://www.ncbi.nlm.nih.gov/bioproject/356817

Article and author information

Author details

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.
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.
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.
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.
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.
Michele Casini

Department of Aquatic Resources, Swedish University of Agricultural Sciences, Lysekil, Sweden

Competing interests
The authors declare that no competing interests exist.
Arild Folkvord

Department of Biology, University of Bergen, Bergen, Norway

Competing interests
The authors declare that no competing interests exist.
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.

"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.

Copyright

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.