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Elife. 2017 Jun 30;6. pii: e23907. doi: 10.7554/eLife.23907.

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

Author information

1
Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
2
Department of Aquatic Resources, Institute of Marine Research, Swedish University of Agricultural Sciences, Lysekil, Sweden.
3
Department of Biology, University of Bergen and the Hjort Center of Marine Ecosystem Dynamics, Bergen, Norway.
4
Institute of Marine Research, Bergen, Norway.
5
Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden.
6
Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, United States.

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 × 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.

KEYWORDS:

evolution; evolutionary biology; genomics; mutation; nucleotide diversity

PMID:
28665273
PMCID:
PMC5524536
DOI:
10.7554/eLife.23907
[Indexed for MEDLINE]
Free PMC Article

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