eLife (Jun 2017)

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

  • Chungang Feng,
  • Mats Pettersson,
  • Sangeet Lamichhaney,
  • Carl-Johan Rubin,
  • Nima Rafati,
  • Michele Casini,
  • Arild Folkvord,
  • Leif Andersson

DOI
https://doi.org/10.7554/eLife.23907
Journal volume & issue
Vol. 6

Abstract

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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.

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