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Research article - Peer-reviewed, 2017

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

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

Abstract

The Atlantic herring is one of the most abundant vertebrates on earth but its nucleotide diversity is moderate (pi = 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.

Keywords

Atlantic herring; Clupea harengus; genetics; mutation rates; nucleotide diversity; whole-genome sequencing

Published in

eLife
2017, volume: 6, article number: e23907
Publisher: ELIFE SCIENCES PUBLICATIONS LTD

Authors' information

Feng, Chungang
Uppsala University
Pettersson, Mats
Uppsala University
Lamichhaney, Sangeet
Uppsala University
Rubin, Carl-Johan
Uppsala University
Rafati, Nima
Uppsala University
Swedish University of Agricultural Sciences, Department of Aquatic Resources
Folkvord, Arild
University of Bergen
Andersson, Leif
Uppsala University
Andersson, Leif
Swedish University of Agricultural Sciences, Department of Animal Breeding and Genetics
Andersson, Leif
Texas A&M University

UKÄ Subject classification

Evolutionary Biology

Publication Identifiers

DOI: https://doi.org/10.7554/eLife.23907

URI (permanent link to this page)

https://res.slu.se/id/publ/92564