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

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.

Figure 1.. Flowchart describing the de novo mutation-calling pipeline.

A schematic illustration of the steps used in calling and filtering the candidate mutations. DOI: http://dx.doi.org/10.7554/eLife.23907.004

Figure 1—figure supplement 1.. Sanger sequencing chromatograms of the de novo mutations.

Chromatograms from the identified target offspring and its parents for each region containing a candidate de novo mutation. DOI: http://dx.doi.org/10.7554/eLife.23907.005