Estimation of the spontaneous mutation rate per nucleotide site in a Drosophila melanogaster full-sib family

Abstract

We employed deep genome sequencing of two parents and 12 of their offspring to estimate the mutation rate per site per generation in a full-sib family of Drosophila melanogaster recently sampled from a natural population. Sites that were homozygous for the same allele in the parents and heterozygous in one or more offspring were categorized as candidate mutations and subjected to detailed analysis. In 1.23 × 10(9) callable sites from 12 individuals, we confirmed six single nucleotide mutations. We estimated the false negative rate in the experiment by generating synthetic mutations using the empirical distributions of numbers of nonreference bases at heterozygous sites in the offspring. The proportion of synthetic mutations at callable sites that we failed to detect was <1%, implying that the false negative rate was extremely low. Our estimate of the point mutation rate is 2.8 × 10(-9) (95% confidence interval = 1.0 × 10(-9) - 6.1 × 10(-9)) per site per generation, which is at the low end of the range of previous estimates, and suggests an effective population size for the species of ∼1.4 × 10(6). At one site, point mutations were present in two individuals, indicating that there had been a premeiotic mutation cluster, although surprisingly one individual had a G→A transition and the other a G→T transversion, possibly associated with error-prone mismatch repair. We also detected three short deletion mutations and no insertions, giving a deletion mutation rate of 1.2 × 10(-9) (95% confidence interval = 0.7 × 10(-9) - 11 × 10(-9)).

Keywords: Drosophilla; Genome sequencing; mutation.

Figure 1

Distributions of read depth of the two parents, (A) female and (B) male and two representative offspring, (C) male and (D) female for the autosomes (blue) and X chromosome (red). Duplicate reads were removed.

Figure 2

Empirical (red) and expected (blue) distributions of the number of nonreference bases at heterozygous sites for offspring having read depths of 40. The empirical distribution shows the relative frequencies of sites having numbers of nonreference bases from 0 to 40. The expected distribution is binomial for equal frequencies of reference and nonreference bases.