Estimation of the spontaneous mutation rate in Heliconius melpomene.

Chris D Jiggins,Rob W Ness,John W Davey,Kanchon K Dasmahapatra,Ana Pinharanda,James Mallet,Fraser Simpson,Peter D Keightley

doi:10.1093/molbev/msu302

Abstract

We estimated the spontaneous mutation rate in Heliconius melpomene by genome sequencing of a pair of parents and 30 of their offspring, based on the ratio of number of de novo heterozygotes to the number of callable site-individuals. We detected nine new mutations, each one affecting a single site in a single offspring. This yields an estimated mutation rate of 2.9 × 10−9 (95% confidence interval, 1.3 × 10−9–5.5 × 10−9), which is similar to recent estimates in Drosophila melanogaster, the only other insect species in which the mutation rate has been directly estimated. We infer that recent effective population size of H. melpomene is about 2 million, a substantially lower value than its census size, suggesting a role for natural selection reducing diversity. We estimate that H. melpomene diverged from its Müllerian comimic H. erato about 6 Ma, a somewhat later date than estimates based on a local molecular clock.

Highlights

We estimated the spontaneous mutation rate in Heliconius melpomene by genome sequencing of a pair of parents and 30 of their offspring, based on the ratio of number of de novo heterozygotes to the number of callable site-individuals
Variation in the mutation rate is expected to contribute to the large range of variation in neutral nucleotide diversity that has been observed in natural populations (Leffler et al 2012)
Mutations were not called in the bait offspring nor did they contribute to the number of site-individuals

Summary

Introduction

We estimated the spontaneous mutation rate in Heliconius melpomene by genome sequencing of a pair of parents and 30 of their offspring, based on the ratio of number of de novo heterozygotes to the number of callable site-individuals. There are, drawbacks to these approaches, including uncertainty about species divergence dates and nonneutral synonymous site evolution (Chamary et al 2006) This has led to efforts to directly estimate the mutation rate by sequencing mutation accumulation (MA) lines or outbred parents and their offspring. Its practical applicability is limited, because inbred lines cannot be produced for most species Sequencing parents and their offspring and searching for de novo mutations in the offspring are more generally applicable, but to date experiments have only been carried out in humans (Roach et al 2010; Conrad et al 2011; Kong et al 2012; Michaelson et al 2012) and Drosophila melanogaster (Keightley et al 2014). Open Access org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited

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