Deep sequencing of natural and experimental populations of Drosophila melanogaster reveals biases in the spectrum of new mutations

Abstract

Mutations provide the raw material of evolution, and thus our ability to study evolution depends fundamentally on having precise measurements of mutational rates and patterns. We generate a data set for this purpose using (1) de novo mutations from mutation accumulation experiments and (2) extremely rare polymorphisms from natural populations. The first, mutation accumulation (MA) lines are the product of maintaining flies in tiny populations for many generations, therefore rendering natural selection ineffective and allowing new mutations to accrue in the genome. The second, rare genetic variation from natural populations allows the study of mutation because extremely rare polymorphisms are relatively unaffected by the filter of natural selection. We use both methods in , first generating our own novel data set of sequenced MA lines and performing a meta-analysis of all published MA mutations (∼2000 events) and then identifying a high quality set of ∼70,000 extremely rare (≤0.1%) polymorphisms that are fully validated with resequencing. We use these data sets to precisely measure mutational rates and patterns. Highlights of our results include: a high rate of multinucleotide mutation events at both short (∼5 bp) and long (∼1 kb) genomic distances, showing that mutation drives GC content lower in already GC-poor regions, and using our precise context-dependent mutation rates to predict long-term evolutionary patterns at synonymous sites. We also show that de novo mutations from independent MA experiments display similar patterns of single nucleotide mutation and well match the patterns of mutation found in natural populations.

Mutational Landscape of Spontaneous Base Substitutions and Small Indels in Experimental Caenorhabditis elegans Populations of Differing Size

“…The base substitution rate in these nematodes is lower relative to other invertebrates for which similar information exists. For example, the base substitution rate in the cladoceran Daphnia pulex (Flynn et al 2017) is roughly twice as high as in nematodes, whereas D. melanogaster has an approximately threefold-higher rate than Caenorhabditis (Huang et al 2016;Sharp and Agrawal 2016;Assaf et al 2017). Furthermore, the spontaneous mitochondrial base substitution rate for the very same C. elegans MA lines (Konrad et al 2017) is 24-fold higher than the nuclear base substitution rate generated from this study.…”

Rapid Low-Cost Assembly of the Drosophila melanogaster Reference Genome Using Low-Coverage, Long-Read Sequencing

“…It is possible that some of these errors are SVs, which are expected to accumulate because the ISO1 stock has been maintained in the laboratory for approximately 350 generations (assuming 20 gen/year) since initial sequencing in 2000. This allows for the accumulation of new mutations by genetic drift, including ones reducing fitness ( Assaf et al 2017 ). Due to the high contiguity in the euchromatic region, our assembly facilitates detection of such euchromatic SVs.…”

Old Trade, New Tricks: Insights into the Spontaneous Mutation Process from the Partnering of Classical Mutation Accumulation Experiments with High-Throughput Genomic Approaches

“…(2013) Drosophila melanogaster b EukaryotaMetazoa—606.00 × 10 −9 5.21 × 10 −9 7.90 × 10 −10 7:1Huang et al. (2016) Drosophila melanogaster EukaryotaMetazoa2526.37 × 10 −9 6.03 × 10 −9 3.38 × 10 −10 18:1Sharp and Agrawal (2016) Drosophila melanogaster EukaryotaMetazoa236–53—4.90 × 10 −9 ——Assaf et al. (2017) Mus musculus EukaryotaMetazoa—20–215.71 × 10 −9 5.40 × 10 −9 3.10 × 10 −10 17:1Uchimura et al.…”