Abstract
Spontaneous mutations play a central role in evolution. Despite their importance, mutation rates are some of the most elusive parameters to measure in evolutionary biology. The combination of mutation accumulation (MA) experiments and whole-genome sequencing now makes it possible to estimate mutation rates by directly observing new mutations at the molecular level across the whole genome. We performed an MA experiment with the social amoeba Dictyostelium discoideum and sequenced the genomes of three randomly chosen lines using high-throughput sequencing to estimate the spontaneous mutation rate in this model organism. The mitochondrial mutation rate of 6.76×10−9, with a Poisson confidence interval of 4.1×10−9 − 9.5×10−9, per nucleotide per generation is slightly lower than estimates for other taxa. The mutation rate estimate for the nuclear DNA of 2.9×10−11, with a Poisson confidence interval ranging from 7.4×10−13 to 1.6×10−10, is the lowest reported for any eukaryote. These results are consistent with low microsatellite mutation rates previously observed in D. discoideum and low levels of genetic variation observed in wild D. discoideum populations. In addition, D. discoideum has been shown to be quite resistant to DNA damage, which suggests an efficient DNA-repair mechanism that could be an adaptation to life in soil and frequent exposure to intracellular and extracellular mutagenic compounds. The social aspect of the life cycle of D. discoideum and a large portion of the genome under relaxed selection during vegetative growth could also select for a low mutation rate. This hypothesis is supported by a significantly lower mutation rate per cell division in multicellular eukaryotes compared with unicellular eukaryotes.
Highlights
Mutations are the ultimate source of genetic variation upon which natural selection acts [1]
The average read coverage per site in the nuclear genome ranged from 9X to 11X, while the average coverage in the considerably smaller and more abundant mitochondrial genome was close to 5000X (4655X for MA31, 7141X for MA47, and 3033X for MA55)
Increasing the minimum coverage required for individual base calls, may come at a cost of reduced information overall, because a smaller percentage of the genome will be covered at the minimum level
Summary
Mutations are the ultimate source of genetic variation upon which natural selection acts [1]. Mutations play a central role in the evolutionary process. How often new mutations arise has been difficult to determine until recently [2,3]; mostly because mutations are very rare events [4]. Many mutations have deleterious fitness effects [5], causing them to be quickly removed by natural selection. Unless methods are used to minimize selection, deleterious mutations can be undercounted. Estimates based on comparative approaches are further hampered by unknown times of divergence and unknown selection pressures imposed by environmental variation during divergence. Direct estimation of mutation rates was mostly limited to the analyses of a few genes based on phenotypic assays [4]
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