The repeatability of genome-wide mutation rate and spectrum estimates

Abstract

Over the last decade, mutation studies have grown in popularity due to the affordability and accessibility of whole genome sequencing. As the number of species in which spontaneous mutation has been directly estimated approaches 20 across two domains of life, questions arise over the repeatability of results in such experiments. Five species were identified in which duplicate mutation studies have been performed. Across these studies the difference in estimated spontaneous mutation rate is at most, weakly significant (p < 0.01). However, a highly significant (p < 10(-5)), threefold difference in the rate of insertions/deletions (indels) exists between two recent studies in Schizosaccharomyces pombe. Upon investigation of the ancestral genome sequence for both studies, a possible anti-mutator allele was identified. The observed variation in indel rate may imply that the use of indel markers, such as microsatellites, for the investigation of genetic diversity within and among populations may be inappropriate because of the assumption of uniform mutation rate within a species.

Keywords: DNA repair; Evolution; Microsatellite; Mutation accumulation; Schizosaccharomyces pombe; Yeast; indel.

Figure 1

Comparison of mutational effects in MA ancestor and MA lines. There is no difference between any of the three spectra (Chi-squared test: p-value = 0.61).

Figure 2

Comparison of mutation accumulation spectra for the four species in which there are sufficient numbers of mutations to make a comparison. In all four species, spectra are not significantly different across studies (Chi-squared test: A: A. thaliana, p-value = 0.75, B: D. melanogaster, p-value = 0.58, C: C. elegans, p-value = 0.164, D: S. pombe, p-value = 0.66) .