1. Spontaneous mutation accumulation in the house mouse.
We set up a replicated mutation accumulation (MA) lines, and controls consisting of frozen embryos to allow us to determine whether the mean values of quantitative traits have changed.
2. Distinguishing low from high frequency variant sites in the genome.
We developed a statistical approach to estimate the frequencies of beneficial and deleterious mutations based on polymorphism data from a sample of individuals. This method has been widely used (Keightley and Jackson 2018).
3. Understanding the causes of variation in nucleotide diversity across the genome.
We attempted to quantify the contributions of background selection and selective sweeps to diversity dips around protein-coding genes and gene regulatory elements in the mouse. Selection in favour of strongly advantageous mutations has been important in shaping patterns of diversity across the genome (Booker and Keightley 2018).
4. The distribution of fitness effects (DFE) for new mutations.
We attempted to characterize properties of the DFE in the single-celled green alga Chlamydomonas reinhardtii by crossing lines carrying known complements of mutations with their ancestral strains (Boendel et al 2019, 2022). Our results suggest that the distribution is L-shaped, and that a high proportion of mutations increase fitness.
5. Sequencing of MA lines and their ancestors to estimate the mutation rate.
The variation present in the ancestors of our MA lines provided a reasonable per nucleotide mutation rate estimate for the colony nucleus (~7.9 × 10^-9) (Chebib et al 2021). In the MA lines, we estimated that the average rate of new SNMs is ∼μ = 6.7 × 10^-9. We followed this up with PacBio sequencing. Among the different types of structural mutations, tandem repeat mutations have the highest mutation rate, followed by insertions of transposable elements (Lopez-Cortegano et al 2025). Studies were complemented by experiments in MA lines of Chlamydomonas (Lopez-Cortegano at al 2021).
6. The fitness consequences of mutation accumulation in the house mouse.
Prior to our study, the phenotypic consequences of MA in vertebrates were largely unknown. We studied the impact of spontaneous MA on the mean and genetic variation for quantitative and fitness-related traits using the MA experimental design, with a cryopreserved control to account for environmental influences. Variation accumulates at a sufficiently high rate to maintain genetic variation and selection response. When extrapolated to humans, our results imply that the rate of fitness loss should not be of concern in the foreseeable future (Chebib et al 2021).
