Biology subjects

Sharp, N. P.

Publications and source records attributed to Sharp, N. P..

10 recordsLinked to original sources

bioRxiv2025

The effect of spontaneous mutations on CUP1 copy number and copper tolerance in Saccharomyces cerevisiae

Genomic regions containing tandem duplications may be subject to particularly high rates of copy number mutations due to recombinational repair of DNA damage. Consequently, changes in copy number may be among the most accessible beneficial mutations during evolution in a new environment. In the budding yeast Saccharomyces cerevisiae, the gene CUP1 occurs in multiple tandem copies and encodes a metallothionein protein that is relevant for copper homeostasis. We examined CUP1 copy number in 220 mutation accumulation lines and their ancestors to quantify spontaneous genetic change at this locus. We also measured copper tolerance in the same strains to understand the phenotypic effects of CUP1 copy number change and other mutations. We found that mutations in CUP1 copy number occurred rapidly, with a bias towards the loss of copies. While copper tolerance also declined due to spontaneous mutations, this change was less rapid overall and was only partly driven by CUP1 copy number. Thus, while this locus is highly susceptible to mutation, such mutations may provide an accessible but insufficient evolutionary path towards increased copper resistance.

evolutionary biology↗

bioRxiv2025

Evolutionary responses to increased opportunity for sexual selection in yeast

Sexual selection contributes to biodiversity and the costs and benefits of sexual reproduction. In organisms where sex is infrequent, these impacts of sexual selection are likely to be limited. An increased frequency of obligate sex would increase the opportunity for sexual selection, which could promote the evolution of sexual traits and sexual differentiation. To study these dynamics, we conducted experimental evolution in the yeast Saccharomyces cerevisiae, which is predominantly asexual, with two isogamous mating types. We used selectable markers to impose frequent obligate sex in 96 populations. We manipulated the opportunity for sexual selection by imposing skewed mating-type ratios and by altering the degree to which mating occurred by selfing versus outcrossing. After just ten sexual cycles, we observed evolution in growth, cell size, pheromone production, and mating, with the mating types responding asymmetrically, but little evolutionary change in sporulation rate. Mating type dimorphism increased, with evident trade-offs between growth, attractiveness, and cell size. Genome sequences from a subset of populations revealed many mutations affecting sex-related genes. Unexpectedly, the selfing populations evolved to become sporulation-competent haploids, unlinking meiosis from ploidy change. Our results illustrate that sexual differentiation can evolve rapidly in response to an increased opportunity for sexual selection.

evolutionary biology↗

bioRxiv2025

Meiotic double strand DNA breaks and spontaneous mutation in Drosophila melanogaster

The exchange of genetic material during meiosis requires the formation and repair of DNA double-strand breaks (DSBs), which may not be repaired with perfect fidelity. If meiotic exchange is mutagenic, this would add to the costs of sexual reproduction and affect patterns of genome evolution, but much of the evidence for this is indirect. In the fruit fly Drosophila melanogaster, it is possible to completely suppress endogenous DSBs while retaining normal fertility. We took advantage of this system to generate fly strains with and without a mutant allele of mei-P22, a gene that is essential for meiotic DSB formation, on a common genetic background. This allowed us to investigate the relationship between DSBs and genome-wide mutation patterns, using a mutation accumulation design to allow un-selected spontaneous mutations to be observed. Following 30 generations of mutation accumulation, we identified over 1800 mutations by whole-genome sequencing. The presence of meiotic DSBs had little effect on the rate and spectrum of point mutations. We found that mutations were more likely to occur in areas of the genome with higher rates of crossover recombination, regardless of whether meiotic DSBs were occurring. We also found that the rate of transposable element insertions across multiple TE families was substantially elevated in the group lacking meiotic DSBs, suggesting that host suppression of mobile genetic elements is closely associated with meiotic recombination mechanisms.

evolutionary biology↗

bioRxiv2025

Quantitative genetics of trauma induced mortality in Drosophila melanogaster

Traumatic brain injury is a major cause of chronic neurological impairment worldwide, and there is evidence that both genetic and environmental variation contribute to the likelihood of recovery. Using an insect model of traumatic brain injury, we examined variation in the risk of mortality using quantitative genetic approaches applied previously for life history traits in Drosophila melanogaster. We quantified additive genetic variance for mortality risk using a controlled breeding design and found levels of variation consistent with existing data on major fitness components. We found no evidence for inbreeding effects on mortality risk, suggesting that dominance genetic variance makes little contribution to this trait. To explain the high level of standing genetic variation, we considered whether mortality risk depends on the metabolic resources available to an individual, also known as "condition". We manipulated condition by inducing random mutations and by restricting calories during larval development. We found that reduced condition due to both random mutations and resource limitation significantly increased the risk of mortality following trauma. Among inbred lines, greater mortality risk was associated with lower viability, fecundity and longevity, consistent with an effect of genome-wide genetic quality. Our results suggest that further consideration of individual condition would be valuable for understanding and predicting variation in the outcomes of traumatic brain injury.

genetics↗

bioRxiv2025

Contrasting mutation patterns in haploid and diploid cells from two yeast species

There is significant variation in the rate and spectrum of spontaneous mutations among taxa. How this variation is shaped by natural selection remains a subject of debate. The drift barrier hypothesis proposes that selection generally favors lower mutation rates due to the risk of deleterious mutations but acts less effectively against weak mutator alleles in smaller populations, allowing the mutation rate to increase due to genetic drift. Given this model, we propose that mutation rates may also be elevated in cell types that appear rarely in a population, where DNA replication and repair processes are subject to selection less often. We can begin to test this prediction in yeast species, some of which can be grown in either a haploid or diploid cell state. Existing data on the budding yeast Saccharomyces cerevisiae support this prediction, with a higher mutation rate observed in haploids, which is the rare cell type in natural populations. However, this pattern could also appear if haploidy is inherently mutagenic, regardless of the dominant cell type. To test these alternatives, we conducted a mutation accumulation experiment with haploid and diploid cells of the fission yeast Schizosaccharomyces pombe, in which diploidy is the rare cell type. In this species, we found a higher mutation rate in diploids, consistent with our prediction. In both species, the spectrum of mutations is also influenced by ploidy state. Our findings suggest that limits to selection on mutation may be evident as variation within species. SignificanceSpontaneous mutation rates vary among organisms. Natural selection may act to reduce mutation rates; if so, we would expect mutation rates to be elevated in cell types where natural selection has historically had less opportunity to act. We studied mutation patterns in two yeast species when grown in the haploid or diploid form. For the typically diploid species, the mutation rate was higher in the haploid form. For the typically haploid species, the mutation rate was higher in the diploid form. The observation that mutation rates increase when selection is ineffective indicates that selection usually acts to reduce mutation rates.

evolutionary biology↗

bioRxiv2024

On the rate of aneuploidy reversion in a wild yeast model

Aneuploidy, arising from gain or loss of chromosomes due to nondisjunction, is a special class of mutation. It can create significant phenotypic changes by altering abundance of hundreds of genes in a single event, providing material for adaptive evolution. But it can also incur large fitness costs relative to other types of mutations. Understanding mutational dynamics of aneuploidy is important for modeling its impact in nature, but aneuploidy rates are difficult to measure accurately. One challenge is that aneuploid karyotypes may revert back to euploidy, biasing forward mutation rate estimates - yet the rate of aneuploidy reversion is largely uncharacterized. Furthermore, current rate estimates are confounded because fitness differences between euploids and aneuploids are typically not accounted for in rate calculations. We developed a unique fluctuation assay in a wild-yeast model to measure the rate of extra-chromosome loss across three aneuploid chromosomes, while accounting for fitness differences between aneuploid and euploid cells. We show that incorporating fitness effects is essential to obtain accurate estimates of aneuploidy rates. Furthermore, the rate of extra-chromosome loss, separate from karyotype fitness differences, varies across chromosomes. We also measured rates in a strain lacking RNA-binding protein Ssd1, important for aneuploidy tolerance and implicated in chromosome segregation. We found no role for Ssd1 in the loss of native aneuploid chromosomes, although it did impact an engineered chromosome XV with a perturbed centromeric sequence. We discuss the impacts and challenges of modeling aneuploidy dynamics in real world situations. ARTICLE SUMMARYErrors in chromosome segregation can produce aneuploid cells with an abnormal number of chromosomes. Aneuploidy is not uncommon in wild populations of fungi and can underlie emergence of drug-resistant pathogens. But modeling the impact of aneuploidy on evolution has been challenging, because rates of aneuploidy emergence and reversion have been difficult to measure. This work used a novel fluctuation assay that incorporates euploid-aneuploid fitness differences to calculate rates of extra-chromosome loss in aneuploid Saccharomyces cerevisiae, across several chromosomes. The results present for the first time estimates of aneuploidy reversion ("back mutation") rates and implications for previously measured rates of aneuploidy.

genetics↗

bioRxiv2024

Sex-specific viability effects of mutations in Drosophila melanogaster

In populations with separate sexes, genetic load due to deleterious mutations may be expressed differently in males and females. Evidence from insect models suggests that selection against mutations is stronger in males, with a positive intersexual correlation for fitness. This pattern will reduce deleterious allele frequencies at the expense of males, such that female mean fitness is greater than expected, preserving population persistence in the face of high mutation rates. While previous studies focus on reproductive success, mutation load depends on total selection in each sex, including selection for viability. In fruit flies, we might expect minimal sex differences in viability effects, since male and female larvae behave similarly, but many genes show sex-biased expression in larvae. We measured the sex-specific viability effects of nine "marker" mutations and 33 mutagenized chromosomes. We find that both types of mutations generally reduce viability in both sexes. Among marker mutations we detect instances of sex biased selection in both directions, but mutagenized chromosomes show little sign of sex-specific mutational variance. We conclude that some mutations can indeed affect viability in a sex-specific manner, but that the pattern of male-biased mutational effects observed previously for reproductive success is not apparent at the pre-reproductive stage.

evolutionary biology↗

bioRxiv2022

Contribution of spontaneous mutations to quantitative and molecular variation at the highly repetitive rDNA locus in yeast

The ribosomal DNA array in Saccharomyces cerevisiae consists of many tandem repeats whose copy number is believed to be functionally important but highly labile. Regulatory mechanisms have evolved to maintain copy number by directed mutation, but how spontaneous variation at this locus is generated and selected has not been well characterized. We applied a mutation accumulation approach to quantify the impacts of mutation and selection on this unique genomic feature across hundreds of mutant strains. We find that mutational variance for this trait is relatively high, and that un-selected mutations throughout the genome can disrupt copy number maintenance. In consequence, copy number generally declines, consistent with a model of regulation where copy number is normally increased when low. This pattern holds across ploidy levels and strains in the standard lab environment, but differs under some stressful conditions. We identify several alleles, gene categories and genomic features that likely affect copy number, including aneuploidy for chromosome XII. Copy number change is associated with reduced growth in diploids, consistent with stabilizing selection. Levels of standing variation in copy number are well predicted by a balance between mutation and stabilizing selection, suggesting this trait is not subject to strong diversifying selection in the wild. The rate and spectrum of point mutations within the rDNA locus itself is distinct from the rest of the genome, and predictive of polymorphism locations. Our findings help differentiate the roles of mutation and selection and indicate that spontaneous mutation patterns shape several aspects of ribosomal DNA evolution.

genetics↗

bioRxiv2018

The genome-wide rate and spectrum of spontaneous mutations differs between haploid and diploid yeast

By altering the dynamics of DNA replication and repair, alternative ploidy states may experience different rates and types of new mutations, leading to divergent evolutionary outcomes. We report the first direct comparison of the genome-wide spectrum of spontaneous mutations arising in haploid and diploid forms of the budding yeast. Characterizing the number, types, locations, and effects of thousands of mutations revealed that haploids were more prone to single-nucleotide and mitochondrial mutations, while larger structural changes were more common in diploids. Mutations were more likely to be detrimental in diploids, even after accounting for the large impact of structural changes, contrary to the prediction that diploidy masks the effects of recessive alleles. Haploidy is expected to reduce the opportunity for conservative DNA repair involving homologous chromosomes, increasing the insertion-deletion rate, but we found little support for this idea. Instead, haploids were more susceptible to particular single-nucleotide mutations in late-replicating genomic regions, resulting in a ploidy difference in the spectrum of substitutions. In diploids we detect mutation rate variation among chromosomes in association with centromere location, a finding that is supported by published polymorphism data. Diploids are Saccharomyces cerevisiae not simply doubled haploids; instead, our results predict that the spectrum of spontaneous mutations will substantially shape the dynamics of genome evolution in haploid and diploid populations.

evolutionary biology↗

bioRxiv2017

An experimental test of the mutation-selection balance model for the maintenance of genetic variance in fitness components

Despite decades of research, the factors that maintain genetic variation for fitness are poorly understood. Mutation selection balance will always contribute to standing variance, but it is unclear what fraction of the variance in a typical fitness component can be explained by mutation-selection balance and whether fitness components differ in this respect. In theory, the level of standing variance in fitness due to mutation-selection balance can be predicted using the rate of fitness decline under mutation accumulation, and this prediction can be directly compared to the actual standing variance observed. This approach allows for controlled statistical tests of the sufficiency of the mutation-selection balance model, and could be used to identify traits or populations where genetic variance is maintained by factors beyond mutation-selection balance. For example, some traits may be influenced by sexually antagonistic balancing selection, resulting in an excess of standing variance beyond that generated by deleterious mutations. To encourage the application of this approach, we describe the underlying theory and use it to test the mutation selection balance model for three traits in Drosophila melanogaster. We find some evidence for non-mutational variance in male mating success and female fecundity relative to larval viability, which is consistent with balancing selection on sexual fitness components. Finally, we discuss the theoretical and practical limitations to this approach, and discuss how to apply it successfully.

evolutionary biology↗