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54 results for “deleterious mutations”
Demographic history shaped geographical patterns of deleterious mutation load in a broadly distributed Pacific Salmon
<p class="17"><span>A thorough reconstruction of historical processes is essential for a comprehensive understanding the mechanisms shaping patterns of genetic diversity. Indeed, past and current conditions influencing effective population size have important evolutionary implications for the efficacy of selection, increased accumulation of deleterious mutations, and loss of adaptive potential. Here, we gather extensive genome-wide data that represent the extant diversity of the Coho salmon (<i><span>Oncorhynchus kisutch</span></i>) to address two objectives. We demonstrate that a single glacial refugium is the source of most of the present-day genetic diversity, with detectable inputs from a putative secondary micro-refugium. We found statistical support for a scenario whereby ancestral populations located south of the ice sheets expanded in postglacial time, swamping out most of the diversity from other putative micro-refugia. Demographic inferences revealed that genetic diversity was also affected by linked selection in large parts of the genome. Moreover, we demonstrate that the recent demographic history of this species generated regional differences in the load of deleterious mutations among populations, a finding that mirrors recent results from human populations and provides increased support for models of expansion load. We propose that insights from these historical inferences should be better integrated in conservation planning of wild organisms, which currently focuses largely on neutral genetic diversity and local adaptation, with the role of potentially maladaptive variation being generally ignored.</span></p>
Data from: Deleterious mutations show increasing negative effects with age in Drosophila melanogaster
<p><strong>Background</strong><br> In order for ageing to evolve in response to a declining strength of selection with age, a genetic architecture that allows for mutations with age-specific effects on organismal performance is required. Our understanding of how selective effects of individual mutations are distributed across ages is however poor. Established evolutionary theories assume that mutations causing ageing have negative late-life effects, coupled to either positive or neutral effects early in life. New theory now suggests evolution of ageing may also result from deleterious mutations with increasing negative effects with age, a possibility that has not yet been empirically explored.</p> <p><strong>Results</strong><br> To directly test how the effects of deleterious mutations are distributed across ages, we separately measure age-specific effects on fecundity for each of 20 mutations in <i>Drosophila melanogaster</i>. We find that deleterious mutations in general have a negative effect that increases with age, and that the rate of increase depends on how deleterious a mutation is early in life.</p> <p><b>Conclusions</b><br> Our findings suggest that ageing does not exclusively depend on genetic variants assumed by the established evolutionary theories of ageing. Instead, ageing can result from deleterious mutations with negative effects that amplify with age. If increasing negative effect with age is a general property of deleterious mutations, the proportion of mutations with the capacity to contribute towards ageing may be considerably larger than previously believed.</p>
Data from: Magnitude and sign epistasis among deleterious mutations in a positive-sense plant RNA virus
How epistatic interactions between mutations determine the genetic architecture of fitness is of central importance in evolution. The study of epistasis is particularly interesting for RNA viruses because of their genomic compactness, lack of genetic redundancy, and apparent low complexity. Moreover, interactions between mutations in viral genomes determine traits such as resistance to antiviral drugs, virulence and host range. In this study we generated 53 Tobacco etch potyvirus genotypes carrying pairs of single-nucleotide substitutions and measured their separated and combined deleterious fitness effects. We found that up to 38% of pairs had significant epistasis for fitness, including both positive and negative deviations from the null hypothesis of multiplicative effects. Interestingly, the sign of epistasis was correlated with viral protein–protein interactions in a model network, being predominantly positive between linked pairs of proteins and negative between unlinked ones. Furthermore, 55% of significant interactions were cases of reciprocal sign epistasis (RSE), indicating that adaptive landscapes for RNA viruses maybe highly rugged. Finally, we found that the magnitude of epistasis correlated negatively with the average effect of mutations. Overall, our results are in good agreement to those previously reported for other viruses and further consolidate the view that positive epistasis is the norm for small and compact genomes that lack genetic robustness.
Data from: Abiotic stress does not magnify the deleterious effects of spontaneous mutations
Although the effects of deleterious alleles often are predicted to be greater in stressful environments, there is no theoretical basis for this prediction and the empirical evidence is mixed. Here we characterized the effects of three types of abiotic stress (thermal, oxidative and hyperosmotic) on two sets of nematode (Caenorhabditis elegans) mutation accumulation (MA) lines that differ by threefold in fitness. We compared the survival and egg-to-adult viability between environments (benign and stressful) and between fitness categories (high-fitness MA, low-fitness MA). If the environment and mutation load have synergistic effects on trait means, then the difference between the high and low-fitness MA lines should be larger in stressful environments. Although the stress treatments consistently decreased survival and/or viability, we did not detect significant interactions between fitness categories and environment types. In contrast, we did find consistent evidence for synergistic effects on (micro)environmental variation. The lack of signal in trait means likely reflects the very low starting fitness of some low-fitness MA lines, the potential for cross-stress responses and the context dependence of mutational effects. In addition, the large increases in the environmental variance in the stressful environments may have masked small changes in trait means. These results do not provide evidence for synergism between mutation and stress.
Data from: Sex-chromosome turnovers induced by deleterious mutation load
In sharp contrast with mammals and birds, many cold-blooded vertebrates present homomorphic sex chromosomes. Empirical evidence supports a role for frequent turnovers, which replace non-recombining sex chromosomes before they have time to decay. Three main mechanisms have been proposed for such turnovers, relying either on neutral processes, sex-ratio selection, or intrinsic benefits of the new sex-determining genes (due e.g. to linkage with sexually antagonistic mutations). Here we suggest an additional mechanism, arising from the load of deleterious mutations that accumulate on non-recombining sex chromosomes. In the absence of dosage compensation, this load should progressively lower survival rate in the heterogametic sex. Turnovers should occur when this cost outweighs the benefits gained from any sexually antagonistic genes carried by the non-recombining sex chromosome. We use individual-based simulations of a Muller's ratchet process to test this prediction, and investigate how the relevant parameters (effective population size, strength and dominance of deleterious mutations, size of non-recombining segment, and strength of sexually antagonistic selection) are expected to affect the rate of turnovers.
Data from: The effect of deleterious mutations and age on recombination in Drosophila melanogaster
At the population level, recombination mediates the efficiency with which selection can eliminate deleterious mutations. At the individual level, deleterious alleles may influence recombination, which would change the rate at which linkage disequilibrium is eroded and thereby alter the efficiency with which deleterious alleles are purged. Here we test whether the presence of a deleterious allele on one autosome affects recombination on another autosome. We find that deleterious alleles not only alter the rate but also the pattern of recombination. However, there is little support that different deleterious alleles affect recombination in a consistent manner. Because we have detailed information on individual females across their life times, we are able to examine how recombination patterns change with age and find that these patterns are also affected by the presence of deleterious alleles. The differences among genotypes or among age classes is large enough to add substantial noise to genetic mapping experiments that do not consider these sources of variation.
Nonlethal deleterious mutation–induced stress accelerates bacterial aging
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Data from: Experiments on the role of deleterious mutations as stepping stones in adaptive evolution
Many evolutionary studies assume that deleterious mutations necessarily impede adaptive evolution. However, a later mutation that is conditionally beneficial may interact with a deleterious predecessor before it is eliminated, thereby providing access to adaptations that might otherwise be inaccessible. It is unknown whether such sign-epistatic recoveries are inconsequential events or an important factor in evolution, owing to the difficulty of monitoring the effects and fates of all mutations during experiments with biological organisms. Here, we used digital organisms to compare the extent of adaptive evolution in populations when deleterious mutations were disallowed with control populations in which such mutations were allowed. Significantly higher fitness levels were achieved over the long term in the control populations because some of the deleterious mutations served as stepping stones across otherwise impassable fitness valleys. As a consequence, initially deleterious mutations facilitated the evolution of complex, beneficial functions. We also examined the effects of disallowing neutral mutations, of varying the mutation rate, and of sexual recombination. Populations evolving without neutral mutations were able to leverage deleterious and compensatory mutation pairs to overcome, at least partially, the absence of neutral mutations. Substantially raising or lowering the mutation rate reduced or eliminated the long-term benefit of deleterious mutations, but introducing recombination did not. Our work demonstrates that deleterious mutations can play an important role in adaptive evolution under at least some conditions.
Rucaparib in Treating Patients With Genomic LOH High and/or Deleterious BRCA1/2 Mutation Stage IV or Recurrent Non-small Cell Lung Cancer (A Lung-MAP Treatment Trial)
ClinicalTrials.gov study NCT03845296. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Data from: The maintenance of obligate sex in finite, structured populations subject to recurrent beneficial and deleterious mutation
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Data from: Environmental stress increases selection against and dominance of deleterious mutations in inbred families of the Pacific oyster Crassostrea gigas
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Data from: The purging of deleterious mutations in simple and complex mating environments
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Data from: The evolution of XY-recombination: sexually antagonistic selection versus deleterious mutation load
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Data from: Experiments on the role of deleterious mutations as stepping stones in adaptive evolution
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Data from: Dietary stress does not strengthen selection against single deleterious mutations in Drosophila melanogaster
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Data from: Purging deleterious mutations in conservation programmes: combining optimal contributions with inbred matings
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Data from: Magnitude and sign epistasis among deleterious mutations in a positive-sense plant RNA virus
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Demographic history shaped geographical patterns of deleterious mutation load in a broadly distributed Pacific Salmon
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Data from: Sex-chromosome turnovers induced by deleterious mutation load
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Data from: Test of synergistic interactions among deleterious mutations in bacteria
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