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54 results for “deleterious mutations”
Demographic history and natural selection shape patterns of deleterious mutation load and barriers to introgression across Populus genome
<p><br> Abbreviation of species names in each folder: Palb, P. alba; Pade, P. adenopoda; Pdav, P. davidiana; Ptra, P. tremula; Ptrs, P. tremuloides; Prot, P. rotundifolia; Pqio,P. qiongdaoensis.</p> <p>1. FST<br> Relative divergence (FST) for pairwise species comparisons was calculated for all sites with 100 Kbp non-overlapping windows. </p> <p>2. dxy<br> Absolute divergence (dxy) was calculated for all sites with 100 Kbp non-overlapping windows. </p> <p>3. Nucleotide diversity<br> Nucleotide diversity (π) was calculated for all sites with 100 Kbp non-overlapping windows. </p> <p>4. Derived allele frequency<br> The derived frequencies of 4 different functional categories. Each folder contains seven Populus resluts</p> <p>5. Derived_allele_statistics<br> The statistics of homozygous and heterozygous derived alleles for loss of function, deleterious, tolerated and synonymous variants for each individual. The last two individuals in each file are outgroups </p> <p>6. dsuite-dinvestigate<br> The outputs of 10 trios using program Dinvestigate from Dsuite. The sliding window is 50 SNPs, and the step is 20 SNPs.</p> <p>7. Recombination rate<br> The result of population-scaled recombination rate was calculated by LDhat v2.2.</p> <p>8. Volcanofinder<br> Genome-wide scans of introgression sweeps within each species was implemented using VolcanFinder v.1.0 with the Model over 10 Kbp non-overlapping windows.</p> <p>9. ihh12<br> phased SNPs were used to computed ihh12 by selscan v1.3.0. </p> <p>10 populus162.phased.recode.vcf.gz<br> SNPs were phased with Beagle v.4.1 for the 162 non-hybrid individuals.</p> <p>11 populus227.snp.rm_indel.para_filter.biallelic.GQ30.max_miss20.bed.recode.vcf.gz <br> The vcf of 227 Populus samples. </p>
Data from: Mutations in yeast are deleterious on average regardless of the degree of adaptation to the testing environment
<p>The role of spontaneous mutations in evolution depends on the distribution of their effects on fitness. Despite a general consensus that new mutations are deleterious on average, a handful of mutation accumulation experiments in diverse organisms instead suggest that of beneficial and deleterious mutations can have comparable fitness impacts, i.e., the product of their respective rates and effects can be roughly equal. We currently lack a general framework for predicting when such a pattern will occur. One idea is that beneficial mutations will be more evident in genotypes that are not well adapted to the testing environment. We tested this prediction experimentally in the laboratory yeast <em>Saccharomyces cerevisiae</em> by allowing nine replicate populations to adapt to novel environments with complex sets of stressors. After >1000 asexual generations interspersed with 41 rounds of sexual reproduction, we assessed the mean effect of induced mutations on yeast growth in both the environment to which they had been adapting and the alternative novel environment. The mutations were deleterious on average, with the severity depending on the testing environment. However, we find no evidence that the adaptive match between genotype and environment is predictive of mutational fitness effects.</p>
A Study to Evaluate Rucaparib in Participants With Solid Tumors and With Deleterious Mutations in HRR Genes
ClinicalTrials.gov study NCT04171700. IPD Sharing: YES. Countries: 1. Publications: 1.
Data from: Mutations in yeast are deleterious on average regardless of the degree of adaptation to the testing environment
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Conditionally deleterious mutation load accumulates in genomic islands but can be purged with sufficient genotypic redundancy
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Negative linkage disequilibrium between amino acid changing variants reveals interference among deleterious mutations in the human genome
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BMN 673 (Talazoparib), an Oral PARP Inhibitor, in People With Deleterious BRCA1/2 Mutation-Associated Ovarian Cancer Who Have Had Prior PARP Inhibitor Treatment
ClinicalTrials.gov study NCT02326844. IPD Sharing: NO. Countries: 1. Publications: 3.
Pilot Trial of BMN 673, an Oral PARP Inhibitor, in Patients With Advanced Solid Tumors and Deleterious BRCA Mutations
ClinicalTrials.gov study NCT01989546. IPD Sharing: NO. Countries: 1. Publications: 4.
Strongly deleterious mutations influence reproducitve output and longevity in an endangered population
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Data from: The accumulation of deleterious mutations as a consequence of domestication and improvement in sunflowers and other Compositae crops
For populations to maintain optimal fitness, harmful mutations must be efficiently purged from the genome. Yet, under circumstances that diminish the effectiveness of natural selection, such as the process of plant and animal domestication, deleterious mutations are predicted to accumulate. Here, we compared the load of deleterious mutations in 21 accessions from natural populations and 19 domesticated accessions of the common sunflower using whole-transcriptome single nucleotide polymorphism data. Although we find that genetic diversity has been greatly reduced during domestication, the remaining mutations were disproportionally biased toward nonsynonymous substitutions. Bioinformatically predicted deleterious mutations affecting protein function were especially strongly over-represented. We also identify similar patterns in two other domesticated species of the sunflower family (globe artichoke and cardoon), indicating that this phenomenon is not due to idiosyncrasies of sunflower domestication or the sunflower genome. Finally, we provide unequivocal evidence that deleterious mutations accumulate in low recombining regions of the genome, due to the reduced efficacy of purifying selection. These results represent a conundrum for crop improvement efforts. Although the elimination of harmful mutations should be a long-term goal of plant and animal breeding programs, it will be difficult to weed them out because of limited recombination.
Data from: Do genetic drift and accumulation of deleterious mutations preclude adaptation? Empirical investigation using RADseq in a northern lacustrine fish
Understanding genomic signatures of divergent selection underlying long-term adaptation in populations located in heterogeneous environments is a key goal in evolutionary biology. In this study, we investigated neutral, adaptive and deleterious genetic variation using 7,192 SNPs in 31 Lake Trout (Salvelinus namaycush) populations (n = 673) from Québec, Canada. Average genetic diversity was low, weakly shared among lakes, and positively correlated to lake size, indicating a major role for genetic drift subsequent to lake isolation. Putatively deleterious mutations were on average at lower frequencies than the other SNPs, and their abundance relative to the entire polymorphism in each population was positively correlated to inbreeding, suggesting that the effectiveness of purifying selection was negatively correlated to inbreeding, as predicted from theory. Despite evidence for pronounced genetic drift and inbreeding, several outlier loci were associated with temperature and found in or close to genes with biologically relevant functions notably related to heat-stress and immune responses. Outcomes of gene-temperature associations were influenced by the inclusion of the most inbred populations, in which allele frequencies deviated the most from model predictions. This result illustrates challenge in identifying gene-environment associations in cases of high genetic drift and restricted gene flow and suggests limited adaptation in populations experiencing higher inbreeding. We discuss the relevance of these findings for the conservation and management, notably regarding stocking and genetic rescue, of Lake Trout populations and other species inhabiting highly fragmented habitats.
Accumulation of deleterious mutations in landlocked threespine stickleback populations
<p></p><p>Colonization of new habitats often reduces population sizes and may result in the accumulation of deleterious mutations by genetic drift. Compared to the genomic basis for adaptation to new environments, genome-wide analysis of deleterious mutations in isolated populations remains limited. In the present study, we investigated the accumulation of deleterious mutations in five endangered freshwater populations of threespine stickleback (Gasterosteus aculeatus) in the central part of the mainland of Japan. Using whole genome resequencing data, we first conducted phylogenomic analysis and confirmed at least two independent freshwater colonization events in the central mainland from ancestral marine ecotypes. Next, analyses of single nucleotide polymorphisms (SNPs) showed a substantial reduction of heterozygosity in freshwater populations compared to marine populations. Reduction in heterozygosity was more apparent at the center of each chromosome than the peripheries and on X-chromosomes compared to autosomes. Third, bioinformatic analysis of deleterious mutations showed increased accumulation of putatively deleterious mutations in the landlocked freshwater populations compared to marine populations. For the majority of populations examined, the frequencies of putatively deleterious mutations were higher on X-chromosomes than on autosomes. The inter-population comparison indicated that the majority of putatively deleterious mutations may have accumulated independently. Thus, whole genome resequencing of endangered populations can help to estimate the accumulation of deleterious mutations and inform us of which populations are the most severely endangered. Furthermore, analysis of variation among chromosomes can give insights into whether any particular chromosomes are likely to accumulate deleterious mutations.</p><p></p>
FIG. 1 in OPINION Testing for the accumulation of deleterious mutations in asexual eukaryote genomes using molecular sequences
FIG. 1. Phylogeny of representative sexual and asexual Lachnidae with estimates of the numbers of replacement and silent substitutions for EF1a and CO2 on each branch. See text for description of estimation of the numbers of substitutions in each category. Phylogeny is from Normark (2000).
InheriteD brEast caNcer iTalian regIsTrY A Retrospective-prospective Observational Cohort Study to Evaluate Cancer Prevention Strategies in Women With a Deleterious Mutation in BRCA1-2
ClinicalTrials.gov study NCT05835739. IPD Sharing: Not stated. Countries: 1. Publications: 6.
Promitil Treatment of Patients With Solid Tumors Associated With Deleterious Mutations Who Have Progressed After Therapy
ClinicalTrials.gov study NCT06478862. IPD Sharing: NO. Countries: 1. Publications: 2.
Data from: Do genetic drift and accumulation of deleterious mutations preclude adaptation? Empirical investigation using RADseq in a northern lacustrine fish
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Data from: The accumulation of deleterious mutations as a consequence of domestication and improvement in sunflowers and other Compositae crops
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Accumulation of deleterious mutations in landlocked threespine stickleback populations
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Data from: Somatic deleterious mutation rate in a woody plant: estimation from phenotypic data
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Data from: Accumulation of deleterious mutations on the neo-Y chromosome of Japan sea stickleback (Gasterosteus nipponicus)
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