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97 results for “genetic variance”
Data from: Can dominance genetic variance be ignored in evolutionary quantitative genetic analyses of wild populations?
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Data from: Hidden genetic variance contributes to increase the short-term adaptive potential of selfing populations
Standing genetic variation is considered a major contributor to the adaptive potential of species. The low heritable genetic variation observed in self-fertilising populations has led to the hypothesis that species with this mating system would be less likely to adapt. However, a non-negligible amount of cryptic genetic variation for polygenic traits, accumulated through negative linkage disequilibrium, could prove to be an important source of standing variation in self-fertilising species. To test this hypothesis we simulated populations under stabilizing selection subjected to an environmental change. We demonstrate that, when the mutation rate is high (but realistic), selfing populations are better able to store genetic variance than outcrossing populations through genetic associations, notably due to the reduced effective recombination rate associated with predominant selfing. Following an environmental shift, this diversity can be partially remobilized, which increases the additive variance and adaptive potential of predominantly (but not completely) selfing populations. In such conditions, despite initially lower observed genetic variance, selfing populations adapt as readily as outcrossing ones within a few generations. For low mutation rates, purifying selection impedes the storage of diversity through genetic associations, in which case, as previously predicted, the lower genetic variance of selfing populations results in lower adaptability compared to their outcrossing counterparts. The population size and the mutation rate are the main parameters to consider, as they are the best predictors of the amount of stored diversity in selfing populations. Our results and their impact on our knowledge of adaptation under high selfing rates are discussed.
Data from Koch et al. 2020 Evolution: Genetic variance in fitness and its cross-sex covariance predict adaptation during experimental evolution.
<p><strong>Abstract</strong></p> <p>In presence of rapid environmental changes, it is of particular importance to assess the adaptive potential of populations, which is mostly determined by the additive genetic variation (V<sub>A</sub>) in fitness. In this study we used <em>Tribolium castaneum </em>(red flour beetles) to investigate its adaptive potential in three new environmental conditions (Dry, Hot, Hot-Dry). We tested for potential constraints that might limit adaptation, including negative genetic covariance between female and male fitness. Based on V<sub>A</sub> estimates for fitness, we expected the highest relative fitness increase in the most stressful condition Hot-Dry and similar increases in single stress conditions Dry and Hot. High adaptive potential in females in Hot was reduced by a negative covariance with male fitness. We tested adaptation to the three conditions after 20 generations of experimental evolution and found that observed adaptation mainly matched our predictions. Given that body size is commonly used as a proxy for fitness, we also tested how this trait and its genetic variance (including non-additive genetic variance) were impacted by environmental stress. In both traits, variances were sex and condition dependent, but they differed in their variance composition, cross-sex and cross-environment genetic covariances, as well as in the environmental impact on V<sub>A</sub>.</p> <p> </p> <p><strong>Method</strong></p> <p><em>Strain and environmental conditions</em></p> <p>We used the <em>Tribolium castaneum</em> Cro1 strain collected from a wild population in 2010 and adapted to lab standard conditions (33°C, 70% relative humidity) for more than 20 generations. Beetles were kept in 24h darkness on organic wheat flour mixed with 10% organic baker's yeast. We sterilized flour and yeast by heating them for 12h at 80°C before use. To test for adaptation to new environmental conditions we used replicate lines and exposed them to three treatments and Control conditions. The conditions in the treatments were: Dry: 33°C and 30% relative humidity; Hot: 37°C and 70% r. h.; Hot-Dry: 37°C and 30% r. h.</p> <p> </p> <p><em>Crossing, fitness assay and measurement of body size</em></p> <p>In order to be able to estimate genetic variances, we applied a split-brood paternal half-sib breeding design. We produced 147 half-sib families by mating virgin males to three virgin females. Half- as well as full-sib families were split across all conditions. Male and female offspring (four females and two males per full-sib family and condition) were separated at the pupal stage and transferred to 10 mL tubes with 1 g of medium and remained there until they were used for the fitness assay eight weeks later.</p> <p>To estimate fitness, we mated each virgin male with two unrelated virgin females from the same condition in 15mL tube with 1g medium. The male was removed after 24h and females transferred into two separate tubes. Females were removed from the tubes after one week of egg laying, and 9g medium was added to provide food for the developing offspring. After five weeks the number of adult offspring was counted. While we conducted the matings for the fitness assay, we followed a specific crossing design and always crossed two pairs of full-sib families. Individuals resulting from these crosses (the F2 genaration) were double first cousins.</p> <p>Body size was measured in the F2, i.e. in the offspring of beetles that were used for the fitness assay. To estimate body size, we used the centroid size of the abdominal segment IV as proxy for total size since it can be measured more accurately than dry weight in very small insects and shows a high correlation with body mass.</p> <p> </p> <p><em>Experimental evolution</em></p> <p>We used ten replicate lines per condition originating from the same ancestral population (Cro1) and let them adapt for 20 generations. Each new generation was set up by randomly selecting 120 pupae and placing them into a new vial with 70g medium. One selection line in Dry became extinct. Adult beetles of generation 20 from all selection lines were transferred to control conditions, in which they stayed for one week to mate and lay eggs. After removal of the adults, we waited until their offspring had reached the pupal stage and separated males and females. These individuals (generation 21) developed completely in control conditions. When they had reached the adult stage, each virgin male was mated with a virgin female of the same selection line and their offspring was transferred to all four conditions in the egg stage, resulting in full-sib families split across all conditions . As soon as these offspring (generation 22) had reached the pupal stage, males and females were separated. To compare fitness of different selection lines and test for adaptation, a virgin male and a virgin female of the same selection line in the same condition, but from different families were mated and the number of adult offspring produced within four days of mating and egg laying was used as a fitness estimate.</p> <p> </p> <p> </p> <p><strong>Files</strong></p> <p>This data publication contains the following files:</p> <p>Fitness_data.txt: Fitness data (offspring number) of the first generation in new environmental conditions.</p> <p>ANIMAL: ID of female individuals; male: ID of mating partner, father of the offspring; fitness: number of adult offspring per female produced within one week of egg laying; condition: condition under which the individuals grew up, mated, reproduced (CTL: control, D: dry, H: hot, HD: hot-dry, see Methods for details); MOTHER: mother of the female; Batch: samples where fitness assay was started on the same day</p> <p> </p> <p>Size_data.txt: Centroid size of abdominal segment IV.</p> <p>ANIMAL: ID of measured individuals; condition: condition under which the individuals grew up (CT: control, D: dry, H: hot, HD: hot-dry, see Methods for details); sex: sex of individuals (f: female, m: male); AS: centroid size [Pixel] of abdominal segment IV; Mother: ID of their mother; batch: Batches represent individuals that grew up at the same time, and thus accounts for variations in the medium or lab temperature</p> <p> </p> <p>Pedigree.txt: Pedigree of measured individuals.</p> <p>ANIMAL: individual ID ; MOTHER: mother ID; FATHER: father ID</p> <p> </p> <p>Transplant_data.txt: Offspring number of different selection lines under different conditions after 20 generations of experimental evolution.</p> <p>Line: Selection-line ID; Selection: condition, in which the selection-line spent 20 generations (CT: Control; D: Dry; Hot; HD: Hot-Dry); Fam: each selection line consisted of several families; Treatment: condition, in which offspring number was measured; offspring: number of adult offspring that a female produced within four days of egg-laying</p>
Data from: Short-term effects of controlled mating and selection on the genetic variance of honeybee populations
<p>Directional selection in a population yields reduced genetic variance due to the Bulmer effect. While this effect has been thoroughly investigated in mammals, it is poorly studied in social insects with biological peculiarities such as haplo-diploidy or the collective expression of traits. In addition to natural adaptation to climate change, parasites, and pesticides, honeybees increasingly experience artificial selection pressure through modern breeding programs. Besides selection, many honeybee breeding schemes introduce controlled mating. We investigated which individual effects selection and controlled mating have on genetic variance. We derived formulas to describe short-term changes of genetic variance in honeybee populations and conducted computer simulations to confirm them. Thereby, we found that the changes in genetic variance depend on whether variance is measured between queens (inheritance criterion), worker groups (selection criterion) or both (performance criterion). All three criteria showed reduced genetic variance under selection. In the selection and performance criteria, our formulas and simulations showed an increased genetic variance through controlled mating.<br> This newly described effect counterbalanced and occasionally outweighed the Bulmer effect. It could not be observed in the inheritance criterion. A good understanding of the different notions of genetic variance in honeybees therefore appears crucial to interpret population parameters correctly.</p>
Data from: Additive genetic variance and developmental plasticity in growth trajectories in a wild cooperative mammal
Individual variation in growth is high in cooperative breeders and may reflect plastic divergence in developmental trajectories leading to breeding vs. helping phenotypes. However, the relative importance of additive genetic variance and developmental plasticity in shaping growth trajectories is largely unknown in cooperative vertebrates. This study exploits weekly sequences of body mass from birth to adulthood to investigate sources of variance in, and covariance between, early and later growth in wild meerkats (Suricata suricatta), a cooperative mongoose. Our results indicate that (i) the correlation between early growth (prior to nutritional independence) and adult mass is positive but weak, and there are frequent changes (compensatory growth) in post-independence growth trajectories; (ii) among parameters describing growth trajectories, those describing growth rate (prior to and at nutritional independence) show undetectable heritability while associated size parameters (mass at nutritional independence and asymptotic mass) are moderately heritable (0.09 ≤ h2 < 0.3); and (iii) additive genetic effects, rather than early environmental effects, mediate the covariance between early growth and adult mass. These results reveal that meerkat growth trajectories remain plastic throughout development, rather than showing early and irreversible divergence, and that the weak effects of early growth on adult mass, an important determinant of breeding success, are partly genetic. In contrast to most cooperative invertebrates, the acquisition of breeding status is often determined after sexual maturity and strongly impacted by chance in many cooperative vertebrates, who may therefore retain the ability to adjust their morphology to environmental changes and social opportunities arising throughout their development, rather than specializing early.
Data from: The genetic structure of Asian corn borer, Ostrinia furnacalis, populations in China: haplotype variance in Northern populations and potential impact on management of resistance to transgenic maize
Asian corn borer, Ostrinia furnacalis (Guenée), is a severe pest that infests cultivated maize in the major production regions of China. Populations show genotype-by-environment variation in voltinism, such that populations with a single generation (univoltine) are fixed in Northern China where growing seasons are short. Low genetic differentiation was found among samples from 33 collection sites across China and one site from North Korea (n = 1,673) using variation at 6 nuclear microsatellite loci (ENA corrected global FST = 0.020; P-value < 0.05). Analysis of molecular variance (AMOVA) indicated that geographic region, number of generations or voltinism accounted for < 0.38% of the total genetic variation at nuclear loci and was corroborated by clustering of co-ancestries among genotypes using the program STRUCTURE. In contrast, a mitochondrial haplotype network identified four distinct clusters, where 70.5% of samples from univoltine populations were within a single group. Univoltine populations were also placed into a unique cluster using Population Graph and Principal Component analyses, which showed significant differentiation with multivoltine populations (ST = 0.400; P-value < 0.01). This study suggests that gene flow among O. furnacalis in China may be high among regions, with the exception of northeastern localities. Haplotype variation may be due to random genetic drift resulting from partial reproductive isolation between univoltine and multivoltine O. furnacalis populations. Such reproductive isolation might impact the potential spread of alleles that confer resistance to transgenic maize in China.
Data from: Genetic correlations and little genetic variance for reaction norms may limit potential for adaptation to pollution by ionic and nanoparticulate silver in a whitefish (Salmonidae)
For natural populations to adapt to anthropogenic threats, heritable variation must persist in tolerance traits. Silver nanoparticles, the most widely used engineered nanoparticles, are expected to increase in concentrations in freshwaters. Little is known about how these particles affect wild populations, and whether genetic variation persists in tolerance to permit rapid evolutionary responses. We sampled wild adult whitefish and crossed them in vitro full factorially. In total, 2896 singly raised embryos of 48 families were exposed to two concentrations (0.5 μg/L; 100 μg/L) of differently sized silver nanoparticles or ions (silver nitrate). These doses were not lethal; yet higher concentrations prompted embryos to hatch earlier and at a smaller size. The induced hatching did not vary with nanoparticle size and was stronger in the silver nitrate group. Additive genetic variation for hatching time was significant across all treatments, with no apparent environmental dependencies. No genetic variation was found for hatching plasticity. We found some treatment-dependent heritable variation for larval length and yolk volume, and one instance of additive genetic variation for the reaction norm on length at hatching. Our assessment suggests that the effects of silver exposure on additive genetic variation vary according to trait and silver source. While the long-term fitness consequences of low-level silver exposure on whitefish embryos must be further investigated to determine whether it is, in fact, detrimental, our results suggest that the evolutionary potential for adaptation to these types of pollutants may be low.
Data from: Quantitative genetic divergence and standing genetic (co)variance in thermal reaction norms along latitude
Although the potential to adapt to warmer climate is constrained by genetic trade-offs, our understanding of how selection and mutation shape genetic (co)variances in thermal reaction norms is poor. Using 71 isofemale lines of the fly Sepsis punctum, originating from northern, central and southern European climates, we tested for divergence in juvenile development rate across latitude at five experimental temperatures. To investigate effects of evolutionary history in different climates on standing genetic variation in reaction norms, we further compared genetic (co)variances between regions. Flies were reared on either high or low food resources to explore the role of energy-acquisition in determining genetic trade-offs between different temperatures. Although the latter had only weak effects on the strength and sign of genetic correlations, genetic architecture differed significantly between climatic regions, implying that evolution of reaction norms proceeds via different trajectories at high versus low latitude in this system. Accordingly, regional genetic architecture was correlated to region-specific differentiation. Moreover, hot development temperatures were associated with low genetic variance and stronger genetic correlations compared to cooler temperatures. We discuss the evolutionary potential of thermal reaction norms in light of their underlying genetic architectures, evolutionary histories and the materialization of trade-offs in natural environments.
Data from: Genetic basis of between-individual and within-individual variance of docility
Between-individual variation in phenotypes within a population is the basis of evolution. However, evolutionary and behavioural ecologists have mainly focused on estimating between-individual variance in mean trait and neglected variation in within-individual variance, or predictability of a trait. In fact, an important assumption of mixed-effects models used to estimate between-individual variance in mean traits is that within-individual residual variance (predictability) is identical across individuals. Individual heterogeneity in the predictability of behaviours is a potentially important effect but rarely estimated and accounted for. We used 11,389 measures of docility behaviour from 1,576 yellow-bellied marmots (Marmota flaviventris) to estimate between-individual variation in both mean docility and its predictability. We then implemented a double hierarchical animal model to decompose the variances of both mean trait and predictability into their environmental and genetic components. We found that individuals differed both in their docility and in their predictability of docility with a negative phenotypic covariance. We also found significant genetic variance for both mean docility and its predictability but no genetic covariance between the two. This analysis is one of the first to estimate the genetic basis of both mean trait and within-individual variance in a wild population. Our results indicate that equal within-individual variance should not be assumed. We demonstrate the evolutionary importance of the variation in the predictability of docility, and illustrate potential bias in models ignoring variation in predictability. We conclude that the variability in the predictability of a trait should not be ignored, and present a coherent approach for its quantification.
Data from: Metapopulation patterns of additive and nonadditive genetic variance in the sea bass (Dicentrarchus labrax)
Describing and explaining the geographic within-species variation in phenotypes ("phenogeography") in the sea over a species distribution range is central to our understanding of a variety of eco-evolutionary topics. However, phenogeographic studies that have a large potential to investigate adaptive variation are overcome by phylogeographic studies, still mainly focusing on neutral markers. How genotypic and phenotypic data could covary over large geographic scales remains poorly understood in marine species. We crossed 75 noninbred sires (five origins) and 26 dams (two origins; each side of a hybrid zone) in a factorial diallel cross in order to investigate geographic variation for early survival and sex ratio in the metapopulation of the European sea bass (Dicentrarchus labrax), a highly prized marine fish species. Full-sib families (N = 1,950) were produced and reared in a common environment. Parentage assignment of 7,200 individuals was performed with seven microsatellite markers. Generalized linear models showed significant additive effects for both traits and pleiotropy between traits. A significant nonadditive genetic effect was detected. Different expression of traits and distinct relative performances were found for reciprocal crosses involving populations located on each side of the main hybrid zone located at the Almeria-Oran front, illustrating asymmetric reproductive isolation. The poor fitness performance observed for the Western Mediterranean population of sea bass is discussed as it represents the main source of seed hatchery production, but also because it potentially illustrates nonadaptive introgression and maladaptation.
Data from: Evolution of genetic variance during adaptive radiation
Genetic correlations between traits can concentrate genetic variance into fewer phenotypic dimensions that can bias evolutionary trajectories along the axis of greatest genetic variance and away from optimal phenotypes, constraining the rate of evolution. If genetic correlations limit adaptation, rapid adaptive divergence between multiple contrasting environments may be difficult. However, if natural selection increases the frequency of rare alleles after colonisation of new environments, an increase in genetic variance in the direction of selection can accelerate adaptive divergence. Here, we explored adaptive divergence of an Australian native wildflower by examining the alignment between divergence in phenotype mean and divergence in genetic variance among four contrasting ecotypes. We found divergence in mean multivariate phenotype along two major axes represented by different combinations of plant architecture and leaf traits. Ecotypes also showed divergence in the level of genetic variance in individual traits, and the multivariate distribution of genetic variance among traits. Divergence in multivariate phenotypic mean aligned with divergence in genetic variance, with much of the divergence in phenotype among ecotypes associated with changes in trait combinations containing substantial levels of genetic variance. Overall, our results suggest that natural selection can alter the distribution of genetic variance underlying phenotypic traits, increasing the amount of genetic variance in the direction of natural selection and potentially facilitating rapid adaptive divergence during an adaptive radiation.
Data from: Female and male genetic effects on offspring paternity: additive genetic (co)variances in female extra-pair reproduction and male paternity success in song sparrows (Melospiza melodia)
Ongoing evolution of polyandry, and consequent extra-pair reproduction in socially monogamous systems, is hypothesised to be facilitated by indirect selection stemming from cross-sex genetic covariances with components of male fitness. Specifically, polyandry is hypothesised to create positive genetic covariance with male paternity success due to inevitable assortative reproduction, driving ongoing coevolution. However, it remains unclear whether such covariances could or do emerge within complex polyandrous systems. First, we illustrate that genetic covariances between female extra-pair reproduction and male within-pair paternity success might be constrained in socially monogamous systems where female and male additive genetic effects can have opposing impacts on the paternity of jointly reared offspring. Second, we demonstrate non-zero additive genetic variance in female liability for extra-pair reproduction and male liability for within-pair paternity success, modelled as direct and associative genetic effects on offspring paternity respectively, in free-living song sparrows (Melospiza melodia). The posterior mean additive genetic covariance between these liabilities was slightly positive, but the credible interval was wide and overlapped zero. Therefore, while substantial total additive genetic variance exists, the hypothesis that ongoing evolution of female extra-pair reproduction is facilitated by genetic covariance with male within-pair paternity success cannot yet be definitively supported or rejected either conceptually or empirically.
Data and R scripts supporting the article: "Evolution of genetic (co)variances during the worldwide invasion of Drosophila suzukii"
<p>This repository contains raw data, processed data (.RData files) and R scripts necessary to replicate the analyses, figures and tables from the manuscript "Evolution of genetic (co)variances during the worldwide invasion of Drosophila suzukii" (Fraimout, A., Chantepie, S., Navarro, N., Teplitsky, C. & Debat, V.).</p> <p>Each R script contains detailed information about the location of each analysis in the manuscript (i.e., line numbering and paragraph title as in Fraimout et al. 2024: https://www.biorxiv.org/content/10.1101/2024.01.02.573869v1)</p>
Genetic and environmental variance of semen quality in Nordic Holstein bulls
<p>Figure S1. Plots of genetic Variance at different age (month) for the semen quality traits. Va: genetic variance, Conc= concentration; Pre= pre-cryopreservation; post= post-cryopreservation; Mot= sperm motility; Via= sperm viability; NDOS= number of doses per ejaculate.</p> <p>Figure S2. Permanent environment Variance at different age (month). Vpe: permanent environment variance, Conc= concentration; Pre= pre-cryopreservation; post= post-cryopreservation; Mot= sperm motility; Via= sperm viability; NDOS= number of doses per ejaculate.</p> <p>Figure S3. Residual Variance at different age (month). Ve= residual variance, Conc= concentration; Pre= pre-cryopreservation; post= post-cryopreservation; Mot= sperm motility; Via= sperm.</p>
Data from: The genetic variance but not the genetic covariance of life-history traits changes towards the north in a time-constrained insect
Seasonal time constraints are usually stronger at higher than lower latitudes and can exert strong selection on life history traits and the correlations among these traits. To predict the response of life history traits to environmental change along a latitudinal gradient, information must be obtained about genetic variance in traits and also genetic correlation between traits, i.e., the genetic variance-covariance matrix, G. Here, we estimated G for key life history traits in an obligate univoltine damselfly that faces seasonal time constraints. We exposed populations to simulated native temperatures and photoperiods and common garden environmental conditions in a laboratory setup. Despite differences in genetic variance in these traits between populations (lower variance at northern latitudes), there was no evidence for latitude-specific covariance of the life history traits. At simulated native conditions, all populations showed strong genetic and phenotypic correlations between traits that shaped growth and development. The variance-covariance matrix changed considerably when populations were exposed to common garden conditions compared with the simulated natural conditions, showing the importance of environmentally induced changes in multivariate genetic structure. Our results highlight the importance of estimating variance-covariance matrixes in environments that mimic selection pressures and not only trait variances or mean trait values in common garden conditions for understanding the trait evolution across populations and environments.
Sex-specific genetic (co)variances of standard metabolic rate, body mass and locomotor activity in Drosophila melanogaster
<p>A longstanding focus in evolutionary physiology concerns the causes and consequences of variation in maintenance metabolism. Insight into this can be gained by estimating the sex-specific genetic architecture of maintenance metabolism alongside other, potentially correlated traits on which selection may also act, such as body mass and locomotor activity. This may reveal potential genetic constraints affecting the evolution of maintenance metabolism. Here, we used a half-sibling breeding design to quantify the sex-specific patterns of genetic (co)variance in standard metabolic rate (SMR), body mass, and daily locomotor activity in <i>Drosophila melanogaster</i>. There was detectable additive genetic variance for all traits in both sexes. As expected, SMR and body mass were strongly and positively correlated, with genetic allometry exponents (<i>b</i><sub>A</sub>±se) of 0.66±0.16 in females and 0.58±0.32 in males. There was a significant and positive genetic correlation between SMR and locomotor activity in males, suggesting that alleles that increase locomotion have pleiotropic effects on SMR. Sexual differences in the genetic architecture were driven in large part by a difference in genetic variance in locomotor activity between the sexes. Overall, genetic variation was mostly shared between males and females, setting the stage for a potential intralocus sexual conflict in the face of sexually antagonistic selection.</p>
Data from: Colour ornamentation in the blue tit: quantitative genetic (co)variances across sexes
Although secondary sexual traits are commonly more developed in males than females, in many animal species females also display elaborate ornaments or weaponry. Indirect selection on correlated traits in males and/or direct sexual or social selection in females are hypothesized to drive the evolution and maintenance of female ornaments. Yet, the relative roles of these evolutionary processes remain unidentified, because little is known about the genetic correlation that might exist between the ornaments of both sexes, and few estimates of sex-specific autosomal or sex-linked genetic variances are available. In this study, we used two wild blue tit populations with 9 years of measurements on two colour ornaments: one structurally based (blue crown) and one carotenoid based (yellow chest). We found significant autosomal heritability for the chromatic part of the structurally based colouration in both sexes, whereas carotenoid chroma was heritable only in males, and the achromatic part of both colour patches was mostly non heritable. Power limitations, which are probably common among most data sets collected so far in wild populations, prevented estimation of sex-linked genetic variance. Bivariate analyses revealed very strong cross-sex genetic correlations in all heritable traits, although the strength of these correlations was not related to the level of sexual dimorphism. In total, our results suggest that males and females share a majority of their genetic variation underlying colour ornamentation, and hence the evolution of these sex-specific traits may depend greatly on correlated responses to selection in the opposite sex.
Genetic & Environmental Determinants Of Immune Phenotype Variance: A Longitudinal Assessment
ClinicalTrials.gov study NCT05381857. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Genetic & Environmental Determinants Of Immune Phenotype Variance: Establishing A Path Towards Personalized Medicine
ClinicalTrials.gov study NCT01699893. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Data from: Genetic basis of between-individual and within-individual variance of docility
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