Phenotypic plasticity for life-history traits in Drosophila melanogaster. III. Effect of the environment on genetic parameters

SummaryWe estimated genetic and environmental variance components for developmental time and dry weight at eclosion in Drosophila melanogaster raised in ten different environments (all combinations of 22, 25 and 28°C and 0·5, 1 and 4% yeast concentration, and 0·25% yeast at 25°C). We used six homozygous lines derived from a natural population for complete diallel crosses in each environment. Additive genetic variances were consistently low for both traits (h2 around 10%). The additive genetic variance of developmental time was larger at lower yeast concentrations, but the heritability did not increase because other components were also larger. The additive genetic effects of the six parental lines changed ranks across environments, suggesting a mechanism for the maintenance of genetic variation in heterogenous environments.The variance due to non-directional dominance was small in most environments. However, there was directional dominance in the form of inbreeding depression for both traits. It was pronounced at high yeast levels and temperatures but disappeared when yeast or temperature were decreased. This meant that the heterozygous flies were more sensitive to environmental differences than homozygous flies. Because dominance effects are not heritable, this suggests that the evolution of plasticity can be constrained when dominance effects are important as a mechanism for plasticity.

Download Full-text

Age-Specific Patterns of Genetic Variance in Drosophila melanogaster. II. Fecundity and Its Genetic Covariance With Age-Specific Mortality

Genetics ◽

10.1093/genetics/143.2.849 ◽

1996 ◽

Vol 143 (2) ◽

pp. 849-858 ◽

Cited By ~ 5

Author(s):

Marc Tatar ◽

Daniel E L Promislow ◽

Aziz A Khazaeli ◽

James W Curtsinger

Keyword(s):

Drosophila Melanogaster ◽

Variance Components ◽

Life History Traits ◽

Genetic Variance ◽

Additive Genetic Variance ◽

Genetic Correlations ◽

Mutation Accumulation ◽

Age Classes ◽

Genetic Covariance ◽

Specific Mortality

Abstract Under the mutation accumulation model of senescence, it was predicted that the additive genetic variance (VA) for fitness traits will increase with age. We measured age-specific mortality and fecundity from 65,134 Drosophila melanogaster and estimated genetic variance components, based on reciprocal crosses of extracted second chromosome lines. Elsewhere we report the results for mortality. Here, for fecundity, we report a bimodal pattern for VA with peaks at 3 days and at 17–31 days. Under the antagonistic pleiotropy model of senescence, it was predicted that negative correlations will exist between early and late life history traits. For fecundity itself we find positive genetic correlations among age classes >3 days but negative nonsignificant correlations between fecundity at 3 days and at older age classes. For fecundity vs. age-specific mortality, we find positive fitness correlations (negative genetic correlations) among the traits at all ages >3 days but a negative fitness correlation between fecundity at 3 days and mortality at the oldest ages (positive genetic correlations). For age-specific mortality itself we find overwhelmingly positive genetic correlations among all age classes. The data suggest that mutation accumulation may be a major source of standing genetic variance for senescence.

Download Full-text

Effects of stress combinations on the expression of additive genetic variation for fecundity in Drosophila melanogaster

Genetics Research ◽

10.1017/s0016672398003310 ◽

1998 ◽

Vol 72 (1) ◽

pp. 13-18 ◽

Cited By ~ 29

Author(s):

CARLA M. SGRÒ ◽

ARY A. HOFFMANN

Keyword(s):

Drosophila Melanogaster ◽

Genetic Variance ◽

Cold Shock ◽

Additive Genetic Variance ◽

Combined Stress ◽

Heritable Variation ◽

Environmental Variance ◽

Apparent Increase ◽

Nutrition Environment ◽

Stress Combinations

To test whether stressful conditions altered levels of heritable variation in fecundity in Drosophila melanogaster, parent–offspring comparisons were undertaken across three generations for flies reared in a combined stress (ethanol, cold shock, low nutrition) environment or a control environment. The stressful conditions did not directly influence fecundity but did lead to a reduced fecundity in the offspring generations, perhaps reflecting cross-generation maternal effects. Both the heritability and evolvability estimates were higher in the combined stress treatment, reflecting an apparent increase in the additive genetic variance under stress. In contrast, there were no consistent changes in the environmental variance across environments.

Download Full-text

Alternative life histories in the Atlantic salmon: genetic covariances within the sneaker sexual tactic in males

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2010.2045 ◽

2010 ◽

Vol 278 (1715) ◽

pp. 2150-2158 ◽

Cited By ~ 18

Author(s):

David James Páez ◽

Louis Bernatchez ◽

Julian J. Dodson

Keyword(s):

Body Size ◽

Atlantic Salmon ◽

Life Histories ◽

Life History Traits ◽

Additive Genetic Variance ◽

Reproductive Tactics ◽

Genetic Covariance ◽

Additive Genetic Effects ◽

Reproductive Tactic ◽

Genetic Covariances

Alternative reproductive tactics are ubiquitous in many species. Tactic expression often depends on whether an individual's condition surpasses thresholds that are responsible for activating particular developmental pathways. Two central goals in understanding the evolution of reproductive tactics are quantifying the extent to which thresholds are explained by additive genetic effects, and describing their covariation with condition-related traits. We monitored the development of early sexual maturation that leads to the sneaker reproductive tactic in Atlantic salmon ( Salmo salar L.). We found evidence for additive genetic variance in the timing of sexual maturity (which is a measure of the surpassing of threshold values) and body-size traits. This suggests that selection can affect the patterns of sexual development by changing the timing of this event and/or body size. Significant levels of covariation between these traits also occurred, implying a potential for correlated responses to selection. Closer examination of genetic covariances suggests that the detected genetic variation is distributed along at least five directions of phenotypic variation. Our results show that the potential for evolution of the life-history traits constituting this reproductive phenotype is greatly influenced by their patterns of genetic covariance.

Download Full-text

The Changes in Genetic and Environmental Variance With Inbreeding in Drosophila melanogaster

Genetics ◽

10.1093/genetics/152.1.345 ◽

1999 ◽

Vol 152 (1) ◽

pp. 345-353 ◽

Cited By ~ 3

Author(s):

Michael C Whitlock ◽

Kevin Fowler

Keyword(s):

Drosophila Melanogaster ◽

Large Scale ◽

Genetic Variance ◽

Additive Genetic Variance ◽

Inbred Lines ◽

Residual Variance ◽

Phenotypic Variance ◽

Population Bottlenecks ◽

Environmental Variance ◽

Components Of Variance

Abstract We performed a large-scale experiment on the effects of inbreeding and population bottlenecks on the additive genetic and environmental variance for morphological traits in Drosophila melanogaster. Fifty-two inbred lines were created from the progeny of single pairs, and 90 parent-offspring families on average were measured in each of these lines for six wing size and shape traits, as well as 1945 families from the outbred population from which the lines were derived. The amount of additive genetic variance has been observed to increase after such population bottlenecks in other studies; in contrast here the mean change in additive genetic variance was in very good agreement with classical additive theory, decreasing proportionally to the inbreeding coefficient of the lines. The residual, probably environmental, variance increased on average after inbreeding. Both components of variance were highly variable among inbred lines, with increases and decreases recorded for both. The variance among lines in the residual variance provides some evidence for a genetic basis of developmental stability. Changes in the phenotypic variance of these traits are largely due to changes in the genetic variance.

Download Full-text

Estimation of additive and dominance variance for litter size components in rabbits

Czech Journal of Animal Science ◽

10.17221/7342-cjas ◽

2014 ◽

Vol 59 (No. 4) ◽

pp. 182-189 ◽

Cited By ~ 7

Author(s):

I. Nagy ◽

J. Farkas ◽

I. Curik ◽

G. Gorjanc ◽

P. Gyovai ◽

...

Keyword(s):

Environmental Effects ◽

Variance Components ◽

Correlation Coefficients ◽

Data File ◽

Breeding Value ◽

Environmental Variance ◽

Relative Significance ◽

Breeding Values ◽

Dead Animal ◽

Additive Genetic Effects

Additive, dominance, and permanent environmental variance components were estimated for the number of kits born alive, number of kits born dead, and total number of kits born of a synthetic rabbit line (called Pannon Ka). The data file consisted of 11 582 kindling records of 2620 does collected between the years 1996–2013. The total number of animals in the pedigree files was 4012. The examined traits were evaluated using single-trait and two-trait (number of kits born alive-dead) animal models containing all or part of the following effects: additive genetic effects, permanent environmental effects, dominance effects. Heritability estimates calculated using the basic single-trait and two-trait models were 0.094 ± 0.018 and 0.090 ± 0.016 for number of kits born alive, 0.037 ± 0.010 and 0.041 ± 0.012 for number of kits born dead, and 0.117 ± 0.018 for total number of kits born, respectively. The relative significance of permanent environmental effects was 0.069 ± 0.014 and 0.069 ± 0.012 for number of kits born alive, 0.025 ± 0.011 and 0.023 ± 0.010 for number of kits born dead, and 0.060 ± 0.013 for total number of kits born, respectively. Using the extended single-trait and two-trait models, the ratios of the dominance components compared to the phenotypic variances were 0.048 ± 0.008 and 0.046 ± 0.007 for number of kits born alive, 0.068 ± 0.006 and 0.065 ± 0.006 for number of kits born dead, and 0.005 ± 0.0073 for total number of kits born, respectively. Genetic correlation coefficients between number of kits born alive and number of kits born dead were 0.401 ± 0.171 and 0.521 ± 0.182, respectively. Spearman’s rank correlations between the breeding values of the different single-trait models were close to unity in all traits (0.992–0.990). Much lower breeding value stability was found for two-trait models (0.384–0.898), especially for number of kits born dead. Results showed that the dominance components for number of kits born alive and number of kits born dead were not zero and affected the ranking of the animals (based on the breeding values).  

Download Full-text

Increased selection response in larger populations. II. Selection for ethanol vapor resistance in Drosophila melanogaster at two population sizes.

Genetics ◽

10.1093/genetics/125.3.585 ◽

1990 ◽

Vol 125 (3) ◽

pp. 585-597 ◽

Cited By ~ 7

Author(s):

K E Weber ◽

L T Diggins

Keyword(s):

Drosophila Melanogaster ◽

Population Size ◽

Additive Genetic Variance ◽

Large Population ◽

Ethanol Vapor ◽

Selection Response ◽

Environmental Variance ◽

Final Treatment ◽

Population Sizes ◽

The Difference

Abstract The effect of large population size on selection response was investigated using Drosophila melanogaster, with four "small" lines of 160 selected parents/generation compared to two "large" lines of 1,600 selected parents/generation. All lines were selected under similar conditions at a selection intensity of approximately 0.55 standard deviations, for 65 generations, for increased ethanol vapor resistance (measured in minutes required to become anesthetized). Two unselected control lines of 320 parents/generation were also maintained. A significant effect of population size was found. The final treatment means and standard errors were: 27.91 +/- 1.28 min (two "large" lines); 19.40 +/- 1.54 min (four "small" lines); and 4.98 +/- 0.35 min (two control lines). To estimate the mutation rate for the trait, two isogenic lines of about 400 selected parents were selected for 29 generations. The mean increase in additive genetic variance per generation was 0.0009 times the initial environmental variance of the outbred lines. This is comparable to other reported mutation rates. Mutation can explain part of the difference in evolved resistance between treatments, but it appears that even at rather large population sizes, a large difference in long-term response can be obtained in larger outbred lines, from more complete utilization of the initial genetic variation.

Download Full-text

SNP-based mate allocation strategies to maximize total genetic value in pigs

Genetics Selection Evolution ◽

10.1186/s12711-019-0498-y ◽

2019 ◽

Vol 51 (1) ◽

Cited By ~ 1

Author(s):

David González-Diéguez ◽

Llibertat Tusell ◽

Céline Carillier-Jacquin ◽

Alban Bouquet ◽

Zulma G. Vitezica

Keyword(s):

Inbreeding Depression ◽

Genetic Gain ◽

Variance Components ◽

Genetic Variance ◽

Additive Genetic Variance ◽

Genetic Effects ◽

Breeding Values ◽

Genetic Merit ◽

Additive Genetic Effects ◽

Allocation Strategies

Abstract Background Mate allocation strategies that account for non-additive genetic effects can be used to maximize the overall genetic merit of future offspring. Accounting for dominance effects in genetic evaluations is easier in a genomic context, than in a classical pedigree-based context because the combinations of alleles at loci are known. The objective of our study was two-fold. First, dominance variance components were estimated for age at 100 kg (AGE), backfat depth (BD) at 140 days, and for average piglet weight at birth within litter (APWL). Second, the efficiency of mate allocation strategies that account for dominance and inbreeding depression to maximize the overall genetic merit of future offspring was explored. Results Genetic variance components were estimated using genomic models that included inbreeding depression with and without non-additive genetic effects (dominance). Models that included dominance effects did not fit the data better than the genomic additive model. Estimates of dominance variances, expressed as a percentage of additive genetic variance, were 20, 11, and 12% for AGE, BD, and APWL, respectively. Estimates of additive and dominance single nucleotide polymorphism effects were retrieved from the genetic variance component estimates and used to predict the outcome of matings in terms of total genetic and breeding values. Maximizing total genetic values instead of breeding values in matings gave the progeny an average advantage of − 0.79 days, − 0.04 mm, and 11.3 g for AGE, BD and APWL, respectively, but slightly reduced the expected additive genetic gain, e.g. by 1.8% for AGE. Conclusions Genomic mate allocation accounting for non-additive genetic effects is a feasible and potential strategy to improve the performance of the offspring without dramatically compromising additive genetic gain.

Download Full-text

Whole-Genome Effects of Ethyl Methanesulfonate-Induced Mutation on Nine Quantitative Traits in Outbred Drosophila melanogaster

Genetics ◽

10.1093/genetics/157.3.1257 ◽

2001 ◽

Vol 157 (3) ◽

pp. 1257-1265 ◽

Cited By ~ 3

Author(s):

Hsiao-Pei Yang ◽

Ana Y Tanikawa ◽

Wayne A Van Voorhies ◽

Joana C Silva ◽

Alexey S Kondrashov

Keyword(s):

Drosophila Melanogaster ◽

Quantitative Traits ◽

Spontaneous Mutation ◽

Developmental Time ◽

Ethyl Methanesulfonate ◽

Induced Mutations ◽

Mean Values ◽

Eye Color ◽

Recessive Mutations ◽

The Mean

Abstract We induced mutations in Drosophila melanogaster males by treating them with 21.2 mm ethyl methanesulfonate (EMS). Nine quantitative traits (developmental time, viability, fecundity, longevity, metabolic rate, motility, body weight, and abdominal and sternopleural bristle numbers) were measured in outbred heterozygous F3 (viability) or F2 (all other traits) offspring from the treated males. The mean values of the first four traits, which are all directly related to the life history, were substantially affected by EMS mutagenesis: the developmental time increased while viability, fecundity, and longevity declined. In contrast, the mean values of the other five traits were not significantly affected. Rates of recessive X-linked lethals and of recessive mutations at several loci affecting eye color imply that our EMS treatment was equivalent to ∼100 generations of spontaneous mutation. If so, our data imply that one generation of spontaneous mutation increases the developmental time by 0.09% at 20° and by 0.04% at 25°, and reduces viability under harsh conditions, fecundity, and longevity by 1.35, 0.21, and 0.08%, respectively. Comparison of flies with none, one, and two grandfathers (or greatgrandfathers, in the case of viability) treated with EMS did not reveal any significant epistasis among the induced mutations.

Download Full-text

Genomic prediction with non-additive effects in beef cattle: stability of variance component and genetic effect estimates against population size

BMC Genomics ◽

10.1186/s12864-021-07792-y ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Akio Onogi ◽

Toshio Watanabe ◽

Atsushi Ogino ◽

Kazuhito Kurogi ◽

Kenji Togashi

Keyword(s):

Population Size ◽

Genomic Prediction ◽

Variance Components ◽

Variance Component ◽

Predictive Accuracy ◽

Genetic Effect ◽

Genetic Effects ◽

Additive Effects ◽

Additive Variance ◽

Additive Genetic Effects

Abstract Background Genomic prediction is now an essential technology for genetic improvement in animal and plant breeding. Whereas emphasis has been placed on predicting the breeding values, the prediction of non-additive genetic effects has also been of interest. In this study, we assessed the potential of genomic prediction using non-additive effects for phenotypic prediction in Japanese Black, a beef cattle breed. In addition, we examined the stability of variance component and genetic effect estimates against population size by subsampling with different sample sizes. Results Records of six carcass traits, namely, carcass weight, rib eye area, rib thickness, subcutaneous fat thickness, yield rate and beef marbling score, for 9850 animals were used for analyses. As the non-additive genetic effects, dominance, additive-by-additive, additive-by-dominance and dominance-by-dominance effects were considered. The covariance structures of these genetic effects were defined using genome-wide SNPs. Using single-trait animal models with different combinations of genetic effects, it was found that 12.6–19.5 % of phenotypic variance were occupied by the additive-by-additive variance, whereas little dominance variance was observed. In cross-validation, adding the additive-by-additive effects had little influence on predictive accuracy and bias. Subsampling analyses showed that estimation of the additive-by-additive effects was highly variable when phenotypes were not available. On the other hand, the estimates of the additive-by-additive variance components were less affected by reduction of the population size. Conclusions The six carcass traits of Japanese Black cattle showed moderate or relatively high levels of additive-by-additive variance components, although incorporating the additive-by-additive effects did not improve the predictive accuracy. Subsampling analysis suggested that estimation of the additive-by-additive effects was highly reliant on the phenotypic values of the animals to be estimated, as supported by low off-diagonal values of the relationship matrix. On the other hand, estimates of the additive-by-additive variance components were relatively stable against reduction of the population size compared with the estimates of the corresponding genetic effects.

Download Full-text

A note on genetic parameters and accuracy of estimated breeding values in honey bees

Genetics Selection Evolution ◽

10.1186/s12711-019-0510-6 ◽

2019 ◽

Vol 51 (1) ◽

Cited By ~ 6

Author(s):

Evert W. Brascamp ◽

Piter Bijma

Keyword(s):

Honey Bees ◽

Variance Components ◽

Genetic Parameters ◽

Additive Genetic Variance ◽

Breeding Value ◽

Phenotypic Variance ◽

Breeding Values ◽

Estimated Breeding Values ◽

Additive Genetic Relationship ◽

The Relationship

Abstract Background In honey bees, observations are usually made on colonies. The phenotype of a colony is affected by the average breeding value for the worker effect of the thousands of workers in the colony (the worker group) and by the breeding value for the queen effect of the queen of the colony. Because the worker group consists of multiple individuals, interpretation of the variance components and heritabilities of phenotypes observed on the colony and of the accuracy of selection is not straightforward. The additive genetic variance among worker groups depends on the additive genetic relationship between the drone-producing queens (DPQ) that produce the drones that mate with the queen. Results Here, we clarify how the relatedness between DPQ affects phenotypic variance, heritability and accuracy of the estimated breeding values of replacement queens. Second, we use simulation to investigate the effect of assumptions about the relatedness between DPQ in the base population on estimates of genetic parameters. Relatedness between DPQ in the base generation may differ considerably between populations because of their history. Conclusions Our results show that estimates of (co)variance components and derived genetic parameters were seriously biased (25% too high or too low) when assumptions on the relationship between DPQ in the statistical analysis did not agree with reality.

Download Full-text