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Sample records for additive genetic variances

  1. Estimation of Additive, Dominance, and Imprinting Genetic Variance Using Genomic Data

    PubMed Central

    Lopes, Marcos S.; Bastiaansen, John W. M.; Janss, Luc; Knol, Egbert F.; Bovenhuis, Henk

    2015-01-01

    Traditionally, exploration of genetic variance in humans, plants, and livestock species has been limited mostly to the use of additive effects estimated using pedigree data. However, with the development of dense panels of single-nucleotide polymorphisms (SNPs), the exploration of genetic variation of complex traits is moving from quantifying the resemblance between family members to the dissection of genetic variation at individual loci. With SNPs, we were able to quantify the contribution of additive, dominance, and imprinting variance to the total genetic variance by using a SNP regression method. The method was validated in simulated data and applied to three traits (number of teats, backfat, and lifetime daily gain) in three purebred pig populations. In simulated data, the estimates of additive, dominance, and imprinting variance were very close to the simulated values. In real data, dominance effects account for a substantial proportion of the total genetic variance (up to 44%) for these traits in these populations. The contribution of imprinting to the total phenotypic variance of the evaluated traits was relatively small (1–3%). Our results indicate a strong relationship between additive variance explained per chromosome and chromosome length, which has been described previously for other traits in other species. We also show that a similar linear relationship exists for dominance and imprinting variance. These novel results improve our understanding of the genetic architecture of the evaluated traits and shows promise to apply the SNP regression method to other traits and species, including human diseases. PMID:26438289

  2. The Evolution of Human Intelligence and the Coefficient of Additive Genetic Variance in Human Brain Size

    ERIC Educational Resources Information Center

    Miller, Geoffrey F.; Penke, Lars

    2007-01-01

    Most theories of human mental evolution assume that selection favored higher intelligence and larger brains, which should have reduced genetic variance in both. However, adult human intelligence remains highly heritable, and is genetically correlated with brain size. This conflict might be resolved by estimating the coefficient of additive genetic…

  3. Simultaneous Estimation of Additive and Mutational Genetic Variance in an Outbred Population of Drosophila serrata.

    PubMed

    McGuigan, Katrina; Aguirre, J David; Blows, Mark W

    2015-11-01

    How new mutations contribute to genetic variation is a key question in biology. Although the evolutionary fate of an allele is largely determined by its heterozygous effect, most estimates of mutational variance and mutational effects derive from highly inbred lines, where new mutations are present in homozygous form. In an attempt to overcome this limitation, middle-class neighborhood (MCN) experiments have been used to assess the fitness effect of new mutations in heterozygous form. However, because MCN populations harbor substantial standing genetic variance, estimates of mutational variance have not typically been available from such experiments. Here we employ a modification of the animal model to analyze data from 22 generations of Drosophila serrata bred in an MCN design. Mutational heritability, measured for eight cuticular hydrocarbons, 10 wing-shape traits, and wing size in this outbred genetic background, ranged from 0.0006 to 0.006 (with one exception), a similar range to that reported from studies employing inbred lines. Simultaneously partitioning the additive and mutational variance in the same outbred population allowed us to quantitatively test the ability of mutation-selection balance models to explain the observed levels of additive and mutational genetic variance. The Gaussian allelic approximation and house-of-cards models, which assume real stabilizing selection on single traits, both overestimated the genetic variance maintained at equilibrium, but the house-of-cards model was a closer fit to the data. This analytical approach has the potential to be broadly applied, expanding our understanding of the dynamics of genetic variance in natural populations. PMID:26384357

  4. The Multi-allelic Genetic Architecture of a Variance-Heterogeneity Locus for Molybdenum Concentration in Leaves Acts as a Source of Unexplained Additive Genetic Variance

    PubMed Central

    Forsberg, Simon K. G.; Andreatta, Matthew E.; Huang, Xin-Yuan; Danku, John; Salt, David E.; Carlborg, Örjan

    2015-01-01

    Genome-wide association (GWA) analyses have generally been used to detect individual loci contributing to the phenotypic diversity in a population by the effects of these loci on the trait mean. More rarely, loci have also been detected based on variance differences between genotypes. Several hypotheses have been proposed to explain the possible genetic mechanisms leading to such variance signals. However, little is known about what causes these signals, or whether this genetic variance-heterogeneity reflects mechanisms of importance in natural populations. Previously, we identified a variance-heterogeneity GWA (vGWA) signal for leaf molybdenum concentrations in Arabidopsis thaliana. Here, fine-mapping of this association reveals that the vGWA emerges from the effects of three independent genetic polymorphisms that all are in strong LD with the markers displaying the genetic variance-heterogeneity. By revealing the genetic architecture underlying this vGWA signal, we uncovered the molecular source of a significant amount of hidden additive genetic variation or “missing heritability”. Two of the three polymorphisms underlying the genetic variance-heterogeneity are promoter variants for Molybdate transporter 1 (MOT1), and the third a variant located ~25 kb downstream of this gene. A fourth independent association was also detected ~600 kb upstream of MOT1. Use of a T-DNA knockout allele highlights Copper Transporter 6; COPT6 (AT2G26975) as a strong candidate gene for this association. Our results show that an extended LD across a complex locus including multiple functional alleles can lead to a variance-heterogeneity between genotypes in natural populations. Further, they provide novel insights into the genetic regulation of ion homeostasis in A. thaliana, and empirically confirm that variance-heterogeneity based GWA methods are a valuable tool to detect novel associations of biological importance in natural populations. PMID:26599497

  5. Pattern of inbreeding depression, condition dependence, and additive genetic variance in Trinidadian guppy ejaculate traits

    PubMed Central

    Gasparini, Clelia; Devigili, Alessandro; Dosselli, Ryan; Pilastro, Andrea

    2013-01-01

    In polyandrous species, a male's reproductive success depends on his fertilization capability and traits enhancing competitive fertilization success will be under strong, directional selection. This leads to the prediction that these traits should show stronger condition dependence and larger genetic variance than other traits subject to weaker or stabilizing selection. While empirical evidence of condition dependence in postcopulatory traits is increasing, the comparison between sexually selected and ‘control’ traits is often based on untested assumption concerning the different strength of selection acting on these traits. Furthermore, information on selection in the past is essential, as both condition dependence and genetic variance of a trait are likely to be influenced by the pattern of selection acting historically on it. Using the guppy (Poecilia reticulata), a livebearing fish with high levels of multiple paternity, we performed three independent experiments on three ejaculate quality traits, sperm number, velocity, and size, which have been previously shown to be subject to strong, intermediate, and weak directional postcopulatory selection, respectively. First, we conducted an inbreeding experiment to determine the pattern of selection in the past. Second, we used a diet restriction experiment to estimate their level of condition dependence. Third, we used a half-sib/full-sib mating design to estimate the coefficients of additive genetic variance (CVA) underlying these traits. Additionally, using a simulated predator evasion test, we showed that both inbreeding and diet restriction significantly reduced condition. According to predictions, sperm number showed higher inbreeding depression, stronger condition dependence, and larger CVA than sperm velocity and sperm size. The lack of significant genetic correlation between sperm number and velocity suggests that the former may respond to selection independently one from other ejaculate quality traits

  6. Additive genetic variance in polyandry enables its evolution, but polyandry is unlikely to evolve through sexy or good sperm processes.

    PubMed

    Travers, L M; Simmons, L W; Garcia-Gonzalez, F

    2016-05-01

    Polyandry is widespread despite its costs. The sexually selected sperm hypotheses ('sexy' and 'good' sperm) posit that sperm competition plays a role in the evolution of polyandry. Two poorly studied assumptions of these hypotheses are the presence of additive genetic variance in polyandry and sperm competitiveness. Using a quantitative genetic breeding design in a natural population of Drosophila melanogaster, we first established the potential for polyandry to respond to selection. We then investigated whether polyandry can evolve through sexually selected sperm processes. We measured lifetime polyandry and offensive sperm competitiveness (P2 ) while controlling for sampling variance due to male × male × female interactions. We also measured additive genetic variance in egg-to-adult viability and controlled for its effect on P2 estimates. Female lifetime polyandry showed significant and substantial additive genetic variance and evolvability. In contrast, we found little genetic variance or evolvability in P2 or egg-to-adult viability. Additive genetic variance in polyandry highlights its potential to respond to selection. However, the low levels of genetic variance in sperm competitiveness suggest that the evolution of polyandry may not be driven by sexy sperm or good sperm processes. PMID:26801640

  7. Heritability of heterozygosity offers a new way of understanding why dominant gene action contributes to additive genetic variance.

    PubMed

    Nietlisbach, Pirmin; Hadfield, Jarrod D

    2015-07-01

    Whenever allele frequencies are unequal, nonadditive gene action contributes to additive genetic variance and therefore the resemblance between parents and offspring. The reason for this has not been easy to understand. Here, we present a new single-locus decomposition of additive genetic variance that may give greater intuition about this important result. We show that the contribution of dominant gene action to parent-offspring resemblance only depends on the degree to which the heterozygosity of parents and offspring covary. Thus, dominant gene action only contributes to additive genetic variance when heterozygosity is heritable. Under most circumstances this is the case because individuals with rare alleles are more likely to be heterozygous, and because they pass rare alleles to their offspring they also tend to have heterozygous offspring. When segregating alleles are at equal frequency there are no rare alleles, the heterozygosities of parents and offspring are uncorrelated and dominant gene action does not contribute to additive genetic variance. PMID:26100570

  8. Additive genetic variance and developmental plasticity in growth trajectories in a wild cooperative mammal.

    PubMed

    Huchard, E; Charmantier, A; English, S; Bateman, A; Nielsen, J F; Clutton-Brock, T

    2014-09-01

    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 ≤ h(2) < 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. PMID:24962704

  9. Very low levels of direct additive genetic variance in fitness and fitness components in a red squirrel population

    PubMed Central

    McFarlane, S Eryn; Gorrell, Jamieson C; Coltman, David W; Humphries, Murray M; Boutin, Stan; McAdam, Andrew G

    2014-01-01

    A trait must genetically correlate with fitness in order to evolve in response to natural selection, but theory suggests that strong directional selection should erode additive genetic variance in fitness and limit future evolutionary potential. Balancing selection has been proposed as a mechanism that could maintain genetic variance if fitness components trade off with one another and has been invoked to account for empirical observations of higher levels of additive genetic variance in fitness components than would be expected from mutation–selection balance. Here, we used a long-term study of an individually marked population of North American red squirrels (Tamiasciurus hudsonicus) to look for evidence of (1) additive genetic variance in lifetime reproductive success and (2) fitness trade-offs between fitness components, such as male and female fitness or fitness in high- and low-resource environments. “Animal model” analyses of a multigenerational pedigree revealed modest maternal effects on fitness, but very low levels of additive genetic variance in lifetime reproductive success overall as well as fitness measures within each sex and environment. It therefore appears that there are very low levels of direct genetic variance in fitness and fitness components in red squirrels to facilitate contemporary adaptation in this population. PMID:24963372

  10. Efficient Markov Chain Monte Carlo Implementation of Bayesian Analysis of Additive and Dominance Genetic Variances in Noninbred Pedigrees

    PubMed Central

    Waldmann, Patrik; Hallander, Jon; Hoti, Fabian; Sillanpää, Mikko J.

    2008-01-01

    Accurate and fast computation of quantitative genetic variance parameters is of great importance in both natural and breeding populations. For experimental designs with complex relationship structures it can be important to include both additive and dominance variance components in the statistical model. In this study, we introduce a Bayesian Gibbs sampling approach for estimation of additive and dominance genetic variances in the traditional infinitesimal model. The method can handle general pedigrees without inbreeding. To optimize between computational time and good mixing of the Markov chain Monte Carlo (MCMC) chains, we used a hybrid Gibbs sampler that combines a single site and a blocked Gibbs sampler. The speed of the hybrid sampler and the mixing of the single-site sampler were further improved by the use of pretransformed variables. Two traits (height and trunk diameter) from a previously published diallel progeny test of Scots pine (Pinus sylvestris L.) and two large simulated data sets with different levels of dominance variance were analyzed. We also performed Bayesian model comparison on the basis of the posterior predictive loss approach. Results showed that models with both additive and dominance components had the best fit for both height and diameter and for the simulated data with high dominance. For the simulated data with low dominance, we needed an informative prior to avoid the dominance variance component becoming overestimated. The narrow-sense heritability estimates in the Scots pine data were lower compared to the earlier results, which is not surprising because the level of dominance variance was rather high, especially for diameter. In general, the hybrid sampler was considerably faster than the blocked sampler and displayed better mixing properties than the single-site sampler. PMID:18558655

  11. Efficient Markov chain Monte Carlo implementation of Bayesian analysis of additive and dominance genetic variances in noninbred pedigrees.

    PubMed

    Waldmann, Patrik; Hallander, Jon; Hoti, Fabian; Sillanpää, Mikko J

    2008-06-01

    Accurate and fast computation of quantitative genetic variance parameters is of great importance in both natural and breeding populations. For experimental designs with complex relationship structures it can be important to include both additive and dominance variance components in the statistical model. In this study, we introduce a Bayesian Gibbs sampling approach for estimation of additive and dominance genetic variances in the traditional infinitesimal model. The method can handle general pedigrees without inbreeding. To optimize between computational time and good mixing of the Markov chain Monte Carlo (MCMC) chains, we used a hybrid Gibbs sampler that combines a single site and a blocked Gibbs sampler. The speed of the hybrid sampler and the mixing of the single-site sampler were further improved by the use of pretransformed variables. Two traits (height and trunk diameter) from a previously published diallel progeny test of Scots pine (Pinus sylvestris L.) and two large simulated data sets with different levels of dominance variance were analyzed. We also performed Bayesian model comparison on the basis of the posterior predictive loss approach. Results showed that models with both additive and dominance components had the best fit for both height and diameter and for the simulated data with high dominance. For the simulated data with low dominance, we needed an informative prior to avoid the dominance variance component becoming overestimated. The narrow-sense heritability estimates in the Scots pine data were lower compared to the earlier results, which is not surprising because the level of dominance variance was rather high, especially for diameter. In general, the hybrid sampler was considerably faster than the blocked sampler and displayed better mixing properties than the single-site sampler. PMID:18558655

  12. Genome-Enabled Estimates of Additive and Nonadditive Genetic Variances and Prediction of Apple Phenotypes Across Environments

    PubMed Central

    Kumar, Satish; Molloy, Claire; Muñoz, Patricio; Daetwyler, Hans; Chagné, David; Volz, Richard

    2015-01-01

    The nonadditive genetic effects may have an important contribution to total genetic variation of phenotypes, so estimates of both the additive and nonadditive effects are desirable for breeding and selection purposes. Our main objectives were to: estimate additive, dominance and epistatic variances of apple (Malus × domestica Borkh.) phenotypes using relationship matrices constructed from genome-wide dense single nucleotide polymorphism (SNP) markers; and compare the accuracy of genomic predictions using genomic best linear unbiased prediction models with or without including nonadditive genetic effects. A set of 247 clonally replicated individuals was assessed for six fruit quality traits at two sites, and also genotyped using an Illumina 8K SNP array. Across several fruit quality traits, the additive, dominance, and epistatic effects contributed about 30%, 16%, and 19%, respectively, to the total phenotypic variance. Models ignoring nonadditive components yielded upwardly biased estimates of additive variance (heritability) for all traits in this study. The accuracy of genomic predicted genetic values (GEGV) varied from about 0.15 to 0.35 for various traits, and these were almost identical for models with or without including nonadditive effects. However, models including nonadditive genetic effects further reduced the bias of GEGV. Between-site genotypic correlations were high (>0.85) for all traits, and genotype-site interaction accounted for <10% of the phenotypic variability. The accuracy of prediction, when the validation set was present only at one site, was generally similar for both sites, and varied from about 0.50 to 0.85. The prediction accuracies were strongly influenced by trait heritability, and genetic relatedness between the training and validation families. PMID:26497141

  13. 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)

    PubMed Central

    Reid, Jane M; Arcese, Peter; Keller, Lukas F; Losdat, Sylvain

    2014-01-01

    Ongoing evolution of polyandry, and consequent extra-pair reproduction in socially monogamous systems, is hypothesized to be facilitated by indirect selection stemming from cross-sex genetic covariances with components of male fitness. Specifically, polyandry is hypothesized 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 nonzero additive genetic variance in female liability for extra-pair reproduction and male liability for within-pair paternity success, modeled 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, although 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. PMID:24724612

  14. Evolution of the additive genetic variance-covariance matrix under continuous directional selection on a complex behavioural phenotype.

    PubMed

    Careau, Vincent; Wolak, Matthew E; Carter, Patrick A; Garland, Theodore

    2015-11-22

    Given the pace at which human-induced environmental changes occur, a pressing challenge is to determine the speed with which selection can drive evolutionary change. A key determinant of adaptive response to multivariate phenotypic selection is the additive genetic variance-covariance matrix ( G: ). Yet knowledge of G: in a population experiencing new or altered selection is not sufficient to predict selection response because G: itself evolves in ways that are poorly understood. We experimentally evaluated changes in G: when closely related behavioural traits experience continuous directional selection. We applied the genetic covariance tensor approach to a large dataset (n = 17 328 individuals) from a replicated, 31-generation artificial selection experiment that bred mice for voluntary wheel running on days 5 and 6 of a 6-day test. Selection on this subset of G: induced proportional changes across the matrix for all 6 days of running behaviour within the first four generations. The changes in G: induced by selection resulted in a fourfold slower-than-predicted rate of response to selection. Thus, selection exacerbated constraints within G: and limited future adaptive response, a phenomenon that could have profound consequences for populations facing rapid environmental change. PMID:26582016

  15. Replication of a Gene-Environment Interaction via Multimodel Inference: Additive-Genetic Variance in Adolescents’ General Cognitive Ability Increases with Family-of-Origin Socioeconomic Status

    PubMed Central

    Kirkpatrick, Robert M.; McGue, Matt; Iacono, William G.

    2015-01-01

    The present study of general cognitive ability attempts to replicate and extend previous investigations of a biometric moderator, family-of-origin socioeconomic status (SES), in a sample of 2,494 pairs of adolescent twins, non-twin biological siblings, and adoptive siblings assessed with individually administered IQ tests. We hypothesized that SES would covary positively with additive-genetic variance and negatively with shared-environmental variance. Important potential confounds unaddressed in some past studies, such as twin-specific effects, assortative mating, and differential heritability by trait level, were found to be negligible. In our main analysis, we compared models by their sample-size corrected AIC, and base our statistical inference on model-averaged point estimates and standard errors. Additive-genetic variance increased with SES—an effect that was statistically significant and robust to model specification. We found no evidence that SES moderated shared-environmental influence. We attempt to explain the inconsistent replication record of these effects, and provide suggestions for future research. PMID:25539975

  16. Replication of a gene-environment interaction Via Multimodel inference: additive-genetic variance in adolescents' general cognitive ability increases with family-of-origin socioeconomic status.

    PubMed

    Kirkpatrick, Robert M; McGue, Matt; Iacono, William G

    2015-03-01

    The present study of general cognitive ability attempts to replicate and extend previous investigations of a biometric moderator, family-of-origin socioeconomic status (SES), in a sample of 2,494 pairs of adolescent twins, non-twin biological siblings, and adoptive siblings assessed with individually administered IQ tests. We hypothesized that SES would covary positively with additive-genetic variance and negatively with shared-environmental variance. Important potential confounds unaddressed in some past studies, such as twin-specific effects, assortative mating, and differential heritability by trait level, were found to be negligible. In our main analysis, we compared models by their sample-size corrected AIC, and base our statistical inference on model-averaged point estimates and standard errors. Additive-genetic variance increased with SES-an effect that was statistically significant and robust to model specification. We found no evidence that SES moderated shared-environmental influence. We attempt to explain the inconsistent replication record of these effects, and provide suggestions for future research. PMID:25539975

  17. Characterizing the evolution of genetic variance using genetic covariance tensors.

    PubMed

    Hine, Emma; Chenoweth, Stephen F; Rundle, Howard D; Blows, Mark W

    2009-06-12

    Determining how genetic variance changes under selection in natural populations has proved to be a very resilient problem in evolutionary genetics. In the same way that understanding the availability of genetic variance within populations requires the simultaneous consideration of genetic variance in sets of functionally related traits, determining how genetic variance changes under selection in natural populations will require ascertaining how genetic variance-covariance (G) matrices evolve. Here, we develop a geometric framework using higher-order tensors, which enables the empirical characterization of how G matrices have diverged among populations. We then show how divergence among populations in genetic covariance structure can then be associated with divergence in selection acting on those traits using key equations from evolutionary theory. Using estimates of G matrices of eight male sexually selected traits from nine geographical populations of Drosophila serrata, we show that much of the divergence in genetic variance occurred in a single trait combination, a conclusion that could not have been reached by examining variation among the individual elements of the nine G matrices. Divergence in G was primarily in the direction of the major axes of genetic variance within populations, suggesting that genetic drift may be a major cause of divergence in genetic variance among these populations. PMID:19414471

  18. Dominance Genetic Variance for Traits Under Directional Selection in Drosophila serrata

    PubMed Central

    Sztepanacz, Jacqueline L.; Blows, Mark W.

    2015-01-01

    In contrast to our growing understanding of patterns of additive genetic variance in single- and multi-trait combinations, the relative contribution of nonadditive genetic variance, particularly dominance variance, to multivariate phenotypes is largely unknown. While mechanisms for the evolution of dominance genetic variance have been, and to some degree remain, subject to debate, the pervasiveness of dominance is widely recognized and may play a key role in several evolutionary processes. Theoretical and empirical evidence suggests that the contribution of dominance variance to phenotypic variance may increase with the correlation between a trait and fitness; however, direct tests of this hypothesis are few. Using a multigenerational breeding design in an unmanipulated population of Drosophila serrata, we estimated additive and dominance genetic covariance matrices for multivariate wing-shape phenotypes, together with a comprehensive measure of fitness, to determine whether there is an association between directional selection and dominance variance. Fitness, a trait unequivocally under directional selection, had no detectable additive genetic variance, but significant dominance genetic variance contributing 32% of the phenotypic variance. For single and multivariate morphological traits, however, no relationship was observed between trait–fitness correlations and dominance variance. A similar proportion of additive and dominance variance was found to contribute to phenotypic variance for single traits, and double the amount of additive compared to dominance variance was found for the multivariate trait combination under directional selection. These data suggest that for many fitness components a positive association between directional selection and dominance genetic variance may not be expected. PMID:25783700

  19. Dominance genetic variance for traits under directional selection in Drosophila serrata.

    PubMed

    Sztepanacz, Jacqueline L; Blows, Mark W

    2015-05-01

    In contrast to our growing understanding of patterns of additive genetic variance in single- and multi-trait combinations, the relative contribution of nonadditive genetic variance, particularly dominance variance, to multivariate phenotypes is largely unknown. While mechanisms for the evolution of dominance genetic variance have been, and to some degree remain, subject to debate, the pervasiveness of dominance is widely recognized and may play a key role in several evolutionary processes. Theoretical and empirical evidence suggests that the contribution of dominance variance to phenotypic variance may increase with the correlation between a trait and fitness; however, direct tests of this hypothesis are few. Using a multigenerational breeding design in an unmanipulated population of Drosophila serrata, we estimated additive and dominance genetic covariance matrices for multivariate wing-shape phenotypes, together with a comprehensive measure of fitness, to determine whether there is an association between directional selection and dominance variance. Fitness, a trait unequivocally under directional selection, had no detectable additive genetic variance, but significant dominance genetic variance contributing 32% of the phenotypic variance. For single and multivariate morphological traits, however, no relationship was observed between trait-fitness correlations and dominance variance. A similar proportion of additive and dominance variance was found to contribute to phenotypic variance for single traits, and double the amount of additive compared to dominance variance was found for the multivariate trait combination under directional selection. These data suggest that for many fitness components a positive association between directional selection and dominance genetic variance may not be expected. PMID:25783700

  20. On the Additive and Dominant Variance and Covariance of Individuals Within the Genomic Selection Scope

    PubMed Central

    Vitezica, Zulma G.; Varona, Luis; Legarra, Andres

    2013-01-01

    Genomic evaluation models can fit additive and dominant SNP effects. Under quantitative genetics theory, additive or “breeding” values of individuals are generated by substitution effects, which involve both “biological” additive and dominant effects of the markers. Dominance deviations include only a portion of the biological dominant effects of the markers. Additive variance includes variation due to the additive and dominant effects of the markers. We describe a matrix of dominant genomic relationships across individuals, D, which is similar to the G matrix used in genomic best linear unbiased prediction. This matrix can be used in a mixed-model context for genomic evaluations or to estimate dominant and additive variances in the population. From the “genotypic” value of individuals, an alternative parameterization defines additive and dominance as the parts attributable to the additive and dominant effect of the markers. This approach underestimates the additive genetic variance and overestimates the dominance variance. Transforming the variances from one model into the other is trivial if the distribution of allelic frequencies is known. We illustrate these results with mouse data (four traits, 1884 mice, and 10,946 markers) and simulated data (2100 individuals and 10,000 markers). Variance components were estimated correctly in the model, considering breeding values and dominance deviations. For the model considering genotypic values, the inclusion of dominant effects biased the estimate of additive variance. Genomic models were more accurate for the estimation of variance components than their pedigree-based counterparts. PMID:24121775

  1. Influence of genetic variance on sodium sensitivity of blood pressure.

    PubMed

    Luft, F C; Miller, J Z; Weinberger, M H; Grim, C E; Daugherty, S A; Christian, J C

    1987-02-01

    To examine the effect of genetic variance on blood pressure, sodium homeostasis, and its regulatory determinants, we studied 37 pairs of monozygotic twins and 18 pairs of dizygotic twins under conditions of volume expansion and contraction. We found that, in addition to blood pressure and body size, sodium excretion in response to provocative maneuvers, glomerular filtration rate, the renin-angiotensin system, and the sympathetic nervous system are influenced by genetic variance. To elucidate the interaction of genetic factors and an environmental influence, namely, salt intake, we restricted dietary sodium in 44 families of twin children. In addition to a modest decrease in blood pressure, we found heterogeneous responses in blood pressure indicative of sodium sensitivity and resistance which were normally distributed. Strong parent-offspring resemblances were found in baseline blood pressures which persisted when adjustments were made for age and weight. Further, mother-offspring resemblances were observed in the change in blood pressure with sodium restriction. We conclude that the control of sodium homeostasis is heritable and that the change in blood pressure with sodium restriction is familial as well. These data speak to the interaction between the genetic susceptibility to hypertension and environmental influences which may result in its expression. PMID:3553721

  2. Argentine Population Genetic Structure: Large Variance in Amerindian Contribution

    PubMed Central

    Seldin, Michael F.; Tian, Chao; Shigeta, Russell; Scherbarth, Hugo R.; Silva, Gabriel; Belmont, John W.; Kittles, Rick; Gamron, Susana; Allevi, Alberto; Palatnik, Simon A.; Alvarellos, Alejandro; Paira, Sergio; Caprarulo, Cesar; Guillerón, Carolina; Catoggio, Luis J.; Prigione, Cristina; Berbotto, Guillermo A.; García, Mercedes A.; Perandones, Carlos E.; Pons-Estel, Bernardo A.; Alarcon-Riquelme, Marta E.

    2011-01-01

    Argentine population genetic structure was examined using a set of 78 ancestry informative markers (AIMs) to assess the contributions of European, Amerindian, and African ancestry in 94 individuals members of this population. Using the Bayesian clustering algorithm STRUCTURE, the mean European contribution was 78%, the Amerindian contribution was 19.4%, and the African contribution was 2.5%. Similar results were found using weighted least mean square method: European, 80.2%; Amerindian, 18.1%; and African, 1.7%. Consistent with previous studies the current results showed very few individuals (four of 94) with greater than 10% African admixture. Notably, when individual admixture was examined, the Amerindian and European admixture showed a very large variance and individual Amerindian contribution ranged from 1.5 to 84.5% in the 94 individual Argentine subjects. These results indicate that admixture must be considered when clinical epidemiology or case control genetic analyses are studied in this population. Moreover, the current study provides a set of informative SNPs that can be used to ascertain or control for this potentially hidden stratification. In addition, the large variance in admixture proportions in individual Argentine subjects shown by this study suggests that this population is appropriate for future admixture mapping studies. PMID:17177183

  3. Analysis of Variance Components for Genetic Markers with Unphased Genotypes

    PubMed Central

    Wang, Tao

    2016-01-01

    An ANOVA type general multi-allele (GMA) model was proposed in Wang (2014) on analysis of variance components for quantitative trait loci or genetic markers with phased or unphased genotypes. In this study, by applying the GMA model, we further examine estimation of the genetic variance components for genetic markers with unphased genotypes based on a random sample from a study population. In one locus and two loci cases, we first derive the least square estimates (LSE) of model parameters in fitting the GMA model. Then we construct estimators of the genetic variance components for one marker locus in a Hardy-Weinberg disequilibrium population and two marker loci in an equilibrium population. Meanwhile, we explore the difference between the classical general linear model (GLM) and GMA based approaches in association analysis of genetic markers with quantitative traits. We show that the GMA model can retain the same partition on the genetic variance components as the traditional Fisher's ANOVA model, while the GLM cannot. We clarify that the standard F-statistics based on the partial reductions in sums of squares from GLM for testing the fixed allelic effects could be inadequate for testing the existence of the variance component when allelic interactions are present. We point out that the GMA model can reduce the confounding between the allelic effects and allelic interactions at least for independent alleles. As a result, the GMA model could be more beneficial than GLM for detecting allelic interactions. PMID:27468297

  4. Genetic Variance in the SES-IQ Correlation.

    ERIC Educational Resources Information Center

    Eckland, Bruce K.

    1979-01-01

    Discusses questions dealing with genetic aspects of the correlation between IQ and socioeconomic status (SES). Questions include: How does assortative mating affect the genetic variance of IQ? Is the relationship between an individual's IQ and adult SES a causal one? And how can IQ research improve schools and schooling? (Author/DB)

  5. Components of genetic variance for plant survival and vigor of apple trees.

    PubMed

    Watkins, R; Spangelo, L P

    1970-01-01

    The additive and non-additive variance components were estimated from progenies derived from two samples of parents (representing a northern continental type climate) for five factors relating to plant survival and two composites of the factors. It was found that additive variance made up 90 and 100%, 91 and 100%, 91 and 100%, 100 and 100%, 82 and 59%, 91 and 100%, and 90 and 100% of the total genetic variance for leafing-out date, leafingout percent, tip injury, stem damage, root damage, a shoot composite, and a shoot-root composite for the two samples respectively. A third sample had 100% additive variance for plant height while, in contrast, a sample of rootstocks, differing from each other in their ability to dwarf grafted scions, had approximately 50-70% additive variance for plant height. It was shown that breeding progress for both winter survival and plant height could be achieved by exploiting the additive variance, the total genetic variance, or (where progenies were the selection unit rather than individuals) by progeny selection. By exploiting the additive variance, it should be possible to improve plant survival and change plant height in each of several successive generations. It is predicted that (with the exception of selection for vigor in a population having a range of dwarfing abilities) potential parents could be efficiently screened phenotypically and so obviate the need for genotypic evaluation. A total of 9180 progeny trees were involved in the analyses considered in this paper. PMID:24435802

  6. Genetic and environmental heterogeneity of residual variance of weight traits in Nellore beef cattle

    PubMed Central

    2012-01-01

    Background Many studies have provided evidence of the existence of genetic heterogeneity of environmental variance, suggesting that it could be exploited to improve robustness and uniformity of livestock by selection. However, little is known about the perspectives of such a selection strategy in beef cattle. Methods A two-step approach was applied to study the genetic heterogeneity of residual variance of weight gain from birth to weaning and long-yearling weight in a Nellore beef cattle population. First, an animal model was fitted to the data and second, the influence of additive and environmental effects on the residual variance of these traits was investigated with different models, in which the log squared estimated residuals for each phenotypic record were analyzed using the restricted maximum likelihood method. Monte Carlo simulation was performed to assess the reliability of variance component estimates from the second step and the accuracy of estimated breeding values for residual variation. Results The results suggest that both genetic and environmental factors have an effect on the residual variance of weight gain from birth to weaning and long-yearling in Nellore beef cattle and that uniformity of these traits could be improved by selecting for lower residual variance, when considering a large amount of information to predict genetic merit for this criterion. Simulations suggested that using the two-step approach would lead to biased estimates of variance components, such that more adequate methods are needed to study the genetic heterogeneity of residual variance in beef cattle. PMID:22672564

  7. 49 CFR 350.345 - How does a State apply for additional variances from the FMCSRs?

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 49 Transportation 5 2010-10-01 2010-10-01 false How does a State apply for additional variances... apply for additional variances from the FMCSRs? Any State may apply to the Administrator for a variance from the FMCSRs for intrastate commerce. The variance will be granted only if the State...

  8. The genetic and environmental roots of variance in negativity toward foreign nationals.

    PubMed

    Kandler, Christian; Lewis, Gary J; Feldhaus, Lea Henrike; Riemann, Rainer

    2015-03-01

    This study quantified genetic and environmental roots of variance in prejudice and discriminatory intent toward foreign nationals and examined potential mediators of these genetic influences: right-wing authoritarianism (RWA), social dominance orientation (SDO), and narrow-sense xenophobia (NSX). In line with the dual process motivational (DPM) model, we predicted that the two basic attitudinal and motivational orientations-RWA and SDO-would account for variance in out-group prejudice and discrimination. In line with other theories, we expected that NSX as an affective component would explain additional variance in out-group prejudice and discriminatory intent. Data from 1,397 individuals (incl. twins as well as their spouses) were analyzed. Univariate analyses of twins' and spouses' data yielded genetic (incl. contributions of assortative mating) and multiple environmental sources (i.e., social homogamy, spouse-specific, and individual-specific effects) of variance in negativity toward strangers. Multivariate analyses suggested an extension to the DPM model by including NSX in addition to RWA and SDO as predictor of prejudice and discrimination. RWA and NSX primarily mediated the genetic influences on the variance in prejudice and discriminatory intent toward foreign nationals. In sum, the findings provide the basis of a behavioral genetic framework integrating different scientific disciplines for the study of negativity toward out-groups. PMID:25534512

  9. Maintenance of Quantitative Genetic Variance Under Partial Self-Fertilization, with Implications for Evolution of Selfing

    PubMed Central

    Lande, Russell; Porcher, Emmanuelle

    2015-01-01

    We analyze two models of the maintenance of quantitative genetic variance in a mixed-mating system of self-fertilization and outcrossing. In both models purely additive genetic variance is maintained by mutation and recombination under stabilizing selection on the phenotype of one or more quantitative characters. The Gaussian allele model (GAM) involves a finite number of unlinked loci in an infinitely large population, with a normal distribution of allelic effects at each locus within lineages selfed for τ consecutive generations since their last outcross. The infinitesimal model for partial selfing (IMS) involves an infinite number of loci in a large but finite population, with a normal distribution of breeding values in lineages of selfing age τ. In both models a stable equilibrium genetic variance exists, the outcrossed equilibrium, nearly equal to that under random mating, for all selfing rates, r, up to critical value, r^, the purging threshold, which approximately equals the mean fitness under random mating relative to that under complete selfing. In the GAM a second stable equilibrium, the purged equilibrium, exists for any positive selfing rate, with genetic variance less than or equal to that under pure selfing; as r increases above r^ the outcrossed equilibrium collapses sharply to the purged equilibrium genetic variance. In the IMS a single stable equilibrium genetic variance exists at each selfing rate; as r increases above r^ the equilibrium genetic variance drops sharply and then declines gradually to that maintained under complete selfing. The implications for evolution of selfing rates, and for adaptive evolution and persistence of predominantly selfing species, provide a theoretical basis for the classical view of Stebbins that predominant selfing constitutes an “evolutionary dead end.” PMID:25969460

  10. Maintenance of Quantitative Genetic Variance Under Partial Self-Fertilization, with Implications for Evolution of Selfing.

    PubMed

    Lande, Russell; Porcher, Emmanuelle

    2015-07-01

    We analyze two models of the maintenance of quantitative genetic variance in a mixed-mating system of self-fertilization and outcrossing. In both models purely additive genetic variance is maintained by mutation and recombination under stabilizing selection on the phenotype of one or more quantitative characters. The Gaussian allele model (GAM) involves a finite number of unlinked loci in an infinitely large population, with a normal distribution of allelic effects at each locus within lineages selfed for τ consecutive generations since their last outcross. The infinitesimal model for partial selfing (IMS) involves an infinite number of loci in a large but finite population, with a normal distribution of breeding values in lineages of selfing age τ. In both models a stable equilibrium genetic variance exists, the outcrossed equilibrium, nearly equal to that under random mating, for all selfing rates, r, up to critical value, [Formula: see text], the purging threshold, which approximately equals the mean fitness under random mating relative to that under complete selfing. In the GAM a second stable equilibrium, the purged equilibrium, exists for any positive selfing rate, with genetic variance less than or equal to that under pure selfing; as r increases above [Formula: see text] the outcrossed equilibrium collapses sharply to the purged equilibrium genetic variance. In the IMS a single stable equilibrium genetic variance exists at each selfing rate; as r increases above [Formula: see text] the equilibrium genetic variance drops sharply and then declines gradually to that maintained under complete selfing. The implications for evolution of selfing rates, and for adaptive evolution and persistence of predominantly selfing species, provide a theoretical basis for the classical view of Stebbins that predominant selfing constitutes an "evolutionary dead end." PMID:25969460

  11. Ontogenetic changes in genetic variances of age-dependent plasticity along a latitudinal gradient.

    PubMed

    Nilsson-Örtman, V; Rogell, B; Stoks, R; Johansson, F

    2015-10-01

    The expression of phenotypic plasticity may differ among life stages of the same organism. Age-dependent plasticity can be important for adaptation to heterogeneous environments, but this has only recently been recognized. Whether age-dependent plasticity is a common outcome of local adaptation and whether populations harbor genetic variation in this respect remains largely unknown. To answer these questions, we estimated levels of additive genetic variation in age-dependent plasticity in six species of damselflies sampled from 18 populations along a latitudinal gradient spanning 3600 km. We reared full sib larvae at three temperatures and estimated genetic variances in the height and slope of thermal reaction norms of body size at three points in time during ontogeny using random regression. Our data show that most populations harbor genetic variation in growth rate (reaction norm height) in all ontogenetic stages, but only some populations and ontogenetic stages were found to harbor genetic variation in thermal plasticity (reaction norm slope). Genetic variances in reaction norm height differed among species, while genetic variances in reaction norm slope differed among populations. The slope of the ontogenetic trend in genetic variances of both reaction norm height and slope increased with latitude. We propose that differences in genetic variances reflect temporal and spatial variation in the strength and direction of natural selection on growth trajectories and age-dependent plasticity. Selection on age-dependent plasticity may depend on the interaction between temperature seasonality and time constraints associated with variation in life history traits such as generation length. PMID:25649500

  12. Quantitative Genetic Analysis of Temperature Regulation in MUS MUSCULUS. I. Partitioning of Variance

    PubMed Central

    Lacy, Robert C.; Lynch, Carol Becker

    1979-01-01

    Heritabilities (from parent-offspring regression) and intraclass correlations of full sibs for a variety of traits were estimated from 225 litters of a heterogeneous stock (HS/Ibg) of laboratory mice. Initial variance partitioning suggested different adaptive functions for physiological, morphological and behavioral adjustments with respect to their thermoregulatory significance. Metabolic heat-production mechanisms appear to have reached their genetic limits, with little additive genetic variance remaining. This study provided no genetic evidence that body size has a close directional association with fitness in cold environments, since heritability estimates for weight gain and adult weight were similar and high, whether or not the animals were exposed to cold. Behavioral heat conservation mechanisms also displayed considerable amounts of genetic variability. However, due to strong evidence from numerous other studies that behavior serves an important adaptive role for temperature regulation in small mammals, we suggest that fluctuating selection pressures may have acted to maintain heritable variation in these traits. PMID:17248909

  13. Increasing Genetic Variance of Body Mass Index during the Swedish Obesity Epidemic

    PubMed Central

    Rokholm, Benjamin; Silventoinen, Karri; Tynelius, Per; Gamborg, Michael; Sørensen, Thorkild I. A.; Rasmussen, Finn

    2011-01-01

    Background and Objectives There is no doubt that the dramatic worldwide increase in obesity prevalence is due to changes in environmental factors. However, twin and family studies suggest that genetic differences are responsible for the major part of the variation in adiposity within populations. Recent studies show that the genetic effects on body mass index (BMI) may be stronger when combined with presumed risk factors for obesity. We tested the hypothesis that the genetic variance of BMI has increased during the obesity epidemic. Methods The data comprised height and weight measurements of 1,474,065 Swedish conscripts at age 18–19 y born between 1951 and 1983. The data were linked to the Swedish Multi-Generation Register and the Swedish Twin Register from which 264,796 full-brother pairs, 1,736 monozygotic (MZ) and 1,961 dizygotic (DZ) twin pairs were identified. The twin pairs were analysed to identify the most parsimonious model for the genetic and environmental contribution to BMI variance. The full-brother pairs were subsequently divided into subgroups by year of birth to investigate trends in the genetic variance of BMI. Results The twin analysis showed that BMI variation could be explained by additive genetic and environmental factors not shared by co-twins. On the basis of the analyses of the full-siblings, the additive genetic variance of BMI increased from 4.3 [95% CI 4.04–4.53] to 7.9 [95% CI 7.28–8.54] within the study period, as did the unique environmental variance, which increased from 1.4 [95% CI 1.32–1.48] to 2.0 [95% CI 1.89–2.22]. The BMI heritability increased from 75% to 78.8%. Conclusion The results confirm the hypothesis that the additive genetic variance of BMI has increased strongly during the obesity epidemic. This suggests that the obesogenic environment has enhanced the influence of adiposity related genes. PMID:22087252

  14. Genetic variance components and heritability of multiallelic heterozygosity under inbreeding.

    PubMed

    Nietlisbach, P; Keller, L F; Postma, E

    2016-01-01

    The maintenance of genetic diversity in fitness-related traits remains a central topic in evolutionary biology, for example, in the context of sexual selection for genetic benefits. Among the solutions that have been proposed is directional sexual selection for heterozygosity. The importance of such selection is highly debated. However, a critical evaluation requires knowledge of the heritability of heterozygosity, a quantity that is rarely estimated in this context, and often assumed to be zero. This is at least partly the result of the lack of a general framework that allows for its quantitative prediction in small and inbred populations, which are the focus of most empirical studies. Moreover, while current predictors are applicable only to biallelic loci, fitness-relevant loci are often multiallelic, as are the neutral markers typically used to estimate genome-wide heterozygosity. To this end, we first review previous, but little-known, work showing that under most circumstances, heterozygosity at biallelic loci and in the absence of inbreeding is heritable. We then derive the heritability of heterozygosity and the underlying variances for multiple alleles and any inbreeding level. We also show that heterozygosity at multiallelic loci can be highly heritable when allele frequencies are unequal, and that this heritability is reduced by inbreeding. Our quantitative genetic framework can provide new insights into the evolutionary dynamics of heterozygosity in inbred and outbred populations. PMID:26174022

  15. Shared genetic variance between obesity and white matter integrity in Mexican Americans

    PubMed Central

    Spieker, Elena A.; Kochunov, Peter; Rowland, Laura M.; Sprooten, Emma; Winkler, Anderson M.; Olvera, Rene L.; Almasy, Laura; Duggirala, Ravi; Fox, Peter T.; Blangero, John; Glahn, David C.; Curran, Joanne E.

    2015-01-01

    Obesity is a chronic metabolic disorder that may also lead to reduced white matter integrity, potentially due to shared genetic risk factors. Genetic correlation analyses were conducted in a large cohort of Mexican American families in San Antonio (N = 761, 58% females, ages 18–81 years; 41.3 ± 14.5) from the Genetics of Brain Structure and Function Study. Shared genetic variance was calculated between measures of adiposity [(body mass index (BMI; kg/m2) and waist circumference (WC; in)] and whole-brain and regional measurements of cerebral white matter integrity (fractional anisotropy). Whole-brain average and regional fractional anisotropy values for 10 major white matter tracts were calculated from high angular resolution diffusion tensor imaging data (DTI; 1.7 × 1.7 × 3 mm; 55 directions). Additive genetic factors explained intersubject variance in BMI (heritability, h2 = 0.58), WC (h2 = 0.57), and FA (h2 = 0.49). FA shared significant portions of genetic variance with BMI in the genu (ρG = −0.25), body (ρG = −0.30), and splenium (ρG = −0.26) of the corpus callosum, internal capsule (ρG = −0.29), and thalamic radiation (ρG = −0.31) (all p's = 0.043). The strongest evidence of shared variance was between BMI/WC and FA in the superior fronto-occipital fasciculus (ρG = −0.39, p = 0.020; ρG = −0.39, p = 0.030), which highlights region-specific variation in neural correlates of obesity. This may suggest that increase in obesity and reduced white matter integrity share common genetic risk factors. PMID:25763009

  16. Age-specific patterns of genetic variance in Drosophila melanogaster. I. Mortality

    SciTech Connect

    Promislow, D.E.L.; Tatar, M.; Curtsinger, J.W.

    1996-06-01

    Peter Medawar proposed that senescence arises from an age-related decline in the force of selection, which allows late-acting deleterious mutations to accumulate. Subsequent workers have suggested that mutation accumulation could produce an age-related increase in additive genetic variance (V{sub A}) for fitness traits, as recently found in Drosophila melanogaster. Here we report results from a genetic analysis of mortality in 65,134 D. melanogaster. Additive genetic variance for female mortality rates increases from 0.007 in the first week of life to 0.325 by the third week, and then declines to 0.002 by the seventh week. Males show a similar pattern, though total variance is lower than in females. In contrast to a predicted divergence in mortality curves, mortality curves of different genotypes are roughly parallel. Using a three-parameter model, we find significant V{sub A} for the slope and constant term of the curve describing age-specific mortality rates, and also for the rate at which mortality decelerates late in life. These results fail to support a prediction derived from Medawar`s {open_quotes}mutation accumulation{close_quotes} theory for the evolution of senescence. However, our results could be consistent with alternative interpretations of evolutionary models of aging. 65 refs., 2 figs., 2 tabs.

  17. Genetic regulatory network motifs constrain adaptation through curvature in the landscape of mutational (co)variance.

    PubMed

    Hether, Tyler D; Hohenlohe, Paul A

    2014-04-01

    Systems biology is accumulating a wealth of understanding about the structure of genetic regulatory networks, leading to a more complete picture of the complex genotype-phenotype relationship. However, models of multivariate phenotypic evolution based on quantitative genetics have largely not incorporated a network-based view of genetic variation. Here we model a set of two-node, two-phenotype genetic network motifs, covering a full range of regulatory interactions. We find that network interactions result in different patterns of mutational (co)variance at the phenotypic level (the M-matrix), not only across network motifs but also across phenotypic space within single motifs. This effect is due almost entirely to mutational input of additive genetic (co)variance. Variation in M has the effect of stretching and bending phenotypic space with respect to evolvability, analogous to the curvature of space-time under general relativity, and similar mathematical tools may apply in each case. We explored the consequences of curvature in mutational variation by simulating adaptation under divergent selection with gene flow. Both standing genetic variation (the G-matrix) and rate of adaptation are constrained by M, so that G and adaptive trajectories are curved across phenotypic space. Under weak selection the phenotypic mean at migration-selection balance also depends on M. PMID:24219635

  18. Impact of nonrandom mating on genetic variance and gene flow in populations with mass selection.

    PubMed

    Sánchez, Leopoldo; Woolliams, John A

    2004-01-01

    The mechanisms by which nonrandom mating affects selected populations are not completely understood and remain a subject of scientific debate in the development of tractable predictors of population characteristics. The main objective of this study was to provide a predictive model for the genetic variance and covariance among mates for traits subjected to directional selection in populations with nonrandom mating based on the pedigree. Stochastic simulations were used to check the validity of this model. Our predictions indicate that the positive covariance among mates that is expected to result with preferential mating of relatives can be severely overpredicted from neutral expectations. The covariance expected from neutral theory is offset by an opposing covariance between the genetic mean of an individual's family and the Mendelian sampling term of its mate. This mechanism was able to predict the reduction in covariance among mates that we observed in the simulated populations and, in consequence, the equilibrium genetic variance and expected long-term genetic contributions. Additionally, this study provided confirmatory evidence on the postulated relationships of long-term genetic contributions with both the rate of genetic gain and the rate of inbreeding (deltaF) with nonrandom mating. The coefficient of variation of the expected gene flow among individuals and deltaF was sensitive to nonrandom mating when heritability was low, but less so as heritability increased, and the theory developed in the study was sufficient to explain this phenomenon. PMID:15020441

  19. Assessment of the genetic variance of late-onset Alzheimer's disease.

    PubMed

    Ridge, Perry G; Hoyt, Kaitlyn B; Boehme, Kevin; Mukherjee, Shubhabrata; Crane, Paul K; Haines, Jonathan L; Mayeux, Richard; Farrer, Lindsay A; Pericak-Vance, Margaret A; Schellenberg, Gerard D; Kauwe, John S K

    2016-05-01

    Alzheimer's disease (AD) is a complex genetic disorder with no effective treatments. More than 20 common markers have been identified, which are associated with AD. Recently, several rare variants have been identified in Amyloid Precursor Protein (APP), Triggering Receptor Expressed On Myeloid Cells 2 (TREM2) and Unc-5 Netrin Receptor C (UNC5C) that affect risk for AD. Despite the many successes, the genetic architecture of AD remains unsolved. We used Genome-wide Complex Trait Analysis to (1) estimate phenotypic variance explained by genetics; (2) calculate genetic variance explained by known AD single nucleotide polymorphisms (SNPs); and (3) identify the genomic locations of variation that explain the remaining unexplained genetic variance. In total, 53.24% of phenotypic variance is explained by genetics, but known AD SNPs only explain 30.62% of the genetic variance. Of the unexplained genetic variance, approximately 41% is explained by unknown SNPs in regions adjacent to known AD SNPs, and the remaining unexplained genetic variance outside these regions. PMID:27036079

  20. Genetic Variance in Processing Speed Drives Variation in Aging of Spatial and Memory Abilities

    PubMed Central

    Finkel, Deborah; McArdle, John J.; Reynolds, Chandra A.; Hamagami, Fumiaki; Pedersen, Nancy L.

    2013-01-01

    Previous analyses have identified a genetic contribution to the correlation between declines with age in processing speed and higher cognitive abilities. The goal of the current analysis was to apply the biometric dual change score model to consider the possibility of temporal dynamics underlying the genetic covariance between aging trajectories for processing speed and cognitive abilities. Longitudinal twin data from the Swedish Adoption/Twin Study of Aging, including up to 5 measurement occasions covering a 16-year period, were available from 806 participants ranging in age from 50 to 88 years at the 1st measurement wave. Factors were generated to tap 4 cognitive domains: verbal ability, spatial ability, memory, and processing speed. Model-fitting indicated that genetic variance for processing speed was a leading indicator of variation in age changes for spatial and memory ability, providing additional support for processing speed theories of cognitive aging. PMID:19413434

  1. Genetic Influence on the Variance in Coincidence Timing and Its Covariance with IQ: A Twin Study.

    ERIC Educational Resources Information Center

    Wright, Margaret J.; Smith, Glen A.; Geffen, Gina M.; Geffen, Laurie B.; Martin, Nicholas G.

    2000-01-01

    Studied whether genetic variability explained some of the variance in coincidence timing and whether common genetic factors accounted for the association with intellectual functioning using 55 pairs of 16-year-old twins. Results suggest that the genetic influence operating on coincidence timing skills was of similar magnitude to that of response…

  2. Estimates for Genetic Variance Components in Reciprocal Recurrent Selection in Populations Derived from Maize Single-Cross Hybrids

    PubMed Central

    dos Reis, Matheus Costa; Pádua, José Maria Villela; Abreu, Guilherme Barbosa; Guedes, Fernando Lisboa; Balbi, Rodrigo Vieira; de Souza, João Cândido

    2014-01-01

    This study was carried out to obtain the estimates of genetic variance and covariance components related to intra- and interpopulation in the original populations (C0) and in the third cycle (C3) of reciprocal recurrent selection (RRS) which allows breeders to define the best breeding strategy. For that purpose, the half-sib progenies of intrapopulation (P11 and P22) and interpopulation (P12 and P21) from populations 1 and 2 derived from single-cross hybrids in the 0 and 3 cycles of the reciprocal recurrent selection program were used. The intra- and interpopulation progenies were evaluated in a 10 × 10 triple lattice design in two separate locations. The data for unhusked ear weight (ear weight without husk) and plant height were collected. All genetic variance and covariance components were estimated from the expected mean squares. The breakdown of additive variance into intrapopulation and interpopulation additive deviations (στ2) and the covariance between these and their intrapopulation additive effects (CovAτ) found predominance of the dominance effect for unhusked ear weight. Plant height for these components shows that the intrapopulation additive effect explains most of the variation. Estimates for intrapopulation and interpopulation additive genetic variances confirm that populations derived from single-cross hybrids have potential for recurrent selection programs. PMID:25009831

  3. Explaining additional genetic variation in complex traits

    PubMed Central

    Robinson, Matthew R.; Wray, Naomi R.; Visscher, Peter M.

    2015-01-01

    Genome-wide association studies (GWAS) have provided valuable insights into the genetic basis of complex traits, discovering >6000 variants associated with >500 quantitative traits and common complex diseases in humans. The associations identified so far represent only a fraction of those which influence phenotype, as there are likely to be very many variants across the entire frequency spectrum, each of which influences multiple traits, with only a small average contribution to the phenotypic variance. This presents a considerable challenge to further dissection of the remaining unexplained genetic variance within populations, which limits our ability to predict disease risk, identify new drug targets, improve and maintain food sources, and understand natural diversity. This challenge will be met within the current framework through larger sample size, better phenotyping including recording of non-genetic risk factors, focused study designs, and an integration of multiple sources of phenotypic and genetic information. The current evidence supports the application of quantitative genetic approaches, and we argue that one should retain simpler theories until simplicity can be traded for greater explanatory power. PMID:24629526

  4. Genetic Variance in Nonverbal Intelligence: Data from the Kinships of Identical Twins.

    ERIC Educational Resources Information Center

    Rose, Richard J.; And Others

    1979-01-01

    Data are presented from families of monozygotic twin pairs which give evidence of genetic variance on the Block Design Test, a nonverbal measure of intelligence. Analyses of genetic and environmental effects on behavior are possible with this kind of information. (SA)

  5. Analysis of Quantitative Traits in Two Long-Term Randomly Mated Soybean Populations I. Genetic Variances

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The genetic effects of long term random mating and natural selection aided by genetic male sterility were evaluated in two soybean [Glycine max (L.) Merr.] populations: RSII and RSIII. Population means, variances, and heritabilities were estimated to determine the effects of 26 generations of random...

  6. Age-specific patterns of genetic variance in Drosophila melanogaster. II. Fecundity and its genetic covariance with age-specific mortality

    SciTech Connect

    Tatar, M.; Promislow, D.E.L.; Khazaeli, A.A.; Curtsinger, J.W.

    1996-06-01

    Under the mutation accumulation model of senescence, it was predicted that the additive genetic variance (V{sub A}) 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 biomodal pattern for V{sub A} 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. 75 refs., 4 figs., 1 tab.

  7. Age-Specific Patterns of Genetic Variance in Drosophila Melanogaster. II. Fecundity and Its Genetic Covariance with Age-Specific Mortality

    PubMed Central

    Tatar, M.; Promislow, DEL.; Khazaeli, A. A.; Curtsinger, J. W.

    1996-01-01

    Under the mutation accumulation model of senescence, it was predicted that the additive genetic variance (V(A)) 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 V(A) 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. PMID:8725233

  8. Quantitative genetic variance and multivariate clines in the Ivyleaf morning glory, Ipomoea hederacea

    PubMed Central

    Stock, Amanda J.; Campitelli, Brandon E.; Stinchcombe, John R.

    2014-01-01

    Clinal variation is commonly interpreted as evidence of adaptive differentiation, although clines can also be produced by stochastic forces. Understanding whether clines are adaptive therefore requires comparing clinal variation to background patterns of genetic differentiation at presumably neutral markers. Although this approach has frequently been applied to single traits at a time, we have comparatively fewer examples of how multiple correlated traits vary clinally. Here, we characterize multivariate clines in the Ivyleaf morning glory, examining how suites of traits vary with latitude, with the goal of testing for divergence in trait means that would indicate past evolutionary responses. We couple this with analysis of genetic variance in clinally varying traits in 20 populations to test whether past evolutionary responses have depleted genetic variance, or whether genetic variance declines approaching the range margin. We find evidence of clinal differentiation in five quantitative traits, with little evidence of isolation by distance at neutral loci that would suggest non-adaptive or stochastic mechanisms. Within and across populations, the traits that contribute most to population differentiation and clinal trends in the multivariate phenotype are genetically variable as well, suggesting that a lack of genetic variance will not cause absolute evolutionary constraints. Our data are broadly consistent theoretical predictions of polygenic clines in response to shallow environmental gradients. Ecologically, our results are consistent with past findings of natural selection on flowering phenology, presumably due to season-length variation across the range. PMID:25002704

  9. Quantitative genetic variance and multivariate clines in the Ivyleaf morning glory, Ipomoea hederacea.

    PubMed

    Stock, Amanda J; Campitelli, Brandon E; Stinchcombe, John R

    2014-08-19

    Clinal variation is commonly interpreted as evidence of adaptive differentiation, although clines can also be produced by stochastic forces. Understanding whether clines are adaptive therefore requires comparing clinal variation to background patterns of genetic differentiation at presumably neutral markers. Although this approach has frequently been applied to single traits at a time, we have comparatively fewer examples of how multiple correlated traits vary clinally. Here, we characterize multivariate clines in the Ivyleaf morning glory, examining how suites of traits vary with latitude, with the goal of testing for divergence in trait means that would indicate past evolutionary responses. We couple this with analysis of genetic variance in clinally varying traits in 20 populations to test whether past evolutionary responses have depleted genetic variance, or whether genetic variance declines approaching the range margin. We find evidence of clinal differentiation in five quantitative traits, with little evidence of isolation by distance at neutral loci that would suggest non-adaptive or stochastic mechanisms. Within and across populations, the traits that contribute most to population differentiation and clinal trends in the multivariate phenotype are genetically variable as well, suggesting that a lack of genetic variance will not cause absolute evolutionary constraints. Our data are broadly consistent theoretical predictions of polygenic clines in response to shallow environmental gradients. Ecologically, our results are consistent with past findings of natural selection on flowering phenology, presumably due to season-length variation across the range. PMID:25002704

  10. Two-Variance-Component Model Improves Genetic Prediction in Family Datasets

    PubMed Central

    Tucker, George; Loh, Po-Ru; MacLeod, Iona M.; Hayes, Ben J.; Goddard, Michael E.; Berger, Bonnie; Price, Alkes L.

    2015-01-01

    Genetic prediction based on either identity by state (IBS) sharing or pedigree information has been investigated extensively with best linear unbiased prediction (BLUP) methods. Such methods were pioneered in plant and animal-breeding literature and have since been applied to predict human traits, with the aim of eventual clinical utility. However, methods to combine IBS sharing and pedigree information for genetic prediction in humans have not been explored. We introduce a two-variance-component model for genetic prediction: one component for IBS sharing and one for approximate pedigree structure, both estimated with genetic markers. In simulations using real genotypes from the Candidate-gene Association Resource (CARe) and Framingham Heart Study (FHS) family cohorts, we demonstrate that the two-variance-component model achieves gains in prediction r2 over standard BLUP at current sample sizes, and we project, based on simulations, that these gains will continue to hold at larger sample sizes. Accordingly, in analyses of four quantitative phenotypes from CARe and two quantitative phenotypes from FHS, the two-variance-component model significantly improves prediction r2 in each case, with up to a 20% relative improvement. We also find that standard mixed-model association tests can produce inflated test statistics in datasets with related individuals, whereas the two-variance-component model corrects for inflation. PMID:26544803

  11. Two-Variance-Component Model Improves Genetic Prediction in Family Datasets.

    PubMed

    Tucker, George; Loh, Po-Ru; MacLeod, Iona M; Hayes, Ben J; Goddard, Michael E; Berger, Bonnie; Price, Alkes L

    2015-11-01

    Genetic prediction based on either identity by state (IBS) sharing or pedigree information has been investigated extensively with best linear unbiased prediction (BLUP) methods. Such methods were pioneered in plant and animal-breeding literature and have since been applied to predict human traits, with the aim of eventual clinical utility. However, methods to combine IBS sharing and pedigree information for genetic prediction in humans have not been explored. We introduce a two-variance-component model for genetic prediction: one component for IBS sharing and one for approximate pedigree structure, both estimated with genetic markers. In simulations using real genotypes from the Candidate-gene Association Resource (CARe) and Framingham Heart Study (FHS) family cohorts, we demonstrate that the two-variance-component model achieves gains in prediction r(2) over standard BLUP at current sample sizes, and we project, based on simulations, that these gains will continue to hold at larger sample sizes. Accordingly, in analyses of four quantitative phenotypes from CARe and two quantitative phenotypes from FHS, the two-variance-component model significantly improves prediction r(2) in each case, with up to a 20% relative improvement. We also find that standard mixed-model association tests can produce inflated test statistics in datasets with related individuals, whereas the two-variance-component model corrects for inflation. PMID:26544803

  12. Estimation of genetic parameters and their sampling variances of quantitative traits in the type 2 modified augmented design

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We proposed a method to estimate the error variance among non-replicated genotypes, thus to estimate the genetic parameters by using replicated controls. We derived formulas to estimate sampling variances of the genetic parameters. Computer simulation indicated that the proposed methods of estimatin...

  13. Variance components for statistical genetics: applications in medical research to characteristics related to human diseases and health.

    PubMed

    Hopper, J L

    1993-01-01

    RA Fisher introduced variance components in 1918. He synthesized Mendelian inheritance with Darwin's theory of evolution by showing that the genetic variance of a continuous trait could be decomposed into additive and non-additive components. The model can be extended to include environmental factors, interactions, covariation, and non-random mating. Identifiability depends critically on design. Methods of analysis include modelling the mean squares from a fixed effects analysis of variance, and covariance structure modelling, which can be extended to multivariate traits and has been used to study ordinal traits by reference to postulated, unmeasured, latent 'liabilities'. These methods operate on dependent observations within independent groups of the same size and structure, and therefore require balanced designs ('regular' pedigrees). A multivariate normal model handles data in its generic form, utilizes data efficiently from all members of pedigrees of unequal size or varying structure, accommodates individuals missing at random, and allows flexible modelling with tests of distributional assumptions and fit. Most analytical methods use least squares or maximum likelihood under normal theory. Robust methods, scale transformation, ascertainment, path diagrams and correlational path models (popular in behavioural genetics through addressing nonrandom mating and social interactions), 'heritability', and the contribution and limitations of statistical modelling to the 'nature-nurture' debate, are discussed. PMID:8261258

  14. Additive genetic effect of APOE and BDNF on hippocampus activity.

    PubMed

    Kauppi, Karolina; Nilsson, Lars-Göran; Persson, Jonas; Nyberg, Lars

    2014-04-01

    Human memory is a highly heritable polygenic trait with complex inheritance patterns. To study the genetics of memory and memory-related diseases, hippocampal functioning has served as an intermediate phenotype. The importance of investigating gene-gene effects on complex phenotypes has been emphasized, but most imaging studies still focus on single polymorphisms. APOE ε4 and BDNF Met, two of the most studied gene variants for variability in memory performance and neuropsychiatric disorders, have both separately been related to poorer episodic memory and altered hippocampal functioning. Here, we investigated the combined effect of APOE and BDNF on hippocampal activation (N=151). No non-additive interaction effects were seen. Instead, the results revealed decreased activation in bilateral hippocampus and parahippocampus as a function of the number of APOE ε4 and BDNF Met alleles present (neither, one, or both). The combined effect was stronger than either of the individual effects, and both gene variables explained significant proportions of variance in BOLD signal change. Thus, there was an additive gene-gene effect of APOE and BDNF on medial temporal lobe (MTL) activation, showing that a larger proportion of variance in brain activation attributed to genetics can be explained by considering more than one gene variant. This effect might be relevant for the understanding of normal variability in memory function as well as memory-related disorders associated with APOE and BDNF. PMID:24321557

  15. Editing genomic DNA in cancer cells with high genetic variance: benefit or risk?

    PubMed

    Wang, Lin; Wang, Yixiang; Guo, Chuanbin

    2014-05-01

    The generation of stably-transfected cell lines is a common and very important technology in cancer science. Considerable knowledge in the field of life sciences has been gained through the modification of the genetic code. However, there is a risk in evaluating exogenous gene function through editing genomic DNA in a cancer cell with high genetic variance. In the present study, we showed that genomic DNA status should be considered when evaluating the exogenous gene function in a cancer cell line with high variant genome through stable transfection technology, immunostaining, wound healing assay, transwell invasion assay, real-time PCR, western blot and karyotyping analysis. Our results showed that the S100P expression level was not related to the migration and invasion abilities in these stably transfected cell lines derived from a human salivary adenoid cystic carcinoma cell line SACC-83. The MMP expression pattern was detected by western blot analysis which matched the biological behaviors in these cells. The genomic analysis showed that SACC-83 presented hypotetraploid karyotyping with high variance. Our data indicated that establishment of stable transgenic cancer cell lines should consider the status of genetic variance in a cancer cell to avoid any biased conclusion. PMID:24604254

  16. Genetic variances and covariances of aerobic metabolic rates in laboratory mice

    PubMed Central

    Wone, Bernard; Sears, Michael W.; Labocha, Marta K.; Donovan, Edward R.; Hayes, Jack P.

    2009-01-01

    The genetic variances and covariances of traits must be known to predict how they may respond to selection and how covariances among them might affect their evolutionary trajectories. We used the animal model to estimate the genetic variances and covariances of basal metabolic rate (BMR) and maximal metabolic rate (MMR) in a genetically heterogeneous stock of laboratory mice. Narrow-sense heritability (h2) was approximately 0.38 ± 0.08 for body mass, 0.26 ± 0.08 for whole-animal BMR, 0.24 ± 0.07 for whole-animal MMR, 0.19 ± 0.07 for mass-independent BMR, and 0.16 ± 0.06 for mass-independent MMR. All h2 estimates were significantly different from zero. The phenotypic correlation of whole animal BMR and MMR was 0.56 ± 0.02, and the corresponding genetic correlation was 0.79 ± 0.12. The phenotypic correlation of mass-independent BMR and MMR was 0.13 ± 0.03, and the corresponding genetic correlation was 0.72 ± 0.03. The genetic correlations of metabolic rates were significantly different from zero, but not significantly different from one. A key assumption of the aerobic capacity model for the evolution of endothermy is that BMR and MMR are linked. The estimated genetic correlation between BMR and MMR is consistent with that assumption, but the genetic correlation is not so high as to preclude independent evolution of BMR and MMR. PMID:19656796

  17. Genetic interactions contribute less than additive effects to quantitative trait variation in yeast

    PubMed Central

    Bloom, Joshua S.; Kotenko, Iulia; Sadhu, Meru J.; Treusch, Sebastian; Albert, Frank W.; Kruglyak, Leonid

    2015-01-01

    Genetic mapping studies of quantitative traits typically focus on detecting loci that contribute additively to trait variation. Genetic interactions are often proposed as a contributing factor to trait variation, but the relative contribution of interactions to trait variation is a subject of debate. Here we use a very large cross between two yeast strains to accurately estimate the fraction of phenotypic variance due to pairwise QTL–QTL interactions for 20 quantitative traits. We find that this fraction is 9% on average, substantially less than the contribution of additive QTL (43%). Statistically significant QTL–QTL pairs typically have small individual effect sizes, but collectively explain 40% of the pairwise interaction variance. We show that pairwise interaction variance is largely explained by pairs of loci at least one of which has a significant additive effect. These results refine our understanding of the genetic architecture of quantitative traits and help guide future mapping studies. PMID:26537231

  18. RFLP variation and genealogical distance, multivariate distance, heterosis, and genetic variance in oats.

    PubMed

    Moser, H; Lee, M

    1994-03-01

    Patterns of restriction fragment length polymorphisms (RFLPs) have been proposed as estimators of genetic diversity among breeding lines and as predictors of heterosis and genetic variance. We evaluated these proposals by using a set of nine elite oat lines crossed in a diallel mating design without reciprocals. RFLP analysis was conducted using HindIII-digested DNA and a total of 107 probes from three different sources: 14 heterologous wheat cDNA clones, 17 oat genomic clones, and 76 oat cDNA clones. Of the 77 probes that produced high-quality autoradiographs, 26 detected polymorphisms among this set of lines, with an average of 2.6 variants per probe. RFLP-based genetic distance (FD) was calculated from these data by using Nei and Li's measure of genetic similarity, and was compared with two other measures of genetic divergence. Genealogical distance (GD (*)) was obtained from the coefficients of parentage based on known parental pedigrees, and multivariate distance (DI) was calculated by using the first five principal components of the parental correlation matrix for 12 agronomic traits. FD was significantly correlated with GD (*) (r=0.63, P<0.01), but not with DI (r=-0.05). Cluster analysis based on these three distance estimates did not produce equivalent groupings, but the FD and GD (*) clusters were more similar to each other than to the DI clusters. These results indicate that: (1) sufficient variation exists for further application of RFLP technologyto oats, (2) RFLPs could provide accurate estimates of genetic divergence among elite oat lines, and (3) it is unlikely that dispersed markers can predict heterosis or population genetic variance in oats. Further investigations will require more parental lines, a larger set of markers, and more information on the linkage relationships between RFLP markers and loci controlling the trait of interest. PMID:24190529

  19. Genetically Determined Variation in Lysis Time Variance in the Bacteriophage φX174

    PubMed Central

    Baker, Christopher W.; Miller, Craig R.; Thaweethai, Tanayott; Yuan, Jeffrey; Baker, Meghan Hollibaugh; Joyce, Paul; Weinreich, Daniel M.

    2016-01-01

    Researchers in evolutionary genetics recently have recognized an exciting opportunity in decomposing beneficial mutations into their proximal, mechanistic determinants. The application of methods and concepts from molecular biology and life history theory to studies of lytic bacteriophages (phages) has allowed them to understand how natural selection sees mutations influencing life history. This work motivated the research presented here, in which we explored whether, under consistent experimental conditions, small differences in the genome of bacteriophage φX174 could lead to altered life history phenotypes among a panel of eight genetically distinct clones. We assessed the clones’ phenotypes by applying a novel statistical framework to the results of a serially sampled parallel infection assay, in which we simultaneously inoculated each of a large number of replicate host volumes with ∼1 phage particle. We sequentially plated the volumes over the course of infection and counted the plaques that formed after incubation. These counts served as a proxy for the number of phage particles in a single volume as a function of time. From repeated assays, we inferred significant, genetically determined heterogeneity in lysis time and burst size, including lysis time variance. These findings are interesting in light of the genetic and phenotypic constraints on the single-protein lysis mechanism of φX174. We speculate briefly on the mechanisms underlying our results, and we discuss the potential importance of lysis time variance in viral evolution. PMID:26921293

  20. Genetic selection for increased mean and reduced variance of twinning rate in Belclare ewes.

    PubMed

    Cottle, D J; Gilmour, A R; Pabiou, T; Amer, P R; Fahey, A G

    2016-04-01

    It is sometimes possible to breed for more uniform individuals by selecting animals with a greater tendency to be less variable, that is, those with a smaller environmental variance. This approach has been applied to reproduction traits in various animal species. We have evaluated fecundity in the Irish Belclare sheep breed by analyses of flocks with differing average litter size (number of lambs per ewe per year, NLB) and have estimated the genetic variance in environmental variance of lambing traits using double hierarchical generalized linear models (DHGLM). The data set comprised of 9470 litter size records from 4407 ewes collected in 56 flocks. The percentage of pedigreed lambing ewes with singles, twins and triplets was 30, 54 and 14%, respectively, in 2013 and has been relatively constant for the last 15 years. The variance of NLB increases with the mean in this data; the correlation of mean and standard deviation across sires is 0.50. The breeding goal is to increase the mean NLB without unduly increasing the incidence of triplets and higher litter sizes. The heritability estimates for lambing traits were NLB, 0.09; triplet occurrence (TRI) 0.07; and twin occurrence (TWN), 0.02. The highest and lowest twinning flocks differed by 23% (75% versus 52%) in the proportion of ewes lambing twins. Fitting bivariate sire models to NLB and the residual from the NLB model using a double hierarchical generalized linear model (DHGLM) model found a strong genetic correlation (0.88 ± 0.07) between the sire effect for the magnitude of the residual (VE ) and sire effects for NLB, confirming the general observation that increased average litter size is associated with increased variability in litter size. We propose a threshold model that may help breeders with low litter size increase the percentage of twin bearers without unduly increasing the percentage of ewes bearing triplets in Belclare sheep. PMID:26081782

  1. Estimating additive and dominance variances for complex traits in pigs combining genomic and pedigree information.

    PubMed

    Costa, E V; Diniz, D B; Veroneze, R; Resende, M D V; Azevedo, C F; Guimaraes, S E F; Silva, F F; Lopes, P S

    2015-01-01

    Knowledge of dominance effects should improve ge-netic evaluations, provide the accurate selection of purebred animals, and enable better breeding strategies, including the exploitation of het-erosis in crossbreeds. In this study, we combined genomic and pedi-gree data to study the relative importance of additive and dominance genetic variation in growth and carcass traits in an F2 pig population. Two GBLUP models were used, a model without a polygenic effect (ADM) and a model with a polygenic effect (ADMP). Additive effects played a greater role in the control of growth and carcass traits than did dominance effects. However, dominance effects were important for all traits, particularly in backfat thickness. The narrow-sense and broad-sense heritability estimates for growth (0.06 to 0.42, and 0.10 to 0.51, respectively) and carcass traits (0.07 to 0.37, and 0.10 to 0.76, respec-tively) exhibited a wide variation. The inclusion of a polygenic effect in the ADMP model changed the broad-sense heritability estimates only for birth weight and weight at 21 days of age. PMID:26125833

  2. Sex chromosome linked genetic variance and the evolution of sexual dimorphism of quantitative traits.

    PubMed

    Husby, Arild; Schielzeth, Holger; Forstmeier, Wolfgang; Gustafsson, Lars; Qvarnström, Anna

    2013-03-01

    Theory predicts that sex chromsome linkage should reduce intersexual genetic correlations thereby allowing the evolution of sexual dimorphism. Empirical evidence for sex linkage has come largely from crosses and few studies have examined how sexual dimorphism and sex linkage are related within outbred populations. Here, we use data on an array of different traits measured on over 10,000 individuals from two pedigreed populations of birds (collared flycatcher and zebra finch) to estimate the amount of sex-linked genetic variance (h(2)z ). Of 17 traits examined, eight showed a nonzero h(2)Z estimate but only four were significantly different from zero (wing patch size and tarsus length in collared flycatchers, wing length and beak color in zebra finches). We further tested how sexual dimorphism and the mode of selection operating on the trait relate to the proportion of sex-linked genetic variance. Sexually selected traits did not show higher h(2)Z than morphological traits and there was only a weak positive relationship between h(2)Z and sexual dimorphism. However, given the relative scarcity of empirical studies, it is premature to make conclusions about the role of sex chromosome linkage in the evolution of sexual dimorphism. PMID:23461313

  3. Planning additional drilling campaign using two-space genetic algorithm: A game theoretical approach

    NASA Astrophysics Data System (ADS)

    Kumral, Mustafa; Ozer, Umit

    2013-03-01

    Grade and tonnage are the most important technical uncertainties in mining ventures because of the use of estimations/simulations, which are mostly generated from drill data. Open pit mines are planned and designed on the basis of the blocks representing the entire orebody. Each block has different estimation/simulation variance reflecting uncertainty to some extent. The estimation/simulation realizations are submitted to mine production scheduling process. However, the use of a block model with varying estimation/simulation variances will lead to serious risk in the scheduling. In the medium of multiple simulations, the dispersion variances of blocks can be thought to regard technical uncertainties. However, the dispersion variance cannot handle uncertainty associated with varying estimation/simulation variances of blocks. This paper proposes an approach that generates the configuration of the best additional drilling campaign to generate more homogenous estimation/simulation variances of blocks. In other words, the objective is to find the best drilling configuration in such a way as to minimize grade uncertainty under budget constraint. Uncertainty measure of the optimization process in this paper is interpolation variance, which considers data locations and grades. The problem is expressed as a minmax problem, which focuses on finding the best worst-case performance i.e., minimizing interpolation variance of the block generating maximum interpolation variance. Since the optimization model requires computing the interpolation variances of blocks being simulated/estimated in each iteration, the problem cannot be solved by standard optimization tools. This motivates to use two-space genetic algorithm (GA) approach to solve the problem. The technique has two spaces: feasible drill hole configuration with minimization of interpolation variance and drill hole simulations with maximization of interpolation variance. Two-space interacts to find a minmax solution

  4. 77 FR 9637 - Process for Requesting a Variance From Vegetation Standards for Levees and Floodwalls; Additional...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-02-17

    .... If the prism is not smaller than the existing levee cross section, it is unlikely that a variance... dimension the levee prism (see Figure 1). The prism is the minimum analytical cross section that, given site... require a larger prism. The prism must also satisfy the requirements of any other applicable standard....

  5. Contrasting genetic architectures of schizophrenia and other complex diseases using fast variance-components analysis.

    PubMed

    Loh, Po-Ru; Bhatia, Gaurav; Gusev, Alexander; Finucane, Hilary K; Bulik-Sullivan, Brendan K; Pollack, Samuela J; de Candia, Teresa R; Lee, Sang Hong; Wray, Naomi R; Kendler, Kenneth S; O'Donovan, Michael C; Neale, Benjamin M; Patterson, Nick; Price, Alkes L

    2015-12-01

    Heritability analyses of genome-wide association study (GWAS) cohorts have yielded important insights into complex disease architecture, and increasing sample sizes hold the promise of further discoveries. Here we analyze the genetic architectures of schizophrenia in 49,806 samples from the PGC and nine complex diseases in 54,734 samples from the GERA cohort. For schizophrenia, we infer an overwhelmingly polygenic disease architecture in which ≥71% of 1-Mb genomic regions harbor ≥1 variant influencing schizophrenia risk. We also observe significant enrichment of heritability in GC-rich regions and in higher-frequency SNPs for both schizophrenia and GERA diseases. In bivariate analyses, we observe significant genetic correlations (ranging from 0.18 to 0.85) for several pairs of GERA diseases; genetic correlations were on average 1.3 tunes stronger than the correlations of overall disease liabilities. To accomplish these analyses, we developed a fast algorithm for multicomponent, multi-trait variance-components analysis that overcomes prior computational barriers that made such analyses intractable at this scale. PMID:26523775

  6. Contrasting genetic architectures of schizophrenia and other complex diseases using fast variance components analysis

    PubMed Central

    Bhatia, Gaurav; Gusev, Alexander; Finucane, Hilary K; Bulik-Sullivan, Brendan K; Pollack, Samuela J; de Candia, Teresa R; Lee, Sang Hong; Wray, Naomi R; Kendler, Kenneth S; O’Donovan, Michael C; Neale, Benjamin M; Patterson, Nick

    2015-01-01

    Heritability analyses of GWAS cohorts have yielded important insights into complex disease architecture, and increasing sample sizes hold the promise of further discoveries. Here, we analyze the genetic architecture of schizophrenia in 49,806 samples from the PGC, and nine complex diseases in 54,734 samples from the GERA cohort. For schizophrenia, we infer an overwhelmingly polygenic disease architecture in which ≥71% of 1Mb genomic regions harbor ≥1 variant influencing schizophrenia risk. We also observe significant enrichment of heritability in GC-rich regions and in higher-frequency SNPs for both schizophrenia and GERA diseases. In bivariate analyses, we observe significant genetic correlations (ranging from 0.18 to 0.85) among several pairs of GERA diseases; genetic correlations were on average 1.3x stronger than correlations of overall disease liabilities. To accomplish these analyses, we developed a fast algorithm for multi-component, multi-trait variance components analysis that overcomes prior computational barriers that made such analyses intractable at this scale. PMID:26523775

  7. Genetic and phenotypic variance and covariance components for methane emission and postweaning traits in Angus cattle.

    PubMed

    Donoghue, K A; Bird-Gardiner, T; Arthur, P F; Herd, R M; Hegarty, R F

    2016-04-01

    Ruminants contribute 80% of the global livestock greenhouse gas (GHG) emissions mainly through the production of methane, a byproduct of enteric microbial fermentation primarily in the rumen. Hence, reducing enteric methane production is essential in any GHG emissions reduction strategy in livestock. Data on 1,046 young bulls and heifers from 2 performance-recording research herds of Angus cattle were analyzed to provide genetic and phenotypic variance and covariance estimates for methane emissions and production traits and to examine the interrelationships among these traits. The cattle were fed a roughage diet at 1.2 times their estimated maintenance energy requirements and measured for methane production rate (MPR) in open circuit respiration chambers for 48 h. Traits studied included DMI during the methane measurement period, MPR, and methane yield (MY; MPR/DMI), with means of 6.1 kg/d (SD 1.3), 132 g/d (SD 25), and 22.0 g/kg (SD 2.3) DMI, respectively. Four forms of residual methane production (RMP), which is a measure of actual minus predicted MPR, were evaluated. For the first 3 forms, predicted MPR was calculated using published equations. For the fourth (RMP), predicted MPR was obtained by regression of MPR on DMI. Growth and body composition traits evaluated were birth weight (BWT), weaning weight (WWT), yearling weight (YWT), final weight (FWT), and ultrasound measures of eye muscle area, rump fat depth, rib fat depth, and intramuscular fat. Heritability estimates were moderate for MPR (0.27 [SE 0.07]), MY (0.22 [SE 0.06]), and the RMP traits (0.19 [SE 0.06] for each), indicating that genetic improvement to reduce methane emissions is possible. The RMP traits and MY were strongly genetically correlated with each other (0.99 ± 0.01). The genetic correlation of MPR with MY as well as with the RMP traits was moderate (0.32 to 0.63). The genetic correlation between MPR and the growth traits (except BWT) was strong (0.79 to 0.86). These results indicate that

  8. High-dimensional variance partitioning reveals the modular genetic basis of adaptive divergence in gene expression during reproductive character displacement.

    PubMed

    McGraw, Elizabeth A; Ye, Yixin H; Foley, Brad; Chenoweth, Stephen F; Higgie, Megan; Hine, Emma; Blows, Mark W

    2011-11-01

    Although adaptive change is usually associated with complex changes in phenotype, few genetic investigations have been conducted on adaptations that involve sets of high-dimensional traits. Microarrays have supplied high-dimensional descriptions of gene expression, and phenotypic change resulting from adaptation often results in large-scale changes in gene expression. We demonstrate how genetic analysis of large-scale changes in gene expression generated during adaptation can be accomplished by determining high-dimensional variance partitioning within classical genetic experimental designs. A microarray experiment conducted on a panel of recombinant inbred lines (RILs) generated from two populations of Drosophila serrata that have diverged in response to natural selection, revealed genetic divergence in 10.6% of 3762 gene products examined. Over 97% of the genetic divergence in transcript abundance was explained by only 12 genetic modules. The two most important modules, explaining 50% of the genetic variance in transcript abundance, were genetically correlated with the morphological traits that are known to be under selection. The expression of three candidate genes from these two important genetic modules was assessed in an independent experiment using qRT-PCR on 430 individuals from the panel of RILs, and confirmed the genetic association between transcript abundance and morphological traits under selection. PMID:22023580

  9. Unnatural reactive amino acid genetic code additions

    SciTech Connect

    Deiters, Alexander; Cropp, T. Ashton; Chin, Jason W.; Anderson, J. Christopher; Schultz, Peter G.

    2011-08-09

    This invention provides compositions and methods for producing translational components that expand the number of genetically encoded amino acids in eukaryotic cells. The components include orthogonal tRNAs, orthogonal aminoacyl-tRNAsyn-thetases, pairs of tRNAs/synthetases and unnatural amino acids. Proteins and methods of producing proteins with unnatural amino acids in eukaryotic cells are also provided.

  10. Unnatural reactive amino acid genetic code additions

    SciTech Connect

    Deiters, Alexander; Cropp, Ashton T; Chin, Jason W; Anderson, Christopher J; Schultz, Peter G

    2013-05-21

    This invention provides compositions and methods for producing translational components that expand the number of genetically encoded amino acids in eukaryotic cells. The components include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, pairs of tRNAs/synthetases and unnatural amino acids. Proteins and methods of producing proteins with unnatural amino acids in eukaryotic cells are also provided.

  11. Unnatural reactive amino acid genetic code additions

    SciTech Connect

    Deiters, Alexander; Cropp, T. Ashton; Chin, Jason W.; Anderson, J. Christopher; Schultz, Peter G.

    2014-08-26

    This invention provides compositions and methods for producing translational components that expand the number of genetically encoded amino acids in eukaryotic cells. The components include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, orthogonal pairs of tRNAs/synthetases and unnatural amino acids. Proteins and methods of producing proteins with unnatural amino acids in eukaryotic cells are also provided.

  12. Unnatural reactive amino acid genetic code additions

    SciTech Connect

    Deiters, Alexander; Cropp, T. Ashton; Chin, Jason W.; Anderson, J. Christopher; Schultz, Peter G.

    2011-02-15

    This invention provides compositions and methods for producing translational components that expand the number of genetically encoded amino acids in eukaryotic cells. The components include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, orthogonal pairs of tRNAs/synthetases and unnatural amino acids. Proteins and methods of producing proteins with unnatural amino acids in eukaryotic cells are also provided.

  13. Deleterious mutations and the genetic variance of male fitness components in Mimulus guttatus.

    PubMed Central

    Kelly, John K

    2003-01-01

    Deleterious mutations are relevant to a broad range of questions in genetics and evolutionary biology. I present an application of the "biometric method" for estimating mutational parameters for male fitness characters of the yellow monkeyflower, Mimulus guttatus. The biometric method rests on two critical assumptions. The first is that experimental inbreeding changes genotype frequencies without changing allele frequencies; i.e., there is no genetic purging during the experiment. I satisfy this condition by employing a breeding design in which the parents are randomly extracted, fully homozygous inbred lines. The second is that all genetic variation is attributable to deleterious mutations maintained in mutation-selection balance. I explicitly test this hypothesis using likelihood ratios. Of the three deleterious mutation models tested, the first two are rejected for all characters. The failure of these models is due to an excess of additive genetic variation relative to the expectation under mutation-selection balance. The third model is not rejected for either of two log-transformed male fitness traits. However, this model imposes only "weak conditions" and is not sufficiently detailed to provide estimates for mutational parameters. The implication is that, if biometric methods are going to yield useful parameter estimates, they will need to consider mutational models more complicated than those typically employed in experimental studies. PMID:12871916

  14. Small Variance in Growth Rate in Annual Plants has Large Effects on Genetic Drift

    Technology Transfer Automated Retrieval System (TEKTRAN)

    When plant size is strongly correlated with plant reproduction, variance in growth rates results in a lognormal distribution of seed production within a population. Fecundity variance affects effective population size (Ne), which reflects the ability of a population to maintain beneficial mutations ...

  15. Variance components and genetic parameters for milk production and lactation pattern in an ethiopian multibreed dairy cattle population.

    PubMed

    Gebreyohannes, Gebregziabher; Koonawootrittriron, Skorn; Elzo, Mauricio A; Suwanasopee, Thanathip

    2013-09-01

    The objective of this study was to estimate variance components and genetic parameters for lactation milk yield (LY), lactation length (LL), average milk yield per day (YD), initial milk yield (IY), peak milk yield (PY), days to peak (DP) and parameters (ln(a) and c) of the modified incomplete gamma function (MIG) in an Ethiopian multibreed dairy cattle population. The dataset was composed of 5,507 lactation records collected from 1,639 cows in three locations (Bako, Debre Zeit and Holetta) in Ethiopia from 1977 to 2010. Parameters for MIG were obtained from regression analysis of monthly test-day milk data on days in milk. The cows were purebred (Bos indicus) Boran (B) and Horro (H) and their crosses with different fractions of Friesian (F), Jersey (J) and Simmental (S). There were 23 breed groups (B, H, and their crossbreds with F, J, and S) in the population. Fixed and mixed models were used to analyse the data. The fixed model considered herd-year-season, parity and breed group as fixed effects, and residual as random. The single and two-traits mixed animal repeatability models, considered the fixed effects of herd-year-season and parity subclasses, breed as a function of cow H, F, J, and S breed fractions and general heterosis as a function of heterozygosity, and the random additive animal, permanent environment, and residual effects. For the analysis of LY, LL was added as a fixed covariate to all models. Variance components and genetic parameters were estimated using average information restricted maximum likelihood procedures. The results indicated that all traits were affected (p<0.001) by the considered fixed effects. High grade B×F cows (3/16B 13/16F) had the highest least squares means (LSM) for LY (2,490±178.9 kg), IY (10.5±0.8 kg), PY (12.7±0.9 kg), YD (7.6±0.55 kg) and LL (361.4±31.2 d), while B cows had the lowest LSM values for these traits. The LSM of LY, IY, YD, and PY tended to increase from the first to the fifth parity. Single

  16. Additive genetic contribution to symptom dimensions in major depressive disorder.

    PubMed

    Pearson, Rahel; Palmer, Rohan H C; Brick, Leslie A; McGeary, John E; Knopik, Valerie S; Beevers, Christopher G

    2016-05-01

    Major depressive disorder (MDD) is a phenotypically heterogeneous disorder with a complex genetic architecture. In this study, genomic-relatedness-matrix restricted maximum-likelihood analysis (GREML) was used to investigate the extent to which variance in depression symptoms/symptom dimensions can be explained by variation in common single nucleotide polymorphisms (SNPs) in a sample of individuals with MDD (N = 1,558) who participated in the National Institute of Mental Health Sequenced Treatment Alternatives to Relieve Depression (STAR*D) study. A principal components analysis of items from the Hamilton Rating Scale for Depression (HRSD) obtained prior to treatment revealed 4 depression symptom components: (a) appetite, (b) core depression symptoms (e.g., depressed mood, anhedonia), (c) insomnia, and (d) anxiety. These symptom dimensions were associated with SNP-based heritability (hSNP2) estimates of 30%, 14%, 30%, and 5%, respectively. Results indicated that the genetic contribution of common SNPs to depression symptom dimensions were not uniform. Appetite and insomnia symptoms in MDD had a relatively strong genetic contribution whereas the genetic contribution was relatively small for core depression and anxiety symptoms. While in need of replication, these results suggest that future gene discovery efforts may strongly benefit from parsing depression into its constituent parts. (PsycINFO Database Record PMID:27124715

  17. Mapping Quantitative Trait Loci Using Naturally Occurring Genetic Variance Among Commercial Inbred Lines of Maize (Zea mays L.)

    PubMed Central

    Zhang, Yuan-Ming; Mao, Yongcai; Xie, Chongqing; Smith, Howie; Luo, Lang; Xu, Shizhong

    2005-01-01

    Many commercial inbred lines are available in crops. A large amount of genetic variation is preserved among these lines. The genealogical history of the inbred lines is usually well documented. However, quantitative trait loci (QTL) responsible for the genetic variances among the lines are largely unexplored due to lack of statistical methods. In this study, we show that the pedigree information of the lines along with the trait values and marker information can be used to map QTL without the need of further crossing experiments. We develop a Monte Carlo method to estimate locus-specific identity-by-descent (IBD) matrices. These IBD matrices are further incorporated into a mixed-model equation for variance component analysis. QTL variance is estimated and tested at every putative position of the genome. The actual QTL are detected by scanning the entire genome. Applying this new method to a well-documented pedigree of maize (Zea mays L.) that consists of 404 inbred lines, we mapped eight QTL for the maize male flowering trait, growing degree day heat units to pollen shedding (GDUSHD). These detected QTL contributed >80% of the variance observed among the inbred lines. The QTL were then used to evaluate all the inbred lines using the best linear unbiased prediction (BLUP) technique. Superior lines were selected according to the estimated QTL allelic values, a technique called marker-assisted selection (MAS). The MAS procedure implemented via BLUP may be routinely used by breeders to select superior lines and line combinations for development of new cultivars. PMID:15716509

  18. Nonlinear Epigenetic Variance: Review and Simulations

    ERIC Educational Resources Information Center

    Kan, Kees-Jan; Ploeger, Annemie; Raijmakers, Maartje E. J.; Dolan, Conor V.; van Der Maas, Han L. J.

    2010-01-01

    We present a review of empirical evidence that suggests that a substantial portion of phenotypic variance is due to nonlinear (epigenetic) processes during ontogenesis. The role of such processes as a source of phenotypic variance in human behaviour genetic studies is not fully appreciated. In addition to our review, we present simulation studies…

  19. Genetic Variance in Processing Speed Drives Variation in Aging of Spatial and Memory Abilities

    ERIC Educational Resources Information Center

    Finkel, Deborah; Reynolds, Chandra A.; McArdle, John J.; Hamagami, Fumiaki; Pedersen, Nancy L.

    2009-01-01

    Previous analyses have identified a genetic contribution to the correlation between declines with age in processing speed and higher cognitive abilities. The goal of the current analysis was to apply the biometric dual change score model to consider the possibility of temporal dynamics underlying the genetic covariance between aging trajectories…

  20. Implementation of the Realized Genomic Relationship Matrix to Open-Pollinated White Spruce Family Testing for Disentangling Additive from Nonadditive Genetic Effects

    PubMed Central

    Gamal El-Dien, Omnia; Ratcliffe, Blaise; Klápště, Jaroslav; Porth, Ilga; Chen, Charles; El-Kassaby, Yousry A.

    2016-01-01

    The open-pollinated (OP) family testing combines the simplest known progeny evaluation and quantitative genetics analyses as candidates’ offspring are assumed to represent independent half-sib families. The accuracy of genetic parameter estimates is often questioned as the assumption of “half-sibling” in OP families may often be violated. We compared the pedigree- vs. marker-based genetic models by analysing 22-yr height and 30-yr wood density for 214 white spruce [Picea glauca (Moench) Voss] OP families represented by 1694 individuals growing on one site in Quebec, Canada. Assuming half-sibling, the pedigree-based model was limited to estimating the additive genetic variances which, in turn, were grossly overestimated as they were confounded by very minor dominance and major additive-by-additive epistatic genetic variances. In contrast, the implemented genomic pairwise realized relationship models allowed the disentanglement of additive from all nonadditive factors through genetic variance decomposition. The marker-based models produced more realistic narrow-sense heritability estimates and, for the first time, allowed estimating the dominance and epistatic genetic variances from OP testing. In addition, the genomic models showed better prediction accuracies compared to pedigree models and were able to predict individual breeding values for new individuals from untested families, which was not possible using the pedigree-based model. Clearly, the use of marker-based relationship approach is effective in estimating the quantitative genetic parameters of complex traits even under simple and shallow pedigree structure. PMID:26801647

  1. Estimation of the Proportion of Variation Accounted for by DNA Tests. I: Genetic Variance

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The proportion of genetic variation accounted for (Rg2) is an important characteristic of a DNA test. For each of 3 levels of narrow sense heritability of the observed trait (h2gy) and 4 levels of Rg2, 500 independent replicates of an observed trait and a molecular breeding value (MBV) for 1000 offs...

  2. Reasoning over genetic variance information in cause-and-effect models of neurodegenerative diseases

    PubMed Central

    Naz, Mufassra; Kodamullil, Alpha Tom

    2016-01-01

    The work we present here is based on the recent extension of the syntax of the Biological Expression Language (BEL), which now allows for the representation of genetic variation information in cause-and-effect models. In our article, we describe, how genetic variation information can be used to identify candidate disease mechanisms in diseases with complex aetiology such as Alzheimer’s disease and Parkinson’s disease. In those diseases, we have to assume that many genetic variants contribute moderately to the overall dysregulation that in the case of neurodegenerative diseases has such a long incubation time until the first clinical symptoms are detectable. Owing to the multilevel nature of dysregulation events, systems biomedicine modelling approaches need to combine mechanistic information from various levels, including gene expression, microRNA (miRNA) expression, protein–protein interaction, genetic variation and pathway. OpenBEL, the open source version of BEL, has recently been extended to match this requirement, and we demonstrate in our article, how candidate mechanisms for early dysregulation events in Alzheimer’s disease can be identified based on an integrative mining approach that identifies ‘chains of causation’ that include single nucleotide polymorphism information in BEL models. PMID:26249223

  3. Temporal Genetic Variance and Propagule-Driven Genetic Structure Characterize Naturalized Rainbow Trout (Oncorhynchus mykiss) from a Patagonian Lake Impacted by Trout Farming

    PubMed Central

    Seeb, Lisa W.; Seeb, James E.; Arismendi, Ivan; Hernández, Cristián E.; Gajardo, Gonzalo; Galleguillos, Ricardo; Cádiz, Maria I.; Musleh, Selim S.

    2015-01-01

    Knowledge about the genetic underpinnings of invasions—a theme addressed by invasion genetics as a discipline—is still scarce amid well documented ecological impacts of non-native species on ecosystems of Patagonia in South America. One of the most invasive species in Patagonia’s freshwater systems and elsewhere is rainbow trout (Oncorhynchus mykiss). This species was introduced to Chile during the early twentieth century for stocking and promoting recreational fishing; during the late twentieth century was reintroduced for farming purposes and is now naturalized. We used population- and individual-based inference from single nucleotide polymorphisms (SNPs) to illuminate three objectives related to the establishment and naturalization of Rainbow Trout in Lake Llanquihue. This lake has been intensively used for trout farming during the last three decades. Our results emanate from samples collected from five inlet streams over two seasons, winter and spring. First, we found that significant intra- population (temporal) genetic variance was greater than inter-population (spatial) genetic variance, downplaying the importance of spatial divergence during the process of naturalization. Allele frequency differences between cohorts, consistent with variation in fish length between spring and winter collections, might explain temporal genetic differences. Second, individual-based Bayesian clustering suggested that genetic structure within Lake Llanquihue was largely driven by putative farm propagules found at one single stream during spring, but not in winter. This suggests that farm broodstock might migrate upstream to breed during spring at that particular stream. It is unclear whether interbreeding has occurred between “pure” naturalized and farm trout in this and other streams. Third, estimates of the annual number of breeders (Nb) were below 73 in half of the collections, suggestive of genetically small and recently founded populations that might experience

  4. Temporal Genetic Variance and Propagule-Driven Genetic Structure Characterize Naturalized Rainbow Trout (Oncorhynchus mykiss) from a Patagonian Lake Impacted by Trout Farming.

    PubMed

    Benavente, Javiera N; Seeb, Lisa W; Seeb, James E; Arismendi, Ivan; Hernández, Cristián E; Gajardo, Gonzalo; Galleguillos, Ricardo; Cádiz, Maria I; Musleh, Selim S; Gomez-Uchida, Daniel

    2015-01-01

    Knowledge about the genetic underpinnings of invasions-a theme addressed by invasion genetics as a discipline-is still scarce amid well documented ecological impacts of non-native species on ecosystems of Patagonia in South America. One of the most invasive species in Patagonia's freshwater systems and elsewhere is rainbow trout (Oncorhynchus mykiss). This species was introduced to Chile during the early twentieth century for stocking and promoting recreational fishing; during the late twentieth century was reintroduced for farming purposes and is now naturalized. We used population- and individual-based inference from single nucleotide polymorphisms (SNPs) to illuminate three objectives related to the establishment and naturalization of Rainbow Trout in Lake Llanquihue. This lake has been intensively used for trout farming during the last three decades. Our results emanate from samples collected from five inlet streams over two seasons, winter and spring. First, we found that significant intra- population (temporal) genetic variance was greater than inter-population (spatial) genetic variance, downplaying the importance of spatial divergence during the process of naturalization. Allele frequency differences between cohorts, consistent with variation in fish length between spring and winter collections, might explain temporal genetic differences. Second, individual-based Bayesian clustering suggested that genetic structure within Lake Llanquihue was largely driven by putative farm propagules found at one single stream during spring, but not in winter. This suggests that farm broodstock might migrate upstream to breed during spring at that particular stream. It is unclear whether interbreeding has occurred between "pure" naturalized and farm trout in this and other streams. Third, estimates of the annual number of breeders (Nb) were below 73 in half of the collections, suggestive of genetically small and recently founded populations that might experience substantial

  5. Noise variance analysis using a flat panel x-ray detector: A method for additive noise assessment with application to breast CT applications

    SciTech Connect

    Yang Kai; Huang, Shih-Ying; Packard, Nathan J.; Boone, John M.

    2010-07-15

    Purpose: A simplified linear model approach was proposed to accurately model the response of a flat panel detector used for breast CT (bCT). Methods: Individual detector pixel mean and variance were measured from bCT projection images acquired both in air and with a polyethylene cylinder, with the detector operating in both fixed low gain and dynamic gain mode. Once the coefficients of the linear model are determined, the fractional additive noise can be used as a quantitative metric to evaluate the system's efficiency in utilizing x-ray photons, including the performance of different gain modes of the detector. Results: Fractional additive noise increases as the object thickness increases or as the radiation dose to the detector decreases. For bCT scan techniques on the UC Davis prototype scanner (80 kVp, 500 views total, 30 frames/s), in the low gain mode, additive noise contributes 21% of the total pixel noise variance for a 10 cm object and 44% for a 17 cm object. With the dynamic gain mode, additive noise only represents approximately 2.6% of the total pixel noise variance for a 10 cm object and 7.3% for a 17 cm object. Conclusions: The existence of the signal-independent additive noise is the primary cause for a quadratic relationship between bCT noise variance and the inverse of radiation dose at the detector. With the knowledge of the additive noise contribution to experimentally acquired images, system modifications can be made to reduce the impact of additive noise and improve the quantum noise efficiency of the bCT system.

  6. Efficient Improvement of Silage Additives by Using Genetic Algorithms

    PubMed Central

    Davies, Zoe S.; Gilbert, Richard J.; Merry, Roger J.; Kell, Douglas B.; Theodorou, Michael K.; Griffith, Gareth W.

    2000-01-01

    The enormous variety of substances which may be added to forage in order to manipulate and improve the ensilage process presents an empirical, combinatorial optimization problem of great complexity. To investigate the utility of genetic algorithms for designing effective silage additive combinations, a series of small-scale proof of principle silage experiments were performed with fresh ryegrass. Having established that significant biochemical changes occur over an ensilage period as short as 2 days, we performed a series of experiments in which we used 50 silage additive combinations (prepared by using eight bacterial and other additives, each of which was added at six different levels, including zero [i.e., no additive]). The decrease in pH, the increase in lactate concentration, and the free amino acid concentration were measured after 2 days and used to calculate a “fitness” value that indicated the quality of the silage (compared to a control silage made without additives). This analysis also included a “cost” element to account for different total additive levels. In the initial experiment additive levels were selected randomly, but subsequently a genetic algorithm program was used to suggest new additive combinations based on the fitness values determined in the preceding experiments. The result was very efficient selection for silages in which large decreases in pH and high levels of lactate occurred along with low levels of free amino acids. During the series of five experiments, each of which comprised 50 treatments, there was a steady increase in the amount of lactate that accumulated; the best treatment combination was that used in the last experiment, which produced 4.6 times more lactate than the untreated silage. The additive combinations that were found to yield the highest fitness values in the final (fifth) experiment were assessed to determine a range of biochemical and microbiological quality parameters during full-term silage

  7. FADS2 Genetic Variance in Combination with Fatty Acid Intake Might Alter Composition of the Fatty Acids in Brain.

    PubMed

    Rizzi, Thais S; van der Sluis, Sophie; Derom, Catherine; Thiery, Evert; van Kesteren, Ronald E; Jacobs, Nele; Van Gestel, Sofie; Vlietinck, Robert; Verhage, Matthijs; Heutink, Peter; Posthuma, Danielle

    2013-01-01

    Multiple lines of evidence suggest that fatty acids (FA) play an important role in cognitive function. However, little is known about the functional genetic pathways involved in cognition. The main goals of this study were to replicate previously reported interaction effects between breast feeding (BF) and FA desaturase (FADS) genetic variation on IQ and to investigate the possible mechanisms by which these variants might moderate BF effect, focusing on brain expression. Using a sample of 534 twins, we observed a trend in the moderation of BF effects on IQ by FADS2 variation. In addition, we made use of publicly available gene expression databases from both humans (193) and mice (93) and showed that FADS2 variants also correlate with FADS1 brain expression (P-value<1.1E-03). Our results provide novel clues for the understanding of the genetic mechanisms regulating FA brain expression and improve the current knowledge of the FADS moderation effect on cognition. PMID:23826354

  8. Locus BoLA-DRB3 is just an ordinary site of the polygene when explaining genetic variance of somatic cell count and milk yield.

    PubMed

    Oprzadek, Jolanta; Sender, Grazyna; Pawlik, Adrianna; Lukaszewicz, Marek

    2015-11-01

    The study aimed at clarifying the problem of the hitherto contradictory results regarding usefulness of BoLA-DRB3 locus as a marker in selection against mastitis and for milk yield. Treating the BoLA-DRB3 locus effect as random was proposed in place of considering it fixed. Somatic cell counts and milk yields recorded monthly on a test day (22,424) of 619 Polish Holstein cows genotyped for BoLA-DRB3 were analysed with an animal model including a random effect for genotype at this locus. The BoLA-DRB3 alleles were defined as restriction patterns obtained with three endonucleases. Two alternative BoLA-DRB3 additive genotype (co)variance structures were constructed for 161 genotypes recorded. One was based on the allelic similarity of the genotypes resulting in element values of 0 (no common allele), 0.5 (one allele in common), and 1 (diagonal). The other considered restriction site similarity (up to 3 in 1 allele) giving element values of 0 (no common restriction sites) and then increasingly in steps of 1/6 up to 6/6 (diagonal), where the numerator represents the number of common sites between genotypes. The DRB3 variance component for the natural logarithm of somatic cell count did not exceed 0.006 of the polygenic additive component or 0.003 for milk yield. Hence, unless we fail to detect the causative site or to properly define traits being the projection of a site, the effect of the genotype at the BoLA-DRB3 locus does not explain variation in somatic cell count and milk yield at a degree expected of a genetic marker. PMID:26333653

  9. Genetic variation and prediction of additive and nonadditive genetic effects for six carcass traits in an Angus-Brahman multibreed herd.

    PubMed

    Elzo, M A; West, R L; Johnson, D D; Wakeman, D L

    1998-07-01

    Estimates of covariances and sire expected progeny differences of additive and nonadditive genetic effects for six carcass traits were obtained using records from 486 straightbred and crossbred steers from 121 sires born between 1989 and 1995 in the Angus-Brahman multibreed herd of the University of Florida. Steers were slaughtered at a similar carcass composition end point. Covariances were estimated by REML procedures, using a generalized expectation-maximization algorithm applied to multibreed populations. Straightbred and crossbred estimates of heritabilities and additive genetic correlations were within ranges found in the literature for steers slaughtered on an age- or weight-constant basis for hot carcass weight, longissimus muscle area, and shear force but equal to or less than the lower bound of these ranges for fat-related traits. Maximum values of interactibilities (i.e., ratios of nonadditive variances to phenotypic variances in the F1) and nonadditive genetic correlations were smaller than heritabilities and additive genetic correlations in straightbreds and crossbred groups. Sire additive and total direct genetic predictions for longissimus muscle area, marbling, and shear force tended to decrease with the fraction of Brahman alleles, whereas those for hot carcass weight and fat thickness over the longissimus were higher, and those for kidney fat were lower in straightbreds and F1 than in other crossbred groups. Nonadditive genetic predictions were similar across sire groups of all Angus and Brahman fractions. These results suggest that slaughtering steers on a similar carcass composition basis reduces variability of fat-related traits while retaining variability for non-fat-related traits comparable to slaughtering steers on a similar age or weight basis. Selection for carcass traits within desirable (narrow) ranges and slaughter of steers at similar compositional end point seems to be a good combination to help produce meat products of consistent

  10. High variance in reproductive success generates a false signature of a genetic bottleneck in populations of constant size: a simulation study

    PubMed Central

    2013-01-01

    Background Demographic bottlenecks can severely reduce the genetic variation of a population or a species. Establishing whether low genetic variation is caused by a bottleneck or a constantly low effective number of individuals is important to understand a species’ ecology and evolution, and it has implications for conservation management. Recent studies have evaluated the power of several statistical methods developed to identify bottlenecks. However, the false positive rate, i.e. the rate with which a bottleneck signal is misidentified in demographically stable populations, has received little attention. We analyse this type of error (type I) in forward computer simulations of stable populations having greater than Poisson variance in reproductive success (i.e., variance in family sizes). The assumption of Poisson variance underlies bottleneck tests, yet it is commonly violated in species with high fecundity. Results With large variance in reproductive success (Vk ≥ 40, corresponding to a ratio between effective and census size smaller than 0.1), tests based on allele frequencies, allelic sizes, and DNA sequence polymorphisms (heterozygosity excess, M-ratio, and Tajima’s D test) tend to show erroneous signals of a bottleneck. Similarly, strong evidence of population decline is erroneously detected when ancestral and current population sizes are estimated with the model based method MSVAR. Conclusions Our results suggest caution when interpreting the results of bottleneck tests in species showing high variance in reproductive success. Particularly in species with high fecundity, computer simulations are recommended to confirm the occurrence of a population bottleneck. PMID:24131797

  11. Factor analysis models for structuring covariance matrices of additive genetic effects: a Bayesian implementation

    PubMed Central

    de los Campos, Gustavo; Gianola, Daniel

    2007-01-01

    Multivariate linear models are increasingly important in quantitative genetics. In high dimensional specifications, factor analysis (FA) may provide an avenue for structuring (co)variance matrices, thus reducing the number of parameters needed for describing (co)dispersion. We describe how FA can be used to model genetic effects in the context of a multivariate linear mixed model. An orthogonal common factor structure is used to model genetic effects under Gaussian assumption, so that the marginal likelihood is multivariate normal with a structured genetic (co)variance matrix. Under standard prior assumptions, all fully conditional distributions have closed form, and samples from the joint posterior distribution can be obtained via Gibbs sampling. The model and the algorithm developed for its Bayesian implementation were used to describe five repeated records of milk yield in dairy cattle, and a one common FA model was compared with a standard multiple trait model. The Bayesian Information Criterion favored the FA model. PMID:17897592

  12. 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).

    PubMed

    Clark, Emily S; Pompini, Manuel; Uppal, Anshu; Wedekind, Claus

    2016-05-01

    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. PMID:27066251

  13. Variance in age-specific sex composition of Pacific halibut catches, and comparison of statistical and genetic methods for reconstructing sex ratios

    NASA Astrophysics Data System (ADS)

    Loher, Timothy; Woods, Monica A.; Jimenez-Hidalgo, Isadora; Hauser, Lorenz

    2016-01-01

    Declines in size at age of Pacific halibut Hippoglossus stenolepis, in concert with sexually-dimorphic growth and a constant minimum commercial size limit, have led to the expectation that the sex composition of commercial catches should be increasingly female-biased. Sensitivity analyses suggest that variance in sex composition of landings may be the most influential source of uncertainty affecting current understanding of spawning stock biomass. However, there is no reliable way to determine sex at landing because all halibut are eviscerated at sea. In 2014, a statistical method based on survey data was developed to estimate the probability that fish of any given length at age (LAA) would be female, derived from the fundamental observation that large, young fish are likely female whereas small, old fish have a high probability of being male. Here, we examine variability in age-specific sex composition using at-sea commercial and closed-season survey catches, and compare the accuracy of the survey-based LAA technique to genetic markers for reconstructing the sex composition of catches. Sexing by LAA performed best for summer-collected samples, consistent with the hypothesis that the ability to characterize catches can be influenced by seasonal demographic shifts. Additionally, differences between survey and commercial selectivity that allow fishers to harvest larger fish within cohorts may generate important mismatch between survey and commercial datasets. Length-at-age-based estimates ranged from 4.7% underestimation of female proportion to 12.0% overestimation, with mean error of 5.8 ± 1.5%. Ratios determined by genetics were closer to true sample proportions and displayed less variability; estimation to within < 1% of true ratios was limited to genetics. Genetic estimation of female proportions ranged from 4.9% underestimation to 2.5% overestimation, with a mean absolute error of 1.2 ± 1.2%. Males were generally more difficult to assign than females: 6.7% of

  14. Modeling variance structure of body shape traits of Lipizzan horses.

    PubMed

    Kaps, M; Curik, I; Baban, M

    2010-09-01

    Heterogeneity of variance of growth traits over age is a common issue in estimating genetic parameters and is addressed in this study by selecting appropriate variance structure models for additive genetic and environmental variances. Modeling and partitioning those variances connected with analyzing small data sets were demonstrated on Lipizzan horses. The following traits were analyzed: withers height, chest girth, and cannon bone circumference. The measurements were taken at birth, and at approximately 6, 12, 24, and 36 mo of age of 660 Lipizzan horses born in Croatia between 1948 and 2000. The corresponding pedigree file consisted of 1,458 horses. Sex, age of dam, and stud-year-season interaction were considered fixed effects; additive genetic and permanent environment effects were defined as random. Linear adjustments of age at measuring were done within measuring groups. Maternal effects were included only for measurements taken at birth and at 6 mo. Additive genetic variance structures were modeled by using uniform structures or structures based on polynomial random regression. Environmental variance structures were modeled by using one of the following models: unstructured, exponential, Gaussian, or combinations of identity or diagonal with structures based on polynomial random regression. The parameters were estimated by using REML. Comparison and fits of the models were assessed by using Akaike and Bayesian information criteria, and by checking graphically the adequacy of the shape of the overall (phenotypic) and component (additive genetic and environmental) variance functions. The best overall fit was obtained from models with unstructured error variance. Compared with the model with uniform additive genetic variance, models with structures based on random regression only slightly improved overall fit. Exponential and Gaussian models were generally not suitable because they do not accommodate adequately heterogeneity of variance. Using the unstructured

  15. Genetic assessment of additional endophenotypes from the Consortium on the Genetics of Schizophrenia Family Study.

    PubMed

    Greenwood, Tiffany A; Lazzeroni, Laura C; Calkins, Monica E; Freedman, Robert; Green, Michael F; Gur, Raquel E; Gur, Ruben C; Light, Gregory A; Nuechterlein, Keith H; Olincy, Ann; Radant, Allen D; Seidman, Larry J; Siever, Larry J; Silverman, Jeremy M; Stone, William S; Sugar, Catherine A; Swerdlow, Neal R; Tsuang, Debby W; Tsuang, Ming T; Turetsky, Bruce I; Braff, David L

    2016-01-01

    The Consortium on the Genetics of Schizophrenia Family Study (COGS-1) has previously reported our efforts to characterize the genetic architecture of 12 primary endophenotypes for schizophrenia. We now report the characterization of 13 additional measures derived from the same endophenotype test paradigms in the COGS-1 families. Nine of the measures were found to discriminate between schizophrenia patients and controls, were significantly heritable (31 to 62%), and were sufficiently independent of previously assessed endophenotypes, demonstrating utility as additional endophenotypes. Genotyping via a custom array of 1536 SNPs from 94 candidate genes identified associations for CTNNA2, ERBB4, GRID1, GRID2, GRIK3, GRIK4, GRIN2B, NOS1AP, NRG1, and RELN across multiple endophenotypes. An experiment-wide p value of 0.003 suggested that the associations across all SNPs and endophenotypes collectively exceeded chance. Linkage analyses performed using a genome-wide SNP array further identified significant or suggestive linkage for six of the candidate endophenotypes, with several genes of interest located beneath the linkage peaks (e.g., CSMD1, DISC1, DLGAP2, GRIK2, GRIN3A, and SLC6A3). While the partial convergence of the association and linkage likely reflects differences in density of gene coverage provided by the distinct genotyping platforms, it is also likely an indication of the differential contribution of rare and common variants for some genes and methodological differences in detection ability. Still, many of the genes implicated by COGS through endophenotypes have been identified by independent studies of common, rare, and de novo variation in schizophrenia, all converging on a functional genetic network related to glutamatergic neurotransmission that warrants further investigation. PMID:26597662

  16. USE OF PRIMITIVE DERIVED COTTON ACCESSIONS FOR AGRONOMIC AND FIBER TRAITS IMPROVEMENT: VARIANCE COMPONENTS AND GENETIC EFFECTS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Upland cotton (Gossypium hirsutum L.) is cultivated in warmer climates throughout the world. The genetic base of modern upland cultivars is narrow. As yield and fiber quality traits are improved the genetic base should be extended by the incorporation of new germplasm into cultivars. In this stud...

  17. School performance and genetic and environmental variance in antisocial behavior at the transition from adolescence to adulthood.

    PubMed

    Johnson, Wendy; McGue, Matt; Iacono, William G

    2009-07-01

    Antisocial behavior increases in adolescence, particularly among those who perform poorly in school. As adolescents move into adulthood, both educational attainment and the extent to which antisocial behavior continues have implications for adolescents' abilities to take on constructive social roles. The authors used a population-representative longitudinal twin study to explore how links among genetic and environmental influences at ages 17 and 24 may be implicated in the developmental processes involved. At age 17, expression of both genetic and nonshared environmental vulnerabilities unique to antisocial behavior was greater among those with low GPA than among those with higher GPA. This suggested that maintenance of high GPA buffered the impact of both genetic and environmental influences encouraging antisocial behavior. When GPA was high, both genetic and environmental influences involved in both traits encouraged good school performance and restrained antisocial behavior. At age 24, however, correlated family environmental influences drove the association between educational attainment and antisocial behavior. Antisocial characteristics involving school performance and educational attainment that transcend generations may slot individuals into social categories that restrict opportunities and reinforce antisocial characteristics. PMID:19586174

  18. Genetic control of the environmental variance for birth weight in seven generations of a divergent selection experiment in mice.

    PubMed

    Formoso-Rafferty, N; Cervantes, I; Ibáñez-Escriche, N; Gutiérrez, J P

    2016-06-01

    Data from seven generations of a divergent selection experiment designed for environmental variability of birth weight were analysed to estimate genetic parameters and to explore signs of selection response. A total of 10 783 birth weight records from 638 females and 1127 litters in combination with 10 007 pedigree records were used. Each record of birth weight was assigned to the mother of the pup in a heteroscedastic model, and after seven generations of selection, evidence of success in the selection process was shown. A Bayesian analysis showed that success of the selection process started from the first generation for birth weight and from the second generation for its environmental variability. Genetic parameters were estimated across generations. However, only from the third generation onwards were the records useful to consider the results to be reliable. The results showed a consistent positive and low genetic correlation between the birth weight trait and its environmental variability, which could allow an independent selection process. This study has demonstrated that the genetic control of the birth weight environmental variability is possible in mice. Nevertheless, before the results are applied directly in farm animals, it would be worth confirming any other implications on other important traits, such as robustness, longevity and welfare. PMID:26150168

  19. School Performance and Genetic and Environmental Variance in Antisocial Behavior at the Transition from Adolescence to Adulthood

    PubMed Central

    Johnson, Wendy; McGue, Matthew K.; Iacono, William G.

    2009-01-01

    Antisocial behavior increases in adolescence, particularly among those who perform poorly in school. As adolescents move into adulthood, both educational attainment and the extent to which antisocial behavior continues have implications for their abilities to take on constructive social roles. We used a population-representative longitudinal twin study to explore how links between genetic and environmental influences at ages 17 and 24 may be implicated in the developmental processes involved. At age 17, expression of both genetic and nonshared environmental vulnerabilities unique to antisocial behavior was greater among those with low GPA than among those with higher GPA. This suggested that maintenance of high GPA buffered the impact of both genetic and environmental influences encouraging antisocial behavior. When GPA was high, both genetic and environmental influences involved in both traits encouraged good school performance and restrained antisocial behavior. At age 24, however, correlated family environmental influences drove the association between educational attainment and antisocial behavior. Antisocial characteristics involving school performance and educational attainment that transcend generations may slot individuals into social categories that restrict opportunities and reinforce antisocial characteristics. PMID:19586174

  20. Prevalence of gene expression additivity in genetically stable wheat allohexaploids.

    PubMed

    Chelaifa, Houda; Chagué, Véronique; Chalabi, Smahane; Mestiri, Imen; Arnaud, Dominique; Deffains, Denise; Lu, Yunhai; Belcram, Harry; Huteau, Virginie; Chiquet, Julien; Coriton, Olivier; Just, Jérémy; Jahier, Joseph; Chalhoub, Boulos

    2013-02-01

    The reprogramming of gene expression appears as the major trend in synthetic and natural allopolyploids where expression of an important proportion of genes was shown to deviate from that of the parents or the average of the parents. In this study, we analyzed gene expression changes in previously reported, highly stable synthetic wheat allohexaploids that combine the D genome of Aegilops tauschii and the AB genome extracted from the natural hexaploid wheat Triticum aestivum. A comprehensive genome-wide analysis of transcriptional changes using the Affymetrix GeneChip Wheat Genome Array was conducted. Prevalence of gene expression additivity was observed where expression does not deviate from the average of the parents for 99.3% of 34,820 expressed transcripts. Moreover, nearly similar expression was observed (for 99.5% of genes) when comparing these synthetic and natural wheat allohexaploids. Such near-complete additivity has never been reported for other allopolyploids and, more interestingly, for other synthetic wheat allohexaploids that differ from the ones studied here by having the natural tetraploid Triticum turgidum as the AB genome progenitor. Our study gave insights into the dynamics of additive gene expression in the highly stable wheat allohexaploids. PMID:23278496

  1. Quantitative genetics of sexually dimorphic traits and capture of genetic variance by a sexually-selected condition-dependent ornament in red junglefowl (Gallus gallus).

    PubMed

    Parker, T H; Garant, D

    2004-11-01

    We studied the quantitative genetics of sexually selected traits in a captive population of red junglefowl (Gallus gallus L.) using a multi-generational 'animal model' approach. We found significant heritability of mass, tarsus length (both strongly sexually dimorphic), residual mass, and male comb (a fleshy head ornament) length. Residual mass has a genetic correlation between the sexes smaller than unity and so could show partially independent responses to selection in the two sexes. In males, tarsus length and mass were not genetically correlated, and this produced a negative genetic correlation between tarsus length and residual mass. The male red junglefowl's comb, an ornament influencing female choice, is highly condition dependent. We show that expression of this ornament is heritable, however, and shows strong genetic correlation with a condition index, residual mass. Because residual mass is partly influenced by various aspects of condition, it appears that comb size has 'captured' genetic variability in condition. PMID:15525412

  2. Additive genetic variation and evolvability of a multivariate trait can be increased by epistatic gene action.

    PubMed

    Griswold, Cortland K

    2015-12-21

    Epistatic gene action occurs when mutations or alleles interact to produce a phenotype. Theoretically and empirically it is of interest to know whether gene interactions can facilitate the evolution of diversity. In this paper, we explore how epistatic gene action affects the additive genetic component or heritable component of multivariate trait variation, as well as how epistatic gene action affects the evolvability of multivariate traits. The analysis involves a sexually reproducing and recombining population. Our results indicate that under stabilizing selection conditions a population with a mixed additive and epistatic genetic architecture can have greater multivariate additive genetic variation and evolvability than a population with a purely additive genetic architecture. That greater multivariate additive genetic variation can occur with epistasis is in contrast to previous theory that indicated univariate additive genetic variation is decreased with epistasis under stabilizing selection conditions. In a multivariate setting, epistasis leads to less relative covariance among individuals in their genotypic, as well as their breeding values, which facilitates the maintenance of additive genetic variation and increases a population׳s evolvability. Our analysis involves linking the combinatorial nature of epistatic genetic effects to the ancestral graph structure of a population to provide insight into the consequences of epistasis on multivariate trait variation and evolution. PMID:26431770

  3. μ-Calpain, calpastatin, and growth hormone receptor genetic effects on preweaning performance, carcass quality traits, and residual variance of tenderness in Angus cattle selected to increase minor haplotype and allele frequencies.

    PubMed

    Tait, R G; Shackelford, S D; Wheeler, T L; King, D A; Casas, E; Thallman, R M; Smith, T P L; Bennett, G L

    2014-02-01

    Genetic marker effects and interactions are estimated with poor precision when minor marker allele frequencies are low. An Angus population was subjected to marker assisted selection for multiple years to increase divergent haplotype and minor marker allele frequencies to 1) estimate effect size and mode of inheritance for previously reported SNP on targeted beef carcass quality traits; 2) estimate effects of previously reported SNP on nontarget performance traits; and 3) evaluate tenderness SNP specific residual variance models compared to a single residual variance model for tenderness. Divergent haplotypes within µ-calpain (CAPN1), and SNP within calpastatin (CAST) and growth hormone receptor (GHR) were successfully selected to increase their frequencies. Traits evaluated were birth BW, weaning BW, final BW, fat thickness, LM area, USDA marbling score, yield grade, slice shear force (SSF), and visible and near infrared predicted slice shear force. Both CAPN1 and CAST exhibited additive (P < 0.001) modes of inheritance for SSF and neither exhibited dominance (P ≥ 0.19). Furthermore, the interaction between CAPN1 and CAST for SSF was not significant (P = 0.55). Estimated additive effects of CAPN1 (1.049 kg) and CAST (1.257 kg) on SSF were large in this study. Animals homozygous for tender alleles at both CAPN1 and CAST would have 4.61 kg lower SSF (38.6% of the mean) than animals homozygous tough for both markers. There was also an effect of CAST on yield grade (P < 0.02). The tender CAST allele was associated with more red meat yield and less trimmable fat. There were no significant effects (P ≥ 0.23) for GHR on any of the traits evaluated in this study. Furthermore, CAST specific residual variance models were found to fit significantly better (P < 0.001) than single residual variance models for SSF, with the tougher genotypes having larger residual variance. Thus, the risk of a tough steak from the undesired CAST genotype is increased through both an

  4. Genetic variance and covariance patterns for body weight and energy balance characters in an advanced intercross population of mice

    PubMed Central

    Leamy, Larry J; Elo, Kari; Nielsen, Merlyn K; Van Vleck, L Dale; Pomp, Daniel

    2005-01-01

    We estimated heritabilities and genetic correlations for a suite of 15 characters in five functional groups in an advanced intercross population of over 2000 mice derived from a cross of inbred lines selected for high and low heat loss. Heritabilities averaged 0.56 for three body weights, 0.23 for two energy balance characters, 0.48 for three bone characters, 0.35 for four measures of adiposity, and 0.27 for three organ weights, all of which were generally consistent in magnitude with estimates derived in previous studies. Genetic correlations varied from -0.65 to +0.98, and were higher within these functional groups than between groups. These correlations generally conformed to a priori expectations, being positive in sign for energy expenditure and consumption (+0.24) and negative in sign for energy expenditure and adiposity (-0.17). The genetic correlations of adiposity with body weight at 3, 6, and 12 weeks of age (-0.29, -0.22, -0.26) all were negative in sign but not statistically significant. The independence of body weight and adiposity suggests that this advanced intercross population is ideal for a comprehensive discovery of genes controlling regulation of mammalian adiposity that are distinct from those for body weight. PMID:16194522

  5. 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.

    PubMed

    Li, Jing; Coates, Brad S; Kim, Kyung Seok; Bourguet, Denis; Ponsard, Sergine; He, Kanglai; Wang, Zhenying

    2014-01-01

    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=1673) using variation at 6 nuclear microsatellite loci (ENA corrected global FST=0.020; P value<0.05). Analysis of molecular variance 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 4 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 (φST=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. PMID:25024271

  6. Estimation of Variance Components of Quantitative Traits in Inbred Populations

    PubMed Central

    Abney, Mark; McPeek, Mary Sara; Ober, Carole

    2000-01-01

    Summary Use of variance-component estimation for mapping of quantitative-trait loci in humans is a subject of great current interest. When only trait values, not genotypic information, are considered, variance-component estimation can also be used to estimate heritability of a quantitative trait. Inbred pedigrees present special challenges for variance-component estimation. First, there are more variance components to be estimated in the inbred case, even for a relatively simple model including additive, dominance, and environmental effects. Second, more identity coefficients need to be calculated from an inbred pedigree in order to perform the estimation, and these are computationally more difficult to obtain in the inbred than in the outbred case. As a result, inbreeding effects have generally been ignored in practice. We describe here the calculation of identity coefficients and estimation of variance components of quantitative traits in large inbred pedigrees, using the example of HDL in the Hutterites. We use a multivariate normal model for the genetic effects, extending the central-limit theorem of Lange to allow for both inbreeding and dominance under the assumptions of our variance-component model. We use simulated examples to give an indication of under what conditions one has the power to detect the additional variance components and to examine their impact on variance-component estimation. We discuss the implications for mapping and heritability estimation by use of variance components in inbred populations. PMID:10677322

  7. Additive and non-additive genetic components of the jack male life history in Chinook salmon (Oncorhynchus tshawytscha).

    PubMed

    Forest, Adriana R; Semeniuk, Christina A D; Heath, Daniel D; Pitcher, Trevor E

    2016-08-01

    Chinook salmon, Oncorhynchus tshawytscha, exhibit alternative reproductive tactics (ARTs) where males exist in two phenotypes: large "hooknose" males and smaller "jacks" that reach sexual maturity after only 1 year in seawater. The mechanisms that determine "jacking rate"-the rate at which males precociously sexually mature-are known to involve both genetics and differential growth rates, where individuals that become jacks exhibit higher growth earlier in life. The additive genetic components have been studied and it is known that jack sires produce significantly more jack offspring than hooknose sires, and vice versa. The current study was the first to investigate both additive and non-additive genetic components underlying jacking through the use of a full-factorial breeding design using all hooknose sires. The effect of dams and sires descendant from a marker-assisted broodstock program that identified "high performance" and "low performance" lines using growth- and survival-related gene markers was also studied. Finally, the relative growth of jack, hooknose, and female offspring was examined. No significant dam, sire, or interaction effects were observed in this study, and the maternal, additive, and non-additive components underlying jacking were small. Differences in jacking rates in this study were determined by dam performance line, where dams that originated from the low performance line produced significantly more jacks. Jack offspring in this study had a significantly larger body size than both hooknose males and females starting 1 year post-fertilization. This study provides novel information regarding the genetic architecture underlying ARTs in Chinook salmon that could have implications for the aquaculture industry, where jacks are not favoured due to their small body size and poor flesh quality. PMID:27450674

  8. Standing genetic variance for female resistance to harm from males and its relationship to intralocus sexual conflict.

    PubMed

    Lew, Timothy A; Morrow, Edward H; Rice, William R

    2006-01-01

    Interlocus sexual conflict theory predicts that some male adaptations are harmful to their mates. Females are therefore expected to evolve resistance to this harm. Using cytogenetic cloning techniques, we tested for heritable genetic variation among females for resistance to harm from males and determined whether propensity to remate, female body size, and intralocus conflict contributes to this variation. We found low but significant heritability for female resistance, but this variation accounted for more than half of the standing genetic variation for net fitness among females. We found no association between female resistance and female body size or level of intralocus sexual conflict. Reluctance to remate was found to be an important factor contributing to the female resistance phenotype, and we found a positive selection gradient on this trait. However, we observed only a nonsignificant positive correlation between a female's resistance and her net fitness. One factor contributing to the observed nominal level of selection on female resistance was that males cause the greatest amount of harm to females with the highest intrinsic fecundity. PMID:16568635

  9. Additive-dominance genetic model analyses for late-maturity alpha-amylase activity in a bread wheat factorial crossing population.

    PubMed

    Rasul, Golam; Glover, Karl D; Krishnan, Padmanaban G; Wu, Jixiang; Berzonsky, William A; Ibrahim, Amir M H

    2015-12-01

    Elevated level of late maturity α-amylase activity (LMAA) can result in low falling number scores, reduced grain quality, and downgrade of wheat (Triticum aestivum L.) class. A mating population was developed by crossing parents with different levels of LMAA. The F2 and F3 hybrids and their parents were evaluated for LMAA, and data were analyzed using the R software package 'qgtools' integrated with an additive-dominance genetic model and a mixed linear model approach. Simulated results showed high testing powers for additive and additive × environment variances, and comparatively low powers for dominance and dominance × environment variances. All variance components and their proportions to the phenotypic variance for the parents and hybrids were significant except for the dominance × environment variance. The estimated narrow-sense heritability and broad-sense heritability for LMAA were 14 and 54%, respectively. High significant negative additive effects for parents suggest that spring wheat cultivars 'Lancer' and 'Chester' can serve as good general combiners, and that 'Kinsman' and 'Seri-82' had negative specific combining ability in some hybrids despite of their own significant positive additive effects, suggesting they can be used as parents to reduce LMAA levels. Seri-82 showed very good general combining ability effect when used as a male parent, indicating the importance of reciprocal effects. High significant negative dominance effects and high-parent heterosis for hybrids demonstrated that the specific hybrid combinations; Chester × Kinsman, 'Lerma52' × Lancer, Lerma52 × 'LoSprout' and 'Janz' × Seri-82 could be generated to produce cultivars with significantly reduced LMAA level. PMID:26403988

  10. Fine-mapping in the MHC region accounts for 18% additional genetic risk for celiac disease

    PubMed Central

    Gutierrez-Achury, Javier; Zhernakova, Alexandra; Pulit, Sara L.; Trynka, Gosia; Hunt, Karen A.; Romanos, Jihane; Raychaudhuri, Soumya; van Heel, David A.; Wijmenga, Cisca; de Bakker, Paul I.W.

    2015-01-01

    Although dietary gluten is the trigger, celiac disease risk is strongly influenced by genetic variation in the major histocompatibility complex (MHC) region. We fine-mapped the MHC association signal to identify additional risk factors independent of the HLA-DQ alleles and observed five novel associations that account for 18% of the genetic risk. Together with the 57 known non-MHC loci, genetic variation can now explain up to 48% of celiac disease heritability. PMID:25894500

  11. Effects of single nucleotide polymorphism marker density on degree of genetic variance explained and genomic evaluation for carcass traits in Japanese Black beef cattle

    PubMed Central

    2014-01-01

    Background Japanese Black cattle are a beef breed whose meat is well known to excel in meat quality, especially in marbling, and whose effective population size is relatively low in Japan. Unlike dairy cattle, the accuracy of genomic evaluation (GE) for carcass traits in beef cattle, including this breed, has been poorly studied. For carcass weight and marbling score in the breed, as well as the extent of whole genome linkage disequilibrium (LD), the effects of equally-spaced single nucleotide polymorphisms (SNPs) density on genomic relationship matrix (G matrix), genetic variance explained and GE were investigated using the genotype data of about 40,000 SNPs and two statistical models. Results Using all pairs of two adjacent SNPs in the whole SNP set, the means of LD (r 2 ) at ranges 0–0.1, 0.1–0.2, 0.2–0.5 and 0.5–1 Mb were 0.22, 0.13, 0.10 and 0.08, respectively, and 25.7, 13.9, 10.4 and 6.4% of the r 2 values exceeded 0.3, respectively. While about 90% of the genetic variance for carcass weight estimated using all available SNPs was explained using 4,000–6,000 SNPs, the corresponding percentage for marbling score was consistently lower. With the conventional linear model incorporating the G matrix, correlation between the genomic estimated breeding values (GEBVs) obtained using 4,000 SNPs and all available SNPs was 0.99 for carcass weight and 0.98 for marbling score, with an underestimation of the former GEBVs, especially for marbling score. Conclusions The Japanese Black is likely to be in a breed group with a relatively high extent of whole genome LD. The results indicated that the degree of marbling is controlled by only QTLs with relatively small effects, compared with carcass weight, and that using at least 4,000 equally-spaced SNPs, there is a possibility of ranking animals genetically for these carcass traits in this breed. PMID:24491120

  12. CAPN1, CAST, and DGAT1 genetic effects on preweaning performance, carcass quality traits, and residual variance of tenderness in a beef cattle population selected for haplotype and allele equalization.

    PubMed

    Tait, R G; Shackelford, S D; Wheeler, T L; King, D A; Keele, J W; Casas, E; Smith, T P L; Bennett, G L

    2014-12-01

    Genetic marker effects and type of inheritance are estimated with poor precision when minor marker allele frequencies are low. A stable composite population (MARC III) was subjected to marker-assisted selection for multiple years to equalize specific marker frequencies to 1) estimate effect size and mode of inheritance for previously reported SNP on targeted beef carcass quality traits (n=254), 2) estimate pleiotropic effects of previously reported SNP on nontarget performance traits (n=542 or 254), and 3) evaluate tenderness SNP specific residual variance for LM tenderness. Three haplotypes within μ-calpain (CAPN1), a SNP in calpastatin (CAST), and a dinucleotide substitution in diacylglycerol O-acyltransferase 1 (DGAT1) were successfully selected to equalize their frequencies. Traits evaluated were birth BW, weaning BW, yearling BW, final BW, dressing percent, HCW, fat thickness, LM area, USDA marbling score, yield grade, LM slice shear force (SSF), and visible and near-infrared (VISNIR)-predicted SSF. While the CAPN1 genotype effect on SSF was not significant (P=0.12), the direction and size of CAPN1 contrasts were consistent with previous research. Effects on SSF between divergent CAPN1 haplotypes (1.153 kg) and the additive effect of CAST (0.902 kg) were large, and animals homozygous for tender alleles at both CAPN1 and CAST would have 4.11 kg lower SSF (27.5% of the mean) than animals homozygous tough for both markers. Furthermore, the interaction between CAPN1 and CAST for SSF was not significant (P=0.40). There were significant effects for DGAT1 on adjusted fat thickness (P=0.02) and VISNIR-predicted SSF (P<0.001) with additive and dominance modes of inheritance (P<0.05) for both traits. Furthermore, CAST genotype specific residual variance models fit significantly better (P<0.001) than single residual variance models for SSF, with the tougher genotypes having progressively larger residual (and hence phenotypic) variances. Therefore, risk of a tough steak

  13. ADJUSTMENT FOR HETEROGENEOUS GENETIC AND NON-GENETIC (CO)VARIANCE STRUCTURES ON TEST-DAY MODELS USING A TRANSFORMATION ON RANDOM REGRESSION EFFECT REGRESSORS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A method of accounting for differences in variation in components of test-day milk production records was developed. This method could improve the accuracy of genetic evaluations. A random regression model is used to analyze the data, then a transformation is applied to the random regression coeffic...

  14. Biclustering with heterogeneous variance.

    PubMed

    Chen, Guanhua; Sullivan, Patrick F; Kosorok, Michael R

    2013-07-23

    In cancer research, as in all of medicine, it is important to classify patients into etiologically and therapeutically relevant subtypes to improve diagnosis and treatment. One way to do this is to use clustering methods to find subgroups of homogeneous individuals based on genetic profiles together with heuristic clinical analysis. A notable drawback of existing clustering methods is that they ignore the possibility that the variance of gene expression profile measurements can be heterogeneous across subgroups, and methods that do not consider heterogeneity of variance can lead to inaccurate subgroup prediction. Research has shown that hypervariability is a common feature among cancer subtypes. In this paper, we present a statistical approach that can capture both mean and variance structure in genetic data. We demonstrate the strength of our method in both synthetic data and in two cancer data sets. In particular, our method confirms the hypervariability of methylation level in cancer patients, and it detects clearer subgroup patterns in lung cancer data. PMID:23836637

  15. [Food additives and genetically modified food--a risk for allergic patients?].

    PubMed

    Wüthrich, B

    1999-04-01

    Adverse reactions to food and food additives must be classified according to pathogenic criteria. It is necessary to strictly differentiate between an allergy, triggered by a substance-specific immunological mechanism, and an intolerance, in which no specific immune reaction can be established. In contrast to views expressed in the media, by laymen and patients, adverse reactions to additives are less frequent than is believed. Due to frequently "alternative" methods of examination, an allergy to food additives is often wrongly blamed as the cause of a wide variety of symptoms and illness. Diagnosing an allergy or intolerance to additives normally involves carrying out double-blind, placebo-controlled oral provocation tests with food additives. Allergic reactions to food additives occur particularly against additives which are organic in origin. In principle, it is possible that during the manufacture of genetically modified plants and food, proteins are transferred which potentially create allergies. However, legislation exists both in the USA (Federal Drug Administration, FDA) and in Switzerland (Ordinance on the approval process for GM food, GM food additives and GM accessory agents for processing) which require a careful analysis before a genetically modified product is launched, particularly where foreign genes are introduced. Products containing genetically modified organisms (GMO) as additives must be declared. In addition, the source of the foreign protein must be identified. The "Round-up ready" (RR) soya flour introduced in Switzerland is no different from natural soya flour in terms of its allergenic potential. Genetically modified food can be a blessing for allergic individuals if gene technology were to succeed in removing the allergen (e.g. such possibilities exist for rice). The same caution shown towards genetically modified food might also be advisable for foreign food in our diet. Luckily, the immune system of the digestive tract in healthy people

  16. Common genetic variants, acting additively, are a major source of risk for autism

    PubMed Central

    2012-01-01

    Background Autism spectrum disorders (ASD) are early onset neurodevelopmental syndromes typified by impairments in reciprocal social interaction and communication, accompanied by restricted and repetitive behaviors. While rare and especially de novo genetic variation are known to affect liability, whether common genetic polymorphism plays a substantial role is an open question and the relative contribution of genes and environment is contentious. It is probable that the relative contributions of rare and common variation, as well as environment, differs between ASD families having only a single affected individual (simplex) versus multiplex families who have two or more affected individuals. Methods By using quantitative genetics techniques and the contrast of ASD subjects to controls, we estimate what portion of liability can be explained by additive genetic effects, known as narrow-sense heritability. We evaluate relatives of ASD subjects using the same methods to evaluate the assumptions of the additive model and partition families by simplex/multiplex status to determine how heritability changes with status. Results By analyzing common variation throughout the genome, we show that common genetic polymorphism exerts substantial additive genetic effects on ASD liability and that simplex/multiplex family status has an impact on the identified composition of that risk. As a fraction of the total variation in liability, the estimated narrow-sense heritability exceeds 60% for ASD individuals from multiplex families and is approximately 40% for simplex families. By analyzing parents, unaffected siblings and alleles not transmitted from parents to their affected children, we conclude that the data for simplex ASD families follow the expectation for additive models closely. The data from multiplex families deviate somewhat from an additive model, possibly due to parental assortative mating. Conclusions Our results, when viewed in the context of results from genome

  17. 45 CFR 146.122 - Additional requirements prohibiting discrimination based on genetic information.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 45 Public Welfare 1 2011-10-01 2011-10-01 false Additional requirements prohibiting discrimination based on genetic information. 146.122 Section 146.122 Public Welfare DEPARTMENT OF HEALTH AND HUMAN SERVICES REQUIREMENTS RELATING TO HEALTH CARE ACCESS REQUIREMENTS FOR THE GROUP HEALTH INSURANCE MARKET Requirements Relating to Access...

  18. 26 CFR 54.9802-3T - Additional requirements prohibiting discrimination based on genetic information (temporary).

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 26 Internal Revenue 17 2014-04-01 2014-04-01 false Additional requirements prohibiting discrimination based on genetic information (temporary). 54.9802-3T Section 54.9802-3T Internal Revenue INTERNAL REVENUE SERVICE, DEPARTMENT OF THE TREASURY (CONTINUED) MISCELLANEOUS EXCISE TAXES (CONTINUED) PENSION EXCISE TAXES § 54.9802-3T...

  19. 29 CFR 2590.702-1 - Additional requirements prohibiting discrimination based on genetic information.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 29 Labor 9 2014-07-01 2014-07-01 false Additional requirements prohibiting discrimination based on genetic information. 2590.702-1 Section 2590.702-1 Labor Regulations Relating to Labor (Continued) EMPLOYEE BENEFITS SECURITY ADMINISTRATION, DEPARTMENT OF LABOR GROUP HEALTH PLANS RULES AND REGULATIONS FOR GROUP HEALTH PLANS Health...

  20. 26 CFR 54.9802-3T - Additional requirements prohibiting discrimination based on genetic information (temporary).

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 26 Internal Revenue 17 2012-04-01 2012-04-01 false Additional requirements prohibiting discrimination based on genetic information (temporary). 54.9802-3T Section 54.9802-3T Internal Revenue INTERNAL REVENUE SERVICE, DEPARTMENT OF THE TREASURY (CONTINUED) MISCELLANEOUS EXCISE TAXES (CONTINUED) PENSION EXCISE TAXES § 54.9802-3T...

  1. 26 CFR 54.9802-3T - Additional requirements prohibiting discrimination based on genetic information (temporary).

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 26 Internal Revenue 17 2013-04-01 2013-04-01 false Additional requirements prohibiting discrimination based on genetic information (temporary). 54.9802-3T Section 54.9802-3T Internal Revenue INTERNAL REVENUE SERVICE, DEPARTMENT OF THE TREASURY (CONTINUED) MISCELLANEOUS EXCISE TAXES (CONTINUED) PENSION EXCISE TAXES § 54.9802-3T...

  2. Additives

    NASA Technical Reports Server (NTRS)

    Smalheer, C. V.

    1973-01-01

    The chemistry of lubricant additives is discussed to show what the additives are chemically and what functions they perform in the lubrication of various kinds of equipment. Current theories regarding the mode of action of lubricant additives are presented. The additive groups discussed include the following: (1) detergents and dispersants, (2) corrosion inhibitors, (3) antioxidants, (4) viscosity index improvers, (5) pour point depressants, and (6) antifouling agents.

  3. Multi-site study of additive genetic effects on fractional anisotropy of cerebral white matter: comparing meta and mega analytical approaches for data pooling

    PubMed Central

    Kochunov, Peter; Jahanshad, Neda; Sprooten, Emma; Nichols, Thomas E.; Mandl, René C.; Almasy, Laura; Booth, Tom; Brouwer, Rachel M.; Curran, Joanne E.; de Zubicaray, Greig I.; Dimitrova, Rali; Duggirala, Ravi; Fox, Peter T.; Hong, L. Elliot; Landman, Bennett A.; Lemaitre, Hervé; Lopez, Lorna; Martin, Nicholas G.; McMahon, Katie L.; Mitchell, Braxton D.; Olvera, Rene L.; Peterson, Charles P.; Starr, John M.; Sussmann, Jessika E.; Toga, Arthur W.; Wardlaw, Joanna M.; Wright, Margaret J.; Wright, Susan N.; Bastin, Mark E.; McIntosh, Andrew M.; Boomsma, Dorret I.; Kahn, René S.; den Braber, Anouk; de Geus, Eco JC; Deary, Ian J.; Hulshoff Pol, Hilleke E.; Williamson, Douglas E.; Blangero, John; van ’t Ent, Dennis; Thompson, Paul M.; Glahn, David C.

    2014-01-01

    Combining datasets across independent studies can boost statistical power by increasing the numbers of observations and can achieve more accurate estimates of effect sizes. This is especially important for genetic studies where a large number of observations are required to obtain sufficient power to detect and replicate genetic effects. There is a need to develop and evaluate methods for joint-analytical analyses of rich datasets collected in imaging genetics studies. The ENIGMA-DTI consortium is developing and evaluating approaches for obtaining pooled estimates of heritability through meta-and mega-genetic analytical approaches, to estimate the general additive genetic contributions to the intersubject variance in fractional anisotropy (FA) measured from diffusion tensor imaging (DTI). We used the ENIGMA-DTI data harmonization protocol for uniform processing of DTI data from multiple sites. We evaluated this protocol in five family-based cohorts providing data from a total of 2248 children and adults (ages: 9–85) collected with various imaging protocols. We used the imaging genetics analysis tool, SOLAR-Eclipse, to combine twin and family data from Dutch, Australian and Mexican-American cohorts into one large “mega-family”. We showed that heritability estimates may vary from one cohort to another. We used two meta-analytical (the sample-size and standard-error weighted) approaches and a mega-genetic analysis to calculate heritability estimates across-population. We performed leave-one-out analysis of the joint estimates of heritability, removing a different cohort each time to understand the estimate variability. Overall, meta- and mega-genetic analyses of heritability produced robust estimates of heritability. PMID:24657781

  4. Multi-site study of additive genetic effects on fractional anisotropy of cerebral white matter: Comparing meta and megaanalytical approaches for data pooling.

    PubMed

    Kochunov, Peter; Jahanshad, Neda; Sprooten, Emma; Nichols, Thomas E; Mandl, René C; Almasy, Laura; Booth, Tom; Brouwer, Rachel M; Curran, Joanne E; de Zubicaray, Greig I; Dimitrova, Rali; Duggirala, Ravi; Fox, Peter T; Hong, L Elliot; Landman, Bennett A; Lemaitre, Hervé; Lopez, Lorna M; Martin, Nicholas G; McMahon, Katie L; Mitchell, Braxton D; Olvera, Rene L; Peterson, Charles P; Starr, John M; Sussmann, Jessika E; Toga, Arthur W; Wardlaw, Joanna M; Wright, Margaret J; Wright, Susan N; Bastin, Mark E; McIntosh, Andrew M; Boomsma, Dorret I; Kahn, René S; den Braber, Anouk; de Geus, Eco J C; Deary, Ian J; Hulshoff Pol, Hilleke E; Williamson, Douglas E; Blangero, John; van 't Ent, Dennis; Thompson, Paul M; Glahn, David C

    2014-07-15

    Combining datasets across independent studies can boost statistical power by increasing the numbers of observations and can achieve more accurate estimates of effect sizes. This is especially important for genetic studies where a large number of observations are required to obtain sufficient power to detect and replicate genetic effects. There is a need to develop and evaluate methods for joint-analytical analyses of rich datasets collected in imaging genetics studies. The ENIGMA-DTI consortium is developing and evaluating approaches for obtaining pooled estimates of heritability through meta-and mega-genetic analytical approaches, to estimate the general additive genetic contributions to the intersubject variance in fractional anisotropy (FA) measured from diffusion tensor imaging (DTI). We used the ENIGMA-DTI data harmonization protocol for uniform processing of DTI data from multiple sites. We evaluated this protocol in five family-based cohorts providing data from a total of 2248 children and adults (ages: 9-85) collected with various imaging protocols. We used the imaging genetics analysis tool, SOLAR-Eclipse, to combine twin and family data from Dutch, Australian and Mexican-American cohorts into one large "mega-family". We showed that heritability estimates may vary from one cohort to another. We used two meta-analytical (the sample-size and standard-error weighted) approaches and a mega-genetic analysis to calculate heritability estimates across-population. We performed leave-one-out analysis of the joint estimates of heritability, removing a different cohort each time to understand the estimate variability. Overall, meta- and mega-genetic analyses of heritability produced robust estimates of heritability. PMID:24657781

  5. Nuclear Material Variance Calculation

    1995-01-01

    MAVARIC (Materials Accounting VARIance Calculations) is a custom spreadsheet that significantly reduces the effort required to make the variance and covariance calculations needed to determine the detection sensitivity of a materials accounting system and loss of special nuclear material (SNM). The user is required to enter information into one of four data tables depending on the type of term in the materials balance (MB) equation. The four data tables correspond to input transfers, output transfers,more » and two types of inventory terms, one for nondestructive assay (NDA) measurements and one for measurements made by chemical analysis. Each data entry must contain an identification number and a short description, as well as values for the SNM concentration, the bulk mass (or solution volume), the measurement error standard deviations, and the number of measurements during an accounting period. The user must also specify the type of error model (additive or multiplicative) associated with each measurement, and possible correlations between transfer terms. Predefined spreadsheet macros are used to perform the variance and covariance calculations for each term based on the corresponding set of entries. MAVARIC has been used for sensitivity studies of chemical separation facilities, fuel processing and fabrication facilities, and gas centrifuge and laser isotope enrichment facilities.« less

  6. Additive genetic risk from five serotonin system polymorphisms interacts with interpersonal stress to predict depression.

    PubMed

    Vrshek-Schallhorn, Suzanne; Stroud, Catherine B; Mineka, Susan; Zinbarg, Richard E; Adam, Emma K; Redei, Eva E; Hammen, Constance; Craske, Michelle G

    2015-11-01

    Behavioral genetic research supports polygenic models of depression in which many genetic variations each contribute a small amount of risk, and prevailing diathesis-stress models suggest gene-environment interactions (G×E). Multilocus profile scores of additive risk offer an approach that is consistent with polygenic models of depression risk. In a first demonstration of this approach in a G×E predicting depression, we created an additive multilocus profile score from 5 serotonin system polymorphisms (1 each in the genes HTR1A, HTR2A, HTR2C, and 2 in TPH2). Analyses focused on 2 forms of interpersonal stress as environmental risk factors. Using 5 years of longitudinal diagnostic and life stress interviews from 387 emerging young adults in the Youth Emotion Project, survival analyses show that this multilocus profile score interacts with major interpersonal stressful life events to predict major depressive episode onsets (hazard ratio [HR] = 1.815, p = .007). Simultaneously, there was a significant protective effect of the profile score without a recent event (HR = 0.83, p = .030). The G×E effect with interpersonal chronic stress was not significant (HR = 1.15, p = .165). Finally, effect sizes for genetic factors examined ignoring stress suggested such an approach could lead to overlooking or misinterpreting genetic effects. Both the G×E effect and the protective simple main effect were replicated in a sample of early adolescent girls (N = 105). We discuss potential benefits of the multilocus genetic profile score approach and caveats for future research. PMID:26595467

  7. Additive Genetic Variation in Schizophrenia Risk Is Shared by Populations of African and European Descent

    PubMed Central

    de Candia, Teresa R.; Lee, S. Hong; Yang, Jian; Browning, Brian L.; Gejman, Pablo V.; Levinson, Douglas F.; Mowry, Bryan J.; Hewitt, John K.; Goddard, Michael E.; O’Donovan, Michael C.; Purcell, Shaun M.; Posthuma, Danielle; Visscher, Peter M.; Wray, Naomi R.; Keller, Matthew C.

    2013-01-01

    To investigate the extent to which the proportion of schizophrenia’s additive genetic variation tagged by SNPs is shared by populations of European and African descent, we analyzed the largest combined African descent (AD [n = 2,142]) and European descent (ED [n = 4,990]) schizophrenia case-control genome-wide association study (GWAS) data set available, the Molecular Genetics of Schizophrenia (MGS) data set. We show how a method that uses genomic similarities at measured SNPs to estimate the additive genetic correlation (SNP correlation [SNP-rg]) between traits can be extended to estimate SNP-rg for the same trait between ethnicities. We estimated SNP-rg for schizophrenia between the MGS ED and MGS AD samples to be 0.66 (SE = 0.23), which is significantly different from 0 (p(SNP-rg = 0) = 0.0003), but not 1 (p(SNP-rg = 1) = 0.26). We re-estimated SNP-rg between an independent ED data set (n = 6,665) and the MGS AD sample to be 0.61 (SE = 0.21, p(SNP-rg = 0) = 0.0003, p(SNP-rg = 1) = 0.16). These results suggest that many schizophrenia risk alleles are shared across ethnic groups and predate African-European divergence. PMID:23954163

  8. Significant variance in genetic diversity among populations of Schistosoma haematobium detected using microsatellite DNA loci from a genome-wide database

    PubMed Central

    2013-01-01

    species (i.e., using DNA sequences conserved among species), as well as other markers that are specific to species or species-groups (i.e., using DNA sequences that differ among species). Full genome-sequencing of additional species and specimens of S. haematobium, S. japonicum, and S. mansoni is desirable to better characterize differences within and among these species, to develop additional genetic markers, and to examine genes as well as conserved non-coding elements associated with drug resistance. PMID:24499537

  9. Searching for additional endocrine functions of the skeleton: genetic approaches and implications for therapeutics

    PubMed Central

    Wei, Jianwen; Flaherty, Stephen; Karsenty, Gerard

    2016-01-01

    Our knowledge of whole organism physiology has greatly advanced in the past decades through mouse genetics. In particular, genetic studies have revealed that most organs interact with one another through hormones in order to maintain normal physiological functions and the homeostasis of the entire organism. Remarkably, through these studies many unexpected novel endocrine means to regulate physiological functions have been uncovered. The skeletal system is one example. In this article, we review a series of studies that over the years have identified bone as an endocrine organ. The mechanism of action, pathological relevance, and therapeutic implications of the functions of the bone-derived hormone osteocalcin are discussed. In the last part of this review we discuss the possibility that additional endocrine functions of the skeleton may exist.

  10. Effect of multiplicative and additive noise on genetic transcriptional regulatory mechanism

    NASA Astrophysics Data System (ADS)

    Liu, Xue-Mei; Xie, Hui-Zhang; Liu, Liang-Gang; Li, Zhi-Bing

    2009-02-01

    A multiplicative noise and an additive noise are introduced in the kinetic model of Smolen-Baxter-Byrne [P. Smolen, D.A. Baxter, J.H. Byrne, Amer. J. Physiol. Cell. Physiol. 274 (1998) 531], in which the expression of gene is controlled by protein concentration of transcriptional activator. The Fokker-Planck equation is solved and the steady-state probability distribution is obtained numerically. It is found that the multiplicative noise converts the bistability to monostability that can be regarded as a noise-induced transition. The additive noise reduces the transcription efficiency. The correlation between the multiplicative noise and the additive noise works as a genetic switch and regulates the gene transcription effectively.

  11. Estimates of variances due to direct and maternal effects for growth traits of Romanov sheep.

    PubMed

    María, G A; Boldman, K G; Van Vleck, L D

    1993-04-01

    Records of growth traits of 2,086 Romanov lambs were used to estimate variance components for an animal model and genetic correlations between growth traits. Traits analyzed were birth weight (BWT), weaning weight (WW), 90-d weight (W90), and daily gain for the periods birth to weaning (DG1) and weaning to 90 d (DG2). Weaning was at approximately 40 d. Variance components were estimated using restricted maximum likelihood with an animal model including fixed effects for year x season, sex, rearing type, and litter size and random effects for the direct genetic effect of the animal (with relative variance h2), the maternal genetic effect (with relative variance m2), the permanent environmental effect (with relative variance c2), and random residual effect. Genetic correlations were estimated for a model with the same fixed effects and only additive genetic effects. Estimates of the variances of random effects, h2, m2, and c2, respectively, as a proportion of phenotypic variance were .04, .22, .10 (BWT); .34, .25, .0 (WW); .09, .01, .07 (W90); .26, .17, .02 (DG1); and .15, .01, .03 (DG2). Estimates of genetic correlations were .12 (BWT with WW); .24 (BWT with W90); .48 (WW with W90); .69 (DG1 with DG2); -.01 (BWT with DG1); .05 (BWT with DG2); .59 (WW with DG1); .47 (WW with DG2); .67 (W90 with DG1); and .98 (W90 with DG2). Results suggest that selection should be effective for WW, DG1, and DG2 but less effective for BWT and W90. An important maternal effect was observed for BWT, WW, and DG1. The estimates of genetic correlations showed no genetic antagonisms among the traits. PMID:8478286

  12. Does variance in drinking motives explain the genetic overlap between personality and alcohol use disorder symptoms? A twin study of young women

    PubMed Central

    Littlefield, Andrew K.; Agrawal, Arpana; Ellingson, Jarrod M.; Kristjansson, Sean; Madden, Pamela A. F.; Bucholz, Kathleen K.; Slutske, Wendy S.; Heath, Andrew C.; Sher, Kenneth J.

    2011-01-01

    Background Genetic risk for alcohol dependence has been shown to overlap with genetic factors contributing to variation in dimensions of personality. Though drinking motives have been posited as important mediators of the alcohol-personality relation, the extent to which the genetic covariance between alcohol use disorder (AUD) symptoms (i.e. abuse and dependence criteria) and personality is explained by genetic factors contributing to variation in drinking motives remains unclear. Methods Using data from 2,904 young adult female twins, the phenotypic and genetic associations among personality dimensions (constraint [measured by the Multidimensional Personality Questionnaire; Tellegen, 1982], conscientiousness, neuroticism, and agreeableness [measured by the NEO-PI; Costa & McCrae, 1985]), internal drinking motives (enhancement and coping motives [measured by the Drinking Motive Questionnaire; Cooper, 1994]), and AUD symptoms were tested. Results Significant genetic associations were found between all personality measures and AUD symptoms. Coping motives showed significant genetic overlap with AUD symptoms and most personality measures, whereas enhancement motives were not significantly heritable. Adjusting for coping motives, genetic correlations between AUD symptoms and traits of neuroticism and agreeableness were no longer statistically significant. Conclusions Findings suggest that genetic variation in drinking to cope might account for a considerable proportion of the genetic covariance between specific personality dimensions and AUD symptoms. PMID:21790670

  13. Heterogeneity of variances for carcass traits by percentage Brahman inheritance.

    PubMed

    Crews, D H; Franke, D E

    1998-07-01

    Heterogeneity of carcass trait variances due to level of Brahman inheritance was investigated using records from straightbred and crossbred steers produced from 1970 to 1988 (n = 1,530). Angus, Brahman, Charolais, and Hereford sires were mated to straightbred and crossbred cows to produce straightbred, F1, back-cross, three-breed cross, and two-, three-, and four-breed rotational crossbred steers in four non-overlapping generations. At weaning (mean age = 220 d), steers were randomly assigned within breed group directly to the feedlot for 200 d, or to a backgrounding and stocker phase before feeding. Stocker steers were fed from 70 to 100 d in generations 1 and 2 and from 60 to 120 d in generations 3 and 4. Carcass traits included hot carcass weight, subcutaneous fat thickness and longissimus muscle area at the 12-13th rib interface, carcass weight-adjusted longissimus muscle area, USDA yield grade, estimated total lean yield, marbling score, and Warner-Bratzler shear force. Steers were classified as either high Brahman (50 to 100% Brahman), moderate Brahman (25 to 49% Brahman), or low Brahman (0 to 24% Brahman) inheritance. Two types of animal models were fit with regard to level of Brahman inheritance. One model assumed similar variances between pairs of Brahman inheritance groups, and the second model assumed different variances between pairs of Brahman inheritance groups. Fixed sources of variation in both models included direct and maternal additive and nonadditive breed effects, year of birth, and slaughter age. Variances were estimated using derivative free REML procedures. Likelihood ratio tests were used to compare models. The model accounting for heterogeneous variances had a greater likelihood (P < .001) than the model assuming homogeneous variances for hot carcass weight, longissimus muscle area, weight-adjusted longissimus muscle area, total lean yield, and Warner-Bratzler shear force, indicating improved fit with percentage Brahman inheritance

  14. Genetic Rearrangements of Six Wheat–Agropyron cristatum 6P Addition Lines Revealed by Molecular Markers

    PubMed Central

    Su, Junji; Zhang, Jinpeng; Song, Liqiang; Gao, Ainong; Yang, Xinming; Li, Xiuquan; Liu, Weihua; Li, Lihui

    2014-01-01

    Agropyron cristatum (L.) Gaertn. (2n = 4x = 28, PPPP) not only is cultivated as pasture fodder but also could provide many desirable genes for wheat improvement. It is critical to obtain common wheat–A. cristatum alien disomic addition lines to locate the desired genes on the P genome chromosomes. Comparative analysis of the homoeologous relationships between the P genome chromosome and wheat genome chromosomes is a key step in transferring different desirable genes into common wheat and producing the desired alien translocation line while compensating for the loss of wheat chromatin. In this study, six common wheat–A. cristatum disomic addition lines were produced and analyzed by phenotypic examination, genomic in situ hybridization (GISH), SSR markers from the ABD genomes and STS markers from the P genome. Comparative maps, six in total, were generated and demonstrated that all six addition lines belonged to homoeologous group 6. However, chromosome 6P had undergone obvious rearrangements in different addition lines compared with the wheat chromosome, indicating that to obtain a genetic compensating alien translocation line, one should recombine alien chromosomal regions with homoeologous wheat chromosomes. Indeed, these addition lines were classified into four types based on the comparative mapping: 6PI, 6PII, 6PIII, and 6PIV. The different types of chromosome 6P possessed different desirable genes. For example, the 6PI type, containing three addition lines, carried genes conferring high numbers of kernels per spike and resistance to powdery mildew, important traits for wheat improvement. These results may prove valuable for promoting the development of conventional chromosome engineering techniques toward molecular chromosome engineering. PMID:24595330

  15. The genetics of maternal care: direct and indirect genetic effects on phenotype in the dung beetle Onthophagus taurus.

    PubMed

    Hunt, John; Simmons, Leigh W

    2002-05-14

    While theoretical models of the evolution of parental care are based on the assumption of underlying genetic variance, surprisingly few quantitative genetic studies of this life-history trait exist. Estimation of the degree of genetic variance in parental care is important because it can be a significant source of maternal effects, which, if genetically based, represent indirect genetic effects. A major prediction of indirect genetic effect theory is that traits without heritable variation can evolve because of the heritable environmental variation that indirect genetic effects provide. In the dung beetle, Onthophagus taurus, females provide care to offspring by provisioning a brood mass. The size of the brood mass has pronounced effects on offspring phenotype. Using a half-sib breeding design we show that the weight of the brood mass females produce exhibits significant levels of additive genetic variance due to sires. However, variance caused by dams is considerably larger, demonstrating that maternal effects are also important. Body size exhibited low additive genetic variance. However, body size exerts a strong maternal influence on the weight of brood masses produced, accounting for 22% of the nongenetic variance in offspring body size. Maternal body size also influenced the number of offspring produced but there was no genetic variance for this trait. Offspring body size and brood mass weight exhibited positive genetic and phenotypic correlations. We conclude that both indirect genetic effects, via maternal care, and nongenetic maternal effects, via female size, play important roles in the evolution of phenotype in this species. PMID:11983863

  16. Variational bayesian method of estimating variance components.

    PubMed

    Arakawa, Aisaku; Taniguchi, Masaaki; Hayashi, Takeshi; Mikawa, Satoshi

    2016-07-01

    We developed a Bayesian analysis approach by using a variational inference method, a so-called variational Bayesian method, to determine the posterior distributions of variance components. This variational Bayesian method and an alternative Bayesian method using Gibbs sampling were compared in estimating genetic and residual variance components from both simulated data and publically available real pig data. In the simulated data set, we observed strong bias toward overestimation of genetic variance for the variational Bayesian method in the case of low heritability and low population size, and less bias was detected with larger population sizes in both methods examined. The differences in the estimates of variance components between the variational Bayesian and the Gibbs sampling were not found in the real pig data. However, the posterior distributions of the variance components obtained with the variational Bayesian method had shorter tails than those obtained with the Gibbs sampling. Consequently, the posterior standard deviations of the genetic and residual variances of the variational Bayesian method were lower than those of the method using Gibbs sampling. The computing time required was much shorter with the variational Bayesian method than with the method using Gibbs sampling. PMID:26877207

  17. Functional Analysis of Variance for Association Studies

    PubMed Central

    Vsevolozhskaya, Olga A.; Zaykin, Dmitri V.; Greenwood, Mark C.; Wei, Changshuai; Lu, Qing

    2014-01-01

    While progress has been made in identifying common genetic variants associated with human diseases, for most of common complex diseases, the identified genetic variants only account for a small proportion of heritability. Challenges remain in finding additional unknown genetic variants predisposing to complex diseases. With the advance in next-generation sequencing technologies, sequencing studies have become commonplace in genetic research. The ongoing exome-sequencing and whole-genome-sequencing studies generate a massive amount of sequencing variants and allow researchers to comprehensively investigate their role in human diseases. The discovery of new disease-associated variants can be enhanced by utilizing powerful and computationally efficient statistical methods. In this paper, we propose a functional analysis of variance (FANOVA) method for testing an association of sequence variants in a genomic region with a qualitative trait. The FANOVA has a number of advantages: (1) it tests for a joint effect of gene variants, including both common and rare; (2) it fully utilizes linkage disequilibrium and genetic position information; and (3) allows for either protective or risk-increasing causal variants. Through simulations, we show that FANOVA outperform two popularly used methods – SKAT and a previously proposed method based on functional linear models (FLM), – especially if a sample size of a study is small and/or sequence variants have low to moderate effects. We conduct an empirical study by applying three methods (FANOVA, SKAT and FLM) to sequencing data from Dallas Heart Study. While SKAT and FLM respectively detected ANGPTL 4 and ANGPTL 3 associated with obesity, FANOVA was able to identify both genes associated with obesity. PMID:25244256

  18. Cosmology without cosmic variance

    SciTech Connect

    Bernstein, Gary M.; Cai, Yan -Chuan

    2011-10-01

    The growth of structures in the Universe is described by a function G that is predicted by the combination of the expansion history of the Universe and the laws of gravity within it. We examine the improvements in constraints on G that are available from the combination of a large-scale galaxy redshift survey with a weak gravitational lensing survey of background sources. We describe a new combination of such observations that in principle this yields a measure of the growth rate that is free of sample variance, i.e. the uncertainty in G can be reduced without bound by increasing the number of redshifts obtained within a finite survey volume. The addition of background weak lensing data to a redshift survey increases information on G by an amount equivalent to a 10-fold increase in the volume of a standard redshift-space distortion measurement - if the lensing signal can be measured to sub-per cent accuracy. This argues that a combined lensing and redshift survey over a common low-redshift volume of the Universe is a more powerful test of general relativity than an isolated redshift survey over larger volume at high redshift, especially as surveys begin to cover most of the available sky.

  19. Cosmology without cosmic variance

    DOE PAGESBeta

    Bernstein, Gary M.; Cai, Yan -Chuan

    2011-10-01

    The growth of structures in the Universe is described by a function G that is predicted by the combination of the expansion history of the Universe and the laws of gravity within it. We examine the improvements in constraints on G that are available from the combination of a large-scale galaxy redshift survey with a weak gravitational lensing survey of background sources. We describe a new combination of such observations that in principle this yields a measure of the growth rate that is free of sample variance, i.e. the uncertainty in G can be reduced without bound by increasing themore » number of redshifts obtained within a finite survey volume. The addition of background weak lensing data to a redshift survey increases information on G by an amount equivalent to a 10-fold increase in the volume of a standard redshift-space distortion measurement - if the lensing signal can be measured to sub-per cent accuracy. This argues that a combined lensing and redshift survey over a common low-redshift volume of the Universe is a more powerful test of general relativity than an isolated redshift survey over larger volume at high redshift, especially as surveys begin to cover most of the available sky.« less

  20. The genetic architecture of fitness in a seed beetle: assessing the potential for indirect genetic benefits of female choice

    PubMed Central

    2008-01-01

    Background Quantifying the amount of standing genetic variation in fitness represents an empirical challenge. Unfortunately, the shortage of detailed studies of the genetic architecture of fitness has hampered progress in several domains of evolutionary biology. One such area is the study of sexual selection. In particular, the evolution of adaptive female choice by indirect genetic benefits relies on the presence of genetic variation for fitness. Female choice by genetic benefits fall broadly into good genes (additive) models and compatibility (non-additive) models where the strength of selection is dictated by the genetic architecture of fitness. To characterize the genetic architecture of fitness, we employed a quantitative genetic design (the diallel cross) in a population of the seed beetle Callosobruchus maculatus, which is known to exhibit post-copulatory female choice. From reciprocal crosses of inbred lines, we assayed egg production, egg-to-adult survival, and lifetime offspring production of the outbred F1 daughters (F1 productivity). Results We used the bio model to estimate six components of genetic and environmental variance in fitness. We found sizeable additive and non-additive genetic variance in F1 productivity, but lower genetic variance in egg-to-adult survival, which was strongly influenced by maternal and paternal effects. Conclusion Our results show that, in order to gain a relevant understanding of the genetic architecture of fitness, measures of offspring fitness should be inclusive and should include quantifications of offspring reproductive success. We note that our estimate of additive genetic variance in F1 productivity (CVA = 14%) is sufficient to generate indirect selection on female choice. However, our results also show that the major determinant of offspring fitness is the genetic interaction between parental genomes, as indicated by large amounts of non-additive genetic variance (dominance and/or epistasis) for F1 productivity. We

  1. 45 CFR 146.122 - Additional requirements prohibiting discrimination based on genetic information.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... individual has a genetic variant associated with hereditary nonpolyposis colorectal cancer is a genetic test... manifested with respect to A. Example 2. (i) Facts. Individual B has several family members with colon cancer... hereditary nonpolyposis colorectal cancer (HNPCC). B's physician, a health care professional with...

  2. 45 CFR 146.122 - Additional requirements prohibiting discrimination based on genetic information.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... individual has a genetic variant associated with hereditary nonpolyposis colorectal cancer is a genetic test... manifested with respect to A. Example 2. (i) Facts. Individual B has several family members with colon cancer... hereditary nonpolyposis colorectal cancer (HNPCC). B's physician, a health care professional with...

  3. 45 CFR 146.122 - Additional requirements prohibiting discrimination based on genetic information.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... individual has a genetic variant associated with hereditary nonpolyposis colorectal cancer is a genetic test... manifested with respect to A. Example 2. (i) Facts. Individual B has several family members with colon cancer... hereditary nonpolyposis colorectal cancer (HNPCC). B's physician, a health care professional with...

  4. 45 CFR 146.122 - Additional requirements prohibiting discrimination based on genetic information.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... individual has a genetic variant associated with hereditary nonpolyposis colorectal cancer is a genetic test... manifested with respect to A. Example 2. (i) Facts. Individual B has several family members with colon cancer... hereditary nonpolyposis colorectal cancer (HNPCC). B's physician, a health care professional with...

  5. Monte Carlo variance reduction

    NASA Technical Reports Server (NTRS)

    Byrn, N. R.

    1980-01-01

    Computer program incorporates technique that reduces variance of forward Monte Carlo method for given amount of computer time in determining radiation environment in complex organic and inorganic systems exposed to significant amounts of radiation.

  6. Genetic variances, heritabilities and maternal effects on body weight, breast meat yield, meat quality traits and the shape of the growth curve in turkey birds

    PubMed Central

    2011-01-01

    Background Turkey is an important agricultural species and is largely used as a meat bird. In 2004, turkey represented 6.5% of the world poultry meat production. The world-wide turkey population has rapidly grown due to increased commercial farming. Due to the high demand for turkey meat from both consumers and industry global turkey stocks increased from 100 million in 1970 to over 276 million in 2004. This rapidly increasing importance of turkeys was a reason to design this study for the estimation of genetic parameters that control body weight, body composition, meat quality traits and parameters that shape the growth curve in turkey birds. Results The average heritability estimate for body weight traits was 0.38, except for early weights that were strongly affected by maternal effects. This study showed that body weight traits, upper asymptote (a growth curve trait), percent breast meat and redness of meat had high heritability whereas heritabilities of breast length, breast width, percent drip loss, ultimate pH, lightness and yellowness of meat were medium to low. We found high positive genetic and phenotypic correlations between body weight, upper asymptote, most breast meat yield traits and percent drip loss but percent drip loss was found strongly negatively correlated with ultimate pH. Percent breast meat, however, showed genetic correlations close to zero with body weight traits and upper asymptote. Conclusion The results of this analysis and the growth curve from the studied population of turkey birds suggest that the turkey birds could be selected for breeding between 60 and 80 days of age in order to improve overall production and the production of desirable cuts of meat. The continuous selection of birds within this age range could promote high growth rates but specific attention to meat quality would be needed to avoid a negative impact on the quality of meat. PMID:21266032

  7. A COSMIC VARIANCE COOKBOOK

    SciTech Connect

    Moster, Benjamin P.; Rix, Hans-Walter; Somerville, Rachel S.; Newman, Jeffrey A. E-mail: rix@mpia.de E-mail: janewman@pitt.edu

    2011-04-20

    Deep pencil beam surveys (<1 deg{sup 2}) are of fundamental importance for studying the high-redshift universe. However, inferences about galaxy population properties (e.g., the abundance of objects) are in practice limited by 'cosmic variance'. This is the uncertainty in observational estimates of the number density of galaxies arising from the underlying large-scale density fluctuations. This source of uncertainty can be significant, especially for surveys which cover only small areas and for massive high-redshift galaxies. Cosmic variance for a given galaxy population can be determined using predictions from cold dark matter theory and the galaxy bias. In this paper, we provide tools for experiment design and interpretation. For a given survey geometry, we present the cosmic variance of dark matter as a function of mean redshift z-bar and redshift bin size {Delta}z. Using a halo occupation model to predict galaxy clustering, we derive the galaxy bias as a function of mean redshift for galaxy samples of a given stellar mass range. In the linear regime, the cosmic variance of these galaxy samples is the product of the galaxy bias and the dark matter cosmic variance. We present a simple recipe using a fitting function to compute cosmic variance as a function of the angular dimensions of the field, z-bar , {Delta}z, and stellar mass m{sub *}. We also provide tabulated values and a software tool. The accuracy of the resulting cosmic variance estimates ({delta}{sigma}{sub v}/{sigma}{sub v}) is shown to be better than 20%. We find that for GOODS at z-bar =2 and with {Delta}z = 0.5, the relative cosmic variance of galaxies with m{sub *}>10{sup 11} M{sub sun} is {approx}38%, while it is {approx}27% for GEMS and {approx}12% for COSMOS. For galaxies of m{sub *} {approx} 10{sup 10} M{sub sun}, the relative cosmic variance is {approx}19% for GOODS, {approx}13% for GEMS, and {approx}6% for COSMOS. This implies that cosmic variance is a significant source of uncertainty at z

  8. A Cosmic Variance Cookbook

    NASA Astrophysics Data System (ADS)

    Moster, Benjamin P.; Somerville, Rachel S.; Newman, Jeffrey A.; Rix, Hans-Walter

    2011-04-01

    Deep pencil beam surveys (<1 deg2) are of fundamental importance for studying the high-redshift universe. However, inferences about galaxy population properties (e.g., the abundance of objects) are in practice limited by "cosmic variance." This is the uncertainty in observational estimates of the number density of galaxies arising from the underlying large-scale density fluctuations. This source of uncertainty can be significant, especially for surveys which cover only small areas and for massive high-redshift galaxies. Cosmic variance for a given galaxy population can be determined using predictions from cold dark matter theory and the galaxy bias. In this paper, we provide tools for experiment design and interpretation. For a given survey geometry, we present the cosmic variance of dark matter as a function of mean redshift \\bar{z} and redshift bin size Δz. Using a halo occupation model to predict galaxy clustering, we derive the galaxy bias as a function of mean redshift for galaxy samples of a given stellar mass range. In the linear regime, the cosmic variance of these galaxy samples is the product of the galaxy bias and the dark matter cosmic variance. We present a simple recipe using a fitting function to compute cosmic variance as a function of the angular dimensions of the field, \\bar{z}, Δz, and stellar mass m *. We also provide tabulated values and a software tool. The accuracy of the resulting cosmic variance estimates (δσ v /σ v ) is shown to be better than 20%. We find that for GOODS at \\bar{z}=2 and with Δz = 0.5, the relative cosmic variance of galaxies with m *>1011 M sun is ~38%, while it is ~27% for GEMS and ~12% for COSMOS. For galaxies of m * ~ 1010 M sun, the relative cosmic variance is ~19% for GOODS, ~13% for GEMS, and ~6% for COSMOS. This implies that cosmic variance is a significant source of uncertainty at \\bar{z}=2 for small fields and massive galaxies, while for larger fields and intermediate mass galaxies, cosmic variance is

  9. Genetic variance and breeding values for resistance to a wind-borne disease [Sphaerotheca macularis (Wallr. ex Fr.)] in strawberry (Fragaria x ananassa Duch.) estimated by exploring mixed and spatial models and pedigree information.

    PubMed

    Davik, Jahn; Honne, Bjørn Ivar

    2005-07-01

    A mixed model approach was used to estimate variance components and heritabilities for resistance to powdery mildew, a wind-borne disease in strawberry. In order to improve precision in the statistical computations, spatial error control effects were included to account for systematic environmental variations in the large field trials. Pedigree information was included where feasible. Seedling families obtained from an incomplete 63-by-63 diallel cross were grown at six locations and scored subjectively for mildew attack three times during the growing season. The 63 parents included both European and American cultivars as well as advanced selections from various breeding programmes. A total of 298 full-sib families were realized, including 26 reciprocal families. No reciprocal differences were found. On a plot-mean basis, the broad-sense heritability was found to be intermediate, H(2) = 0.44-0.50, depending on whether the pedigree information was included in the model or not. The increase was mainly due to a substantial increase in the additive variance component. Likewise, the narrow-sense heritability increased from h(2) = 0.39 to h(2) = 0.45 when the pedigree information was included, while the ratio of the specific combining ability variance to the general combining ability variance fell from 13% to 10%. The predicted breeding values of the 63 parents demonstrate that important cultivars such as Elsanta and Korona are unlikely to produce progenies with a high degree of resistance. On the other hand, the Norwegian cultivar Solprins, the Canadian cultivar Kent and the Italian cultivar Patty appeared to give highly resistant progeny. At the full-sib level, the estimated disease scores ranged from 1.15 (Kent x Induka) to 4.19 (Cavendish x Avanta), revealing a huge range of variation for powdery mildew resistance available for selection. PMID:15937703

  10. Unraveling Additive from Nonadditive Effects Using Genomic Relationship Matrices

    PubMed Central

    Muñoz, Patricio R.; Resende, Marcio F. R.; Gezan, Salvador A.; Resende, Marcos Deon Vilela; de los Campos, Gustavo; Kirst, Matias; Huber, Dudley; Peter, Gary F.

    2014-01-01

    The application of quantitative genetics in plant and animal breeding has largely focused on additive models, which may also capture dominance and epistatic effects. Partitioning genetic variance into its additive and nonadditive components using pedigree-based models (P-genomic best linear unbiased predictor) (P-BLUP) is difficult with most commonly available family structures. However, the availability of dense panels of molecular markers makes possible the use of additive- and dominance-realized genomic relationships for the estimation of variance components and the prediction of genetic values (G-BLUP). We evaluated height data from a multifamily population of the tree species Pinus taeda with a systematic series of models accounting for additive, dominance, and first-order epistatic interactions (additive by additive, dominance by dominance, and additive by dominance), using either pedigree- or marker-based information. We show that, compared with the pedigree, use of realized genomic relationships in marker-based models yields a substantially more precise separation of additive and nonadditive components of genetic variance. We conclude that the marker-based relationship matrices in a model including additive and nonadditive effects performed better, improving breeding value prediction. Moreover, our results suggest that, for tree height in this population, the additive and nonadditive components of genetic variance are similar in magnitude. This novel result improves our current understanding of the genetic control and architecture of a quantitative trait and should be considered when developing breeding strategies. PMID:25324160

  11. Genetic predisposition to coronary heart disease and stroke using an additive genetic risk score: a population-based study in Greece

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Objective: To determine the extent to which the risk for incident coronary heart disease (CHD) increases in relation to a genetic risk score (GRS) that additively integrates the influence of high-risk alleles in nine documented single nucleotide polymorphisms (SNPs) for CHD, and to examine whether t...

  12. Getting around cosmic variance

    SciTech Connect

    Kamionkowski, M.; Loeb, A.

    1997-10-01

    Cosmic microwave background (CMB) anisotropies probe the primordial density field at the edge of the observable Universe. There is a limiting precision ({open_quotes}cosmic variance{close_quotes}) with which anisotropies can determine the amplitude of primordial mass fluctuations. This arises because the surface of last scatter (SLS) probes only a finite two-dimensional slice of the Universe. Probing other SLS{close_quote}s observed from different locations in the Universe would reduce the cosmic variance. In particular, the polarization of CMB photons scattered by the electron gas in a cluster of galaxies provides a measurement of the CMB quadrupole moment seen by the cluster. Therefore, CMB polarization measurements toward many clusters would probe the anisotropy on a variety of SLS{close_quote}s within the observable Universe, and hence reduce the cosmic-variance uncertainty. {copyright} {ital 1997} {ital The American Physical Society}

  13. Variance Anisotropy in Kinetic Plasmas

    NASA Astrophysics Data System (ADS)

    Parashar, Tulasi N.; Oughton, Sean; Matthaeus, William H.; Wan, Minping

    2016-06-01

    Solar wind fluctuations admit well-documented anisotropies of the variance matrix, or polarization, related to the mean magnetic field direction. Typically, one finds a ratio of perpendicular variance to parallel variance of the order of 9:1 for the magnetic field. Here we study the question of whether a kinetic plasma spontaneously generates and sustains parallel variances when initiated with only perpendicular variance. We find that parallel variance grows and saturates at about 5% of the perpendicular variance in a few nonlinear times irrespective of the Reynolds number. For sufficiently large systems (Reynolds numbers) the variance approaches values consistent with the solar wind observations.

  14. Conversations across Meaning Variance

    ERIC Educational Resources Information Center

    Cordero, Alberto

    2013-01-01

    Progressive interpretations of scientific theories have long been denounced as naive, because of the inescapability of meaning variance. The charge reportedly applies to recent realist moves that focus on theory-parts rather than whole theories. This paper considers the question of what "theory-parts" of epistemic significance (if any) relevantly…

  15. Minimum variance geographic sampling

    NASA Technical Reports Server (NTRS)

    Terrell, G. R. (Principal Investigator)

    1980-01-01

    Resource inventories require samples with geographical scatter, sometimes not as widely spaced as would be hoped. A simple model of correlation over distances is used to create a minimum variance unbiased estimate population means. The fitting procedure is illustrated from data used to estimate Missouri corn acreage.

  16. Naive Analysis of Variance

    ERIC Educational Resources Information Center

    Braun, W. John

    2012-01-01

    The Analysis of Variance is often taught in introductory statistics courses, but it is not clear that students really understand the method. This is because the derivation of the test statistic and p-value requires a relatively sophisticated mathematical background which may not be well-remembered or understood. Thus, the essential concept behind…

  17. Spectral Ambiguity of Allan Variance

    NASA Technical Reports Server (NTRS)

    Greenhall, C. A.

    1996-01-01

    We study the extent to which knowledge of Allan variance and other finite-difference variances determines the spectrum of a random process. The variance of first differences is known to determine the spectrum. We show that, in general, the Allan variance does not. A complete description of the ambiguity is given.

  18. Additive genetic variation for tolerance to estrogen pollution in natural populations of Alpine whitefish (Coregonus sp., Salmonidae)

    PubMed Central

    Brazzola, Gregory; Chèvre, Nathalie; Wedekind, Claus

    2014-01-01

    The evolutionary potential of natural populations to adapt to anthropogenic threats critically depends on whether there exists additive genetic variation for tolerance to the threat. A major problem for water-dwelling organisms is chemical pollution, and among the most common pollutants is 17α-ethinylestradiol (EE2), the synthetic estrogen that is used in oral contraceptives and that can affect fish at various developmental stages, including embryogenesis. We tested whether there is variation in the tolerance to EE2 within Alpine whitefish. We sampled spawners from two species of different lakes, bred them in vitro in a full-factorial design each, and studied growth and mortality of embryos. Exposure to EE2 turned out to be toxic in all concentrations we tested (≥1 ng/L). It reduced embryo viability and slowed down embryogenesis. We found significant additive genetic variation in EE2-induced mortality in both species, that is, genotypes differed in their tolerance to estrogen pollution. We also found maternal effects on embryo development to be influenced by EE2, that is, some maternal sib groups were more susceptible to EE2 than others. In conclusion, the toxic effects of EE2 were strong, but both species demonstrated the kind of additive genetic variation that is necessary for an evolutionary response to this type of pollution. PMID:25553069

  19. Additive genetic variation for tolerance to estrogen pollution in natural populations of Alpine whitefish (Coregonus sp., Salmonidae).

    PubMed

    Brazzola, Gregory; Chèvre, Nathalie; Wedekind, Claus

    2014-11-01

    The evolutionary potential of natural populations to adapt to anthropogenic threats critically depends on whether there exists additive genetic variation for tolerance to the threat. A major problem for water-dwelling organisms is chemical pollution, and among the most common pollutants is 17α-ethinylestradiol (EE2), the synthetic estrogen that is used in oral contraceptives and that can affect fish at various developmental stages, including embryogenesis. We tested whether there is variation in the tolerance to EE2 within Alpine whitefish. We sampled spawners from two species of different lakes, bred them in vitro in a full-factorial design each, and studied growth and mortality of embryos. Exposure to EE2 turned out to be toxic in all concentrations we tested (≥1 ng/L). It reduced embryo viability and slowed down embryogenesis. We found significant additive genetic variation in EE2-induced mortality in both species, that is, genotypes differed in their tolerance to estrogen pollution. We also found maternal effects on embryo development to be influenced by EE2, that is, some maternal sib groups were more susceptible to EE2 than others. In conclusion, the toxic effects of EE2 were strong, but both species demonstrated the kind of additive genetic variation that is necessary for an evolutionary response to this type of pollution. PMID:25553069

  20. Estimation of variance components including competitive effects of Large White growing gilts.

    PubMed

    Arango, J; Misztal, I; Tsuruta, S; Culbertson, M; Herring, W

    2005-06-01

    Records of on-test ADG of Large White gilts were analyzed to estimate variance components of direct and associative genetic effects. Models included the effects of contemporary group (farm-barn-batch), birth litter, pen group, and direct and associative additive genetic effects. The area of each pen was 14 m2. The additive genetic variance was a function of the number of competitors in a group, the additive relationships between the animal performing the record and its pen mates, and the additive relationships between pen mates. To partially account for differences in the number of pen mates, a covariable (qi = 1, 1/n, or 1/n(1/2)) was added to the associative genetic effect. There were 4,946 records from 2,409 litters and 362 pen groups. Pen group size ranged from 12 to 16 gilts. Analyses by REML converged very slowly. A grid search showed that the likelihood function was almost flat when the additive genetic associative effect was fitted. Estimates of direct and associative heritability were 0.15 and 0.03, respectively. Within the BLUPF90 family of programs, the mixed-model equations can be set up directly. For variance component estimation, simple programs (REMLF90 and GIBBSF90) worked without modifications, but more optimized programs did not. Estimates obtained using the three values of qi were similar. With the data structure available for this study and under an environment with relative low competition among animals, accurate estimation of associative genetic effects was not possible. Estimation of competitive effects with large pen size is difficult. The magnitude of competition effects may be larger in commercial populations, where housing is denser and food is limited. PMID:15890801

  1. Genetic and Epigenetic Changes in Oilseed Rape (Brassica napus L.) Extracted from Intergeneric Allopolyploid and Additions with Orychophragmus.

    PubMed

    Gautam, Mayank; Dang, Yanwei; Ge, Xianhong; Shao, Yujiao; Li, Zaiyun

    2016-01-01

    Allopolyploidization with the merger of the genomes from different species has been shown to be associated with genetic and epigenetic changes. But the maintenance of such alterations related to one parental species after the genome is extracted from the allopolyploid remains to be detected. In this study, the genome of Brassica napus L. (2n = 38, genomes AACC) was extracted from its intergeneric allohexaploid (2n = 62, genomes AACCOO) with another crucifer Orychophragmus violaceus (2n = 24, genome OO), by backcrossing and development of alien addition lines. B. napus-type plants identified in the self-pollinated progenies of nine monosomic additions were analyzed by the methods of amplified fragment length polymorphism, sequence-specific amplified polymorphism, and methylation-sensitive amplified polymorphism. They showed modifications to certain extents in genomic components (loss and gain of DNA segments and transposons, introgression of alien DNA segments) and DNA methylation, compared with B. napus donor. The significant differences in the changes between the B. napus types extracted from these additions likely resulted from the different effects of individual alien chromosomes. Particularly, the additions which harbored the O. violaceus chromosome carrying dominant rRNA genes over those of B. napus tended to result in the development of plants which showed fewer changes, suggesting a role of the expression levels of alien rRNA genes in genomic stability. These results provided new cues for the genetic alterations in one parental genome that are maintained even after the genome becomes independent. PMID:27148282

  2. Genetic and Epigenetic Changes in Oilseed Rape (Brassica napus L.) Extracted from Intergeneric Allopolyploid and Additions with Orychophragmus

    PubMed Central

    Gautam, Mayank; Dang, Yanwei; Ge, Xianhong; Shao, Yujiao; Li, Zaiyun

    2016-01-01

    Allopolyploidization with the merger of the genomes from different species has been shown to be associated with genetic and epigenetic changes. But the maintenance of such alterations related to one parental species after the genome is extracted from the allopolyploid remains to be detected. In this study, the genome of Brassica napus L. (2n = 38, genomes AACC) was extracted from its intergeneric allohexaploid (2n = 62, genomes AACCOO) with another crucifer Orychophragmus violaceus (2n = 24, genome OO), by backcrossing and development of alien addition lines. B. napus-type plants identified in the self-pollinated progenies of nine monosomic additions were analyzed by the methods of amplified fragment length polymorphism, sequence-specific amplified polymorphism, and methylation-sensitive amplified polymorphism. They showed modifications to certain extents in genomic components (loss and gain of DNA segments and transposons, introgression of alien DNA segments) and DNA methylation, compared with B. napus donor. The significant differences in the changes between the B. napus types extracted from these additions likely resulted from the different effects of individual alien chromosomes. Particularly, the additions which harbored the O. violaceus chromosome carrying dominant rRNA genes over those of B. napus tended to result in the development of plants which showed fewer changes, suggesting a role of the expression levels of alien rRNA genes in genomic stability. These results provided new cues for the genetic alterations in one parental genome that are maintained even after the genome becomes independent. PMID:27148282

  3. Complete nucleotide sequence of a Spanish isolate of alfalfa mosaic virus: evidence for additional genetic variability.

    PubMed

    Parrella, Giuseppe; Acanfora, Nadia; Orílio, Anelise F; Navas-Castillo, Jesús

    2011-06-01

    Alfalfa mosaic virus (AMV) is a plant virus that is distributed worldwide and can induce necrosis and/or yellow mosaic on a large variety of plant species, including commercially important crops. It is the only virus of the genus Alfamovirus in the family Bromoviridae. AMV isolates can be clustered into two genetic groups that correlate with their geographic origin. Here, we report for the first time the complete nucleotide sequence of a Spanish isolate of AMV found infecting Cape honeysuckle (Tecoma capensis) and named Tec-1. The tripartite genome of Tec-1 is composed of 3643 nucleotides (nt) for RNA1, 2594 nt for RNA2 and 2037 nt for RNA3. Comparative sequence analysis of the coat protein gene revealed that the isolate Tec-1 is distantly related to subgroup I of AMV and more closely related to subgroup II, although forming a distinct phylogenetic clade. Therefore, we propose to split subgroup II of AMV into two subgroups, namely IIA, comprising isolates previously included in subgroup II, and IIB, including the novel Spanish isolate Tec-1. PMID:21327783

  4. Additional records of metazoan parasites from Caribbean marine mammals, including genetically identified anisakid nematodes.

    PubMed

    Colón-Llavina, Marlene M; Mignucci-Giannoni, Antonio A; Mattiucci, Simonetta; Paoletti, Michela; Nascetti, Giuseppe; Williams, Ernest H

    2009-10-01

    Studies of marine mammal parasites in the Caribbean are scarce. An assessment for marine mammal endo- and ectoparasites from Puerto Rico and the Virgin Islands, but extending to other areas of the Caribbean, was conducted between 1989 and 1994. The present study complements the latter and enhances identification of anisakid nematodes using molecular markers. Parasites were collected from 59 carcasses of stranded cetaceans and manatees from 1994 to 2006, including Globicephala macrorhynchus, Kogia breviceps, Kogia sima, Lagenodelphis hosei, Mesoplodon densirostris, Peponocephala electra, Stenella longirostris, Steno bredanensis, Trichechus manatus. Tursiops truncatus, and Ziphius cavirostris. Sixteen species of endoparasitic helminthes were morphologically identified, including two species of acanthocephalans (Bolbosoma capitatum, Bolbosoma vasculosum), nine species of nematodes (Anisakis sp., Anisakis brevispiculata, Anisakis paggiae, Anisakis simplex, Anisakis typica, Anisakis ziphidarium, Crassicauda anthonyi, Heterocheilus tunicatus, Pseudoterranova ceticola), two species of cestodes (Monorygma grimaldi, Phyllobothrium delphini), and three species of trematodes (Chiorchis groschafti, Pulmonicola cochleotrema, Monoligerum blairi). The nematodes belonging to the genus Anisakis recovered in some stranded animals were genetically identified to species level based on their sequence analysis of mitochondrial DNA (629 bp of mtDNA cox 2). A total of five new host records and six new geographic records are presented. PMID:19582477

  5. Variance component estimates for alternative litter size traits in swine.

    PubMed

    Putz, A M; Tiezzi, F; Maltecca, C; Gray, K A; Knauer, M T

    2015-11-01

    Litter size at d 5 (LS5) has been shown to be an effective trait to increase total number born (TNB) while simultaneously decreasing preweaning mortality. The objective of this study was to determine the optimal litter size day for selection (i.e., other than d 5). Traits included TNB, number born alive (NBA), litter size at d 2, 5, 10, 30 (LS2, LS5, LS10, LS30, respectively), litter size at weaning (LSW), number weaned (NW), piglet mortality at d 30 (MortD30), and average piglet birth weight (BirthWt). Litter size traits were assigned to biological litters and treated as a trait of the sow. In contrast, NW was the number of piglets weaned by the nurse dam. Bivariate animal models included farm, year-season, and parity as fixed effects. Number born alive was fit as a covariate for BirthWt. Random effects included additive genetics and the permanent environment of the sow. Variance components were plotted for TNB, NBA, and LS2 to LS30 using univariate animal models to determine how variances changed over time. Additive genetic variance was minimized at d 7 in Large White and at d 14 in Landrace pigs. Total phenotypic variance for litter size traits decreased over the first 10 d and then stabilized. Heritability estimates increased between TNB and LS30. Genetic correlations between TNB, NBA, and LS2 to LS29 with LS30 plateaued within the first 10 d. A genetic correlation with LS30 of 0.95 was reached at d 4 for Large White and at d 8 for Landrace pigs. Heritability estimates ranged from 0.07 to 0.13 for litter size traits and MortD30. Birth weight had an h of 0.24 and 0.26 for Large White and Landrace pigs, respectively. Genetic correlations among LS30, LSW, and NW ranged from 0.97 to 1.00. In the Large White breed, genetic correlations between MortD30 with TNB and LS30 were 0.23 and -0.64, respectively. These correlations were 0.10 and -0.61 in the Landrace breed. A high genetic correlation of 0.98 and 0.97 was observed between LS10 and NW for Large White and

  6. Decomposing genomic variance using information from GWA, GWE and eQTL analysis.

    PubMed

    Ehsani, A; Janss, L; Pomp, D; Sørensen, P

    2016-04-01

    A commonly used procedure in genome-wide association (GWA), genome-wide expression (GWE) and expression quantitative trait locus (eQTL) analyses is based on a bottom-up experimental approach that attempts to individually associate molecular variants with complex traits. Top-down modeling of the entire set of genomic data and partitioning of the overall variance into subcomponents may provide further insight into the genetic basis of complex traits. To test this approach, we performed a whole-genome variance components analysis and partitioned the genomic variance using information from GWA, GWE and eQTL analyses of growth-related traits in a mouse F2 population. We characterized the mouse trait genetic architecture by ordering single nucleotide polymorphisms (SNPs) based on their P-values and studying the areas under the curve (AUCs). The observed traits were found to have a genomic variance profile that differed significantly from that expected of a trait under an infinitesimal model. This situation was particularly true for both body weight and body fat, for which the AUCs were much higher compared with that of glucose. In addition, SNPs with a high degree of trait-specific regulatory potential (SNPs associated with subset of transcripts that significantly associated with a specific trait) explained a larger proportion of the genomic variance than did SNPs with high overall regulatory potential (SNPs associated with transcripts using traditional eQTL analysis). We introduced AUC measures of genomic variance profiles that can be used to quantify relative importance of SNPs as well as degree of deviation of a trait's inheritance from an infinitesimal model. The shape of the curve aids global understanding of traits: The steeper the left-hand side of the curve, the fewer the number of SNPs controlling most of the phenotypic variance. PMID:26678352

  7. Spectral variance of aeroacoustic data

    NASA Technical Reports Server (NTRS)

    Rao, K. V.; Preisser, J. S.

    1981-01-01

    An asymptotic technique for estimating the variance of power spectra is applied to aircraft flyover noise data. The results are compared with directly estimated variances and they are in reasonable agreement. The basic time series need not be Gaussian for asymptotic theory to apply. The asymptotic variance formulae can be useful tools both in the design and analysis phase of experiments of this type.

  8. Genetics

    MedlinePlus

    Homozygous; Inheritance; Heterozygous; Inheritance patterns; Heredity and disease; Heritable; Genetic markers ... The chromosomes are made up of strands of genetic information called DNA. Each chromosome contains sections of ...

  9. Genetics

    MedlinePlus

    ... Inheritance; Heterozygous; Inheritance patterns; Heredity and disease; Heritable; Genetic markers ... The chromosomes are made up of strands of genetic information called DNA. Each chromosome contains sections of ...

  10. Selection for increased desiccation resistance in Drosophila melanogaster: Additive genetic control and correlated responses for other stresses

    SciTech Connect

    Hoffmann, A.A.; Parsons, P.A. )

    1989-08-01

    Previously we found that Drosophila melanogaster lines selected for increased desiccation resistance have lowered metabolic rate and behavioral activity levels, and show correlated responses for resistance to starvation and a toxic ethanol level. These results were consistent with a prediction that increased resistance to many environmental stresses may be genetically correlated because of a reduction in metabolic energy expenditure. Here we present experiments on the genetic basis of the selection response and extend the study of correlated responses to other stresses. The response to selection was not sex-specific and involved X-linked and autosomal genes acting additively. Activity differences contributed little to differences in desiccation resistance between selected and control lines. Selected lines had lower metabolic rates than controls in darkness when activity was inhibited. Adults from selected lines showed increased resistance to a heat shock, {sup 60}Co-gamma-radiation, and acute ethanol and acetic acid stress. The desiccation, ethanol and starvation resistance of isofemale lines set up from the F2s of a cross between one of the selected and one of the control lines were correlated. Selected and control lines did not differ in ether-extractable lipid content or in resistance to acetone, ether or a cold shock.

  11. Budget variance analysis using RVUs.

    PubMed

    Berlin, M F; Budzynski, M R

    1998-01-01

    This article details the use of the variance analysis as management tool to evaluate the financial health of the practice. A common financial tool for administrators has been a simple calculation measuring the difference between actual financials vs. budget financials. Standard cost accounting provides a methodology known as variance analysis to better understand the actual vs. budgeted financial streams. The standard variance analysis has been modified by applying relative value units (RVUs) as standards for the practice. PMID:10387247

  12. Minimum variance beamformer weights revisited.

    PubMed

    Moiseev, Alexander; Doesburg, Sam M; Grunau, Ruth E; Ribary, Urs

    2015-10-15

    Adaptive minimum variance beamformers are widely used analysis tools in MEG and EEG. When the target brain activity presents in the form of spatially localized responses, the procedure usually involves two steps. First, positions and orientations of the sources of interest are determined. Second, the filter weights are calculated and source time courses reconstructed. This last step is the object of the current study. Despite different approaches utilized at the source localization stage, basic expressions for the weights have the same form, dictated by the minimum variance condition. These classic expressions involve covariance matrix of the measured field, which includes contributions from both the sources of interest and the noise background. We show analytically that the same weights can alternatively be obtained, if the full field covariance is replaced with that of the noise, provided the beamformer points to the true sources precisely. In practice, however, a certain mismatch is always inevitable. We show that such mismatch results in partial suppression of the true sources if the traditional weights are used. To avoid this effect, the "alternative" weights based on properly estimated noise covariance should be applied at the second, source time course reconstruction step. We demonstrate mathematically and using simulated and real data that in many situations the alternative weights provide significantly better time course reconstruction quality than the traditional ones. In particular, they a) improve source-level SNR and yield more accurately reconstructed waveforms; b) provide more accurate estimates of inter-source correlations; and c) reduce the adverse influence of the source correlations on the performance of single-source beamformers, which are used most often. Importantly, the alternative weights come at no additional computational cost, as the structure of the expressions remains the same. PMID:26143207

  13. Decomposition of Variance for Spatial Cox Processes

    PubMed Central

    Jalilian, Abdollah; Guan, Yongtao; Waagepetersen, Rasmus

    2012-01-01

    Spatial Cox point processes is a natural framework for quantifying the various sources of variation governing the spatial distribution of rain forest trees. We introduce a general criterion for variance decomposition for spatial Cox processes and apply it to specific Cox process models with additive or log linear random intensity functions. We moreover consider a new and flexible class of pair correlation function models given in terms of normal variance mixture covariance functions. The proposed methodology is applied to point pattern data sets of locations of tropical rain forest trees. PMID:23599558

  14. The modified ultrasound pattern sum score mUPSS as additional diagnostic tool for genetically distinct hereditary neuropathies.

    PubMed

    Grimm, Alexander; Rasenack, Maria; Athanasopoulou, Ioanna M; Dammeier, Nele Maria; Lipski, Christina; Wolking, Stefan; Vittore, Debora; Décard, Bernhard F; Axer, Hubertus

    2016-02-01

    The objective of this study is to evaluate the nerve ultrasound characteristics in genetically distinct inherited neuropathies, the value of the modified ultrasound pattern sum score (mUPSS) to differentiate between the subtypes and the correlation of ultrasound with nerve conduction studies (NCS), disease duration and severity. All patients underwent a standardized neurological examination, ultrasound, and NCS. In addition, genetic testing was performed. Consequently, mUPSS was applied, which is a sum-score of cross-sectional areas (CSA) at predefined anatomical points in different nerves. 31 patients were included (10xCharcot-Marie-Tooth (CMT)1a, 3xCMT1b, 3xCMTX, 9xCMT2, 6xHNPP [Hereditary neuropathy with liability to pressure palsies]). Generalized, homogeneous nerve enlargement and significantly increased UPS scores emphasized the diagnosis of demyelinating neuropathy, particularly CMT1a and CMT1b. The amount of enlargement did not depend on disease duration, symptom severity, height and weight. In CMTX the nerves were enlarged, as well, however, only in the roots and lower limbs, most prominent in men. In CMT2 no significant enlargement was detectable. In HNPP the CSA values were increased at entrapped sites, and not elsewhere. However, a distinction from CMT1, which also showed enlarged CSA values at entrapment sites, was only possible by calculating the entrapment ratios and entrapment score. The mUPSS allowed distinction between CMT1a (increased UPS scores, entrapment ratios <1.0) and HNPP (low UPS scores, entrapment ratios >1.4), while CMT1b and CMTX showed intermediate UPS types and entrapment ratios <1.0. Although based on few cases, ultrasound revealed consistent and homogeneous nerve alteration in certain inherited neuropathies. The modified UPSS is a quantitative tool, which may provide useful information for diagnosis, differentiation and follow-up evaluation in addition to NCS and molecular testing. PMID:26559821

  15. Characterizing nonconstant instrumental variance in emerging miniaturized analytical techniques.

    PubMed

    Noblitt, Scott D; Berg, Kathleen E; Cate, David M; Henry, Charles S

    2016-04-01

    Measurement variance is a crucial aspect of quantitative chemical analysis. Variance directly affects important analytical figures of merit, including detection limit, quantitation limit, and confidence intervals. Most reported analyses for emerging analytical techniques implicitly assume constant variance (homoskedasticity) by using unweighted regression calibrations. Despite the assumption of constant variance, it is known that most instruments exhibit heteroskedasticity, where variance changes with signal intensity. Ignoring nonconstant variance results in suboptimal calibrations, invalid uncertainty estimates, and incorrect detection limits. Three techniques where homoskedasticity is often assumed were covered in this work to evaluate if heteroskedasticity had a significant quantitative impact-naked-eye, distance-based detection using paper-based analytical devices (PADs), cathodic stripping voltammetry (CSV) with disposable carbon-ink electrode devices, and microchip electrophoresis (MCE) with conductivity detection. Despite these techniques representing a wide range of chemistries and precision, heteroskedastic behavior was confirmed for each. The general variance forms were analyzed, and recommendations for accounting for nonconstant variance discussed. Monte Carlo simulations of instrument responses were performed to quantify the benefits of weighted regression, and the sensitivity to uncertainty in the variance function was tested. Results show that heteroskedasticity should be considered during development of new techniques; even moderate uncertainty (30%) in the variance function still results in weighted regression outperforming unweighted regressions. We recommend utilizing the power model of variance because it is easy to apply, requires little additional experimentation, and produces higher-precision results and more reliable uncertainty estimates than assuming homoskedasticity. PMID:26995641

  16. The Effect of an Experimental Bottleneck upon Quantitative Genetic Variation in the Housefly

    PubMed Central

    Bryant, Edwin H.; McCommas, Steven A.; Combs, Lisa M.

    1986-01-01

    Effects of a population bottleneck (founder-flush cycle) upon quantitative genetic variation of morphometric traits were examined in replicated experimental lines of the housefly founded with one, four or 16 pairs of flies. Heritability and additive genetic variances for eight morphometric traits generally increased as a result of the bottleneck, but the pattern of increase among bottleneck sizes differed among traits. Principal axes of the additive genetic correlation matrix for the control line yielded two suites of traits, one associated with general body size and another set largely independent of body size. In the former set containing five of the traits, additive genetic variance was greatest in the bottleneck size of four pairs, whereas in the latter set of two traits the largest additive genetic variance occurred in the smallest bottleneck size of one pair. One trait exhibited changes in additive genetic variance intermediate between these two major responses. These results were inconsistent with models of additive effects of alleles within loci or of additive effects among loci. An observed decline in viability measures and body size in the bottleneck lines also indicated that there was nonadditivity of allelic effects for these traits. Several possible nonadditive models were explored that increased additive genetic variance as a result of a bottleneck. These included a model with complete dominance, a model with overdominance and a model incorporating multiplicative epistasis. PMID:17246359

  17. Integrating Variances into an Analytical Database

    NASA Technical Reports Server (NTRS)

    Sanchez, Carlos

    2010-01-01

    For this project, I enrolled in numerous SATERN courses that taught the basics of database programming. These include: Basic Access 2007 Forms, Introduction to Database Systems, Overview of Database Design, and others. My main job was to create an analytical database that can handle many stored forms and make it easy to interpret and organize. Additionally, I helped improve an existing database and populate it with information. These databases were designed to be used with data from Safety Variances and DCR forms. The research consisted of analyzing the database and comparing the data to find out which entries were repeated the most. If an entry happened to be repeated several times in the database, that would mean that the rule or requirement targeted by that variance has been bypassed many times already and so the requirement may not really be needed, but rather should be changed to allow the variance's conditions permanently. This project did not only restrict itself to the design and development of the database system, but also worked on exporting the data from the database to a different format (e.g. Excel or Word) so it could be analyzed in a simpler fashion. Thanks to the change in format, the data was organized in a spreadsheet that made it possible to sort the data by categories or types and helped speed up searches. Once my work with the database was done, the records of variances could be arranged so that they were displayed in numerical order, or one could search for a specific document targeted by the variances and restrict the search to only include variances that modified a specific requirement. A great part that contributed to my learning was SATERN, NASA's resource for education. Thanks to the SATERN online courses I took over the summer, I was able to learn many new things about computers and databases and also go more in depth into topics I already knew about.

  18. Selection enhanced estimates of µ-calpain, calpastatin, and dacylglycerol O-acyltransferase 1 genetic effects on pre-weaning performance, carcass quality traits, and residual variance of tenderness in composite ... cattle

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Selection of the composite MARC III population for markers allowed better estimates of effects and inheritance of markers for targeted carcass quality traits (n=254) and nontargeted traits and an evaluation of SNP specific residual variance models for tenderness. Genotypic effects of CAPN1 haplotyp...

  19. A Computer Program to Determine Reliability Using Analysis of Variance

    ERIC Educational Resources Information Center

    Burns, Edward

    1976-01-01

    A computer program, written in Fortran IV, is described which assesses reliability by using analysis of variance. It produces a complete analysis of variance table in addition to reliability coefficients for unadjusted and adjusted data as well as the intraclass correlation for m subjects and n items. (Author)

  20. Metabolic Profiles and Genetic Diversity of Denitrifying Communities in Activated Sludge after Addition of Methanol or Ethanol†

    PubMed Central

    Hallin, Sara; Throbäck, Ingela Noredal; Dicksved, Johan; Pell, Mikael

    2006-01-01

    External carbon sources can enhance denitrification rates and thus improve nitrogen removal in wastewater treatment plants. The effects of adding methanol and ethanol on the genetic and metabolic diversity of denitrifying communities in activated sludge were compared using a pilot-scale plant with two parallel lines. A full-scale plant receiving the same municipal wastewater, but without external carbon source addition, was the reference. Metabolic profiles obtained from potential denitrification rates with 10 electron donors showed that the denitrifying communities altered their preferences for certain compounds after supplementation with methanol or ethanol and that methanol had the greater impact. Clone libraries of nirK and nirS genes, encoding the two different nitrite reductases in denitrifiers, revealed that methanol also increased the diversity of denitrifiers of the nirS type, which indicates that denitrifiers favored by methanol were on the rise in the community. This suggests that there might be a niche differentiation between nirS and nirK genotypes during activated sludge processes. The composition of nirS genotypes also varied greatly among all samples, whereas the nirK communities were more stable. The latter was confirmed by denaturing gradient gel electrophoresis of nirK communities on all sampling occasions. Our results support earlier hypotheses that the compositions of denitrifier communities change during predenitrification processes when external carbon sources are added, although no severe effect could be observed from an operational point of view. PMID:16885297

  1. Additive transgene expression and genetic introgression in multiple green-fluorescent protein transgenic crop x weed hybrid generations.

    PubMed

    Halfhill, M D; Millwood, R J; Weissinger, A K; Warwick, S I; Stewart, C N

    2003-11-01

    The level of transgene expression in crop x weed hybrids and the degree to which crop-specific genes are integrated into hybrid populations are important factors in assessing the potential ecological and agricultural risks of gene flow associated with genetic engineering. The average transgene zygosity and genetic structure of transgenic hybrid populations change with the progression of generations, and the green fluorescent protein (GFP) transgene is an ideal marker to quantify transgene expression in advancing populations. The homozygous T(1) single-locus insert GFP/ Bacillus thuringiensis (Bt) transgenic canola ( Brassica napus, cv Westar) with two copies of the transgene fluoresced twice as much as hemizygous individuals with only one copy of the transgene. These data indicate that the expression of the GFP gene was additive, and fluorescence could be used to determine zygosity status. Several hybrid generations (BC(1)F(1), BC(2)F(1)) were produced by backcrossing various GFP/Bt transgenic canola ( B. napus, cv Westar) and birdseed rape ( Brassica rapa) hybrid generations onto B. rapa. Intercrossed generations (BC(2)F(2) Bulk) were generated by crossing BC(2)F(1) individuals in the presence of a pollinating insect ( Musca domestica L.). The ploidy of plants in the BC(2)F(2) Bulk hybrid generation was identical to the weedy parental species, B. rapa. AFLP analysis was used to quantify the degree of B. napus introgression into multiple backcross hybrid generations with B. rapa. The F(1) hybrid generations contained 95-97% of the B. napus-specific AFLP markers, and each successive backcross generation demonstrated a reduction of markers resulting in the 15-29% presence in the BC(2)F(2) Bulk population. Average fluorescence of each successive hybrid generation was analyzed, and homozygous canola lines and hybrid populations that contained individuals homozygous for GFP (BC(2)F(2) Bulk) demonstrated significantly higher fluorescence than hemizygous hybrid

  2. Evidence of Shared Genome-Wide Additive Genetic Effects on Interpersonal Trauma Exposure and Generalized Vulnerability to Drug Dependence in a Population of Substance Users.

    PubMed

    Palmer, Rohan H C; Nugent, Nicole R; Brick, Leslie A; Bidwell, Cinnamon L; McGeary, John E; Keller, Matthew C; Knopik, Valerie S

    2016-06-01

    Exposure to traumatic experiences is associated with an increased risk for drug dependence and poorer response to substance abuse treatment (Claus & Kindleberger, 2002; Jaycox, Ebener, Damesek, & Becker, 2004). Despite this evidence, the reasons for the observed associations of trauma and the general tendency to be dependent upon drugs of abuse remain unclear. Data (N = 2,596) from the Study of Addiction: Genetics and Environment were used to analyze (a) the degree to which commonly occurring single nucleotide polymorphisms (SNPs; minor allele frequency > 1%) in the human genome explains exposure to interpersonal traumatic experiences, and (b) the extent to which additive genetic effects on trauma are shared with additive genetic effects on drug dependence. Our results suggested moderate additive genetic influences on interpersonal trauma, h(2) SNP-Interpersonal = .47, 95% confidence interval (CI) [.10, .85], that are partially shared with additive genetic effects on generalized vulnerability to drug dependence, h(2) SNP-DD = .36, 95% CI [.11, .61]; rG-SNP = .49, 95% CI [.02, .96]. Although the design/technique does not exclude the possibility that substance abuse causally increases risk for traumatic experiences (or vice versa), these findings raise the possibility that commonly occurring SNPs influence both the general tendency towards drug dependence and interpersonal trauma. PMID:27214850

  3. A pathway-based analysis provides additional support for an immune-related genetic susceptibility to Parkinson's disease

    PubMed Central

    Holmans, Peter; Moskvina, Valentina; Jones, Lesley; Sharma, Manu; Vedernikov, Alexey; Buchel, Finja; Sadd, Mohamad; Bras, Jose M.; Bettella, Francesco; Nicolaou, Nayia; Simón-Sánchez, Javier; Mittag, Florian; Gibbs, J. Raphael; Schulte, Claudia; Durr, Alexandra; Guerreiro, Rita; Hernandez, Dena; Brice, Alexis; Stefánsson, Hreinn; Majamaa, Kari; Gasser, Thomas; Heutink, Peter; Wood, Nicholas W.; Martinez, Maria; Singleton, Andrew B.; Nalls, Michael A.; Hardy, John; Morris, Huw R.; Williams, Nigel M.; Arepalli, Sampath; Barker, Roger; Barrett, Jeffrey; Ben-Shlomo, Yoav; Berendse, Henk W.; Berg, Daniela; Bhatia, Kailash; de Bie, Rob M.A.; Biffi, Alessandro; Bloem, Bas; Brice, Alexis; Bochdanovits, Zoltan; Bonin, Michael; Bras, Jose M.; Brockmann, Kathrin; Brooks, Janet; Burn, David J.; Charlesworth, Gavin; Chen, Honglei; Chinnery, Patrick F.; Chong, Sean; Clarke, Carl E.; Cookson, Mark R.; Cooper, Jonathan M.; Corvol, Jen-Christophe; Counsell, Carl; Damier, Philippe; Dartigues, Jean Francois; Deloukas, Panagiotis; Deuschl, Günther; Dexter, David T.; van Dijk, Karin D.; Dillman, Allissa; Durif, Frank; Durr, Alexandra; Edkins, Sarah; Evans, Jonathan R.; Foltynie, Thomas; Gao, Jianjun; Gardner, Michelle; Gasser, Thomas; Gibbs, J. Raphael; Goate, Alison; Gray, Emma; Guerreiro, Rita; Gústafsson, Ómar; Hardy, John; Harris, Clare; Hernandez, Dena G.; Heutink, Peter; van Hilten, Jacobus J.; Hofman, Albert; Hollenbeck, Albert; Holmans, Peter; Holton, Janice; Hu, Michele; Huber, Heiko; Hudson, Gavin; Hunt, Sarah E.; Huttenlocher, Johanna; Illig, Thomas; Langford, Cordelia; Lees, Andrew; Lesage, Suzanne; Lichtner, Peter; Limousin, Patricia; Lopez, Grisel; Lorenz, Delia; Martinez, Maria; McNeill, Alisdair; Moorby, Catriona; Moore, Matthew; Morris, Huw; Morrison, Karen E.; Moskvina, Valentina; Mudanohwo, Ese; Nalls, Michael A.; Pearson, Justin; Perlmutter, Joel S.; Pétursson, Hjörvar; Plagnol, Vincent; Pollak, Pierre; Post, Bart; Potter, Simon; Ravina, Bernard; Revesz, Tamas; Riess, Olaf; Rivadeneira, Fernando; Rizzu, Patrizia; Ryten, Mina; Saad, Mohamad; Sawcer, Stephen; Schapira, Anthony; Scheffer, Hans; Sharma, Manu; Shaw, Karen; Sheerin, Una-Marie; Shoulson, Ira; Schulte, Claudia; Sidransky, Ellen; Simón-Sánchez, Javier; Singleton, Andrew B.; Smith, Colin; Stefánsson, Hreinn; Stefánsson, Kári; Steinberg, Stacy; Stockton, Joanna D.; Sveinbjornsdottir, Sigurlaug; Talbot, Kevin; Tanner, Carlie M.; Tashakkori-Ghanbaria, Avazeh; Tison, François; Trabzuni, Daniah; Traynor, Bryan J.; Uitterlinden, André G.; Velseboer, Daan; Vidailhet, Marie; Walker, Robert; van de Warrenburg, Bart; Wickremaratchi, Mirdhu; Williams, Nigel; Williams-Gray, Caroline H.; Winder-Rhodes, Sophie; Wood, Nicholas

    2013-01-01

    Parkinson's disease (PD) is the second most common neurodegenerative disease affecting 1–2% in people >60 and 3–4% in people >80. Genome-wide association (GWA) studies have now implicated significant evidence for association in at least 18 genomic regions. We have studied a large PD-meta analysis and identified a significant excess of SNPs (P < 1 × 10−16) that are associated with PD but fall short of the genome-wide significance threshold. This result was independent of variants at the 18 previously implicated regions and implies the presence of additional polygenic risk alleles. To understand how these loci increase risk of PD, we applied a pathway-based analysis, testing for biological functions that were significantly enriched for genes containing variants associated with PD. Analysing two independent GWA studies, we identified that both had a significant excess in the number of functional categories enriched for PD-associated genes (minimum P = 0.014 and P = 0.006, respectively). Moreover, 58 categories were significantly enriched for associated genes in both GWA studies (P < 0.001), implicating genes involved in the ‘regulation of leucocyte/lymphocyte activity’ and also ‘cytokine-mediated signalling’ as conferring an increased susceptibility to PD. These results were unaltered by the exclusion of all 178 genes that were present at the 18 genomic regions previously reported to be strongly associated with PD (including the HLA locus). Our findings, therefore, provide independent support to the strong association signal at the HLA locus and imply that the immune-related genetic susceptibility to PD is likely to be more widespread in the genome than previously appreciated. PMID:23223016

  4. Influence of a Dopamine Pathway Additive Genetic Efficacy Score on Smoking Cessation: Results from Two Randomized Clinical Trials of Bupropion

    PubMed Central

    David, Sean P.; Strong, David R.; Leventhal, Adam M.; Lancaster, Molly A.; McGeary, John E.; Munafò, Marcus R.; Bergen, Andrew W.; Swan, Gary E.; Benowitz, Neal L.; Tyndale, Rachel F.; Conti, David V.; Brown, Richard A.; Lerman, Caryn; Niaura, Raymond

    2013-01-01

    Aims To evaluate associations of treatment and an ‘additive genetic efficacy score’ (AGES) based on dopamine functional polymorphisms with time to first smoking lapse and point prevalence abstinence at end of treatment among participants enrolled in two randomized clinical trials of smoking cessation therapies. Design Double-blind pharmacogenetic efficacy trials randomizing participants to active or placebo bupropion. Study 1 also randomized participants to cognitive-behavioral smoking cessation treatment (CBT) or this treatment with CBT for depression. Study 2 provided standardized behavioural support. Setting Two Hospital-affiliated clinics (Study 1), and two University-affiliated clinics (Study 2). Participants N=792 self-identified white treatment-seeking smokers aged ≥18 years smoking ≥10 cigarettes per day over the last year. Measurements Age, gender, Fagerström Test for Nicotine Dependence, dopamine pathway genotypes (rs1800497 [ANKK1 E713K], rs4680 [COMT V158M], DRD4 exon 3 Variable Number of Tandem Repeats polymorphism [DRD4 VNTR], SLC6A3 3' VNTR) analyzed both separately and as part of an AGES, time to first lapse, and point prevalence abstinence at end of treatment. Findings Significant associations of the AGES (hazard ratio = 1.10, 95% Confidence Interval [CI] = 1.06–1.14], p=0.0099) and of the DRD4 VNTR (HR = 1.29, 95%CI 1.17–1.41, p=0.0073) were observed with time to first lapse. A significant AGES by pharmacotherapy interaction was observed (β [SE]=−0.18 [0.07], p=0.016), such that AGES predicted risk for time to first lapse only for individuals randomized to placebo. Conclusions A score based on functional polymorphisms relating to dopamine pathways appears to predict lapse to smoking following a quit attempt, and the association is mitigated in smokers using bupropion. PMID:23941313

  5. Latitude dependence of eddy variances

    NASA Technical Reports Server (NTRS)

    Bowman, Kenneth P.; Bell, Thomas L.

    1987-01-01

    The eddy variance of a meteorological field must tend to zero at high latitudes due solely to the nature of spherical polar coordinates. The zonal averaging operator defines a length scale: the circumference of the latitude circle. When the circumference of the latitude circle is greater than the correlation length of the field, the eddy variance from transient eddies is the result of differences between statistically independent regions. When the circumference is less than the correlation length, the eddy variance is computed from points that are well correlated with each other, and so is reduced. The expansion of a field into zonal Fourier components is also influenced by the use of spherical coordinates. As is well known, a phenomenon of fixed wavelength will have different zonal wavenumbers at different latitudes. Simple analytical examples of these effects are presented along with an observational example from satellite ozone data. It is found that geometrical effects can be important even in middle latitudes.

  6. Additive influence of genetic predisposition and conventional risk factors in the incidence of coronary heart disease: a population-based study in Greece

    Technology Transfer Automated Retrieval System (TEKTRAN)

    An additive genetic risk score (GRS) for coronary heart disease (CHD) has previously been associated with incident CHD in the population-based Greek European Prospective Investigation into Cancer and nutrition (EPIC) cohort. In this study, we explore GRS-‘environment’ joint actions on CHD for severa...

  7. The Variance Reaction Time Model

    ERIC Educational Resources Information Center

    Sikstrom, Sverker

    2004-01-01

    The variance reaction time model (VRTM) is proposed to account for various recognition data on reaction time, the mirror effect, receiver-operating-characteristic (ROC) curves, etc. The model is based on simple and plausible assumptions within a neural network: VRTM is a two layer neural network where one layer represents items and one layer…

  8. Analysis of Variance: Variably Complex

    ERIC Educational Resources Information Center

    Drummond, Gordon B.; Vowler, Sarah L.

    2012-01-01

    These authors have previously described how to use the "t" test to compare two groups. In this article, they describe the use of a different test, analysis of variance (ANOVA) to compare more than two groups. ANOVA is a test of group differences: do at least two of the means differ from each other? ANOVA assumes (1) normal distribution of…

  9. Variance of a Few Observations

    ERIC Educational Resources Information Center

    Joarder, Anwar H.

    2009-01-01

    This article demonstrates that the variance of three or four observations can be expressed in terms of the range and the first order differences of the observations. A more general result, which holds for any number of observations, is also stated.

  10. Relating the Hadamard Variance to MCS Kalman Filter Clock Estimation

    NASA Technical Reports Server (NTRS)

    Hutsell, Steven T.

    1996-01-01

    The Global Positioning System (GPS) Master Control Station (MCS) currently makes significant use of the Allan Variance. This two-sample variance equation has proven excellent as a handy, understandable tool, both for time domain analysis of GPS cesium frequency standards, and for fine tuning the MCS's state estimation of these atomic clocks. The Allan Variance does not explicitly converge for the nose types of alpha less than or equal to minus 3 and can be greatly affected by frequency drift. Because GPS rubidium frequency standards exhibit non-trivial aging and aging noise characteristics, the basic Allan Variance analysis must be augmented in order to (a) compensate for a dynamic frequency drift, and (b) characterize two additional noise types, specifically alpha = minus 3, and alpha = minus 4. As the GPS program progresses, we will utilize a larger percentage of rubidium frequency standards than ever before. Hence, GPS rubidium clock characterization will require more attention than ever before. The three sample variance, commonly referred to as a renormalized Hadamard Variance, is unaffected by linear frequency drift, converges for alpha is greater than minus 5, and thus has utility for modeling noise in GPS rubidium frequency standards. This paper demonstrates the potential of Hadamard Variance analysis in GPS operations, and presents an equation that relates the Hadamard Variance to the MCS's Kalman filter process noises.

  11. Genetics

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The genus Capsicum represents one of several well characterized Solanaceous genera. A wealth of classical and molecular genetics research is available for the genus. Information gleaned from its cultivated relatives, tomato and potato, provide further insight for basic and applied studies. Early ...

  12. Genetics

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Maintaining genetic variation in wild populations of Arctic organisms is fundamental to the long-term persistence of high latitude biodiversity. Variability is important because it provides options for species to respond to changing environmental conditions and novel challenges such as emerging path...

  13. 10 CFR 851.31 - Variance process.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 10 Energy 4 2010-01-01 2010-01-01 false Variance process. 851.31 Section 851.31 Energy DEPARTMENT OF ENERGY WORKER SAFETY AND HEALTH PROGRAM Variances § 851.31 Variance process. (a) Application. Contractors desiring a variance from a safety and health standard, or portion thereof, may submit a...

  14. 13 CFR 307.22 - Variances.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 13 Business Credit and Assistance 1 2010-01-01 2010-01-01 false Variances. 307.22 Section 307.22....22 Variances. EDA may approve variances to the requirements contained in this subpart, provided such variances: (a) Are consistent with the goals of the Economic Adjustment Assistance program and with an...

  15. 29 CFR 1920.2 - Variances.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 29 Labor 7 2010-07-01 2010-07-01 false Variances. 1920.2 Section 1920.2 Labor Regulations Relating...' COMPENSATION ACT § 1920.2 Variances. (a) Variances from standards in parts 1915 through 1918 of this chapter may be granted in the same circumstances in which variances may be granted under sections 6(b)...

  16. CAPN1, CAST, and DGAT1 genetic effects on preweaning performance, carcass quality traits, and residual variance of tenderness in a beef cattle population selected for haplotype and allele equalization

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic marker effects and type of inheritance are estimated with poor precision when minor marker allele frequencies are low. A stable composite population (MARC III) was subjected to marker assisted selection for multiple years to equalize specific marker frequencies to 1) estimate effect size an...

  17. µ-Calpain, calpastatin, and growth hormone receptor genetic effects on preweaning performance, carcass quality traits, and residual variance of tenderness in Angus cattle selected to increase minor haplotype ... frequencies

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic marker effects and interactions are estimated with poor precision when minor marker allele frequencies are low. An Angus population was subjected to marker assisted selection for multiple years to increase divergent haplotype and minor marker allele frequencies to 1) estimate effect size an...

  18. Intrauterine diabetic environment confers risks for type 2 diabetes mellitus and obesity in the offspring, in addition to genetic susceptibility.

    PubMed

    Dabelea, D; Pettitt, D J

    2001-01-01

    Numerous studies have reported that offspring whose mothers had type 2 diabetes mellitus (DM) are more likely to develop type 2 DM, impaired glucose tolerance, and obesity at an early age than offspring whose fathers had DM. Exposure to the diabetic intrauterine environment has been shown to be an important risk factor for all these conditions. To what extent transmission of type 2 DM from mother to offspring is the effect of genetic inheritance and to what extent it is the long-term consequence of exposure to maternal hyperglycemia is still uncertain. There are, of course, interactions between the diabetic intrauterine environment and genetics. Several data in experimental animals as well as in humans suggest, however, that exposure of the fetus to the mother's DM confers a risk for type 2 DM and obesity that is above any genetically transmitted susceptibility. In the Pima Indian population much of the increase in childhood type 2 DM can be attributed to the diabetic intrauterine environment. This suggests that intensive glucose control during pregnancy might have extended beneficial effects, contributing to a decrease in the prevalence of childhood type 2 DM. PMID:11592564

  19. Variance decomposition in stochastic simulators

    SciTech Connect

    Le Maître, O. P.; Knio, O. M.; Moraes, A.

    2015-06-28

    This work aims at the development of a mathematical and computational approach that enables quantification of the inherent sources of stochasticity and of the corresponding sensitivities in stochastic simulations of chemical reaction networks. The approach is based on reformulating the system dynamics as being generated by independent standardized Poisson processes. This reformulation affords a straightforward identification of individual realizations for the stochastic dynamics of each reaction channel, and consequently a quantitative characterization of the inherent sources of stochasticity in the system. By relying on the Sobol-Hoeffding decomposition, the reformulation enables us to perform an orthogonal decomposition of the solution variance. Thus, by judiciously exploiting the inherent stochasticity of the system, one is able to quantify the variance-based sensitivities associated with individual reaction channels, as well as the importance of channel interactions. Implementation of the algorithms is illustrated in light of simulations of simplified systems, including the birth-death, Schlögl, and Michaelis-Menten models.

  20. Variance decomposition in stochastic simulators

    NASA Astrophysics Data System (ADS)

    Le Maître, O. P.; Knio, O. M.; Moraes, A.

    2015-06-01

    This work aims at the development of a mathematical and computational approach that enables quantification of the inherent sources of stochasticity and of the corresponding sensitivities in stochastic simulations of chemical reaction networks. The approach is based on reformulating the system dynamics as being generated by independent standardized Poisson processes. This reformulation affords a straightforward identification of individual realizations for the stochastic dynamics of each reaction channel, and consequently a quantitative characterization of the inherent sources of stochasticity in the system. By relying on the Sobol-Hoeffding decomposition, the reformulation enables us to perform an orthogonal decomposition of the solution variance. Thus, by judiciously exploiting the inherent stochasticity of the system, one is able to quantify the variance-based sensitivities associated with individual reaction channels, as well as the importance of channel interactions. Implementation of the algorithms is illustrated in light of simulations of simplified systems, including the birth-death, Schlögl, and Michaelis-Menten models.

  1. Estimating the Modified Allan Variance

    NASA Technical Reports Server (NTRS)

    Greenhall, Charles

    1995-01-01

    The third-difference approach to modified Allan variance (MVAR) leads to a tractable formula for a measure of MVAR estimator confidence, the equivalent degrees of freedom (edf), in the presence of power-law phase noise. The effect of estimation stride on edf is tabulated. A simple approximation for edf is given, and its errors are tabulated. A theorem allowing conservative estimates of edf in the presence of compound noise processes is given.

  2. Neutrino mass without cosmic variance

    NASA Astrophysics Data System (ADS)

    LoVerde, Marilena

    2016-05-01

    Measuring the absolute scale of the neutrino masses is one of the most exciting opportunities available with near-term cosmological data sets. Two quantities that are sensitive to neutrino mass, scale-dependent halo bias b (k ) and the linear growth parameter f (k ) inferred from redshift-space distortions, can be measured without cosmic variance. Unlike the amplitude of the matter power spectrum, which always has a finite error, the error on b (k ) and f (k ) continues to decrease as the number density of tracers increases. This paper presents forecasts for statistics of galaxy and lensing fields that are sensitive to neutrino mass via b (k ) and f (k ). The constraints on neutrino mass from the auto- and cross-power spectra of spectroscopic and photometric galaxy samples are weakened by scale-dependent bias unless a very high density of tracers is available. In the high-density limit, using multiple tracers allows cosmic variance to be beaten, and the forecasted errors on neutrino mass shrink dramatically. In practice, beating the cosmic-variance errors on neutrino mass with b (k ) will be a challenge, but this signal is nevertheless a new probe of neutrino effects on structure formation that is interesting in its own right.

  3. The severity of retinal pathology in homozygous Crb1rd8/rd8 mice is dependent on additional genetic factors

    PubMed Central

    Luhmann, Ulrich F.O.; Carvalho, Livia S.; Holthaus, Sophia-Martha kleine; Cowing, Jill A.; Greenaway, Simon; Chu, Colin J.; Herrmann, Philipp; Smith, Alexander J.; Munro, Peter M.G.; Potter, Paul; Bainbridge, James W.B.; Ali, Robin R.

    2015-01-01

    Understanding phenotype–genotype correlations in retinal degeneration is a major challenge. Mutations in CRB1 lead to a spectrum of autosomal recessive retinal dystrophies with variable phenotypes suggesting the influence of modifying factors. To establish the contribution of the genetic background to phenotypic variability associated with the Crb1rd8/rd8 mutation, we compared the retinal pathology of Crb1rd8/rd8/J inbred mice with that of two Crb1rd8/rd8 lines backcrossed with C57BL/6JOlaHsd mice. Topical endoscopic fundal imaging and scanning laser ophthalmoscopy fundus images of all three Crb1rd8/rd8 lines showed a significant increase in the number of inferior retinal lesions that was strikingly variable between the lines. Optical coherence tomography, semithin, ultrastructural morphology and assessment of inflammatory and vascular marker by immunohistochemistry and quantitative reverse transcriptase-polymerase chain reaction revealed that the lesions were associated with photoreceptor death, Müller and microglia activation and telangiectasia-like vascular remodelling—features that were stable in the inbred, variable in the second, but virtually absent in the third Crb1rd8/rd8 line, even at 12 months of age. This suggests that the Crb1rd8/rd8 mutation is necessary, but not sufficient for the development of these degenerative features. By whole-genome SNP analysis of the genotype–phenotype correlation, a candidate region on chromosome 15 was identified. This may carry one or more genetic modifiers for the manifestation of the retinal pathology associated with mutations in Crb1. This study also provides insight into the nature of the retinal vascular lesions that likely represent a clinical correlate for the formation of retinal telangiectasia or Coats-like vasculopathy in patients with CRB1 mutations that are thought to depend on such genetic modifiers. PMID:25147295

  4. The severity of retinal pathology in homozygous Crb1rd8/rd8 mice is dependent on additional genetic factors.

    PubMed

    Luhmann, Ulrich F O; Carvalho, Livia S; Holthaus, Sophia-Martha Kleine; Cowing, Jill A; Greenaway, Simon; Chu, Colin J; Herrmann, Philipp; Smith, Alexander J; Munro, Peter M G; Potter, Paul; Bainbridge, James W B; Ali, Robin R

    2015-01-01

    Understanding phenotype-genotype correlations in retinal degeneration is a major challenge. Mutations in CRB1 lead to a spectrum of autosomal recessive retinal dystrophies with variable phenotypes suggesting the influence of modifying factors. To establish the contribution of the genetic background to phenotypic variability associated with the Crb1(rd8/rd8) mutation, we compared the retinal pathology of Crb1(rd8/rd8)/J inbred mice with that of two Crb1(rd8/rd8) lines backcrossed with C57BL/6JOlaHsd mice. Topical endoscopic fundal imaging and scanning laser ophthalmoscopy fundus images of all three Crb1(rd8/rd8) lines showed a significant increase in the number of inferior retinal lesions that was strikingly variable between the lines. Optical coherence tomography, semithin, ultrastructural morphology and assessment of inflammatory and vascular marker by immunohistochemistry and quantitative reverse transcriptase-polymerase chain reaction revealed that the lesions were associated with photoreceptor death, Müller and microglia activation and telangiectasia-like vascular remodelling-features that were stable in the inbred, variable in the second, but virtually absent in the third Crb1(rd8/rd8) line, even at 12 months of age. This suggests that the Crb1(rd8/rd8) mutation is necessary, but not sufficient for the development of these degenerative features. By whole-genome SNP analysis of the genotype-phenotype correlation, a candidate region on chromosome 15 was identified. This may carry one or more genetic modifiers for the manifestation of the retinal pathology associated with mutations in Crb1. This study also provides insight into the nature of the retinal vascular lesions that likely represent a clinical correlate for the formation of retinal telangiectasia or Coats-like vasculopathy in patients with CRB1 mutations that are thought to depend on such genetic modifiers. PMID:25147295

  5. Heritable environmental variance causes nonlinear relationships between traits: application to birth weight and stillbirth of pigs.

    PubMed

    Mulder, Herman A; Hill, William G; Knol, Egbert F

    2015-04-01

    There is recent evidence from laboratory experiments and analysis of livestock populations that not only the phenotype itself, but also its environmental variance, is under genetic control. Little is known about the relationships between the environmental variance of one trait and mean levels of other traits, however. A genetic covariance between these is expected to lead to nonlinearity between them, for example between birth weight and survival of piglets, where animals of extreme weights have lower survival. The objectives were to derive this nonlinear relationship analytically using multiple regression and apply it to data on piglet birth weight and survival. This study provides a framework to study such nonlinear relationships caused by genetic covariance of environmental variance of one trait and the mean of the other. It is shown that positions of phenotypic and genetic optima may differ and that genetic relationships are likely to be more curvilinear than phenotypic relationships, dependent mainly on the environmental correlation between these traits. Genetic correlations may change if the population means change relative to the optimal phenotypes. Data of piglet birth weight and survival show that the presence of nonlinearity can be partly explained by the genetic covariance between environmental variance of birth weight and survival. The framework developed can be used to assess effects of artificial and natural selection on means and variances of traits and the statistical method presented can be used to estimate trade-offs between environmental variance of one trait and mean levels of others. PMID:25631318

  6. Heritable Environmental Variance Causes Nonlinear Relationships Between Traits: Application to Birth Weight and Stillbirth of Pigs

    PubMed Central

    Mulder, Herman A.; Hill, William G.; Knol, Egbert F.

    2015-01-01

    There is recent evidence from laboratory experiments and analysis of livestock populations that not only the phenotype itself, but also its environmental variance, is under genetic control. Little is known about the relationships between the environmental variance of one trait and mean levels of other traits, however. A genetic covariance between these is expected to lead to nonlinearity between them, for example between birth weight and survival of piglets, where animals of extreme weights have lower survival. The objectives were to derive this nonlinear relationship analytically using multiple regression and apply it to data on piglet birth weight and survival. This study provides a framework to study such nonlinear relationships caused by genetic covariance of environmental variance of one trait and the mean of the other. It is shown that positions of phenotypic and genetic optima may differ and that genetic relationships are likely to be more curvilinear than phenotypic relationships, dependent mainly on the environmental correlation between these traits. Genetic correlations may change if the population means change relative to the optimal phenotypes. Data of piglet birth weight and survival show that the presence of nonlinearity can be partly explained by the genetic covariance between environmental variance of birth weight and survival. The framework developed can be used to assess effects of artificial and natural selection on means and variances of traits and the statistical method presented can be used to estimate trade-offs between environmental variance of one trait and mean levels of others. PMID:25631318

  7. A Wavelet Perspective on the Allan Variance.

    PubMed

    Percival, Donald B

    2016-04-01

    The origins of the Allan variance trace back 50 years ago to two seminal papers, one by Allan (1966) and the other by Barnes (1966). Since then, the Allan variance has played a leading role in the characterization of high-performance time and frequency standards. Wavelets first arose in the early 1980s in the geophysical literature, and the discrete wavelet transform (DWT) became prominent in the late 1980s in the signal processing literature. Flandrin (1992) briefly documented a connection between the Allan variance and a wavelet transform based upon the Haar wavelet. Percival and Guttorp (1994) noted that one popular estimator of the Allan variance-the maximal overlap estimator-can be interpreted in terms of a version of the DWT now widely referred to as the maximal overlap DWT (MODWT). In particular, when the MODWT is based on the Haar wavelet, the variance of the resulting wavelet coefficients-the wavelet variance-is identical to the Allan variance when the latter is multiplied by one-half. The theory behind the wavelet variance can thus deepen our understanding of the Allan variance. In this paper, we review basic wavelet variance theory with an emphasis on the Haar-based wavelet variance and its connection to the Allan variance. We then note that estimation theory for the wavelet variance offers a means of constructing asymptotically correct confidence intervals (CIs) for the Allan variance without reverting to the common practice of specifying a power-law noise type a priori. We also review recent work on specialized estimators of the wavelet variance that are of interest when some observations are missing (gappy data) or in the presence of contamination (rogue observations or outliers). It is a simple matter to adapt these estimators to become estimators of the Allan variance. Finally we note that wavelet variances based upon wavelets other than the Haar offer interesting generalizations of the Allan variance. PMID:26529757

  8. Estimating the Modified Allan Variance

    NASA Technical Reports Server (NTRS)

    Greenhall, Charles

    1995-01-01

    A paper at the 1992 FCS showed how to express the modified Allan variance (mvar) in terms of the third difference of the cumulative sum of time residuals. Although this reformulated definition was presented merely as a computational trick for simplifying the calculation of mvar estimates, it has since turned out to be a powerful theoretical tool for deriving the statistical quality of those estimates in terms of their equivalent degrees of freedom (edf), defined for an estimator V by edf V = 2(EV)2/(var V). Confidence intervals for mvar can then be constructed from levels of the appropriate 2 distribution.

  9. The genetic basis of photoperiodism and its evolutionary divergence among populations of the pitcher-plant mosquito, Wyeomyia smithii.

    PubMed

    Hard, J J; Bradshaw, W E; Holzapfel, C M

    1993-09-01

    We measured the additive genetic variance within populations and the composite additive, dominance, and epistatic effects contributing to differentiation of photoperiodic response between two southern (ancestral) and each of four progressively more northern (derived) populations of the pitcher-plant mosquito, Wyeomyia smithii. Critical photoperiod and its additive genetic variance but not its heritability increased with latitude. Directional selection on critical photoperiod during the northward divergence of W. smithii has therefore not eroded the additive genetic variance underlying this trait. Joint scaling tests of crosses between populations showed that epistatic effects, especially additive x additive and dominance x dominance interactions, overwhelm composite additive and dominance effects on critical photoperiod. The presence of substantial epistasis suggests that multiple founder events during the northward divergence of W. smithii may have been responsible for the release of progressively greater additive genetic variance in derived populations, despite directional and stabilizing selection to reduce it. If epistasis makes a similar contribution to the genetic differentiation of populations in other species, then current models of adaptive evolution that consider only additive genetic variation and covariation within populations may be of limited value in predicting how natural populations differentiate in life history. PMID:19425986

  10. The Effects of Spontaneous Mutation on Quantitative Traits. I. Variances and Covariances of Life History Traits

    PubMed Central

    Houle, D.; Hughes, K. A.; Hoffmaster, D. K.; Ihara, J.; Assimacopoulos, S.; Canada, D.; Charlesworth, B.

    1994-01-01

    We have accumulated spontaneous mutations in the absence of natural selection in Drosophila melanogaster by backcrossing 200 heterozygous replicates of a single high fitness second chromosome to a balancer stock for 44 generations. At generations 33 and 44 of accumulation, we extracted samples of chromosomes and assayed their homozygous performance for female fecundity early and late in adult life, male and female longevity, male mating ability early and late in adult life, productivity (a measure of fecundity times viability) and body weight. The variance among lines increased significantly for all traits except male mating ability and weight. The rate of increase in variance was similar to that found in previous studies of egg-to-adult viability, when calculated relative to trait means. The mutational correlations among traits were all strongly positive. Many correlations were significantly different from 0, while none was significantly different from 1. These data suggest that the mutation-accumulation hypothesis is not a sufficient explanation for the evolution of senescence in D. melanogaster. Mutation-selection balance does seem adequate to explain a substantial proportion of the additive genetic variance for fecundity and longevity. PMID:7851773

  11. Variance decomposition in stochastic simulators.

    PubMed

    Le Maître, O P; Knio, O M; Moraes, A

    2015-06-28

    This work aims at the development of a mathematical and computational approach that enables quantification of the inherent sources of stochasticity and of the corresponding sensitivities in stochastic simulations of chemical reaction networks. The approach is based on reformulating the system dynamics as being generated by independent standardized Poisson processes. This reformulation affords a straightforward identification of individual realizations for the stochastic dynamics of each reaction channel, and consequently a quantitative characterization of the inherent sources of stochasticity in the system. By relying on the Sobol-Hoeffding decomposition, the reformulation enables us to perform an orthogonal decomposition of the solution variance. Thus, by judiciously exploiting the inherent stochasticity of the system, one is able to quantify the variance-based sensitivities associated with individual reaction channels, as well as the importance of channel interactions. Implementation of the algorithms is illustrated in light of simulations of simplified systems, including the birth-death, Schlögl, and Michaelis-Menten models. PMID:26133418

  12. Variance analysis. Part I, Extending flexible budget variance analysis to acuity.

    PubMed

    Finkler, S A

    1991-01-01

    The author reviews the concepts of flexible budget variance analysis, including the price, quantity, and volume variances generated by that technique. He also introduces the concept of acuity variance and provides direction on how such a variance measure can be calculated. Part II in this two-part series on variance analysis will look at how personal computers can be useful in the variance analysis process. PMID:1870002

  13. 40 CFR 52.2183 - Variance provision.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ...) APPROVAL AND PROMULGATION OF IMPLEMENTATION PLANS (CONTINUED) South Dakota § 52.2183 Variance provision. The revisions to the variance provisions in Chapter 74:26:01:31.01 of the South Dakota Air...

  14. 40 CFR 52.2183 - Variance provision.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ...) APPROVAL AND PROMULGATION OF IMPLEMENTATION PLANS (CONTINUED) South Dakota § 52.2183 Variance provision. The revisions to the variance provisions in Chapter 74:26:01:31.01 of the South Dakota Air...

  15. 40 CFR 52.2183 - Variance provision.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ...) APPROVAL AND PROMULGATION OF IMPLEMENTATION PLANS (CONTINUED) South Dakota § 52.2183 Variance provision. The revisions to the variance provisions in Chapter 74:26:01:31.01 of the South Dakota Air...

  16. Additive genetic variation in resistance traits of an exotic pine species: little evidence for constraints on evolution of resistance against native herbivores

    PubMed Central

    Moreira, X; Zas, R; Sampedro, L

    2013-01-01

    The apparent failure of invasions by alien pines in Europe has been explained by the co-occurrence of native pine congeners supporting herbivores that might easily recognize the new plants as hosts. Previous studies have reported that exotic pines show reduced tolerance and capacity to induce resistance to those native herbivores. We hypothesize that limited genetic variation in resistance to native herbivores and the existence of evolutionary trade-offs between growth and resistance could represent additional potential constraints on the evolution of invasiveness of exotic pines outside their natural range. In this paper, we examined genetic variation for constitutive and induced chemical defences (measured as non-volatile resin in the stem and total phenolics in the needles) and resistance to two major native generalist herbivores of pines in cafeteria bioassays (the phloem-feeder Hylobius abietis and the defoliator Thaumetopoea pityocampa) using half-sib families drawn from a sample of the population of Pinus radiata introduced to Spain in the mid-19th century. We found (i) significant genetic variation, with moderate-to-high narrow-sense heritabilities for both the production of constitutive non-volatile resin and induced total phenolics, and for constitutive resistance against T. pityocampa in bioassays, (ii) no evolutionary trade-offs between plant resistance and growth traits or between the production of different quantitative chemical defences and (iii) a positive genetic correlation between constitutive resistance to the two studied herbivores. Overall, results of our study indicate that the exotic pine P. radiata has limited genetic constraints on the evolution of resistance against herbivores in its introduced range, suggesting that, at least in terms of interactions with these enemies, this pine species has potential to become invasive in the future. PMID:23232833

  17. Additive genetic variation in resistance traits of an exotic pine species: little evidence for constraints on evolution of resistance against native herbivores.

    PubMed

    Moreira, X; Zas, R; Sampedro, L

    2013-05-01

    The apparent failure of invasions by alien pines in Europe has been explained by the co-occurrence of native pine congeners supporting herbivores that might easily recognize the new plants as hosts. Previous studies have reported that exotic pines show reduced tolerance and capacity to induce resistance to those native herbivores. We hypothesize that limited genetic variation in resistance to native herbivores and the existence of evolutionary trade-offs between growth and resistance could represent additional potential constraints on the evolution of invasiveness of exotic pines outside their natural range. In this paper, we examined genetic variation for constitutive and induced chemical defences (measured as non-volatile resin in the stem and total phenolics in the needles) and resistance to two major native generalist herbivores of pines in cafeteria bioassays (the phloem-feeder Hylobius abietis and the defoliator Thaumetopoea pityocampa) using half-sib families drawn from a sample of the population of Pinus radiata introduced to Spain in the mid-19th century. We found (i) significant genetic variation, with moderate-to-high narrow-sense heritabilities for both the production of constitutive non-volatile resin and induced total phenolics, and for constitutive resistance against T. pityocampa in bioassays, (ii) no evolutionary trade-offs between plant resistance and growth traits or between the production of different quantitative chemical defences and (iii) a positive genetic correlation between constitutive resistance to the two studied herbivores. Overall, results of our study indicate that the exotic pine P. radiata has limited genetic constraints on the evolution of resistance against herbivores in its introduced range, suggesting that, at least in terms of interactions with these enemies, this pine species has potential to become invasive in the future. PMID:23232833

  18. Speed Variance and Its Influence on Accidents.

    ERIC Educational Resources Information Center

    Garber, Nicholas J.; Gadirau, Ravi

    A study was conducted to investigate the traffic engineering factors that influence speed variance and to determine to what extent speed variance affects accident rates. Detailed analyses were carried out to relate speed variance with posted speed limit, design speeds, and other traffic variables. The major factor identified was the difference…

  19. 21 CFR 1010.4 - Variances.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 8 2013-04-01 2013-04-01 false Variances. 1010.4 Section 1010.4 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) RADIOLOGICAL HEALTH PERFORMANCE STANDARDS FOR ELECTRONIC PRODUCTS: GENERAL General Provisions § 1010.4 Variances. (a) Criteria for variances. (1) Upon application by...

  20. 40 CFR 52.2183 - Variance provision.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 4 2010-07-01 2010-07-01 false Variance provision. 52.2183 Section 52...) APPROVAL AND PROMULGATION OF IMPLEMENTATION PLANS (CONTINUED) South Dakota § 52.2183 Variance provision. The revisions to the variance provisions in Chapter 74:26:01:31.01 of the South Dakota Air...

  1. 40 CFR 142.41 - Variance request.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 22 2010-07-01 2010-07-01 false Variance request. 142.41 Section 142...) NATIONAL PRIMARY DRINKING WATER REGULATIONS IMPLEMENTATION Variances Issued by the Administrator Under Section 1415(a) of the Act § 142.41 Variance request. A supplier of water may request the granting of...

  2. 10 CFR 851.31 - Variance process.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 10 Energy 4 2014-01-01 2014-01-01 false Variance process. 851.31 Section 851.31 Energy DEPARTMENT OF ENERGY WORKER SAFETY AND HEALTH PROGRAM Variances § 851.31 Variance process. (a) Application..., practices, means, methods, operations, or processes used or proposed to be used by the contractor; and...

  3. 10 CFR 851.31 - Variance process.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 10 Energy 4 2011-01-01 2011-01-01 false Variance process. 851.31 Section 851.31 Energy DEPARTMENT OF ENERGY WORKER SAFETY AND HEALTH PROGRAM Variances § 851.31 Variance process. (a) Application..., practices, means, methods, operations, or processes used or proposed to be used by the contractor; and...

  4. 10 CFR 851.31 - Variance process.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 10 Energy 4 2013-01-01 2013-01-01 false Variance process. 851.31 Section 851.31 Energy DEPARTMENT OF ENERGY WORKER SAFETY AND HEALTH PROGRAM Variances § 851.31 Variance process. (a) Application..., practices, means, methods, operations, or processes used or proposed to be used by the contractor; and...

  5. 10 CFR 851.31 - Variance process.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 10 Energy 4 2012-01-01 2012-01-01 false Variance process. 851.31 Section 851.31 Energy DEPARTMENT OF ENERGY WORKER SAFETY AND HEALTH PROGRAM Variances § 851.31 Variance process. (a) Application..., practices, means, methods, operations, or processes used or proposed to be used by the contractor; and...

  6. 40 CFR 52.2183 - Variance provision.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 4 2011-07-01 2011-07-01 false Variance provision. 52.2183 Section 52.2183 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED) APPROVAL AND PROMULGATION OF IMPLEMENTATION PLANS (CONTINUED) South Dakota § 52.2183 Variance provision. The revisions to the variance provisions...

  7. Genetic covariance between components of male reproductive success: within-pair vs. extra-pair paternity in song sparrows

    PubMed Central

    Reid, J M; Arcese, P; Losdat, S

    2014-01-01

    The evolutionary trajectories of reproductive systems, including both male and female multiple mating and hence polygyny and polyandry, are expected to depend on the additive genetic variances and covariances in and among components of male reproductive success achieved through different reproductive tactics. However, genetic covariances among key components of male reproductive success have not been estimated in wild populations. We used comprehensive paternity data from socially monogamous but genetically polygynandrous song sparrows (Melospiza melodia) to estimate additive genetic variance and covariance in the total number of offspring a male sired per year outside his social pairings (i.e. his total extra-pair reproductive success achieved through multiple mating) and his liability to sire offspring produced by his socially paired female (i.e. his success in defending within-pair paternity). Both components of male fitness showed nonzero additive genetic variance, and the estimated genetic covariance was positive, implying that males with high additive genetic value for extra-pair reproduction also have high additive genetic propensity to sire their socially paired female's offspring. There was consequently no evidence of a genetic or phenotypic trade-off between male within-pair paternity success and extra-pair reproductive success. Such positive genetic covariance might be expected to facilitate ongoing evolution of polygyny and could also shape the ongoing evolution of polyandry through indirect selection. PMID:25186454

  8. Quantitative Genetics of the Aging of Reproductive Traits in the Houbara Bustard

    PubMed Central

    Chantepie, Stéphane; Robert, Alexandre; Sorci, Gabriele; Hingrat, Yves; Charmantier, Anne; Leveque, Gwénaëlle; Lacroix, Frédéric; Teplitsky, Céline

    2015-01-01

    Do all traits within an organism age for the same reason? Evolutionary theories of aging share a common assumption: the strength of natural selection declines with age. A corollary is that additive genetic variance should increase with age. However, not all senescent traits display such increases suggesting that other mechanisms may be at play. Using longitudinal data collected from more than 5400 houbara bustards (Chlamydotis undulata) with an exhaustive recorded pedigree, we investigated the genetics of aging in one female reproductive trait (egg production) and three male reproductive traits (courtship display rate, ejaculate size and sperm viability), that display senescence at the phenotypic level. Animal models revealed an increase in additive genetic variance with age for courtship display rate and egg production but an unexpected absence of increased additive genetic variance for ejaculate size and no additive genetic variance for sperm viability. Our results suggest that the mechanisms behind the senescence of some traits are linked with a change in genetic expression, whereas for some other traits, aging may result from the constraints associated with physiological wear and tear on the organism throughout the life of the individual. PMID:26218735

  9. Additive influence of genetic predisposition and conventional risk factors in the incidence of coronary heart disease: a population-based study in Greece

    PubMed Central

    Yiannakouris, Nikos; Katsoulis, Michail; Trichopoulou, Antonia; Ordovas, Jose M; Trichopoulos, Dimitrios

    2014-01-01

    Objectives An additive genetic risk score (GRS) for coronary heart disease (CHD) has previously been associated with incident CHD in the population-based Greek European Prospective Investigation into Cancer and nutrition (EPIC) cohort. In this study, we explore GRS-‘environment’ joint actions on CHD for several conventional cardiovascular risk factors (ConvRFs), including smoking, hypertension, type-2 diabetes mellitus (T2DM), body mass index (BMI), physical activity and adherence to the Mediterranean diet. Design A case–control study. Setting The general Greek population of the EPIC study. Participants and outcome measures 477 patients with medically confirmed incident CHD and 1271 controls participated in this study. We estimated the ORs for CHD by dividing participants at higher or lower GRS and, alternatively, at higher or lower ConvRF, and calculated the relative excess risk due to interaction (RERI) as a measure of deviation from additivity. Results The joint presence of higher GRS and higher risk ConvRF was in all instances associated with an increased risk of CHD, compared with the joint presence of lower GRS and lower risk ConvRF. The OR (95% CI) was 1.7 (1.2 to 2.4) for smoking, 2.7 (1.9 to 3.8) for hypertension, 4.1 (2.8 to 6.1) for T2DM, 1.9 (1.4 to 2.5) for lower physical activity, 2.0 (1.3 to 3.2) for high BMI and 1.5 (1.1 to 2.1) for poor adherence to the Mediterranean diet. In all instances, RERI values were fairly small and not statistically significant, suggesting that the GRS and the ConvRFs do not have effects beyond additivity. Conclusions Genetic predisposition to CHD, operationalised through a multilocus GRS, and ConvRFs have essentially additive effects on CHD risk. PMID:24500614

  10. Physiological basis of tolerance to complete submergence in rice involves genetic factors in addition to the SUB1 gene.

    PubMed

    Singh, Sudhanshu; Mackill, David J; Ismail, Abdelbagi M

    2014-01-01

    1 lines. This suggests the possibility of further improvements in submergence tolerance by incorporating additional traits present in FR13A or other similar landraces. PMID:25281725

  11. Physiological basis of tolerance to complete submergence in rice involves genetic factors in addition to the SUB1 gene

    PubMed Central

    Singh, Sudhanshu; Mackill, David J.; Ismail, Abdelbagi M.

    2014-01-01

    1 lines. This suggests the possibility of further improvements in submergence tolerance by incorporating additional traits present in FR13A or other similar landraces. PMID:25281725

  12. Comparing G: multivariate analysis of genetic variation in multiple populations.

    PubMed

    Aguirre, J D; Hine, E; McGuigan, K; Blows, M W

    2014-01-01

    The additive genetic variance-covariance matrix (G) summarizes the multivariate genetic relationships among a set of traits. The geometry of G describes the distribution of multivariate genetic variance, and generates genetic constraints that bias the direction of evolution. Determining if and how the multivariate genetic variance evolves has been limited by a number of analytical challenges in comparing G-matrices. Current methods for the comparison of G typically share several drawbacks: metrics that lack a direct relationship to evolutionary theory, the inability to be applied in conjunction with complex experimental designs, difficulties with determining statistical confidence in inferred differences and an inherently pair-wise focus. Here, we present a cohesive and general analytical framework for the comparative analysis of G that addresses these issues, and that incorporates and extends current methods with a strong geometrical basis. We describe the application of random skewers, common subspace analysis, the 4th-order genetic covariance tensor and the decomposition of the multivariate breeders equation, all within a Bayesian framework. We illustrate these methods using data from an artificial selection experiment on eight traits in Drosophila serrata, where a multi-generational pedigree was available to estimate G in each of six populations. One method, the tensor, elegantly captures all of the variation in genetic variance among populations, and allows the identification of the trait combinations that differ most in genetic variance. The tensor approach is likely to be the most generally applicable method to the comparison of G-matrices from any sampling or experimental design. PMID:23486079

  13. 40 CFR 142.43 - Disposition of a variance request.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ...) Compliance (including increments of progress) by the public water system with each contaminant level... control measures as the Administrator may require for each contaminant covered by the variance. (d) The... the Administrator. (f) The proposed schedule for implementation of additional interim control...

  14. Estimation of Epistatic Variance Components and Heritability in Founder Populations and Crosses

    PubMed Central

    Young, Alexander I.; Durbin, Richard

    2014-01-01

    Genetic association studies have explained only a small proportion of the estimated heritability of complex traits, leaving the remaining heritability “missing.” Genetic interactions have been proposed as an explanation for this, because they lead to overestimates of the heritability and are hard to detect. Whether this explanation is true depends on the proportion of variance attributable to genetic interactions, which is difficult to measure in outbred populations. Founder populations exhibit a greater range of kinship than outbred populations, which helps in fitting the epistatic variance. We extend classic theory to founder populations, giving the covariance between individuals due to epistasis of any order. We recover the classic theory as a limit, and we derive a recently proposed estimator of the narrow sense heritability as a corollary. We extend the variance decomposition to include dominance. We show in simulations that it would be possible to estimate the variance from pairwise interactions with samples of a few thousand from strongly bottlenecked human founder populations, and we provide an analytical approximation of the standard error. Applying these methods to 46 traits measured in a yeast (Saccharomyces cerevisiae) cross, we estimate that pairwise interactions explain 10% of the phenotypic variance on average and that third- and higher-order interactions explain 14% of the phenotypic variance on average. We search for third-order interactions, discovering an interaction that is shared between two traits. Our methods will be relevant to future studies of epistatic variance in founder populations and crosses. PMID:25326236

  15. Simulation testing of unbiasedness of variance estimators

    USGS Publications Warehouse

    Link, W.A.

    1993-01-01

    In this article I address the evaluation of estimators of variance for parameter estimates. Given an unbiased estimator X of a parameter 0, and an estimator V of the variance of X, how does one test (via simulation) whether V is an unbiased estimator of the variance of X? The derivation of the test statistic illustrates the need for care in substituting consistent estimators for unknown parameters.

  16. 40 CFR 59.106 - Variance.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... VOLATILE ORGANIC COMPOUND EMISSION STANDARDS FOR CONSUMER AND COMMERCIAL PRODUCTS National Volatile Organic Compound Emission Standards for Automobile Refinish Coatings § 59.106 Variance. (a) Any regulated...

  17. 40 CFR 59.106 - Variance.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... VOLATILE ORGANIC COMPOUND EMISSION STANDARDS FOR CONSUMER AND COMMERCIAL PRODUCTS National Volatile Organic Compound Emission Standards for Automobile Refinish Coatings § 59.106 Variance. (a) Any regulated...

  18. 40 CFR 59.106 - Variance.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... VOLATILE ORGANIC COMPOUND EMISSION STANDARDS FOR CONSUMER AND COMMERCIAL PRODUCTS National Volatile Organic Compound Emission Standards for Automobile Refinish Coatings § 59.106 Variance. (a) Any regulated...

  19. 40 CFR 59.106 - Variance.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... VOLATILE ORGANIC COMPOUND EMISSION STANDARDS FOR CONSUMER AND COMMERCIAL PRODUCTS National Volatile Organic Compound Emission Standards for Automobile Refinish Coatings § 59.106 Variance. (a) Any regulated...

  20. 40 CFR 59.106 - Variance.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... VOLATILE ORGANIC COMPOUND EMISSION STANDARDS FOR CONSUMER AND COMMERCIAL PRODUCTS National Volatile Organic Compound Emission Standards for Automobile Refinish Coatings § 59.106 Variance. (a) Any regulated...

  1. Sensor/Actuator Selection for the Constrained Variance Control Problem

    NASA Technical Reports Server (NTRS)

    Delorenzo, M. L.; Skelton, R. E.

    1985-01-01

    The problem of designing a linear controller for systems subject to inequality variance constraints is considered. A quadratic penalty function approach is used to yield a linear controller. Both the weights in the quadratic penalty function and the locations of sensors and actuators are selected by successive approximations to obtain an optimal design which satisfies the input/output variance constraints. The method is applied to NASA's 64 meter Hoop-Column Space Antenna for satellite communications. In addition the solution for the control law, the main feature of these results is the systematic determination of actuator design requirements which allow the given input/output performance constraints to be satisfied.

  2. Trends in the Genetic Influences on Smoking

    PubMed Central

    Boardman, Jason D.; Blalock, Casey L.; Pampel, Fred C.

    2011-01-01

    Using twin pairs from the National Survey of Midlife Development in the United States, we estimate that 35 percent of the variance in regular smoking is due to additive genetic influences. When we disaggregate the sample by birth cohort we witness strong genetic influences on smoking for those born in the 1920s, 1930s, and 1950s, but negligible influences for those born in the 1940s and 1960s. We show that the timing of the first Surgeon General’s Report coincides with an increase in the genetic influences on regular smoking, but subsequent legislation prohibiting smoking in public places has significantly reduced these influences. These results are in line with existing gene-environment interaction theory, and we argue that variation in genetic influences across cohorts makes it difficult and potentially misleading to estimate genetic effects on health behaviors from data obtained from a single point in time. PMID:20420298

  3. Genetics of Growth Reaction Norms in Farmed Rainbow Trout

    PubMed Central

    Sae-Lim, Panya; Mulder, Han; Gjerde, Bjarne; Koskinen, Heikki; Lillehammer, Marie; Kause, Antti

    2015-01-01

    Rainbow trout is farmed globally under diverse uncontrollable environments. Fish with low macroenvironmental sensitivity (ES) of growth is important to thrive and grow under these uncontrollable environments. The ES may evolve as a correlated response to selection for growth in one environment when the genetic correlation between ES and growth is nonzero. The aims of this study were to quantify additive genetic variance for ES of body weight (BW), defined as the slope of reaction norm across breeding environment (BE) and production environment (PE), and to estimate the genetic correlation (rg(int, sl)) between BW and ES. To estimate heritable variance of ES, the coheritability of ES was derived using selection index theory. The BW records from 43,040 rainbow trout performing either in freshwater or seawater were analysed using a reaction norm model. High additive genetic variance for ES (9584) was observed, inferring that genetic changes in ES can be expected. The coheritability for ES was either -0.06 (intercept at PE) or -0.08 (intercept at BE), suggesting that BW observation in either PE or BE results in low accuracy of selection for ES. Yet, the rg(int, sl) was negative (-0.41 to -0.33) indicating that selection for BW in one environment is expected to result in more sensitive fish. To avoid an increase of ES while selecting for BW, it is possible to have equal genetic gain in BW in both environments so that ES is maintained stable. PMID:26267268

  4. 20 CFR 654.402 - Variances.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 20 Employees' Benefits 3 2011-04-01 2011-04-01 false Variances. 654.402 Section 654.402 Employees' Benefits EMPLOYMENT AND TRAINING ADMINISTRATION, DEPARTMENT OF LABOR SPECIAL RESPONSIBILITIES OF THE EMPLOYMENT SERVICE SYSTEM Housing for Agricultural Workers Purpose and Applicability § 654.402 Variances. (a) An employer may apply for a...

  5. 20 CFR 654.402 - Variances.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 20 Employees' Benefits 3 2010-04-01 2010-04-01 false Variances. 654.402 Section 654.402 Employees' Benefits EMPLOYMENT AND TRAINING ADMINISTRATION, DEPARTMENT OF LABOR SPECIAL RESPONSIBILITIES OF THE EMPLOYMENT SERVICE SYSTEM Housing for Agricultural Workers Purpose and Applicability § 654.402 Variances....

  6. 40 CFR 142.41 - Variance request.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... nature and duration of variance requested. (b) Relevant analytical results of water quality sampling of... relevant to ability to comply. (3) Analytical results of raw water quality relevant to the variance request... request made under § 142.40(b), a statement that the system will perform monitoring and other...

  7. 40 CFR 142.41 - Variance request.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... nature and duration of variance requested. (b) Relevant analytical results of water quality sampling of... relevant to ability to comply. (3) Analytical results of raw water quality relevant to the variance request... request made under § 142.40(b), a statement that the system will perform monitoring and other...

  8. 40 CFR 142.41 - Variance request.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... nature and duration of variance requested. (b) Relevant analytical results of water quality sampling of... relevant to ability to comply. (3) Analytical results of raw water quality relevant to the variance request... request made under § 142.40(b), a statement that the system will perform monitoring and other...

  9. 21 CFR 1010.4 - Variances.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Variances. 1010.4 Section 1010.4 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) RADIOLOGICAL HEALTH... and Radiological Health, Food and Drug Administration, may grant a variance from one or...

  10. 21 CFR 1010.4 - Variances.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 8 2012-04-01 2012-04-01 false Variances. 1010.4 Section 1010.4 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) RADIOLOGICAL HEALTH... and Radiological Health, Food and Drug Administration, may grant a variance from one or...

  11. 21 CFR 1010.4 - Variances.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Variances. 1010.4 Section 1010.4 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) RADIOLOGICAL HEALTH... and Radiological Health, Food and Drug Administration, may grant a variance from one or...

  12. On Some Representations of Sample Variance

    ERIC Educational Resources Information Center

    Joarder, Anwar H.

    2002-01-01

    The usual formula for variance depending on rounding off the sample mean lacks precision, especially when computer programs are used for the calculation. The well-known simplification of the total sums of squares does not always give benefit. Since the variance of two observations is easily calculated without the use of a sample mean, and the…

  13. 10 CFR 1021.343 - Variances.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... Procedures § 1021.343 Variances. (a) Emergency actions. DOE may take an action without observing all provisions of this part or the CEQ Regulations, in accordance with 40 CFR 1506.11, in emergency situations... 10 Energy 4 2010-01-01 2010-01-01 false Variances. 1021.343 Section 1021.343 Energy DEPARTMENT...

  14. 18 CFR 1304.408 - Variances.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 18 Conservation of Power and Water Resources 2 2010-04-01 2010-04-01 false Variances. 1304.408 Section 1304.408 Conservation of Power and Water Resources TENNESSEE VALLEY AUTHORITY APPROVAL OF... § 1304.408 Variances. The Vice President or the designee thereof is authorized, following...

  15. Measurement of Allan variance and phase noise at fractions of a millihertz

    NASA Technical Reports Server (NTRS)

    Conroy, Bruce L.; Le, Duc

    1990-01-01

    Although the measurement of Allan variance of oscillators is well documented, there is a need for a simplified system for finding the degradation of phase noise and Allan variance step-by-step through a system. This article describes an instrumentation system for simultaneous measurement of additive phase noise and degradation in Allan variance through a transmitter system. Also included are measurements of a 20-kW X-band transmitter showing the effect of adding a pass tube regulator.

  16. A quantitative model of the relationship between phenotypic variance and heterozygosity at marker loci under partial selfing.

    PubMed Central

    David, P

    1999-01-01

    Negative relationships between allozyme heterozygosity and morphological variance have often been observed and interpreted as evidence for increased developmental stability in heterozygotes. However, inbreeding can also generate such relationships by decreasing heterozygosity at neutral loci and redistributing genetic variance at the same time. I here provide a quantitative genetic model of this process by analogy with heterozygosity-fitness relationships. Inbreeding generates negative heterozygosity-variance relationships irrespective of the genetic architecture of the trait. This holds for fitness traits as well as neutral traits, the effect being stronger for fitness traits under directional dominance or overdominance. The order of magnitude of heterozygosity-variance regressions is compatible with empirical data even with very low inbreeding. Although developmental stability effects cannot be excluded, inbreeding is a parsimonious explanation that should be seriously considered to explain correlations between heterozygosity and both mean and variance of phenotypes in natural populations. PMID:10545474

  17. Portfolio optimization with mean-variance model

    NASA Astrophysics Data System (ADS)

    Hoe, Lam Weng; Siew, Lam Weng

    2016-06-01

    Investors wish to achieve the target rate of return at the minimum level of risk in their investment. Portfolio optimization is an investment strategy that can be used to minimize the portfolio risk and can achieve the target rate of return. The mean-variance model has been proposed in portfolio optimization. The mean-variance model is an optimization model that aims to minimize the portfolio risk which is the portfolio variance. The objective of this study is to construct the optimal portfolio using the mean-variance model. The data of this study consists of weekly returns of 20 component stocks of FTSE Bursa Malaysia Kuala Lumpur Composite Index (FBMKLCI). The results of this study show that the portfolio composition of the stocks is different. Moreover, investors can get the return at minimum level of risk with the constructed optimal mean-variance portfolio.

  18. Genetic parameters related to environmental variability of weight traits in a selection experiment for weight gain in mice; signs of correlated canalised response

    PubMed Central

    Ibáñez-Escriche, Noelia; Moreno, Almudena; Nieto, Blanca; Piqueras, Pepa; Salgado, Concepción; Gutiérrez, Juan Pablo

    2008-01-01

    Data from an experimental mice population selected from 18 generations to increase weight gain were used to estimate the genetic parameters associated with environmental variability. The analysis involved three traits: weight at 21 days, weight at 42 days and weight gain between 21 and 42 days. A dataset of 5273 records for males was studied. Data were analysed using Bayesian procedures by comparing the Deviance Information Criterion (DIC) value of two different models: one assuming homogeneous environmental variances and another assuming them as heterogeneous. The model assuming heterogeneity was better in all cases and also showed higher additive genetic variances and lower common environmental variances. The heterogeneity of residual variance was associated with systematic and additive genetic effects thus making reduction by selection possible. Genetic correlations between the additive genetic effects on mean and environmental variance of the traits analysed were always negative, ranging from -0.19 to -0.38. An increase in the heritability of the traits was found when considering the genetic determination of the environmental variability. A suggested correlated canalised response was found in terms of coefficient of variation but it could be insufficient to compensate for the scale effect associated with an increase of the mean. PMID:18400150

  19. The relation between the genetic architecture of quantitative traits and long-term genetic response.

    PubMed

    Abdollahi-Arpanahi, Rostam; Pakdel, Abbas; Nejati-Javaremi, Ardeshir; Shahrbabak, Mohammad Moradi; Ghafouri-Kesbi, Farhad

    2014-08-01

    The genetic architecture of a quantitative trait refers to the number of genetic variants, allele frequencies, and effect sizes of variants that affect a trait and their mode of gene action. This study was conducted to investigate the effect of four shapes of allelic frequency distributions (constant, uniform, L-shaped and U-shaped) and different number of trait-affecting loci (50, 100, 200, 500) on allelic frequency changes, long term genetic response, and maintaining genetic variance. To this end, a population of 440 individuals composed of 40 males and 400 females as well as a genome of 200 cM consisting of two chromosomes and with a mutation rate of 2.5 × 10(-5) per locus was simulated. Selection of superior animals was done using best linear unbiased prediction (BLUP) with assumption of infinitesimal model. Selection intensity was constant over 30 generations of selection. The highest genetic progress obtained when the allelic frequency had L-shaped distribution and number of trait-affecting loci was high (500). Although quantitative genetic theories predict the extinction of genetic variance due to artificial selection in long time, our results showed that under L- and U-shapped allelic frequency distributions, the additive genetic variance is persistent after 30 generations of selection. Further, presence or absence of selection limit can be an indication of low (<50) or high (>100) number of trait-affecting loci, respectively. It was concluded that the genetic architecture of complex traits is an important subject which should be considered in studies concerning long-term response to selection. PMID:24671636

  20. Quantitative genetics of response to competitors in Nemophila menziesii: a field experiment.

    PubMed

    Shaw, R G; Platenkamp, G A; Shaw, F H; Podolsky, R H

    1995-01-01

    Recent investigations of evolution in heterogeneous environments have begun to accommodate genetic and environmental complexity typical of natural populations. Theoretical studies demonstrate that evolution of polygenic characters depends heavily on the genetic interdependence of the expression of traits in the different environments in which selection occurs, but information concerning this issue is scarce. We conducted a field experiment to assess the genetic variability of the annual plant Nemophila menziesii in five biotic regimes differing in plant density and composition. Significant, though modest, additive genetic variance in plant size was expressed in particular treatments. Evidence of additive genetic tradeoffs between interspecific and intraspecific competitive performance was found, but this result was not consistent throughout the experiment. Two aspects of experimental design may tend to obscure genetically based tradeoffs across environments in many previously published experiments: (1) inability to isolate additive genetic from other sources of variation and (2) use of novel (e.g., laboratory) environments. PMID:7705640

  1. Quantitative Genetics of Response to Competitors in Nemophila Menziesii: A Field Experiment

    PubMed Central

    Shaw, R. G.; Platenkamp, GAJ.; Shaw, F. H.; Podolsky, R. H.

    1995-01-01

    Recent investigations of evolution in heterogeneous environments have begun to accommodate genetic and environmental complexity typical of natural populations. Theoretical studies demonstrate that evolution of polygenic characters depends heavily on the genetic interdependence of the expression of traits in the different environments in which selection occurs, but information concerning this issue is scarce. We conducted a field experiment to assess the genetic variability of the annual plant Nemophila menziesii in five biotic regimes differing in plant density and composition. Significant, though modest, additive genetic variance in plant size was expressed in particular treatments. Evidence of additive genetic tradeoffs between interspecific and intraspecific competitive performance was found, but this result was not consistent throughout the experiment. Two aspects of experimental design may tend to obscure genetically based tradeoffs across environments in many previously published experiments: (1) inability to isolate additive genetic from other sources of variation and (2) use of novel (e.g., laboratory) environments. PMID:7705640

  2. Portfolio optimization using median-variance approach

    NASA Astrophysics Data System (ADS)

    Wan Mohd, Wan Rosanisah; Mohamad, Daud; Mohamed, Zulkifli

    2013-04-01

    Optimization models have been applied in many decision-making problems particularly in portfolio selection. Since the introduction of Markowitz's theory of portfolio selection, various approaches based on mathematical programming have been introduced such as mean-variance, mean-absolute deviation, mean-variance-skewness and conditional value-at-risk (CVaR) mainly to maximize return and minimize risk. However most of the approaches assume that the distribution of data is normal and this is not generally true. As an alternative, in this paper, we employ the median-variance approach to improve the portfolio optimization. This approach has successfully catered both types of normal and non-normal distribution of data. With this actual representation, we analyze and compare the rate of return and risk between the mean-variance and the median-variance based portfolio which consist of 30 stocks from Bursa Malaysia. The results in this study show that the median-variance approach is capable to produce a lower risk for each return earning as compared to the mean-variance approach.

  3. Rate of evolutionary change in cranial morphology of the marsupial genus Monodelphis is constrained by the availability of additive genetic variation.

    PubMed

    Porto, A; Sebastião, H; Pavan, S E; VandeBerg, J L; Marroig, G; Cheverud, J M

    2015-04-01

    We tested the hypothesis that the rate of marsupial cranial evolution is dependent on the distribution of genetic variation in multivariate space. To do so, we carried out a genetic analysis of cranial morphological variation in laboratory strains of Monodelphis domestica and used estimates of genetic covariation to analyse the morphological diversification of the Monodelphis brevicaudata species group. We found that within-species genetic variation is concentrated in only a few axes of the morphospace and that this strong genetic covariation influenced the rate of morphological diversification of the brevicaudata group, with between-species divergence occurring fastest when occurring along the genetic line of least resistance. Accounting for the geometric distribution of genetic variation also increased our ability to detect the selective regimen underlying species diversification, with several instances of selection only being detected when genetic covariances were taken into account. Therefore, this work directly links patterns of genetic covariation among traits to macroevolutionary patterns of morphological divergence. Our findings also suggest that the limited distribution of Monodelphis species in morphospace is the result of a complex interplay between the limited dimensionality of available genetic variation and strong stabilizing selection along two major axes of genetic variation. PMID:25818173

  4. Rate of evolutionary change in cranial morphology of the marsupial genus Monodelphis is constrained by the availability of additive genetic variation

    PubMed Central

    Porto, Arthur; Sebastião, Harley; Pavan, Silvia Eliza; VandeBerg, John L.; Marroig, Gabriel; Cheverud, James M.

    2015-01-01

    We tested the hypothesis that the rate of marsupial cranial evolution is dependent on the distribution of genetic variation in multivariate space. To do so, we carried out a genetic analysis of cranial morphological variation in laboratory strains of Monodelphis domestica and used estimates of genetic covariation to analyze the morphological diversification of the Monodelphis brevicaudata species group. We found that within-species genetic variation is concentrated in only a few axes of the morphospace and that this strong genetic covariation influenced the rate of morphological diversification of the brevicaudata group, with between-species divergence occurring fastest when occurring along the genetic line of least resistance. Accounting for the geometric distribution of genetic variation also increased our ability to detect the selective regimen underlying species diversification, with several instances of selection only being detected when genetic covariances were taken into account. Therefore, this work directly links patterns of genetic covariation among traits to macroevolutionary patterns of morphological divergence. Our findings also suggest that the limited distribution of Monodelphis species in morphospace is the result of a complex interplay between the limited dimensionality of available genetic variation and strong stabilizing selection along two major axes of genetic variation. PMID:25818173

  5. Automatic variance analysis of multistage care pathways.

    PubMed

    Li, Xiang; Liu, Haifeng; Zhang, Shilei; Mei, Jing; Xie, Guotong; Yu, Yiqin; Li, Jing; Lakshmanan, Geetika T

    2014-01-01

    A care pathway (CP) is a standardized process that consists of multiple care stages, clinical activities and their relations, aimed at ensuring and enhancing the quality of care. However, actual care may deviate from the planned CP, and analysis of these deviations can help clinicians refine the CP and reduce medical errors. In this paper, we propose a CP variance analysis method to automatically identify the deviations between actual patient traces in electronic medical records (EMR) and a multistage CP. As the care stage information is usually unavailable in EMR, we first align every trace with the CP using a hidden Markov model. From the aligned traces, we report three types of deviations for every care stage: additional activities, absent activities and violated constraints, which are identified by using the techniques of temporal logic and binomial tests. The method has been applied to a CP for the management of congestive heart failure and real world EMR, providing meaningful evidence for the further improvement of care quality. PMID:25160280

  6. A multivariate analysis of genetic variation in the advertisement call of the gray treefrog, Hyla versicolor.

    PubMed

    Welch, Allison M; Smith, Michael J; Gerhardt, H Carl

    2014-06-01

    Genetic variation in sexual displays is crucial for an evolutionary response to sexual selection, but can be eroded by strong selection. Identifying the magnitude and sources of additive genetic variance underlying sexually selected traits is thus an important issue in evolutionary biology. We conducted a quantitative genetics experiment with gray treefrogs (Hyla versicolor) to investigate genetic variances and covariances among features of the male advertisement call. Two energetically expensive traits showed significant genetic variation: call duration, expressed as number of pulses per call, and call rate, represented by its inverse, call period. These two properties also showed significant genetic covariance, consistent with an energetic constraint to call production. Combining the genetic variance-covariance matrix with previous estimates of directional sexual selection imposed by female preferences predicts a limited increase in call duration but no change in call rate despite significant selection on both traits. In addition to constraints imposed by the genetic covariance structure, an evolutionary response to sexual selection may also be limited by high energetic costs of long-duration calls and by preferences that act most strongly against very short-duration calls. Meanwhile, the persistence of these preferences could be explained by costs of mating with males with especially unattractive calls. PMID:24621402

  7. On Studying Common Factor Variance in Multiple-Component Measuring Instruments

    ERIC Educational Resources Information Center

    Raykov, Tenko; Pohl, Steffi

    2013-01-01

    A method for examining common factor variance in multiple-component measuring instruments is outlined. The procedure is based on an application of the latent variable modeling methodology and is concerned with evaluating observed variance explained by a global factor and by one or more additional component-specific factors. The approach furnishes…

  8. Child externalizing behavior problems linked to genetic and non-genetic variation in dental caries.

    PubMed

    Lorber, Michael F; Smith Slep, Amy M; Heyman, Richard E; Bretz, Walter A

    2014-01-01

    The association of environmental and genetic variation in caries with child externalizing behavior problems (inattention, hyperactivity, impulsivity, and defiance) was studied in a sample of 239 pairs of 3- to 8-year-old impoverished Brazilian twins. It was hypothesized that externalizing problems would show a stronger positive association with environmental than genetic variation in caries. Univariate twin models were estimated to parse variation in caries into three components: additive genetic (A), shared environment (C) and non-shared environment/error (E). Age-adjusted associations between externalizing problems and each variance component were tested. Contrary to the hypothesis, modest but very consistent negative associations were found between externalizing problems and both genetic and environmental variation in caries. Mutans streptococci and sweetness preference did not explain the negative associations of caries and externalizing problems. Externalizing problems in non-medicated children were associated with less dental decay that could be explained by both genetic and environmental factors. PMID:24852763

  9. 40 CFR 59.206 - Variances.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... VOLATILE ORGANIC COMPOUND EMISSION STANDARDS FOR CONSUMER AND COMMERCIAL PRODUCTS National Volatile Organic Compound Emission Standards for Consumer Products § 59.206 Variances. (a) Any regulated entity who...

  10. 40 CFR 59.206 - Variances.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... VOLATILE ORGANIC COMPOUND EMISSION STANDARDS FOR CONSUMER AND COMMERCIAL PRODUCTS National Volatile Organic Compound Emission Standards for Consumer Products § 59.206 Variances. (a) Any regulated entity who...

  11. 40 CFR 59.206 - Variances.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... VOLATILE ORGANIC COMPOUND EMISSION STANDARDS FOR CONSUMER AND COMMERCIAL PRODUCTS National Volatile Organic Compound Emission Standards for Consumer Products § 59.206 Variances. (a) Any regulated entity who...

  12. 40 CFR 59.206 - Variances.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... VOLATILE ORGANIC COMPOUND EMISSION STANDARDS FOR CONSUMER AND COMMERCIAL PRODUCTS National Volatile Organic Compound Emission Standards for Consumer Products § 59.206 Variances. (a) Any regulated entity who...

  13. 40 CFR 59.206 - Variances.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... VOLATILE ORGANIC COMPOUND EMISSION STANDARDS FOR CONSUMER AND COMMERCIAL PRODUCTS National Volatile Organic Compound Emission Standards for Consumer Products § 59.206 Variances. (a) Any regulated entity who...

  14. Reducing variance in batch partitioning measurements

    SciTech Connect

    Mariner, Paul E.

    2010-08-11

    The partitioning experiment is commonly performed with little or no attention to reducing measurement variance. Batch test procedures such as those used to measure K{sub d} values (e.g., ASTM D 4646 and EPA402 -R-99-004A) do not explain how to evaluate measurement uncertainty nor how to minimize measurement variance. In fact, ASTM D 4646 prescribes a sorbent:water ratio that prevents variance minimization. Consequently, the variance of a set of partitioning measurements can be extreme and even absurd. Such data sets, which are commonplace, hamper probabilistic modeling efforts. An error-savvy design requires adjustment of the solution:sorbent ratio so that approximately half of the sorbate partitions to the sorbent. Results of Monte Carlo simulations indicate that this simple step can markedly improve the precision and statistical characterization of partitioning uncertainty.

  15. Variance anisotropy in compressible 3-D MHD

    NASA Astrophysics Data System (ADS)

    Oughton, S.; Matthaeus, W. H.; Wan, Minping; Parashar, Tulasi

    2016-06-01

    We employ spectral method numerical simulations to examine the dynamical development of anisotropy of the variance, or polarization, of the magnetic and velocity field in compressible magnetohydrodynamic (MHD) turbulence. Both variance anisotropy and spectral anisotropy emerge under influence of a large-scale mean magnetic field B0; these are distinct effects, although sometimes related. Here we examine the appearance of variance parallel to B0, when starting from a highly anisotropic state. The discussion is based on a turbulence theoretic approach rather than a wave perspective. We find that parallel variance emerges over several characteristic nonlinear times, often attaining a quasi-steady level that depends on plasma beta. Consistency with solar wind observations seems to occur when the initial state is dominated by quasi-two-dimensional fluctuations.

  16. Another Line for the Analysis of Variance

    ERIC Educational Resources Information Center

    Brown, Bruce L.; Harshbarger, Thad R.

    1976-01-01

    A test is developed for hypotheses about the grand mean in the analysis of variance, using the known relationship between the t distribution and the F distribution with 1 df (degree of freedom) for the numerator. (Author/RC)

  17. Nonorthogonal Analysis of Variance Programs: An Evaluation.

    ERIC Educational Resources Information Center

    Hosking, James D.; Hamer, Robert M.

    1979-01-01

    Six computer programs for four methods of nonorthogonal analysis of variance are compared for capabilities, accuracy, cost, transportability, quality of documentation, associated computational capabilities, and ease of use: OSIRIS; SAS; SPSS; MANOVA; BMDP2V; and MULTIVARIANCE. (CTM)

  18. Automated variance reduction for Monte Carlo shielding analyses with MCNP

    NASA Astrophysics Data System (ADS)

    Radulescu, Georgeta

    Variance reduction techniques are employed in Monte Carlo analyses to increase the number of particles in the space phase of interest and thereby lower the variance of statistical estimation. Variance reduction parameters are required to perform Monte Carlo calculations. It is well known that adjoint solutions, even approximate ones, are excellent biasing functions that can significantly increase the efficiency of a Monte Carlo calculation. In this study, an automated method of generating Monte Carlo variance reduction parameters, and of implementing the source energy biasing and the weight window technique in MCNP shielding calculations has been developed. The method is based on the approach used in the SAS4 module of the SCALE code system, which derives the biasing parameters from an adjoint one-dimensional Discrete Ordinates calculation. Unlike SAS4 that determines the radial and axial dose rates of a spent fuel cask in separate calculations, the present method provides energy and spatial biasing parameters for the entire system that optimize the simulation of particle transport towards all external surfaces of a spent fuel cask. The energy and spatial biasing parameters are synthesized from the adjoint fluxes of three one-dimensional Discrete Ordinates adjoint calculations. Additionally, the present method accommodates multiple source regions, such as the photon sources in light-water reactor spent nuclear fuel assemblies, in one calculation. With this automated method, detailed and accurate dose rate maps for photons, neutrons, and secondary photons outside spent fuel casks or other containers can be efficiently determined with minimal efforts.

  19. Logistics for Working Together to Facilitate Genomic/Quantitative Genetic Prediction

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The incorporation of DNA tests into the national cattle evaluation system will require estimation of variances of and covariances among the additive genetic components of the DNA tests and the phenotypic traits they are intended to predict. Populations with both DNA test results and phenotypes will ...

  20. Analysis and application of minimum variance discrete time system identification

    NASA Technical Reports Server (NTRS)

    Kaufman, H.; Kotob, S.

    1975-01-01

    An on-line minimum variance parameter identifier is developed which embodies both accuracy and computational efficiency. The formulation results in a linear estimation problem with both additive and multiplicative noise. The resulting filter which utilizes both the covariance of the parameter vector itself and the covariance of the error in identification is proven to be mean square convergent and mean square consistent. The MV parameter identification scheme is then used to construct a stable state and parameter estimation algorithm.

  1. The quantitative genetics of indirect genetic effects: a selective review of modelling issues.

    PubMed

    Bijma, P

    2014-01-01

    Indirect genetic effects (IGE) occur when the genotype of an individual affects the phenotypic trait value of another conspecific individual. IGEs can have profound effects on both the magnitude and the direction of response to selection. Models of inheritance and response to selection in traits subject to IGEs have been developed within two frameworks; a trait-based framework in which IGEs are specified as a direct consequence of individual trait values, and a variance-component framework in which phenotypic variance is decomposed into a direct and an indirect additive genetic component. This work is a selective review of the quantitative genetics of traits affected by IGEs, with a focus on modelling, estimation and interpretation issues. It includes a discussion on variance-component vs trait-based models of IGEs, a review of issues related to the estimation of IGEs from field data, including the estimation of the interaction coefficient Ψ (psi), and a discussion on the relevance of IGEs for response to selection in cases where the strength of interaction varies among pairs of individuals. An investigation of the trait-based model shows that the interaction coefficient Ψ may deviate considerably from the corresponding regression coefficient when feedback occurs. The increasing research effort devoted to IGEs suggests that they are a widespread phenomenon, probably particularly in natural populations and plants. Further work in this field should considerably broaden our understanding of the quantitative genetics of inheritance and response to selection in relation to the social organisation of populations. PMID:23512010

  2. A Fast Method that Uses Polygenic Scores to Estimate the Variance Explained by Genome-wide Marker Panels and the Proportion of Variants Affecting a Trait

    PubMed Central

    Palla, Luigi; Dudbridge, Frank

    2015-01-01

    Several methods have been proposed to estimate the variance in disease liability explained by large sets of genetic markers. However, current methods do not scale up well to large sample sizes. Linear mixed models require solving high-dimensional matrix equations, and methods that use polygenic scores are very computationally intensive. Here we propose a fast analytic method that uses polygenic scores, based on the formula for the non-centrality parameter of the association test of the score. We estimate model parameters from the results of multiple polygenic score tests based on markers with p values in different intervals. We estimate parameters by maximum likelihood and use profile likelihood to compute confidence intervals. We compare various options for constructing polygenic scores, based on nested or disjoint intervals of p values, weighted or unweighted effect sizes, and different numbers of intervals, in estimating the variance explained by a set of markers, the proportion of markers with effects, and the genetic covariance between a pair of traits. Our method provides nearly unbiased estimates and confidence intervals with good coverage, although estimation of the variance is less reliable when jointly estimated with the covariance. We find that disjoint p value intervals perform better than nested intervals, but the weighting did not affect our results. A particular advantage of our method is that it can be applied to summary statistics from single markers, and so can be quickly applied to large consortium datasets. Our method, named AVENGEME (Additive Variance Explained and Number of Genetic Effects Method of Estimation), is implemented in R software. PMID:26189816

  3. Discrimination of frequency variance for tonal sequencesa)

    PubMed Central

    Byrne, Andrew J.; Viemeister, Neal F.; Stellmack, Mark A.

    2014-01-01

    Real-world auditory stimuli are highly variable across occurrences and sources. The present study examined the sensitivity of human listeners to differences in global stimulus variability. In a two-interval, forced-choice task, variance discrimination was measured using sequences of five 100-ms tone pulses. The frequency of each pulse was sampled randomly from a distribution that was Gaussian in logarithmic frequency. In the non-signal interval, the sampled distribution had a variance of σSTAN2, while in the signal interval, the variance of the sequence was σSIG2 (with σSIG2 > σSTAN2). The listener's task was to choose the interval with the larger variance. To constrain possible decision strategies, the mean frequency of the sampling distribution of each interval was randomly chosen for each presentation. Psychometric functions were measured for various values of σSTAN2. Although the performance was remarkably similar across listeners, overall performance was poorer than that of an ideal observer (IO) which perfectly compares interval variances. However, like the IO, Weber's Law behavior was observed, with a constant ratio of (σSIG2-σSTAN2) to σSTAN2 yielding similar performance. A model which degraded the IO with a frequency-resolution noise and a computational noise provided a reasonable fit to the real data. PMID:25480064

  4. Kernel-based variance component estimation and whole-genome prediction of pre-corrected phenotypes and progeny tests for dairy cow health traits

    PubMed Central

    Morota, Gota; Boddhireddy, Prashanth; Vukasinovic, Natascha; Gianola, Daniel; DeNise, Sue

    2014-01-01

    Prediction of complex trait phenotypes in the presence of unknown gene action is an ongoing challenge in animals, plants, and humans. Development of flexible predictive models that perform well irrespective of genetic and environmental architectures is desirable. Methods that can address non-additive variation in a non-explicit manner are gaining attention for this purpose and, in particular, semi-parametric kernel-based methods have been applied to diverse datasets, mostly providing encouraging results. On the other hand, the gains obtained from these methods have been smaller when smoothed values such as estimated breeding value (EBV) have been used as response variables. However, less emphasis has been placed on the choice of phenotypes to be used in kernel-based whole-genome prediction. This study aimed to evaluate differences between semi-parametric and parametric approaches using two types of response variables and molecular markers as inputs. Pre-corrected phenotypes (PCP) and EBV obtained for dairy cow health traits were used for this comparison. We observed that non-additive genetic variances were major contributors to total genetic variances in PCP, whereas additivity was the largest contributor to variability of EBV, as expected. Within the kernels evaluated, non-parametric methods yielded slightly better predictive performance across traits relative to their additive counterparts regardless of the type of response variable used. This reinforces the view that non-parametric kernels aiming to capture non-linear relationships between a panel of SNPs and phenotypes are appealing for complex trait prediction. However, like past studies, the gain in predictive correlation was not large for either PCP or EBV. We conclude that capturing non-additive genetic variation, especially epistatic variation, in a cross-validation framework remains a significant challenge even when it is important, as seems to be the case for health traits in dairy cows. PMID:24715901

  5. Cross-bispectrum computation and variance estimation

    NASA Technical Reports Server (NTRS)

    Lii, K. S.; Helland, K. N.

    1981-01-01

    A method for the estimation of cross-bispectra of discrete real time series is developed. The asymptotic variance properties of the bispectrum are reviewed, and a method for the direct estimation of bispectral variance is given. The symmetry properties are described which minimize the computations necessary to obtain a complete estimate of the cross-bispectrum in the right-half-plane. A procedure is given for computing the cross-bispectrum by subdividing the domain into rectangular averaging regions which help reduce the variance of the estimates and allow easy application of the symmetry relationships to minimize the computational effort. As an example of the procedure, the cross-bispectrum of a numerically generated, exponentially distributed time series is computed and compared with theory.

  6. Inhomogeneity-induced variance of cosmological parameters

    NASA Astrophysics Data System (ADS)

    Wiegand, A.; Schwarz, D. J.

    2012-02-01

    Context. Modern cosmology relies on the assumption of large-scale isotropy and homogeneity of the Universe. However, locally the Universe is inhomogeneous and anisotropic. This raises the question of how local measurements (at the ~102 Mpc scale) can be used to determine the global cosmological parameters (defined at the ~104 Mpc scale)? Aims: We connect the questions of cosmological backreaction, cosmic averaging and the estimation of cosmological parameters and show how they relate to the problem of cosmic variance. Methods: We used Buchert's averaging formalism and determined a set of locally averaged cosmological parameters in the context of the flat Λ cold dark matter model. We calculated their ensemble means (i.e. their global value) and variances (i.e. their cosmic variance). We applied our results to typical survey geometries and focused on the study of the effects of local fluctuations of the curvature parameter. Results: We show that in the context of standard cosmology at large scales (larger than the homogeneity scale and in the linear regime), the question of cosmological backreaction and averaging can be reformulated as the question of cosmic variance. The cosmic variance is found to be highest in the curvature parameter. We propose to use the observed variance of cosmological parameters to measure the growth factor. Conclusions: Cosmological backreaction and averaging are real effects that have been measured already for a long time, e.g. by the fluctuations of the matter density contrast averaged over spheres of a certain radius. Backreaction and averaging effects from scales in the linear regime, as considered in this work, are shown to be important for the precise measurement of cosmological parameters.

  7. Large-scale magnetic variances near the South Solar Pole

    NASA Technical Reports Server (NTRS)

    Jokipii, J. R.; Kota, J.; Smith, E.; Horbury, T.; Giacalone, J.

    1995-01-01

    We summarize recent Ulysses observations of the variances over large temporal scales in the interplanetary magnetic field components and their increase as Ulysses approached the South Solar Pole. A model of these fluctuations is shown to provide a very good fit to the observed amplitude and temporal variation of the fluctuations. In addition, the model predicts that the transport of cosmic rays in the heliosphere will be significantly altered by this level of fluctuations. In addition to altering the inward diffusion and drift access of cosmic rays over the solar poles, we find that the magnetic fluctuations also imply a large latitudinal diffusion, caused primarily by the associated field-line random walk.

  8. Wave propagation analysis using the variance matrix.

    PubMed

    Sharma, Richa; Ivan, J Solomon; Narayanamurthy, C S

    2014-10-01

    The propagation of a coherent laser wave-field through a pseudo-random phase plate is studied using the variance matrix estimated from Shack-Hartmann wavefront sensor data. The uncertainty principle is used as a tool in discriminating the data obtained from the Shack-Hartmann wavefront sensor. Quantities of physical interest such as the twist parameter, and the symplectic eigenvalues, are estimated from the wavefront sensor measurements. A distance measure between two variance matrices is introduced and used to estimate the spatial asymmetry of a wave-field in the experiment. The estimated quantities are then used to compare a distorted wave-field with its undistorted counterpart. PMID:25401243

  9. Variance in binary stellar population synthesis

    NASA Astrophysics Data System (ADS)

    Breivik, Katelyn; Larson, Shane L.

    2016-03-01

    In the years preceding LISA, Milky Way compact binary population simulations can be used to inform the science capabilities of the mission. Galactic population simulation efforts generally focus on high fidelity models that require extensive computational power to produce a single simulated population for each model. Each simulated population represents an incomplete sample of the functions governing compact binary evolution, thus introducing variance from one simulation to another. We present a rapid Monte Carlo population simulation technique that can simulate thousands of populations in less than a week, thus allowing a full exploration of the variance associated with a binary stellar evolution model.

  10. Variance Reduction Using Nonreversible Langevin Samplers

    NASA Astrophysics Data System (ADS)

    Duncan, A. B.; Lelièvre, T.; Pavliotis, G. A.

    2016-05-01

    A standard approach to computing expectations with respect to a given target measure is to introduce an overdamped Langevin equation which is reversible with respect to the target distribution, and to approximate the expectation by a time-averaging estimator. As has been noted in recent papers [30, 37, 61, 72], introducing an appropriately chosen nonreversible component to the dynamics is beneficial, both in terms of reducing the asymptotic variance and of speeding up convergence to the target distribution. In this paper we present a detailed study of the dependence of the asymptotic variance on the deviation from reversibility. Our theoretical findings are supported by numerical simulations.

  11. Random regression models for the estimation of genetic and environmental covariance functions for growth traits in Santa Ines sheep.

    PubMed

    Sarmento, J L R; Torres, R A; Sousa, W H; Lôbo, R N B; Albuquerque, L G; Lopes, P S; Santos, N P S; Bignard, A B

    2016-01-01

    Polynomial functions of different orders were used to model random effects associated with weight of Santa Ines sheep from birth to 196 days. Fixed effects included in the models were contemporary groups, age of ewe at lambing, and fourth-order Legendre polynomials for age to represent the average growth curve. In the random part, functions of different orders were included to model variances associated with direct additive and maternal genetic effects and with permanent environmental effects of the animal and mother. Residual variance was fitted by a sixth-order ordinary polynomial for age. The higher the order of the functions, the better the model fit the data. According to the Akaike information criterion and likelihood ratio test, a continuous function of order, five, five, seven, and three for direct additive genetic, maternal genetic, animal permanent environmental, and maternal permanent environmental effects (k = 5573), respectively, was sufficient to model changes in (co)variances with age. However, a more parsimonious model of order three, three, five, and three (k = 3353) was suggested based on Schwarz's Bayesian information criterion for the same effects. Since it was a more flexible model, model k = 5573 provided inconsistent genetic parameter estimates when compared to the biologically expected result. Predicted breeding values obtained with models k = 3353 and k = 5573 differed, especially at young ages. Model k = 3353 adequately fit changes in variances and covariances with time, and may be used to describe changes in variances with age in the Santa Ines sheep studied. PMID:27323203

  12. A new variance-based global sensitivity analysis technique

    NASA Astrophysics Data System (ADS)

    Wei, Pengfei; Lu, Zhenzhou; Song, Jingwen

    2013-11-01

    A new set of variance-based sensitivity indices, called W-indices, is proposed. Similar to the Sobol's indices, both main and total effect indices are defined. The W-main effect indices measure the average reduction of model output variance when the ranges of a set of inputs are reduced, and the total effect indices quantify the average residual variance when the ranges of the remaining inputs are reduced. Geometrical interpretations show that the W-indices gather the full information of the variance ratio function, whereas, Sobol's indices only reflect the marginal information. Then the double-loop-repeated-set Monte Carlo (MC) (denoted as DLRS MC) procedure, the double-loop-single-set MC (denoted as DLSS MC) procedure and the model emulation procedure are introduced for estimating the W-indices. It is shown that the DLRS MC procedure is suitable for computing all the W-indices despite its highly computational cost. The DLSS MC procedure is computationally efficient, however, it is only applicable for computing low order indices. The model emulation is able to estimate all the W-indices with low computational cost as long as the model behavior is correctly captured by the emulator. The Ishigami function, a modified Sobol's function and two engineering models are utilized for comparing the W- and Sobol's indices and verifying the efficiency and convergence of the three numerical methods. Results show that, for even an additive model, the W-total effect index of one input may be significantly larger than its W-main effect index. This indicates that there may exist interaction effects among the inputs of an additive model when their distribution ranges are reduced.

  13. A Simple Algorithm for Approximating Confidence on the Modified Allan Variance and the Time Variance

    NASA Technical Reports Server (NTRS)

    Weiss, Marc A.; Greenhall, Charles A.

    1996-01-01

    An approximating algorithm for computing equvalent degrees of freedom of the Modified Allan Variance and its square root, the Modified Allan Deviation (MVAR and MDEV), and the Time Variance and Time Deviation (TVAR and TDEV) is presented, along with an algorithm for approximating the inverse chi-square distribution.

  14. Epistasis and the Genetic Divergence of Photoperiodism between Populations of the Pitcher-Plant Mosquito, Wyeomyia Smithii

    PubMed Central

    Hard, J. J.; Bradshaw, W. E.; Holzapfel, C. M.

    1992-01-01

    Parallel crosses between each of two southern (ancestral) and one northern (derived) population of the pitcher-plant mosquito, Wyeomyia smithii, were made to determine the genetic components of population divergence in critical photoperiod, a phenological trait that measures adaptation to seasonality along a climatic gradient. Joint scaling tests were used to analyze means and variances of first- and second-generation hybrids in order to determine whether nonadditive genetic variance, especially epistatic variance, contributed to divergence in critical photoperiod. In both crosses, digenic epistatic effects were highly significant, indicating that genetic divergence cannot have resulted solely from differences in additively acting loci. For one cross that could be tested directly for such effects, higher order epistasis and/or linkage did not contribute to the divergence of critical photoperiod between the constituent populations. PMID:1353737

  15. Epistasis and the genetic divergence of photoperiodism between populations of the pitcher-plant mosquito, Wyeomyia smithii.

    PubMed

    Hard, J J; Bradshaw, W E; Holzapfel, C M

    1992-06-01

    Parallel crosses between each of two southern (ancestral) and one northern (derived) population of the pitcher-plant mosquito, Wyeomyia smithii, were made to determine the genetic components of population divergence in critical photoperiod, a phenological trait that measures adaptation to seasonality along a climatic gradient. Joint scaling tests were used to analyze means and variances of first- and second-generation hybrids in order to determine whether nonadditive genetic variance, especially epistatic variance, contributed to divergence in critical photoperiod. In both crosses, digenic epistatic effects were highly significant, indicating that genetic divergence cannot have resulted solely from differences in additively acting loci. For one cross that could be tested directly for such effects, higher order epistasis and/or linkage did not contribute to the divergence of critical photoperiod between the constituent populations. PMID:1353737

  16. Videotape Project in Child Variance. Final Report.

    ERIC Educational Resources Information Center

    Morse, William C.; Smith, Judith M.

    The design, production, dissemination, and evaluation of a series of videotaped training packages designed to enable teachers, parents, and paraprofessionals to interpret child variance in light of personal and alternative perspectives of behavior are discussed. The goal of each package is to highlight unique contributions of different theoretical…

  17. Testing Variances in Psychological and Educational Research.

    ERIC Educational Resources Information Center

    Ramsey, Philip H.

    1994-01-01

    A review of the literature indicates that the two best procedures for testing variances are one that was proposed by O'Brien (1981) and another that was proposed by Brown and Forsythe (1974). An examination of these procedures for a variety of populations confirms their robustness and indicates how optimal power can usually be obtained. (SLD)

  18. 10 CFR 1022.16 - Variances.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... such an action) DOE shall document the emergency actions in accordance with NEPA procedures at 10 CFR... ENERGY (GENERAL PROVISIONS) COMPLIANCE WITH FLOODPLAIN AND WETLAND ENVIRONMENTAL REVIEW REQUIREMENTS Procedures for Floodplain and Wetland Reviews § 1022.16 Variances. (a) Emergency actions. DOE may...

  19. 10 CFR 1022.16 - Variances.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... such an action) DOE shall document the emergency actions in accordance with NEPA procedures at 10 CFR... ENERGY (GENERAL PROVISIONS) COMPLIANCE WITH FLOODPLAIN AND WETLAND ENVIRONMENTAL REVIEW REQUIREMENTS Procedures for Floodplain and Wetland Reviews § 1022.16 Variances. (a) Emergency actions. DOE may...

  20. 10 CFR 1022.16 - Variances.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... such an action) DOE shall document the emergency actions in accordance with NEPA procedures at 10 CFR... ENERGY (GENERAL PROVISIONS) COMPLIANCE WITH FLOODPLAIN AND WETLAND ENVIRONMENTAL REVIEW REQUIREMENTS Procedures for Floodplain and Wetland Reviews § 1022.16 Variances. (a) Emergency actions. DOE may...

  1. 10 CFR 1022.16 - Variances.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... such an action) DOE shall document the emergency actions in accordance with NEPA procedures at 10 CFR... ENERGY (GENERAL PROVISIONS) COMPLIANCE WITH FLOODPLAIN AND WETLAND ENVIRONMENTAL REVIEW REQUIREMENTS Procedures for Floodplain and Wetland Reviews § 1022.16 Variances. (a) Emergency actions. DOE may...

  2. 10 CFR 1022.16 - Variances.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... such an action) DOE shall document the emergency actions in accordance with NEPA procedures at 10 CFR... ENERGY (GENERAL PROVISIONS) COMPLIANCE WITH FLOODPLAIN AND WETLAND ENVIRONMENTAL REVIEW REQUIREMENTS Procedures for Floodplain and Wetland Reviews § 1022.16 Variances. (a) Emergency actions. DOE may...

  3. Variance Reduction for a Discrete Velocity Gas

    NASA Astrophysics Data System (ADS)

    Morris, A. B.; Varghese, P. L.; Goldstein, D. B.

    2011-05-01

    We extend a variance reduction technique developed by Baker and Hadjiconstantinou [1] to a discrete velocity gas. In our previous work, the collision integral was evaluated by importance sampling of collision partners [2]. Significant computational effort may be wasted by evaluating the collision integral in regions where the flow is in equilibrium. In the current approach, substantial computational savings are obtained by only solving for the deviations from equilibrium. In the near continuum regime, the deviations from equilibrium are small and low noise evaluation of the collision integral can be achieved with very coarse statistical sampling. Spatially homogenous relaxation of the Bobylev-Krook-Wu distribution [3,4], was used as a test case to verify that the method predicts the correct evolution of a highly non-equilibrium distribution to equilibrium. When variance reduction is not used, the noise causes the entropy to undershoot, but the method with variance reduction matches the analytic curve for the same number of collisions. We then extend the work to travelling shock waves and compare the accuracy and computational savings of the variance reduction method to DSMC over Mach numbers ranging from 1.2 to 10.

  4. Multiple Comparison Procedures when Population Variances Differ.

    ERIC Educational Resources Information Center

    Olejnik, Stephen; Lee, JaeShin

    A review of the literature on multiple comparison procedures suggests several alternative approaches for comparing means when population variances differ. These include: (1) the approach of P. A. Games and J. F. Howell (1976); (2) C. W. Dunnett's C confidence interval (1980); and (3) Dunnett's T3 solution (1980). These procedures control the…

  5. Variance Anisotropy of Solar Wind fluctuations

    NASA Astrophysics Data System (ADS)

    Oughton, S.; Matthaeus, W. H.; Wan, M.; Osman, K.

    2013-12-01

    Solar wind observations at MHD scales indicate that the energy associated with velocity and magnetic field fluctuations transverse to the mean magnetic field is typically much larger than that associated with parallel fluctuations [eg, 1]. This is often referred to as variance anisotropy. Various explanations for it have been suggested, including that the fluctuations are predominantly shear Alfven waves [1] and that turbulent dynamics leads to such states [eg, 2]. Here we investigate the origin and strength of such variance anisotropies, using spectral method simulations of the compressible (polytropic) 3D MHD equations. We report on results from runs with initial conditions that are either (i) broadband turbulence or (ii) fluctuations polarized in the same sense as shear Alfven waves. The dependence of the variance anisotropy on the plasma beta and Mach number is examined [3], along with the timescale for any variance anisotropy to develop. Implications for solar wind fluctuations will be discussed. References: [1] Belcher, J. W. and Davis Jr., L. (1971), J. Geophys. Res., 76, 3534. [2] Matthaeus, W. H., Ghosh, S., Oughton, S. and Roberts, D. A. (1996), J. Geophys. Res., 101, 7619. [3] Smith, C. W., B. J. Vasquez and K. Hamilton (2006), J. Geophys. Res., 111, A09111.

  6. Comparing the Variances of Two Dependent Groups.

    ERIC Educational Resources Information Center

    Wilcox, Rand R.

    1990-01-01

    Recently, C. E. McCulloch (1987) suggested a modification of the Morgan-Pitman test for comparing the variances of two dependent groups. This paper demonstrates that there are situations where the procedure is not robust. A subsample approach, similar to the Box-Scheffe test, and the Sandvik-Olsson procedure are also assessed. (TJH)

  7. Formative Use of Intuitive Analysis of Variance

    ERIC Educational Resources Information Center

    Trumpower, David L.

    2013-01-01

    Students' informal inferential reasoning (IIR) is often inconsistent with the normative logic underlying formal statistical methods such as Analysis of Variance (ANOVA), even after instruction. In two experiments reported here, student's IIR was assessed using an intuitive ANOVA task at the beginning and end of a statistics course. In…

  8. 78 FR 14122 - Revocation of Permanent Variances

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-03-04

    ... OSHA's scaffolds standards for construction (77 FR 46948). Today's notice revoking the variances takes... Safety and Health Act of 1970 (OSH Act; 29 U.S.C. 651, 655) in 1971 (see 36 FR 7340). Paragraphs (a)(4..., construction, and use of scaffolds (61 FR 46026). In the preamble to the final rule, OSHA stated that it...

  9. 7 CFR 205.290 - Temporary variances.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 3 2011-01-01 2011-01-01 false Temporary variances. 205.290 Section 205.290 Agriculture Regulations of the Department of Agriculture (Continued) AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing Practices), DEPARTMENT OF AGRICULTURE (CONTINUED) ORGANIC FOODS PRODUCTION ACT PROVISIONS NATIONAL ORGANIC PROGRAM...

  10. 18 CFR 1304.408 - Variances.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 18 Conservation of Power and Water Resources 2 2012-04-01 2012-04-01 false Variances. 1304.408 Section 1304.408 Conservation of Power and Water Resources TENNESSEE VALLEY AUTHORITY APPROVAL OF CONSTRUCTION IN THE TENNESSEE RIVER SYSTEM AND REGULATION OF STRUCTURES AND OTHER ALTERATIONS...

  11. 18 CFR 1304.408 - Variances.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 18 Conservation of Power and Water Resources 2 2011-04-01 2011-04-01 false Variances. 1304.408 Section 1304.408 Conservation of Power and Water Resources TENNESSEE VALLEY AUTHORITY APPROVAL OF CONSTRUCTION IN THE TENNESSEE RIVER SYSTEM AND REGULATION OF STRUCTURES AND OTHER ALTERATIONS...

  12. Evolutionary quantitative genetics of nonlinear developmental systems.

    PubMed

    Morrissey, Michael B

    2015-08-01

    In quantitative genetics, the effects of developmental relationships among traits on microevolution are generally represented by the contribution of pleiotropy to additive genetic covariances. Pleiotropic additive genetic covariances arise only from the average effects of alleles on multiple traits, and therefore the evolutionary importance of nonlinearities in development is generally neglected in quantitative genetic views on evolution. However, nonlinearities in relationships among traits at the level of whole organisms are undeniably important to biology in general, and therefore critical to understanding evolution. I outline a system for characterizing key quantitative parameters in nonlinear developmental systems, which yields expressions for quantities such as trait means and phenotypic and genetic covariance matrices. I then develop a system for quantitative prediction of evolution in nonlinear developmental systems. I apply the system to generating a new hypothesis for why direct stabilizing selection is rarely observed. Other uses will include separation of purely correlative from direct and indirect causal effects in studying mechanisms of selection, generation of predictions of medium-term evolutionary trajectories rather than immediate predictions of evolutionary change over single generation time-steps, and the development of efficient and biologically motivated models for separating additive from epistatic genetic variances and covariances. PMID:26174586

  13. The Column Density Variance-{\\cal M}_s Relationship

    NASA Astrophysics Data System (ADS)

    Burkhart, Blakesley; Lazarian, A.

    2012-08-01

    Although there is a wealth of column density tracers for both the molecular and diffuse interstellar medium, there are few observational studies investigating the relationship between the density variance (σ2) and the sonic Mach number ({\\cal M}_s). This is in part due to the fact that the σ2-{\\cal M}_s relationship is derived, via MHD simulations, for the three-dimensional (3D) density variance only, which is not a direct observable. We investigate the utility of a 2D column density \\sigma _{\\Sigma /\\Sigma _0}^2-{\\cal M}_s relationship using solenoidally driven isothermal MHD simulations and find that the best fit follows closely the form of the 3D density \\sigma _{\\rho /\\rho _0}^2-{\\cal M}_s trend but includes a scaling parameter A such that \\sigma _{\\ln (\\Sigma /\\Sigma _0)}^2=A\\times \\ln (1+b^2{\\cal M}_s^2), where A = 0.11 and b = 1/3. This relation is consistent with the observational data reported for the Taurus and IC 5146 molecular clouds with b = 0.5 and A = 0.16, and b = 0.5 and A = 0.12, respectively. These results open up the possibility of using the 2D column density values of σ2 for investigations of the relation between the sonic Mach number and the probability distribution function (PDF) variance in addition to existing PDF sonic Mach number relations.

  14. R package MVR for Joint Adaptive Mean-Variance Regularization and Variance Stabilization

    PubMed Central

    Dazard, Jean-Eudes; Xu, Hua; Rao, J. Sunil

    2015-01-01

    We present an implementation in the R language for statistical computing of our recent non-parametric joint adaptive mean-variance regularization and variance stabilization procedure. The method is specifically suited for handling difficult problems posed by high-dimensional multivariate datasets (p ≫ n paradigm), such as in ‘omics’-type data, among which are that the variance is often a function of the mean, variable-specific estimators of variances are not reliable, and tests statistics have low powers due to a lack of degrees of freedom. The implementation offers a complete set of features including: (i) normalization and/or variance stabilization function, (ii) computation of mean-variance-regularized t and F statistics, (iii) generation of diverse diagnostic plots, (iv) synthetic and real ‘omics’ test datasets, (v) computationally efficient implementation, using C interfacing, and an option for parallel computing, (vi) manual and documentation on how to setup a cluster. To make each feature as user-friendly as possible, only one subroutine per functionality is to be handled by the end-user. It is available as an R package, called MVR (‘Mean-Variance Regularization’), downloadable from the CRAN. PMID:26819572

  15. Genetic parameter estimation for pre- and post-weaning traits in Brahman cattle in Brazil.

    PubMed

    Vargas, Giovana; Buzanskas, Marcos Eli; Guidolin, Diego Gomes Freire; Grossi, Daniela do Amaral; Bonifácio, Alexandre da Silva; Lôbo, Raysildo Barbosa; da Fonseca, Ricardo; Oliveira, João Ademir de; Munari, Danísio Prado

    2014-10-01

    Beef cattle producers in Brazil use body weight traits as breeding program selection criteria due to their great economic importance. The objectives of this study were to evaluate different animal models, estimate genetic parameters, and define the most fitting model for Brahman cattle body weight standardized at 120 (BW120), 210 (BW210), 365 (BW365), 450 (BW450), and 550 (BW550) days of age. To estimate genetic parameters, single-, two-, and multi-trait analyses were performed using the animal model. The likelihood ratio test was verified between all models. For BW120 and BW210, additive direct genetic, maternal genetic, maternal permanent environment, and residual effects were considered, while for BW365 and BW450, additive direct genetic, maternal genetic, and residual effects were considered. Finally, for BW550, additive direct genetic and residual effects were considered. Estimates of direct heritability for BW120 were similar in all analyses; however, for the other traits, multi-trait analysis resulted in higher estimates. The maternal heritability and proportion of maternal permanent environmental variance to total variance were minimal in multi-trait analyses. Genetic, environmental, and phenotypic correlations were of high magnitude between all traits. Multi-trait analyses would aid in the parameter estimation for body weight at older ages because they are usually affected by a lower number of animals with phenotypic information due to culling and mortality. PMID:25037588

  16. Genetic constraints predict evolutionary divergence in Dalechampia blossoms

    PubMed Central

    Bolstad, Geir H.; Hansen, Thomas F.; Pélabon, Christophe; Falahati-Anbaran, Mohsen; Pérez-Barrales, Rocío; Armbruster, W. Scott

    2014-01-01

    If genetic constraints are important, then rates and direction of evolution should be related to trait evolvability. Here we use recently developed measures of evolvability to test the genetic constraint hypothesis with quantitative genetic data on floral morphology from the Neotropical vine Dalechampia scandens (Euphorbiaceae). These measures were compared against rates of evolution and patterns of divergence among 24 populations in two species in the D. scandens species complex. We found clear evidence for genetic constraints, particularly among traits that were tightly phenotypically integrated. This relationship between evolvability and evolutionary divergence is puzzling, because the estimated evolvabilities seem too large to constitute real constraints. We suggest that this paradox can be explained by a combination of weak stabilizing selection around moving adaptive optima and small realized evolvabilities relative to the observed additive genetic variance. PMID:25002700

  17. Genetic constraints predict evolutionary divergence in Dalechampia blossoms.

    PubMed

    Bolstad, Geir H; Hansen, Thomas F; Pélabon, Christophe; Falahati-Anbaran, Mohsen; Pérez-Barrales, Rocío; Armbruster, W Scott

    2014-08-19

    If genetic constraints are important, then rates and direction of evolution should be related to trait evolvability. Here we use recently developed measures of evolvability to test the genetic constraint hypothesis with quantitative genetic data on floral morphology from the Neotropical vine Dalechampia scandens (Euphorbiaceae). These measures were compared against rates of evolution and patterns of divergence among 24 populations in two species in the D. scandens species complex. We found clear evidence for genetic constraints, particularly among traits that were tightly phenotypically integrated. This relationship between evolvability and evolutionary divergence is puzzling, because the estimated evolvabilities seem too large to constitute real constraints. We suggest that this paradox can be explained by a combination of weak stabilizing selection around moving adaptive optima and small realized evolvabilities relative to the observed additive genetic variance. PMID:25002700

  18. Complex Genotype by Environment interactions and changing genetic architectures across thermal environments in the Australian field cricket, Teleogryllus oceanicus

    PubMed Central

    2011-01-01

    Background Biologists studying adaptation under sexual selection have spent considerable effort assessing the relative importance of two groups of models, which hinge on the idea that females gain indirect benefits via mate discrimination. These are the good genes and genetic compatibility models. Quantitative genetic studies have advanced our understanding of these models by enabling assessment of whether the genetic architectures underlying focal phenotypes are congruent with either model. In this context, good genes models require underlying additive genetic variance, while compatibility models require non-additive variance. Currently, we know very little about how the expression of genotypes comprised of distinct parental haplotypes, or how levels and types of genetic variance underlying key phenotypes, change across environments. Such knowledge is important, however, because genotype-environment interactions can have major implications on the potential for evolutionary responses to selection. Results We used a full diallel breeding design to screen for complex genotype-environment interactions, and genetic architectures underlying key morphological traits, across two thermal environments (the lab standard 27°C, and the cooler 23°C) in the Australian field cricket, Teleogryllus oceanicus. In males, complex three-way interactions between sire and dam parental haplotypes and the rearing environment accounted for up to 23 per cent of the scaled phenotypic variance in the traits we measured (body mass, pronotum width and testes mass), and each trait harboured significant additive genetic variance in the standard temperature (27°C) only. In females, these three-way interactions were less important, with interactions between the paternal haplotype and rearing environment accounting for about ten per cent of the phenotypic variance (in body mass, pronotum width and ovary mass). Of the female traits measured, only ovary mass for crickets reared at the cooler

  19. 42 CFR 456.525 - Request for renewal of variance.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 42 Public Health 4 2010-10-01 2010-10-01 false Request for renewal of variance. 456.525 Section..., and Variances for Hospitals and Mental Hospitals Ur Plan: Remote Facility Variances from Time Requirements § 456.525 Request for renewal of variance. (a) The agency must submit a request for renewal of...

  20. 10 CFR 851.32 - Action on variance requests.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 10 Energy 4 2010-01-01 2010-01-01 false Action on variance requests. 851.32 Section 851.32 Energy DEPARTMENT OF ENERGY WORKER SAFETY AND HEALTH PROGRAM Variances § 851.32 Action on variance requests. (a... approval of a variance application, the Chief Health, Safety and Security Officer must forward to the...

  1. 41 CFR 50-204.1a - Variances.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 41 Public Contracts and Property Management 1 2010-07-01 2010-07-01 true Variances. 50-204.1a... and Application § 50-204.1a Variances. (a) Variances from standards in this part may be granted in the same circumstances in which variances may be granted under sections 6(b)(6)(A) or 6(d) of the...

  2. 21 CFR 898.14 - Exemptions and variances.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Exemptions and variances. 898.14 Section 898.14... variances. (a) A request for an exemption or variance shall be submitted in the form of a petition under... with the device; and (4) Other information justifying the exemption or variance. (b) An exemption...

  3. 10 CFR 851.30 - Consideration of variances.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 10 Energy 4 2010-01-01 2010-01-01 false Consideration of variances. 851.30 Section 851.30 Energy DEPARTMENT OF ENERGY WORKER SAFETY AND HEALTH PROGRAM Variances § 851.30 Consideration of variances. (a) Variances shall be granted by the Under Secretary after considering the recommendation of the Chief...

  4. 42 CFR 456.521 - Conditions for granting variance requests.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 42 Public Health 4 2010-10-01 2010-10-01 false Conditions for granting variance requests. 456.521..., and Variances for Hospitals and Mental Hospitals Ur Plan: Remote Facility Variances from Time Requirements § 456.521 Conditions for granting variance requests. (a) Except as described under paragraph...

  5. Genome Sequence of EU-Unauthorized Genetically Modified Bacillus subtilis Strain 2014-3557 Overproducing Riboflavin, Isolated from a Vitamin B2 80% Feed Additive

    PubMed Central

    Barbau-Piednoir, Elodie; De Keersmaecker, Sigrid C. J.; Wuyts, Véronique; Gau, Céline; Pirovano, Walter; Costessi, Adalberto; Philipp, Patrick

    2015-01-01

    This paper announces the genome sequence and annotation of the genetically modified (GM) Bacillus subtilis strain 2014-3557 overproducing riboflavin (vitamin B2). This GM-strain is unauthorized in the European Union. Nevertheless, it has been isolated from a lot of vitamin B2 (riboflavin) 80% feed grade imported to Europe from China. PMID:25858836

  6. Progress in unraveling the genetic etiology of Parkinson disease in a genomic era.

    PubMed

    Verstraeten, Aline; Theuns, Jessie; Van Broeckhoven, Christine

    2015-03-01

    Parkinson disease (PD) and Parkinson-plus syndromes are genetically heterogeneous neurological diseases. Initial studies into the genetic causes of PD relied on classical molecular genetic approaches in well-documented case families. More recently, these approaches have been combined with exome sequencing and together have identified 15 causal genes. Additionally, genome-wide association studies (GWASs) have discovered over 25 genetic risk factors. Elucidation of the genetic architecture of sporadic and familial parkinsonism, however, has lagged behind that of simple Mendelian conditions, suggesting the existence of features confounding genetic data interpretation. Here we discuss the successes and potential pitfalls of gene discovery in PD and related disorders in the post-genomic era. With an estimated 30% of trait variance currently unexplained, tackling current limitations will further expedite gene discovery and lead to increased application of these genetic insights in molecular diagnostics using gene panel and exome sequencing strategies. PMID:25703649

  7. Analysis of variance of microarray data.

    PubMed

    Ayroles, Julien F; Gibson, Greg

    2006-01-01

    Analysis of variance (ANOVA) is an approach used to identify differentially expressed genes in complex experimental designs. It is based on testing for the significance of the magnitude of effect of two or more treatments taking into account the variance within and between treatment classes. ANOVA is a highly flexible analytical approach that allows investigators to simultaneously assess the contributions of multiple factors to gene expression variation, including technical (dye, batch) effects and biological (sex, genotype, drug, time) ones, as well as interactions between factors. This chapter provides an overview of the theory of linear mixture modeling and the sequence of steps involved in fitting gene-specific models and discusses essential features of experimental design. Commercial and open-source software for performing ANOVA is widely available. PMID:16939792

  8. PHD filtering with localised target number variance

    NASA Astrophysics Data System (ADS)

    Delande, Emmanuel; Houssineau, Jérémie; Clark, Daniel

    2013-05-01

    Mahler's Probability Hypothesis Density (PHD filter), proposed in 2000, addresses the challenges of the multipletarget detection and tracking problem by propagating a mean density of the targets in any region of the state space. However, when retrieving some local evidence on the target presence becomes a critical component of a larger process - e.g. for sensor management purposes - the local target number is insufficient unless some confidence on the estimation of the number of targets can be provided as well. In this paper, we propose a first implementation of a PHD filter that also includes an estimation of localised variance in the target number following each update step; we then illustrate the advantage of the PHD filter + variance on simulated data from a multiple-target scenario.

  9. Changes in variance explained by top SNP windows over generations for three traits in broiler chicken

    PubMed Central

    Fragomeni, Breno de Oliveira; Misztal, Ignacy; Lourenco, Daniela Lino; Aguilar, Ignacio; Okimoto, Ronald; Muir, William M.

    2014-01-01

    The purpose of this study was to determine if the set of genomic regions inferred as accounting for the majority of genetic variation in quantitative traits remain stable over multiple generations of selection. The data set contained phenotypes for five generations of broiler chicken for body weight, breast meat, and leg score. The population consisted of 294,632 animals over five generations and also included genotypes of 41,036 single nucleotide polymorphism (SNP) for 4,866 animals, after quality control. The SNP effects were calculated by a GWAS type analysis using single step genomic BLUP approach for generations 1–3, 2–4, 3–5, and 1–5. Variances were calculated for windows of 20 SNP. The top ten windows for each trait that explained the largest fraction of the genetic variance across generations were examined. Across generations, the top 10 windows explained more than 0.5% but less than 1% of the total variance. Also, the pattern of the windows was not consistent across generations. The windows that explained the greatest variance changed greatly among the combinations of generations, with a few exceptions. In many cases, a window identified as top for one combination, explained less than 0.1% for the other combinations. We conclude that identification of top SNP windows for a population may have little predictive power for genetic selection in the following generations for the traits here evaluated. PMID:25324857

  10. Applications of non-parametric statistics and analysis of variance on sample variances

    NASA Technical Reports Server (NTRS)

    Myers, R. H.

    1981-01-01

    Nonparametric methods that are available for NASA-type applications are discussed. An attempt will be made here to survey what can be used, to attempt recommendations as to when each would be applicable, and to compare the methods, when possible, with the usual normal-theory procedures that are avavilable for the Gaussion analog. It is important here to point out the hypotheses that are being tested, the assumptions that are being made, and limitations of the nonparametric procedures. The appropriateness of doing analysis of variance on sample variances are also discussed and studied. This procedure is followed in several NASA simulation projects. On the surface this would appear to be reasonably sound procedure. However, difficulties involved center around the normality problem and the basic homogeneous variance assumption that is mase in usual analysis of variance problems. These difficulties discussed and guidelines given for using the methods.

  11. Analysis and application of minimum variance discrete time system identification

    NASA Technical Reports Server (NTRS)

    Kotob, S.; Kaufman, H.

    1976-01-01

    An on-line minimum variance parameter identifier was developed which embodies both accuracy and computational efficiency. The new formulation resulted in a linear estimation problem with both additive and multiplicative noise. The resulting filter is shown to utilize both the covariance of the parameter vector itself and the covariance of the error in identification. It is proven that the identification filter is mean square covergent and mean square consistent. The MV parameter identification scheme is then used to construct a stable state and parameter estimation algorithm.

  12. Analysis and application of minimum variance discrete linear system identification

    NASA Technical Reports Server (NTRS)

    Kotob, S.; Kaufman, H.

    1977-01-01

    An on-line minimum variance (MV) parameter identifier is developed which embodies both accuracy and computational efficiency. The formulation results in a linear estimation problem with both additive and multiplicative noise (AMN). The resulting filter which utilizes both the covariance of the parameter vector itself and the covariance of the error in identification is proven to be mean-square convergent and mean-square consistent. The MV parameter identification scheme is then used to construct a stable state and parameter estimation algorithm.

  13. Systems Engineering Programmatic Estimation Using Technology Variance

    NASA Technical Reports Server (NTRS)

    Mog, Robert A.

    2000-01-01

    Unique and innovative system programmatic estimation is conducted using the variance of the packaged technologies. Covariance analysis is performed on the subsystems and components comprising the system of interest. Technological "return" and "variation" parameters are estimated. These parameters are combined with the model error to arrive at a measure of system development stability. The resulting estimates provide valuable information concerning the potential cost growth of the system under development.

  14. Systems Engineering Programmatic Estimation Using Technology Variance

    NASA Technical Reports Server (NTRS)

    Mog, Robert A.

    2000-01-01

    Unique and innovative system programmatic estimation is conducted using the variance of the packaged technologies. Covariance analysis is performed oil the subsystems and components comprising the system of interest. Technological "returns" and "variation" parameters, are estimated. These parameters are combined with the model error to arrive at a measure of system development stability. The resulting estimates provide valuable information concerning the potential cost growth of the system under development.

  15. Analysis of variance based on fuzzy observations

    NASA Astrophysics Data System (ADS)

    Nourbakhsh, M.; Mashinchi, M.; Parchami, A.

    2013-04-01

    Analysis of variance (ANOVA) is an important method in exploratory and confirmatory data analysis. The simplest type of ANOVA is one-way ANOVA for comparison among means of several populations. In this article, we extend one-way ANOVA to a case where observed data are fuzzy observations rather than real numbers. Two real-data examples are given to show the performance of this method.

  16. The Theory of Variances in Equilibrium Reconstruction

    SciTech Connect

    Zakharov, Leonid E.; Lewandowski, Jerome; Foley, Elizabeth L.; Levinton, Fred M.; Yuh, Howard Y.; Drozdov, Vladimir; McDonald, Darren

    2008-01-14

    The theory of variances of equilibrium reconstruction is presented. It complements existing practices with information regarding what kind of plasma profiles can be reconstructed, how accurately, and what remains beyond the abilities of diagnostic systems. The σ-curves, introduced by the present theory, give a quantitative assessment of quality of effectiveness of diagnostic systems in constraining equilibrium reconstructions. The theory also suggests a method for aligning the accuracy of measurements of different physical nature.

  17. Minimum variance and variance of outgoing quality limit MDS-1(c1, c2) plans

    NASA Astrophysics Data System (ADS)

    Raju, C.; Vidya, R.

    2016-06-01

    In this article, the outgoing quality (OQ) and total inspection (TI) of multiple deferred state sampling plans MDS-1(c1,c2) are studied. It is assumed that the inspection is rejection rectification. Procedures for designing MDS-1(c1,c2) sampling plans with minimum variance of OQ and TI are developed. A procedure for obtaining a plan for a designated upper limit for the variance of the OQ (VOQL) is outlined.

  18. Hypothesis exploration with visualization of variance

    PubMed Central

    2014-01-01

    Background The Consortium for Neuropsychiatric Phenomics (CNP) at UCLA was an investigation into the biological bases of traits such as memory and response inhibition phenotypes—to explore whether they are linked to syndromes including ADHD, Bipolar disorder, and Schizophrenia. An aim of the consortium was in moving from traditional categorical approaches for psychiatric syndromes towards more quantitative approaches based on large-scale analysis of the space of human variation. It represented an application of phenomics—wide-scale, systematic study of phenotypes—to neuropsychiatry research. Results This paper reports on a system for exploration of hypotheses in data obtained from the LA2K, LA3C, and LA5C studies in CNP. ViVA is a system for exploratory data analysis using novel mathematical models and methods for visualization of variance. An example of these methods is called VISOVA, a combination of visualization and analysis of variance, with the flavor of exploration associated with ANOVA in biomedical hypothesis generation. It permits visual identification of phenotype profiles—patterns of values across phenotypes—that characterize groups. Visualization enables screening and refinement of hypotheses about variance structure of sets of phenotypes. Conclusions The ViVA system was designed for exploration of neuropsychiatric hypotheses by interdisciplinary teams. Automated visualization in ViVA supports ‘natural selection’ on a pool of hypotheses, and permits deeper understanding of the statistical architecture of the data. Large-scale perspective of this kind could lead to better neuropsychiatric diagnostics. PMID:25097666

  19. Directional variance analysis of annual rings

    NASA Astrophysics Data System (ADS)

    Kumpulainen, P.; Marjanen, K.

    2010-07-01

    The wood quality measurement methods are of increasing importance in the wood industry. The goal is to produce more high quality products with higher marketing value than is produced today. One of the key factors for increasing the market value is to provide better measurements for increased information to support the decisions made later in the product chain. Strength and stiffness are important properties of the wood. They are related to mean annual ring width and its deviation. These indicators can be estimated from images taken from the log ends by two-dimensional power spectrum analysis. The spectrum analysis has been used successfully for images of pine. However, the annual rings in birch, for example are less distinguishable and the basic spectrum analysis method does not give reliable results. A novel method for local log end variance analysis based on Radon-transform is proposed. The directions and the positions of the annual rings can be estimated from local minimum and maximum variance estimates. Applying the spectrum analysis on the maximum local variance estimate instead of the original image produces more reliable estimate of the annual ring width. The proposed method is not limited to log end analysis only. It is usable in other two-dimensional random signal and texture analysis tasks.

  20. Irreversible Langevin samplers and variance reduction: a large deviations approach

    NASA Astrophysics Data System (ADS)

    Rey-Bellet, Luc; Spiliopoulos, Konstantinos

    2015-07-01

    In order to sample from a given target distribution (often of Gibbs type), the Monte Carlo Markov chain method consists of constructing an ergodic Markov process whose invariant measure is the target distribution. By sampling the Markov process one can then compute, approximately, expectations of observables with respect to the target distribution. Often the Markov processes used in practice are time-reversible (i.e. they satisfy detailed balance), but our main goal here is to assess and quantify how the addition of a non-reversible part to the process can be used to improve the sampling properties. We focus on the diffusion setting (overdamped Langevin equations) where the drift consists of a gradient vector field as well as another drift which breaks the reversibility of the process but is chosen to preserve the Gibbs measure. In this paper we use the large deviation rate function for the empirical measure as a tool to analyze the speed of convergence to the invariant measure. We show that the addition of an irreversible drift leads to a larger rate function and it strictly improves the speed of convergence of ergodic average for (generic smooth) observables. We also deduce from this result that the asymptotic variance decreases under the addition of the irreversible drift and we give an explicit characterization of the observables whose variance is not reduced reduced, in terms of a nonlinear Poisson equation. Our theoretical results are illustrated and supplemented by numerical simulations.

  1. Integrating Nonadditive Genomic Relationship Matrices into the Study of Genetic Architecture of Complex Traits.

    PubMed

    Nazarian, Alireza; Gezan, Salvador A

    2016-03-01

    The study of genetic architecture of complex traits has been dramatically influenced by implementing genome-wide analytical approaches during recent years. Of particular interest are genomic prediction strategies which make use of genomic information for predicting phenotypic responses instead of detecting trait-associated loci. In this work, we present the results of a simulation study to improve our understanding of the statistical properties of estimation of genetic variance components of complex traits, and of additive, dominance, and genetic effects through best linear unbiased prediction methodology. Simulated dense marker information was used to construct genomic additive and dominance matrices, and multiple alternative pedigree- and marker-based models were compared to determine if including a dominance term into the analysis may improve the genetic analysis of complex traits. Our results showed that a model containing a pedigree- or marker-based additive relationship matrix along with a pedigree-based dominance matrix provided the best partitioning of genetic variance into its components, especially when some degree of true dominance effects was expected to exist. Also, we noted that the use of a marker-based additive relationship matrix along with a pedigree-based dominance matrix had the best performance in terms of accuracy of correlations between true and estimated additive, dominance, and genetic effects. PMID:26712858

  2. Estimation of Noise-Free Variance to Measure Heterogeneity

    PubMed Central

    Winkler, Tilo; Melo, Marcos F. Vidal; Degani-Costa, Luiza H.; Harris, R. Scott; Correia, John A.; Musch, Guido; Venegas, Jose G.

    2015-01-01

    Variance is a statistical parameter used to characterize heterogeneity or variability in data sets. However, measurements commonly include noise, as random errors superimposed to the actual value, which may substantially increase the variance compared to a noise-free data set. Our aim was to develop and validate a method to estimate noise-free spatial heterogeneity of pulmonary perfusion using dynamic positron emission tomography (PET) scans. On theoretical grounds, we demonstrate a linear relationship between the total variance of a data set derived from averages of n multiple measurements, and the reciprocal of n. Using multiple measurements with varying n yields estimates of the linear relationship including the noise-free variance as the constant parameter. In PET images, n is proportional to the number of registered decay events, and the variance of the image is typically normalized by the square of its mean value yielding a coefficient of variation squared (CV2). The method was evaluated with a Jaszczak phantom as reference spatial heterogeneity (CVr2) for comparison with our estimate of noise-free or ‘true’ heterogeneity (CVt2). We found that CVt2 was only 5.4% higher than CVr2. Additional evaluations were conducted on 38 PET scans of pulmonary perfusion using 13NN-saline injection. The mean CVt2 was 0.10 (range: 0.03–0.30), while the mean CV2 including noise was 0.24 (range: 0.10–0.59). CVt2 was in average 41.5% of the CV2 measured including noise (range: 17.8–71.2%). The reproducibility of CVt2 was evaluated using three repeated PET scans from five subjects. Individual CVt2 were within 16% of each subject's mean and paired t-tests revealed no difference among the results from the three consecutive PET scans. In conclusion, our method provides reliable noise-free estimates of CVt2 in PET scans, and may be useful for similar statistical problems in experimental data. PMID:25906374

  3. A proxy for variance in dense matching over homogeneous terrain

    NASA Astrophysics Data System (ADS)

    Altena, Bas; Cockx, Liesbet; Goedemé, Toon

    2014-05-01

    variance in intensity, the topography was reconstructed entirely. This indicates that to a large extent interpolation was applied. To assess this amount of interpolation processing is done with imagery which is gradually downgraded. Through linking these products with the variance indicator (SNR) this results in a quantitative relation of the interpolation influence onto the topography estimation in respect to contrast. Our proposed method is capable of providing a clear indication of variance in reconstructions from UAV photogrammetry. This indicator has a practical advantage, as it can be implemented before the computational intensive matching phase. As such an acquired dataset can be tested in the field. If an area with too little contrast is identified, camera settings can be adjusted for a new flight, or additional measurements can be done through traditional means.

  4. Evolutionary genetics of maternal effects

    PubMed Central

    Wolf, Jason B.; Wade, Michael J.

    2016-01-01

    Maternal genetic effects (MGEs), where genes expressed by mothers affect the phenotype of their offspring, are important sources of phenotypic diversity in a myriad of organisms. We use a single‐locus model to examine how MGEs contribute patterns of heritable and nonheritable variation and influence evolutionary dynamics in randomly mating and inbreeding populations. We elucidate the influence of MGEs by examining the offspring genotype‐phenotype relationship, which determines how MGEs affect evolutionary dynamics in response to selection on offspring phenotypes. This approach reveals important results that are not apparent from classic quantitative genetic treatments of MGEs. We show that additive and dominance MGEs make different contributions to evolutionary dynamics and patterns of variation, which are differentially affected by inbreeding. Dominance MGEs make the offspring genotype‐phenotype relationship frequency dependent, resulting in the appearance of negative frequency‐dependent selection, while additive MGEs contribute a component of parent‐of‐origin dependent variation. Inbreeding amplifies the contribution of MGEs to the additive genetic variance and, therefore enhances their evolutionary response. Considering evolutionary dynamics of allele frequency change on an adaptive landscape, we show that this landscape differs from the mean fitness surface, and therefore, under some condition, fitness peaks can exist but not be “available” to the evolving population. PMID:26969266

  5. Evolutionary genetics of maternal effects.

    PubMed

    Wolf, Jason B; Wade, Michael J

    2016-04-01

    Maternal genetic effects (MGEs), where genes expressed by mothers affect the phenotype of their offspring, are important sources of phenotypic diversity in a myriad of organisms. We use a single-locus model to examine how MGEs contribute patterns of heritable and nonheritable variation and influence evolutionary dynamics in randomly mating and inbreeding populations. We elucidate the influence of MGEs by examining the offspring genotype-phenotype relationship, which determines how MGEs affect evolutionary dynamics in response to selection on offspring phenotypes. This approach reveals important results that are not apparent from classic quantitative genetic treatments of MGEs. We show that additive and dominance MGEs make different contributions to evolutionary dynamics and patterns of variation, which are differentially affected by inbreeding. Dominance MGEs make the offspring genotype-phenotype relationship frequency dependent, resulting in the appearance of negative frequency-dependent selection, while additive MGEs contribute a component of parent-of-origin dependent variation. Inbreeding amplifies the contribution of MGEs to the additive genetic variance and, therefore enhances their evolutionary response. Considering evolutionary dynamics of allele frequency change on an adaptive landscape, we show that this landscape differs from the mean fitness surface, and therefore, under some condition, fitness peaks can exist but not be "available" to the evolving population. PMID:26969266

  6. FMRI group analysis combining effect estimates and their variances.

    PubMed

    Chen, Gang; Saad, Ziad S; Nath, Audrey R; Beauchamp, Michael S; Cox, Robert W

    2012-03-01

    Conventional functional magnetic resonance imaging (FMRI) group analysis makes two key assumptions that are not always justified. First, the data from each subject is condensed into a single number per voxel, under the assumption that within-subject variance for the effect of interest is the same across all subjects or is negligible relative to the cross-subject variance. Second, it is assumed that all data values are drawn from the same Gaussian distribution with no outliers. We propose an approach that does not make such strong assumptions, and present a computationally efficient frequentist approach to FMRI group analysis, which we term mixed-effects multilevel analysis (MEMA), that incorporates both the variability across subjects and the precision estimate of each effect of interest from individual subject analyses. On average, the more accurate tests result in higher statistical power, especially when conventional variance assumptions do not hold, or in the presence of outliers. In addition, various heterogeneity measures are available with MEMA that may assist the investigator in further improving the modeling. Our method allows group effect t-tests and comparisons among conditions and among groups. In addition, it has the capability to incorporate subject-specific covariates such as age, IQ, or behavioral data. Simulations were performed to illustrate power comparisons and the capability of controlling type I errors among various significance testing methods, and the results indicated that the testing statistic we adopted struck a good balance between power gain and type I error control. Our approach is instantiated in an open-source, freely distributed program that may be used on any dataset stored in the universal neuroimaging file transfer (NIfTI) format. To date, the main impediment for more accurate testing that incorporates both within- and cross-subject variability has been the high computational cost. Our efficient implementation makes this approach

  7. Heritability and genetic correlations of personality traits in a wild population of yellow-bellied marmots (Marmota flaviventris).

    PubMed

    Petelle, M B; Martin, J G A; Blumstein, D T

    2015-10-01

    Describing and quantifying animal personality is now an integral part of behavioural studies because individually distinctive behaviours have ecological and evolutionary consequences. Yet, to fully understand how personality traits may respond to selection, one must understand the underlying heritability and genetic correlations between traits. Previous studies have reported a moderate degree of heritability of personality traits, but few of these studies have either been conducted in the wild or estimated the genetic correlations between personality traits. Estimating the additive genetic variance and covariance in the wild is crucial to understand the evolutionary potential of behavioural traits. Enhanced environmental variation could reduce heritability and genetic correlations, thus leading to different evolutionary predictions. We estimated the additive genetic variance and covariance of docility in the trap, sociability (mirror image stimulation), and exploration and activity in two different contexts (open-field and mirror image simulation experiments) in a wild population of yellow-bellied marmots (Marmota flaviventris). We estimated both heritability of behaviours and of personality traits and found nonzero additive genetic variance in these traits. We also found nonzero maternal, permanent environment and year effects. Finally, we found four phenotypic correlations between traits, and one positive genetic correlation between activity in the open-field test and sociability. We also found permanent environment correlations between activity in both tests and docility and exploration in the MIS test. This is one of a handful of studies to adopt a quantitative genetic approach to explain variation in personality traits in the wild and, thus, provides important insights into the potential variance available for selection. PMID:26214760

  8. Genetic variation in personality traits explains genetic overlap between borderline personality features and substance use disorders

    PubMed Central

    Few, Lauren R.; Grant, Julia D; Trull, Timothy J.; Statham, Dixie J.; Martin, Nicholas G.; Lynskey, Michael T.; Agrawal, Arpana

    2014-01-01

    Aims To examine the genetic overlap between borderline personality features (BPF) and substance use disorders (SUDs) and the extent to which variation in personality traits contributes to this covariance. Design Genetic structural equation modelling was used to partition the variance in and covariance between personality traits, BPF, and SUDs into additive genetic, shared, and individual-specific environmental factors. Setting All participants were registered with the Australian Twin Registry. Participants A total of 3,127 Australian adult twins participated in the study. Measurements Diagnoses of DSM-IV alcohol and cannabis abuse/dependence (AAD; CAD), and nicotine dependence (ND) were derived via computer-assisted telephone interview. BPF and five-factor model personality traits were derived via self-report questionnaires. Findings Genetic factors were responsible for 49% (95%CI: 42%–55%) of the variance in BPF, 38–42% (95%CI range: 32%–49%) for personality traits and 47% (95%CI: 17%–77%), 54% (95%CI: 43%–64%), and 78% (67%–86%) for ND, AAD and CAD, respectively. Genetic and individual-specific environmental correlations between BPF and SUDs ranged from .33–.56 (95%CI range: .19–.74) and .19–.32 (95%CI range: .06–.43), respectively. Overall, there was substantial support for genetic influences that were specific to AAD, ND and CAD (31%–69%). Finally, genetic variation in personality traits was responsible for 11% (Extraversion for CAD) to 59% (Neuroticism for AAD) of the correlation between BPF and SUDs. Conclusions Both genetic and individual-specific environmental factors contribute to comorbidity between borderline personality features and substance use disorders. A substantial proportion of this comorbidity can be attributed to variation in normal personality traits, particularly Neuroticism. PMID:25041562

  9. Genome-wide analysis of BMI in adolescents and young adults reveals additional insight into the effects of genetic loci over the life course

    PubMed Central

    Graff, Mariaelisa; Ngwa, Julius S.; Workalemahu, Tsegaselassie; Homuth, Georg; Schipf, Sabine; Teumer, Alexander; Völzke, Henry; Wallaschofski, Henri; Abecasis, Goncalo R.; Edward, Lakatta; Francesco, Cucca; Sanna, Serena; Scheet, Paul; Schlessinger, David; Sidore, Carlo; Xiao, Xiangjun; Wang, Zhaoming; Chanock, Stephen J.; Jacobs, Kevin B.; Hayes, Richard B.; Hu, Frank; Van Dam, Rob M.; Crout, Richard J.; Marazita, Mary L.; Shaffer, John R; Atwood, Larry D.; Fox, Caroline S.; Heard-Costa, Nancy L.; White, Charles; Choh, Audrey C.; Czerwinski, Stefan A.; Demerath, Ellen W.; Dyer, Thomas D.; Towne, Bradford; Amin, Najaf; Oostra, Ben A.; Van Duijn, Cornelia M.; Zillikens, M. Carola; Esko, Tõnu; Nelis, Mari; Nikopensius, Tit; Metspalu, Andres; Strachan, David P.; Monda, Keri; Qi, Lu; North, Kari E.; Cupples, L. Adrienne; Gordon-Larsen, Penny; Berndt, Sonja I.

    2013-01-01

    Genetic loci for body mass index (BMI) in adolescence and young adulthood, a period of high risk for weight gain, are understudied, yet may yield important insight into the etiology of obesity and early intervention. To identify novel genetic loci and examine the influence of known loci on BMI during this critical time period in late adolescence and early adulthood, we performed a two-stage meta-analysis using 14 genome-wide association studies in populations of European ancestry with data on BMI between ages 16 and 25 in up to 29 880 individuals. We identified seven independent loci (P < 5.0 × 10−8) near FTO (P = 3.72 × 10−23), TMEM18 (P = 3.24 × 10−17), MC4R (P = 4.41 × 10−17), TNNI3K (P = 4.32 × 10−11), SEC16B (P = 6.24 × 10−9), GNPDA2 (P = 1.11 × 10−8) and POMC (P = 4.94 × 10−8) as well as a potential secondary signal at the POMC locus (rs2118404, P = 2.4 × 10−5 after conditioning on the established single-nucleotide polymorphism at this locus) in adolescents and young adults. To evaluate the impact of the established genetic loci on BMI at these young ages, we examined differences between the effect sizes of 32 published BMI loci in European adult populations (aged 18–90) and those observed in our adolescent and young adult meta-analysis. Four loci (near PRKD1, TNNI3K, SEC16B and CADM2) had larger effects and one locus (near SH2B1) had a smaller effect on BMI during adolescence and young adulthood compared with older adults (P < 0.05). These results suggest that genetic loci for BMI can vary in their effects across the life course, underlying the importance of evaluating BMI at different ages. PMID:23669352

  10. [Relation between variance and the arithmetic mean in frequency distributions under conditions of stochastic dependence].

    PubMed

    Mitolo, V; Saccia, M

    1984-06-30

    While the average value of the mitotic index in a primordium is determined by genetic and epigenetic factors, the spatial location of the single mitotic events is stochastic; consequently mitotic density is uneven even in homogeneous areas of the primordium. The statistical frequency distribution of the mitotic events has been studied under three different conditions: (a) no stochastic dependence between adjoining events (random distribution); (b) positive stochastic dependence (facilitation) between adjoining events; (c) negative stochastic dependence (inhibition) between adjoining events. It is concluded that in the first case the variance of the distribution equals the arithmetic mean; in the second case the variance is higher than mean; in the third case variance is lower than mean. PMID:6477729

  11. Evidence for parent-of-origin effects on genetic variability of beef traits.

    PubMed

    Neugebauer, N; Räder, I; Schild, H J; Zimmer, D; Reinsch, N

    2010-02-01

    Imprinted genes are involved in many aspects of development in mammals, plants, and perhaps birds and may play a role in growth and carcass composition of slaughter animals. In the presence of genomic imprinting the expression and, consequently, the effect on the phenotype of maternal and paternal alleles are different. For genetic evaluation genomic imprinting can be accounted for by incorporating 2 additive genetic effects per animal; the first corresponds to a paternal and the second to a maternal expression pattern of imprinted genes. This model holds whatever the mode of imprinting may be: paternal or maternal, full or partial, or any combination thereof. A set of slaughter data from 65,233 German Simmental fattening bulls was analyzed with respect to the relative importance of the genetic imprinting variance. Besides slaughter weight, net daily BW gain, and killing out percentage, there were 22 other traits describing the carcass composition. The latter traits were evaluated by automatic video-imaging devices and were composed of weights of valuable cuts as well as fat and meatiness grade. The number of ancestors in the pedigree was 356,880. Genomic imprinting significantly contributed to the genetic variance of 10 traits, with estimated proportions between 8 and 25% of the total additive genetic variance. For 6 of these traits, the maternal contribution to the imprinting variance was larger than the paternal, whereas for all other traits the reverse was true. Fat grade only showed a paternal contribution to the imprinting variance. Estimates of animal model heritabilities of automatic video-imaging-recorded carcass traits ranged between 20 and 30%. PMID:19854988

  12. Visual SLAM Using Variance Grid Maps

    NASA Technical Reports Server (NTRS)

    Howard, Andrew B.; Marks, Tim K.

    2011-01-01

    An algorithm denoted Gamma-SLAM performs further processing, in real time, of preprocessed digitized images acquired by a stereoscopic pair of electronic cameras aboard an off-road robotic ground vehicle to build accurate maps of the terrain and determine the location of the vehicle with respect to the maps. Part of the name of the algorithm reflects the fact that the process of building the maps and determining the location with respect to them is denoted simultaneous localization and mapping (SLAM). Most prior real-time SLAM algorithms have been limited in applicability to (1) systems equipped with scanning laser range finders as the primary sensors in (2) indoor environments (or relatively simply structured outdoor environments). The few prior vision-based SLAM algorithms have been feature-based and not suitable for real-time applications and, hence, not suitable for autonomous navigation on irregularly structured terrain. The Gamma-SLAM algorithm incorporates two key innovations: Visual odometry (in contradistinction to wheel odometry) is used to estimate the motion of the vehicle. An elevation variance map (in contradistinction to an occupancy or an elevation map) is used to represent the terrain. The Gamma-SLAM algorithm makes use of a Rao-Blackwellized particle filter (RBPF) from Bayesian estimation theory for maintaining a distribution over poses and maps. The core idea of the RBPF approach is that the SLAM problem can be factored into two parts: (1) finding the distribution over robot trajectories, and (2) finding the map conditioned on any given trajectory. The factorization involves the use of a particle filter in which each particle encodes both a possible trajectory and a map conditioned on that trajectory. The base estimate of the trajectory is derived from visual odometry, and the map conditioned on that trajectory is a Cartesian grid of elevation variances. In comparison with traditional occupancy or elevation grid maps, the grid elevation variance

  13. Combined genetic analysis of partial blast resistance in an upland rice population and recurrent selection for line and hybrid values.

    PubMed

    Veillet, S; Filippi, M C; Gallais, A

    1996-05-01

    The CNA-IRAT 5 upland rice population has been improved for 4 years by recurrent selection for blast resistance in Brazil. In order to predict the efficiency of recurrent selection in different test systems and to compare the relative advantage of hybrids versus pure line breeding, a combined genetic analysis of partial blast resistance in the CNA-IRAT 5 population was undertaken. A three-level hierarchical design in inbreeding and a factorial design were derived from the base population. Partial blast resistance of lines and hybrids was evaluated in the greenhouse and in the field by inoculation with one virulent blast isolate. The means and genetic variances of the hybrids and lines were estimated. Genetic advance by recurrent selection was predicted from estimates of variance components. The inheritance of partial blast resistance was mainly additive but non-additive effects were detected at both levels of means and variances. Mean heterosis ranged from 4%-8% for lesion size and lesion density to 10-12% for leaf and panicle resistance. High dominance or homozygous dominance variances relative to additive variance and negative covariance between additive and homozygous dominance effects were estimated. A low frequency of favourable alleles for partial resistance would explain the observed organisation of genetic variability in the base population. Recurrent selection will efficiently improve partial blast resistance of the CNA-IRAT 5 population. Genetic advance for line or hybrid values was expected to be higher testing doubled haploid lines than S1 lines, or than general combining ability. Two components of partial resistance assessed in the greenhouse, lesion size and lesion density, could be used as indirect selection criteria to improve field resistance. On the whole, hybrid breeding for partial blast resistance appeared to be slightly more advantageous than pure line breeding. PMID:24166386

  14. Probability of the residual wavefront variance of an adaptive optics system and its application.

    PubMed

    Huang, Jian; Liu, Chao; Deng, Ke; Yao, Zhousi; Xian, Hao; Li, Xinyang

    2016-02-01

    For performance evaluation of an adaptive optics (AO) system, the probability of the system residual wavefront variance can provide more information than the wavefront variance average. By studying the Zernike coefficients of an AO system residual wavefront, we derived the exact expressions for the probability density functions of the wavefront variance and the Strehl ratio, for instantaneous and long-term exposures owing to the insufficient control loop bandwidth of the AO system. Our calculations agree with the residual wavefront data of a closed loop AO system. Using these functions, we investigated the relationship between the AO system bandwidth and the distribution of the residual wavefront variance. Additionally, we analyzed the availability of an AO system for evaluating the AO performance. These results will assist in designing and probabilistic analysis of AO systems. PMID:26906850

  15. An Empirical Temperature Variance Source Model in Heated Jets

    NASA Technical Reports Server (NTRS)

    Khavaran, Abbas; Bridges, James

    2012-01-01

    An acoustic analogy approach is implemented that models the sources of jet noise in heated jets. The equivalent sources of turbulent mixing noise are recognized as the differences between the fluctuating and Favre-averaged Reynolds stresses and enthalpy fluxes. While in a conventional acoustic analogy only Reynolds stress components are scrutinized for their noise generation properties, it is now accepted that a comprehensive source model should include the additional entropy source term. Following Goldstein s generalized acoustic analogy, the set of Euler equations are divided into two sets of equations that govern a non-radiating base flow plus its residual components. When the base flow is considered as a locally parallel mean flow, the residual equations may be rearranged to form an inhomogeneous third-order wave equation. A general solution is written subsequently using a Green s function method while all non-linear terms are treated as the equivalent sources of aerodynamic sound and are modeled accordingly. In a previous study, a specialized Reynolds-averaged Navier-Stokes (RANS) solver was implemented to compute the variance of thermal fluctuations that determine the enthalpy flux source strength. The main objective here is to present an empirical model capable of providing a reasonable estimate of the stagnation temperature variance in a jet. Such a model is parameterized as a function of the mean stagnation temperature gradient in the jet, and is evaluated using commonly available RANS solvers. The ensuing thermal source distribution is compared with measurements as well as computational result from a dedicated RANS solver that employs an enthalpy variance and dissipation rate model. Turbulent mixing noise predictions are presented for a wide range of jet temperature ratios from 1.0 to 3.20.

  16. Genetic and environmental influences on antisocial behavior: a meta-analysis of twin and adoption studies.

    PubMed

    Rhee, Soo Hyun; Waldman, Irwin D

    2002-05-01

    A meta-analysis of 51 twin and adoption studies was conducted to estimate the magnitude of genetic and environmental influences on antisocial behavior. The best fitting model included moderate proportions of variance due to additive genetic influences (.32), nonadditive genetic influences (.09), shared environmental influences (.16), and nonshared environmental influences (.43). The magnitude of familial influences (i.e., both genetic and shared environmental influences) was lower in parent-offspring adoption studies than in both twin studies and sibling adoption studies. Operationalization, assessment method, zygosity determination method, and age were significant moderators of the magnitude of genetic and environmental influences on antisocial behavior, but there were no significant differences in the magnitude of genetic and environmental influences for males and females. PMID:12002699

  17. Estimators for variance components in structured stair nesting models

    NASA Astrophysics Data System (ADS)

    Monteiro, Sandra; Fonseca, Miguel; Carvalho, Francisco

    2016-06-01

    The purpose of this paper is to present the estimation of the components of variance in structured stair nesting models. The relationship between the canonical variance components and the original ones, will be very important in obtaining that estimators.

  18. Genetic Influences on the Development of Grip Strength in Adolescence

    PubMed Central

    Isen, Joshua; McGue, Matt; Iacono, William

    2014-01-01

    Enhanced physical strength is a secondary sex characteristic in males. Sexual dimorphism in physical strength far exceeds sex differences in stature or total body mass, suggesting a legacy of intense sexual selection. Upper-body strength is a particularly promising marker of intra-sexual competitiveness in young men. Consequently, it is assumed that sex-influenced gene expression contributes to the development of physical strength. It is unclear, however, whether the underlying sources of individual differences in strength development are comparable across sex. We obtained three measurements of hand-grip strength (HGS) over a six-year period spanning adolescence in male and female same-sex twins (N= 2,513). Biometrical latent growth models were used to partition the HGS variance at age 11 (intercept) and its growth over time (slope) into genetic and environmental components. Results demonstrated that variance around the intercept was highly heritable in both males and females (88% and 79%, respectively). In males, variance around the slope exceeded that of the intercept, while the reverse held for females. Additive genetic effects accounted for most (80%) of the variance around the slope in males, but were of less importance in females (heritability = 28%). Absolute genetic variance around the slope was nearly nine-fold higher in males. This striking disparity suggests that the developmental processes shaping HGS growth are different between the sexes. We propose that this might account for the sex-specific pattern of associations between HGS and external measures (e.g., digit ratio and physical aggression) typically reported in the literature. Our results underscore the role of endogenous androgenic influences in the development of physical strength. PMID:24936605

  19. Quantitative genetic analysis of injury liability in infants and toddlers

    SciTech Connect

    Phillips, K.; Matheny, A.P. Jr.

    1995-02-27

    A threshold model of latent liability was applied to infant and toddler twin data on total count of injuries sustained during the interval from birth to 36 months of age. A quantitative genetic analysis of estimated twin correlations in injury liability indicated strong genetic dominance effects, but no additive genetic variance was detected. Because interpretations involving overdominance have little research support, the results may be due to low order epistasis or other interaction effects. Boys had more injuries than girls, but this effect was found only for groups whose parents were prompted and questioned in detail about their children`s injuries. Activity and impulsivity are two behavioral predictors of childhood injury, and the results are discussed in relation to animal research on infant and adult activity levels, and impulsivity in adult humans. Genetic epidemiological approaches to childhood injury should aid in targeting higher risk children for preventive intervention. 30 refs., 4 figs., 3 tabs.

  20. Progress in genetic association studies of plasma lipids

    PubMed Central

    Asselbergs, Folkert W.; Lovering, Ruth C.; Drenos, Fotios

    2013-01-01

    Purpose of review This review summarizes recently published large-scale efforts elucidating the genetic architecture of lipid levels. A supplemental file with all genetic loci is provided for research purposes and we performed bioinformatic analyses of the genetic variants to give an oversight of involved pathways. Recent findings In total, 52 genes for HDL cholesterol, 42 genes for LDL cholesterol, 59 genes for total cholesterol, and 39 genes for triglycerides have been identified. Genetic overlap is present between the different traits and similar pathways are involved. Most of the SNPs that were detected in the European studies could be replicated in other ethnicities and these SNPs show the same direction of effect suggesting that the underlying genetic architecture of blood lipids is similar between ethnicities. Summary Genetic studies have identified many loci associated with plasma lipids and have provided insight into the underlying mechanisms of lipid homeostasis. Future research is needed to determine whether these loci may be novel targets for lipid-lowering therapy and for reducing cardiovascular disease risk. In addition, the proportion of genetic variance explained by these lipid loci is still limited and new large-scale genetic studies are ongoing to identify additional common and rare variants associated with lipid levels. PMID:23385652

  1. Estimation of Genetic Parameters for First Lactation Monthly Test-day Milk Yields using Random Regression Test Day Model in Karan Fries Cattle.

    PubMed

    Singh, Ajay; Singh, Avtar; Singh, Manvendra; Prakash, Ved; Ambhore, G S; Sahoo, S K; Dash, Soumya

    2016-06-01

    A single trait linear mixed random regression test-day model was applied for the first time for analyzing the first lactation monthly test-day milk yield records in Karan Fries cattle. The test-day milk yield data was modeled using a random regression model (RRM) considering different order of Legendre polynomial for the additive genetic effect (4th order) and the permanent environmental effect (5th order). Data pertaining to 1,583 lactation records spread over a period of 30 years were recorded and analyzed in the study. The variance component, heritability and genetic correlations among test-day milk yields were estimated using RRM. RRM heritability estimates of test-day milk yield varied from 0.11 to 0.22 in different test-day records. The estimates of genetic correlations between different test-day milk yields ranged 0.01 (test-day 1 [TD-1] and TD-11) to 0.99 (TD-4 and TD-5). The magnitudes of genetic correlations between test-day milk yields decreased as the interval between test-days increased and adjacent test-day had higher correlations. Additive genetic and permanent environment variances were higher for test-day milk yields at both ends of lactation. The residual variance was observed to be lower than the permanent environment variance for all the test-day milk yields. PMID:26954137

  2. Estimation of Genetic Parameters for First Lactation Monthly Test-day Milk Yields using Random Regression Test Day Model in Karan Fries Cattle

    PubMed Central

    Singh, Ajay; Singh, Avtar; Singh, Manvendra; Prakash, Ved; Ambhore, G. S.; Sahoo, S. K.; Dash, Soumya

    2016-01-01

    A single trait linear mixed random regression test-day model was applied for the first time for analyzing the first lactation monthly test-day milk yield records in Karan Fries cattle. The test-day milk yield data was modeled using a random regression model (RRM) considering different order of Legendre polynomial for the additive genetic effect (4th order) and the permanent environmental effect (5th order). Data pertaining to 1,583 lactation records spread over a period of 30 years were recorded and analyzed in the study. The variance component, heritability and genetic correlations among test-day milk yields were estimated using RRM. RRM heritability estimates of test-day milk yield varied from 0.11 to 0.22 in different test-day records. The estimates of genetic correlations between different test-day milk yields ranged 0.01 (test-day 1 [TD-1] and TD-11) to 0.99 (TD-4 and TD-5). The magnitudes of genetic correlations between test-day milk yields decreased as the interval between test-days increased and adjacent test-day had higher correlations. Additive genetic and permanent environment variances were higher for test-day milk yields at both ends of lactation. The residual variance was observed to be lower than the permanent environment variance for all the test-day milk yields. PMID:26954137

  3. 40 CFR 124.62 - Decision on variances.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 21 2010-07-01 2010-07-01 false Decision on variances. 124.62 Section... FOR DECISIONMAKING Specific Procedures Applicable to NPDES Permits § 124.62 Decision on variances... following variances (subject to EPA objection under § 123.44 for State permits): (1) Extensions under...

  4. 40 CFR 59.509 - Can I get a variance?

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 5 2010-07-01 2010-07-01 false Can I get a variance? 59.509 Section 59... Volatile Organic Compound Emission Standards for Aerosol Coatings § 59.509 Can I get a variance? (a) Any... its reasonable control may apply in writing to the Administrator for a temporary variance....

  5. 36 CFR 27.4 - Variances and exceptions.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 36 Parks, Forests, and Public Property 1 2010-07-01 2010-07-01 false Variances and exceptions. 27... CAPE COD NATIONAL SEASHORE; ZONING STANDARDS § 27.4 Variances and exceptions. (a) Zoning bylaws may provide for variances and exceptions. (b) Bylaws adopted pursuant to these standards shall...

  6. 20 CFR 901.40 - Proof; variance; amendment of pleadings.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 20 Employees' Benefits 3 2010-04-01 2010-04-01 false Proof; variance; amendment of pleadings. 901... Suspension or Termination of Enrollment § 901.40 Proof; variance; amendment of pleadings. In the case of a variance between the allegations in a pleading and the evidence adduced in support of the pleading,...

  7. 31 CFR 10.67 - Proof; variance; amendment of pleadings.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 31 Money and Finance: Treasury 1 2010-07-01 2010-07-01 false Proof; variance; amendment of... BEFORE THE INTERNAL REVENUE SERVICE Rules Applicable to Disciplinary Proceedings § 10.67 Proof; variance; amendment of pleadings. In the case of a variance between the allegations in pleadings and the...

  8. 7 CFR 718.105 - Tolerances, variances, and adjustments.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 7 2010-01-01 2010-01-01 false Tolerances, variances, and adjustments. 718.105... APPLICABLE TO MULTIPLE PROGRAMS Determination of Acreage and Compliance § 718.105 Tolerances, variances, and... marketing quota crop allotment. (d) An administrative variance is applicable to all allotment crop...

  9. 40 CFR 52.1390 - Missoula variance provision.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 4 2010-07-01 2010-07-01 false Missoula variance provision. 52.1390... (CONTINUED) APPROVAL AND PROMULGATION OF IMPLEMENTATION PLANS (CONTINUED) Montana § 52.1390 Missoula variance provision. The Missoula City-County Air Pollution Control Program's Chapter X, Variances, which was...

  10. 29 CFR 1905.5 - Effect of variances.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 29 Labor 5 2010-07-01 2010-07-01 false Effect of variances. 1905.5 Section 1905.5 Labor... RULES OF PRACTICE FOR VARIANCES, LIMITATIONS, VARIATIONS, TOLERANCES, AND EXEMPTIONS UNDER THE WILLIAMS-STEIGER OCCUPATIONAL SAFETY AND HEALTH ACT OF 1970 General § 1905.5 Effect of variances. All...

  11. 40 CFR 190.11 - Variances for unusual operations.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 24 2010-07-01 2010-07-01 false Variances for unusual operations. 190... Standards for the Uranium Fuel Cycle § 190.11 Variances for unusual operations. The standards specified in § 190.10 may be exceeded if: (a) The regulatory agency has granted a variance based upon...

  12. 40 CFR 124.64 - Appeals of variances.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 21 2010-07-01 2010-07-01 false Appeals of variances. 124.64 Section... FOR DECISIONMAKING Specific Procedures Applicable to NPDES Permits § 124.64 Appeals of variances. (a) When a State issues a permit on which EPA has made a variance decision, separate appeals of the...

  13. 31 CFR 8.59 - Proof; variance; amendment of pleadings.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 31 Money and Finance: Treasury 1 2010-07-01 2010-07-01 false Proof; variance; amendment of... BEFORE THE BUREAU OF ALCOHOL, TOBACCO AND FIREARMS Disciplinary Proceedings § 8.59 Proof; variance; amendment of pleadings. In the case of a variance between the allegations in a pleading, the...

  14. 36 CFR 30.5 - Variances, exceptions, and use permits.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 36 Parks, Forests, and Public Property 1 2010-07-01 2010-07-01 false Variances, exceptions, and... UNIT § 30.5 Variances, exceptions, and use permits. (a) Zoning ordinances or amendments thereto, for... Recreation Area may provide for the granting of variances and exceptions. (b) Zoning ordinances or...

  15. 40 CFR 141.4 - Variances and exemptions.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 23 2014-07-01 2014-07-01 false Variances and exemptions. 141.4 Section 141.4 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) WATER PROGRAMS (CONTINUED) NATIONAL PRIMARY DRINKING WATER REGULATIONS General § 141.4 Variances and exemptions. (a) Variances or exemptions from certain provisions...

  16. 29 CFR 1905.5 - Effect of variances.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 29 Labor 5 2014-07-01 2014-07-01 false Effect of variances. 1905.5 Section 1905.5 Labor...-STEIGER OCCUPATIONAL SAFETY AND HEALTH ACT OF 1970 General § 1905.5 Effect of variances. All variances granted pursuant to this part shall have only future effect. In his discretion, the Assistant...

  17. Psychopathic personality traits in middle-aged male twins: a behavior genetic investigation.

    PubMed

    Brook, Michael; Panizzon, Matthew S; Kosson, David S; Sullivan, Elizabeth A; Lyons, Michael J; Franz, Carol E; Eisen, Seth A; Kremen, William S

    2010-08-01

    Psychopathic personality is characterized by interpersonal dominance, impulsivity, sensation seeking, poor planning, and aggressiveness. Studies have shown that the Multidimensional Personality Questionnaire (MPQ) can be used to estimate scores on the fearless-dominant (FD) and the impulsive-antisocial (IA) dimensions of the Psychopathic Personality Inventory (PPI), the best validated self-report measure of psychopathic personality traits. Prior behavior genetic studies reported roughly equal genetic and nonshared environmental influences for both FD and IA, which remained stable from adolescence to young adulthood. However, no prior studies address genetic and environmental influences on these dimensions beyond early adulthood. We utilized the classic twin method to examine genetic and environmental influences on variance in FD and IA in a sample of middle-aged male twins. Biometric modeling indicated that the variance in both factors is best explained by additive genetic and nonshared environmental influences. FD showed roughly equal contributions from genetic and environmental factors, whereas IA showed greater contributions from environmental than genetic factors. Additionally, the small phenotypic correlation between FD and IA was explained entirely by nonshared environmental factors. PMID:20695807

  18. Recognition by variance: learning rules for spatiotemporal patterns.

    PubMed

    Barak, Omri; Tsodyks, Misha

    2006-10-01

    Recognizing specific spatiotemporal patterns of activity, which take place at timescales much larger than the synaptic transmission and membrane time constants, is a demand from the nervous system exemplified, for instance, by auditory processing. We consider the total synaptic input that a single readout neuron receives on presentation of spatiotemporal spiking input patterns. Relying on the monotonic relation between the mean and the variance of a neuron's input current and its spiking output, we derive learning rules that increase the variance of the input current evoked by learned patterns relative to that obtained from random background patterns. We demonstrate that the model can successfully recognize a large number of patterns and exhibits a slow deterioration in performance with increasing number of learned patterns. In addition, robustness to time warping of the input patterns is revealed to be an emergent property of the model. Using a leaky integrate-and-fire realization of the readout neuron, we demonstrate that the above results also apply when considering spiking output. PMID:16907629

  19. The Parabolic Variance (PVAR): A Wavelet Variance Based on the Least-Square Fit.

    PubMed

    Vernotte, Francois; Lenczner, Michel; Bourgeois, Pierre-Yves; Rubiola, Enrico

    2016-04-01

    This paper introduces the parabolic variance (PVAR), a wavelet variance similar to the Allan variance (AVAR), based on the linear regression (LR) of phase data. The companion article arXiv:1506.05009 [physics.ins-det] details the Ω frequency counter, which implements the LR estimate. The PVAR combines the advantages of AVAR and modified AVAR (MVAR). PVAR is good for long-term analysis because the wavelet spans over 2τ, the same as the AVAR wavelet, and good for short-term analysis because the response to white and flicker PM is 1/τ(3) and 1/τ(2), the same as the MVAR. After setting the theoretical framework, we study the degrees of freedom and the confidence interval for the most common noise types. Then, we focus on the detection of a weak noise process at the transition-or corner-where a faster process rolls off. This new perspective raises the question of which variance detects the weak process with the shortest data record. Our simulations show that PVAR is a fortunate tradeoff. PVAR is superior to MVAR in all cases, exhibits the best ability to divide between fast noise phenomena (up to flicker FM), and is almost as good as AVAR for the detection of random walk and drift. PMID:26571523

  20. Dynamics of mean-variance-skewness of cumulative crop yield impact temporal yield variance

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Production risk associated with cropping systems influences farmers’ decisions to adopt a new management practice or a production system. Cumulative yield (CY), temporal yield variance (TYV) and coefficient of variation (CV) were used to assess the risk associated with adopting combinations of new m...

  1. The variance of the adjusted Rand index.

    PubMed

    Steinley, Douglas; Brusco, Michael J; Hubert, Lawrence

    2016-06-01

    For 30 years, the adjusted Rand index has been the preferred method for comparing 2 partitions (e.g., clusterings) of a set of observations. Although the index is widely used, little is known about its variability. Herein, the variance of the adjusted Rand index (Hubert & Arabie, 1985) is provided and its properties are explored. It is shown that a normal approximation is appropriate across a wide range of sample sizes and varying numbers of clusters. Further, it is shown that confidence intervals based on the normal distribution have desirable levels of coverage and accuracy. Finally, the first power analysis evaluating the ability to detect differences between 2, different adjusted Rand indices is provided. (PsycINFO Database Record PMID:26881693

  2. Motion Detection Using Mean Normalized Temporal Variance

    SciTech Connect

    Chan, C W

    2003-08-04

    Scene-Based Wave Front Sensing uses the correlation between successive wavelets to determine the phase aberrations which cause the blurring of digital images. Adaptive Optics technology uses that information to control deformable mirrors to correct for the phase aberrations making the image clearer. The correlation between temporal subimages gives tip-tilt information. If these images do not have identical image content, tip-tilt estimations may be incorrect. Motion detection is necessary to help avoid errors initiated by dynamic subimage content. With a finely limited number of pixels per subaperature, most conventional motion detection algorithms fall apart on our subimages. Despite this fact, motion detection based on the normalized variance of individual pixels proved to be effective.

  3. Calculating bone-lead measurement variance.

    PubMed Central

    Todd, A C

    2000-01-01

    The technique of (109)Cd-based X-ray fluorescence (XRF) measurements of lead in bone is well established. A paper by some XRF researchers [Gordon CL, et al. The Reproducibility of (109)Cd-based X-ray Fluorescence Measurements of Bone Lead. Environ Health Perspect 102:690-694 (1994)] presented the currently practiced method for calculating the variance of an in vivo measurement once a calibration line has been established. This paper corrects typographical errors in the method published by those authors; presents a crude estimate of the measurement error that can be acquired without computational peak fitting programs; and draws attention to the measurement error attributable to covariance, an important feature in the construct of the currently accepted method that is flawed under certain circumstances. PMID:10811562

  4. Variance-based interaction index measuring heteroscedasticity

    NASA Astrophysics Data System (ADS)

    Ito, Keiichi; Couckuyt, Ivo; Poles, Silvia; Dhaene, Tom

    2016-06-01

    This work is motivated by the need to deal with models with high-dimensional input spaces of real variables. One way to tackle high-dimensional problems is to identify interaction or non-interaction among input parameters. We propose a new variance-based sensitivity interaction index that can detect and quantify interactions among the input variables of mathematical functions and computer simulations. The computation is very similar to first-order sensitivity indices by Sobol'. The proposed interaction index can quantify the relative importance of input variables in interaction. Furthermore, detection of non-interaction for screening can be done with as low as 4 n + 2 function evaluations, where n is the number of input variables. Using the interaction indices based on heteroscedasticity, the original function may be decomposed into a set of lower dimensional functions which may then be analyzed separately.

  5. Individualized Additional Instruction for Calculus

    ERIC Educational Resources Information Center

    Takata, Ken

    2010-01-01

    College students enrolling in the calculus sequence have a wide variance in their preparation and abilities, yet they are usually taught from the same lecture. We describe another pedagogical model of Individualized Additional Instruction (IAI) that assesses each student frequently and prescribes further instruction and homework based on the…

  6. Methods to estimate the between‐study variance and its uncertainty in meta‐analysis†

    PubMed Central

    Jackson, Dan; Viechtbauer, Wolfgang; Bender, Ralf; Bowden, Jack; Knapp, Guido; Kuss, Oliver; Higgins, Julian PT; Langan, Dean; Salanti, Georgia

    2015-01-01

    Meta‐analyses are typically used to estimate the overall/mean of an outcome of interest. However, inference about between‐study variability, which is typically modelled using a between‐study variance parameter, is usually an additional aim. The DerSimonian and Laird method, currently widely used by default to estimate the between‐study variance, has been long challenged. Our aim is to identify known methods for estimation of the between‐study variance and its corresponding uncertainty, and to summarise the simulation and empirical evidence that compares them. We identified 16 estimators for the between‐study variance, seven methods to calculate confidence intervals, and several comparative studies. Simulation studies suggest that for both dichotomous and continuous data the estimator proposed by Paule and Mandel and for continuous data the restricted maximum likelihood estimator are better alternatives to estimate the between‐study variance. Based on the scenarios and results presented in the published studies, we recommend the Q‐profile method and the alternative approach based on a ‘generalised Cochran between‐study variance statistic’ to compute corresponding confidence intervals around the resulting estimates. Our recommendations are based on a qualitative evaluation of the existing literature and expert consensus. Evidence‐based recommendations require an extensive simulation study where all methods would be compared under the same scenarios. © 2015 The Authors. Research Synthesis Methods published by John Wiley & Sons Ltd. PMID:26332144

  7. Methods to estimate the between-study variance and its uncertainty in meta-analysis.

    PubMed

    Veroniki, Areti Angeliki; Jackson, Dan; Viechtbauer, Wolfgang; Bender, Ralf; Bowden, Jack; Knapp, Guido; Kuss, Oliver; Higgins, Julian P T; Langan, Dean; Salanti, Georgia

    2016-03-01

    Meta-analyses are typically used to estimate the overall/mean of an outcome of interest. However, inference about between-study variability, which is typically modelled using a between-study variance parameter, is usually an additional aim. The DerSimonian and Laird method, currently widely used by default to estimate the between-study variance, has been long challenged. Our aim is to identify known methods for estimation of the between-study variance and its corresponding uncertainty, and to summarise the simulation and empirical evidence that compares them. We identified 16 estimators for the between-study variance, seven methods to calculate confidence intervals, and several comparative studies. Simulation studies suggest that for both dichotomous and continuous data the estimator proposed by Paule and Mandel and for continuous data the restricted maximum likelihood estimator are better alternatives to estimate the between-study variance. Based on the scenarios and results presented in the published studies, we recommend the Q-profile method and the alternative approach based on a 'generalised Cochran between-study variance statistic' to compute corresponding confidence intervals around the resulting estimates. Our recommendations are based on a qualitative evaluation of the existing literature and expert consensus. Evidence-based recommendations require an extensive simulation study where all methods would be compared under the same scenarios. PMID:26332144

  8. Potential variance affecting homeotic Ultrabithorax and Antennapedia phenotypes in Drosophila melanogaster.

    PubMed Central

    Gibson, G; Wemple, M; van Helden, S

    1999-01-01

    Introgression of homeotic mutations into wild-type genetic backgrounds results in a wide variety of phenotypes and implies that major effect modifiers of extreme phenotypes are not uncommon in natural populations of Drosophila. A composite interval mapping procedure was used to demonstrate that one major effect locus accounts for three-quarters of the variance for haltere to wing margin transformation in Ultrabithorax flies, yet has no obvious effect on wild-type development. Several other genetic backgrounds result in enlargement of the haltere significantly beyond the normal range of haploinsufficient phenotypes, suggesting genetic variation in cofactors that mediate homeotic protein function. Introgression of Antennapedia produces lines with heritable phenotypes ranging from almost complete suppression to perfect antennal leg formation, as well as transformations that are restricted to either the distal or proximal portion of the appendage. It is argued that the existence of "potential" variance, which is genetic variation whose effects are not observable in wild-type individuals, is a prerequisite for the uncoupling of genetic from phenotypic divergence. PMID:10049924

  9. Genetics of quantitative and qualitative traits of isabgol (Plantago ovata).

    PubMed

    Singh, N; Lal, R K

    2009-01-01

    Isabgol is a medicinal plant known for its high-quality dietary fiber. The genetics and inheritance of economic characters, such as number of panicles, panicle length, seed yield, and swelling factor, were measured by diallel analysis of F(1) progenies from seven parents. The additive component of genetic variance was significant for days to flowering, plant height, branches/plant, peduncle length, panicle length, days to maturity, and swelling factor, whereas the dominance component of genetic variance was significant for all the characters except panicles/plant. Additivity was not significant for all the characters, indicating absence of non-allelic interactions (epistasis) in controlling gene expression. Heritability in the narrow sense was very high for panicle length, days to flowering, and plant height, and moderate for branches/plant, panicles/plant, days to maturity, seed yield, husk yield, and swelling factor. However, the degree of genetic improvement was only high for panicle length, seed yield and husk yield. We conclude that hybridizations, isolation of superior genotypes by sib selection and recurrent selection, and exploitation of hybrid vigor in specific parental-cross combinations are good strategies for isabgol crop improvement. PMID:19731195

  10. Estimating discharge measurement uncertainty using the interpolated variance estimator

    USGS Publications Warehouse

    Cohn, T.; Kiang, J.; Mason, R., Jr.

    2012-01-01

    Methods for quantifying the uncertainty in discharge measurements typically identify various sources of uncertainty and then estimate the uncertainty from each of these sources by applying the results of empirical or laboratory studies. If actual measurement conditions are not consistent with those encountered in the empirical or laboratory studies, these methods may give poor estimates of discharge uncertainty. This paper presents an alternative method for estimating discharge measurement uncertainty that uses statistical techniques and at-site observations. This Interpolated Variance Estimator (IVE) estimates uncertainty based on the data collected during the streamflow measurement and therefore reflects the conditions encountered at the site. The IVE has the additional advantage of capturing all sources of random uncertainty in the velocity and depth measurements. It can be applied to velocity-area discharge measurements that use a velocity meter to measure point velocities at multiple vertical sections in a channel cross section.

  11. Dissection of the genetics of Parkinson's disease identifies an additional association 5′ of SNCA and multiple associated haplotypes at 17q21

    PubMed Central

    Spencer, Chris C.A.; Plagnol, Vincent; Strange, Amy; Gardner, Michelle; Paisan-Ruiz, Coro; Band, Gavin; Barker, Roger A.; Bellenguez, Celine; Bhatia, Kailash; Blackburn, Hannah; Blackwell, Jennie M.; Bramon, Elvira; Brown, Martin A.; Brown, Matthew A.; Burn, David; Casas, Juan-Pablo; Chinnery, Patrick F.; Clarke, Carl E.; Corvin, Aiden; Craddock, Nicholas; Deloukas, Panos; Edkins, Sarah; Evans, Jonathan; Freeman, Colin; Gray, Emma; Hardy, John; Hudson, Gavin; Hunt, Sarah; Jankowski, Janusz; Langford, Cordelia; Lees, Andrew J.; Markus, Hugh S.; Mathew, Christopher G.; McCarthy, Mark I.; Morrison, Karen E.; Palmer, Colin N.A.; Pearson, Justin P.; Peltonen, Leena; Pirinen, Matti; Plomin, Robert; Potter, Simon; Rautanen, Anna; Sawcer, Stephen J.; Su, Zhan; Trembath, Richard C.; Viswanathan, Ananth C.; Williams, Nigel W.; Morris, Huw R.; Donnelly, Peter; Wood, Nicholas W.

    2011-01-01

    We performed a genome-wide association study (GWAS) in 1705 Parkinson's disease (PD) UK patients and 5175 UK controls, the largest sample size so far for a PD GWAS. Replication was attempted in an additional cohort of 1039 French PD cases and 1984 controls for the 27 regions showing the strongest evidence of association (P< 10−4). We replicated published associations in the 4q22/SNCA and 17q21/MAPT chromosome regions (P< 10−10) and found evidence for an additional independent association in 4q22/SNCA. A detailed analysis of the haplotype structure at 17q21 showed that there are three separate risk groups within this region. We found weak but consistent evidence of association for common variants located in three previously published associated regions (4p15/BST1, 4p16/GAK and 1q32/PARK16). We found no support for the previously reported SNP association in 12q12/LRRK2. We also found an association of the two SNPs in 4q22/SNCA with the age of onset of the disease. PMID:21044948

  12. Genetic Inheritance of Female and Male Morphotypes in Giant Freshwater Prawn Macrobrachium rosenbergii

    PubMed Central

    2014-01-01

    Giant freshwater prawn (GFP) Macrobrachium rosenbergii is unique with males categorized in five different morphotypes (small claw, orange claw, blue claw, old blue claw and no claw males) and females in three reproductive statuses (mature ovary, berried and spawned females). In the present study we examined genetic inheritance of female and male morphotypes, their body weights and genetic associations between morphotypes and body traits. Restricted maximum likelihood fitting a multi-trait animal model was performed on a total of 21,459 body records collected over five generations in a GFP population selected for high growth rate. The estimates of variance components showed that there were substantial differences in additive genetic variance in body weight between male morphotypes. The low and significantly different from one genetic correlations between the expressions of body weight in male morphotypes also suggest that these traits should be treated as genetically different traits in selective breeding programs. By contrast, body weights of female types are essentially the same characters as indicated by the high genetic correlations between homologous trait expressions. In addition to body weight, male morphotypes and female reproductive statuses were treated as traits in themselves and were analysed as binary observations using animal and sire linear mixed models, and logit and probit threshold models. The estimates of heritability back-transformed from the liability scale were in good agreement with those obtained from linear mixed models, ranging from 0.02 to 0.43 for male morphotypes and 0.06 to 0.10 for female types. The genetic correlations among male morphoptypes were generally favourable. Body weight showed negative genetic associations with SM (−0.96), whereas those of body weight with other male morphotypes were positive (0.25 to 0.76). Our results showed that there is existence of heritable (additive genetic) component for male morphotypes, giving

  13. Explanatory Variance in Maximal Oxygen Uptake

    PubMed Central

    Robert McComb, Jacalyn J.; Roh, Daesung; Williams, James S.

    2006-01-01

    The purpose of this study was to develop a prediction equation that could be used to estimate maximal oxygen uptake (VO2max) from a submaximal water running protocol. Thirty-two volunteers (n =19 males, n = 13 females), ages 18 - 24 years, underwent the following testing procedures: (a) a 7-site skin fold assessment; (b) a land VO2max running treadmill test; and (c) a 6 min water running test. For the water running submaximal protocol, the participants were fitted with an Aqua Jogger Classic Uni-Sex Belt and a Polar Heart Rate Monitor; the participants’ head, shoulders, hips and feet were vertically aligned, using a modified running/bicycle motion. A regression model was used to predict VO2max. The criterion variable, VO2max, was measured using open-circuit calorimetry utilizing the Bruce Treadmill Protocol. Predictor variables included in the model were percent body fat (% BF), height, weight, gender, and heart rate following a 6 min water running protocol. Percent body fat accounted for 76% (r = -0.87, SEE = 3.27) of the variance in VO2max. No other variables significantly contributed to the explained variance in VO2max. The equation for the estimation of VO2max is as follows: VO2max ml.kg-1·min-1 = 56.14 - 0.92 (% BF). Key Points Body Fat is an important predictor of VO2 max. Individuals with low skill level in water running may shorten their stride length to avoid the onset of fatigue at higher work-loads, therefore, the net oxygen cost of the exercise cannot be controlled in inexperienced individuals in water running at fatiguing workloads. Experiments using water running protocols to predict VO2max should use individuals trained in the mechanics of water running. A submaximal water running protocol is needed in the research literature for individuals trained in the mechanics of water running, given the popularity of water running rehabilitative exercise programs and training programs. PMID:24260003

  14. Cyclostationary analysis with logarithmic variance stabilisation

    NASA Astrophysics Data System (ADS)

    Borghesani, Pietro; Shahriar, Md Rifat

    2016-03-01

    Second order cyclostationary (CS2) components in vibration or acoustic emission signals are typical symptoms of a wide variety of faults in rotating and alternating mechanical systems. The square envelope spectrum (SES), obtained via Hilbert transform of the original signal, is at the basis of the most common indicators used for detection of CS2 components. It has been shown that the SES is equivalent to an autocorrelation of the signal's discrete Fourier transform, and that CS2 components are a cause of high correlations in the frequency domain of the signal, thus resulting in peaks in the SES. Statistical tests have been proposed to determine if peaks in the SES are likely to belong to a normal variability in the signal or if they are proper symptoms of CS2 components. Despite the need for automated fault recognition and the theoretical soundness of these tests, this approach to machine diagnostics has been mostly neglected in industrial applications. In fact, in a series of experimental applications, even with proper pre-whitening steps, it has been found that healthy machines might produce high spectral correlations and therefore result in a highly biased SES distribution which might cause a series of false positives. In this paper a new envelope spectrum is defined, with the theoretical intent of rendering the hypothesis test variance-free. This newly proposed indicator will prove unbiased in case of multiple CS2 sources of spectral correlation, thus reducing the risk of false alarms.

  15. Genetic and environmental influences on impulsivity: A meta-analysis of twin, family and adoption studies

    PubMed Central

    Bezdjian, Serena; Baker, Laura A.; Tuvblad, Catherine

    2011-01-01

    A meta-analysis of twin, family and adoption studies was conducted to estimate the magnitude of genetic and environmental influences on impulsivity. The best fitting model for 41 key studies (58 independent samples from 14 month old infants to adults; N = 27,147) included equal proportions of variance due to genetic (0.50) and non-shared environmental (0.50) influences, with genetic effects being both additive (0.38) and non-additive (0.12). Shared environmental effects were unimportant in explaining individual differences in impulsivity. Age, sex, and study design (twin vs. adoption) were all significant moderators of the magnitude of genetic and environmental influences on impulsivity. The relative contribution of genetic effects (broad sense heritability) and unique environmental effects were also found to be important throughout development from childhood to adulthood. Total genetic effects were found to be important for all ages, but appeared to be strongest in children. Analyses also demonstrated that genetic effects appeared to be stronger in males than in females. Method of assessment (laboratory tasks vs. questionnaires), however, was not a significant moderator of the genetic and environmental influences on impulsivity. These results provide a structured synthesis of existing behavior genetic studies on impulsivity by providing a clearer understanding of the relative genetic and environmental contributions in impulsive traits through various stages of development. PMID:21889436

  16. Food additives

    MedlinePlus

    Food additives are substances that become part of a food product when they are added during the processing or making of that food. "Direct" food additives are often added during processing to: Add nutrients ...

  17. Genetic pleiotropy between asthma and obesity in a community-based sample of twins

    PubMed Central

    Hallstrand, Teal S.; Fischer, Mary E.; Wurfel, Mark M.; Afari, Niloofar; Buchwald, Dedra; Goldberg, Jack

    2007-01-01

    Background Asthma and obesity are common conditions that are strongly associated. This association might be due to shared genetic or environmental causes. Objective We sought to determine whether a shared genetic cause is responsible for the association between asthma and obesity and to estimate the magnitude of shared genetic cause. Methods The analyses were performed with 1001 monozygotic and 383 dizygotic same-sex twin pairs within the University of Washington Twin Registry. The presence of asthma was determined by self-report of a physician diagnosis of asthma, and body mass index (BMI) was calculated by using self-reported height and weight. Obesity was defined as a BMI of 30 or greater. The association between asthma and BMI was assessed by means of mixed-effects ordinal regression. Twin correlations examined the association of asthma and obesity. Univariate and bivariate structural equation models estimated the components of variance attributable to genetic and environmental effects. Results A strong association between asthma and BMI was identified in the sample population (P < .001). Substantial heritability was detected for asthma (53%) and obesity (77%), which is indicative of additive genetic influences on each disorder. The best-fitting model of shared components of variance indicated that 8% of the genetic component of obesity is shared with asthma. Conclusion The covariation between obesity and asthma is predominantly caused by shared genetic risk factors for both conditions. PMID:16337451

  18. Estimating the encounter rate variance in distance sampling

    USGS Publications Warehouse

    Fewster, R.M.; Buckland, S.T.; Burnham, K.P.; Borchers, D.L.; Jupp, P.E.; Laake, J.L.; Thomas, L.

    2009-01-01

    The dominant source of variance in line transect sampling is usually the encounter rate variance. Systematic survey designs are often used to reduce the true variability among different realizations of the design, but estimating the variance is difficult and estimators typically approximate the variance by treating the design as a simple random sample of lines. We explore the properties of different encounter rate variance estimators under random and systematic designs. We show that a design-based variance estimator improves upon the model-based estimator of Buckland et al. (2001, Introduction to Distance Sampling. Oxford: Oxford University Press, p. 79) when transects are positioned at random. However, if populations exhibit strong spatial trends, both estimators can have substantial positive bias under systematic designs. We show that poststratification is effective in reducing this bias. ?? 2008, The International Biometric Society.

  19. A Note on Noncentrality Parameters for Contrast Tests in a One-Way Analysis of Variance

    ERIC Educational Resources Information Center

    Liu, Xiaofeng Steven

    2010-01-01

    The noncentrality parameter for a contrast test in a one-way analysis of variance is based on the dot product of 2 vectors whose geometric meaning in a Euclidian space offers mnemonic hints about its constituents. Additionally, the noncentrality parameters for a set of orthogonal contrasts sum up to the noncentrality parameter for the omnibus "F"…

  20. The Operating Characteristics of the Nonparametric Levene Test for Equal Variances with Assessment and Evaluation Data

    ERIC Educational Resources Information Center

    Nordstokke, David W.; Zumbo, Bruno D.; Cairns, Sharon L.; Saklofske, Donald H.

    2011-01-01

    Many assessment and evaluation studies use statistical hypothesis tests, such as the independent samples t test or analysis of variance, to test the equality of two or more means for gender, age groups, cultures or language group comparisons. In addition, some, but far fewer, studies compare variability across these same groups or research…

  1. Food additives

    PubMed Central

    Spencer, Michael

    1974-01-01

    Food additives are discussed from the food technology point of view. The reasons for their use are summarized: (1) to protect food from chemical and microbiological attack; (2) to even out seasonal supplies; (3) to improve their eating quality; (4) to improve their nutritional value. The various types of food additives are considered, e.g. colours, flavours, emulsifiers, bread and flour additives, preservatives, and nutritional additives. The paper concludes with consideration of those circumstances in which the use of additives is (a) justified and (b) unjustified. PMID:4467857

  2. Variance analysis. Part II, The use of computers.

    PubMed

    Finkler, S A

    1991-09-01

    This is the second in a two-part series on variance analysis. In the first article (JONA, July/August 1991), the author discussed flexible budgeting, including the calculation of price, quantity, volume, and acuity variances. In this second article, the author focuses on the use of computers by nurse managers to aid in the process of calculating, understanding, and justifying variances. PMID:1919788

  3. Network Structure and Biased Variance Estimation in Respondent Driven Sampling

    PubMed Central

    Verdery, Ashton M.; Mouw, Ted; Bauldry, Shawn; Mucha, Peter J.

    2015-01-01

    This paper explores bias in the estimation of sampling variance in Respondent Driven Sampling (RDS). Prior methodological work on RDS has focused on its problematic assumptions and the biases and inefficiencies of its estimators of the population mean. Nonetheless, researchers have given only slight attention to the topic of estimating sampling variance in RDS, despite the importance of variance estimation for the construction of confidence intervals and hypothesis tests. In this paper, we show that the estimators of RDS sampling variance rely on a critical assumption that the network is First Order Markov (FOM) with respect to the dependent variable of interest. We demonstrate, through intuitive examples, mathematical generalizations, and computational experiments that current RDS variance estimators will always underestimate the population sampling variance of RDS in empirical networks that do not conform to the FOM assumption. Analysis of 215 observed university and school networks from Facebook and Add Health indicates that the FOM assumption is violated in every empirical network we analyze, and that these violations lead to substantially biased RDS estimators of sampling variance. We propose and test two alternative variance estimators that show some promise for reducing biases, but which also illustrate the limits of estimating sampling variance with only partial information on the underlying population social network. PMID:26679927

  4. Multiperiod Mean-Variance Portfolio Optimization via Market Cloning

    SciTech Connect

    Ankirchner, Stefan; Dermoune, Azzouz

    2011-08-15

    The problem of finding the mean variance optimal portfolio in a multiperiod model can not be solved directly by means of dynamic programming. In order to find a solution we therefore first introduce independent market clones having the same distributional properties as the original market, and we replace the portfolio mean and variance by their empirical counterparts. We then use dynamic programming to derive portfolios maximizing a weighted sum of the empirical mean and variance. By letting the number of market clones converge to infinity we are able to solve the original mean variance problem.

  5. Network Structure and Biased Variance Estimation in Respondent Driven Sampling.

    PubMed

    Verdery, Ashton M; Mouw, Ted; Bauldry, Shawn; Mucha, Peter J

    2015-01-01

    This paper explores bias in the estimation of sampling variance in Respondent Driven Sampling (RDS). Prior methodological work on RDS has focused on its problematic assumptions and the biases and inefficiencies of its estimators of the population mean. Nonetheless, researchers have given only slight attention to the topic of estimating sampling variance in RDS, despite the importance of variance estimation for the construction of confidence intervals and hypothesis tests. In this paper, we show that the estimators of RDS sampling variance rely on a critical assumption that the network is First Order Markov (FOM) with respect to the dependent variable of interest. We demonstrate, through intuitive examples, mathematical generalizations, and computational experiments that current RDS variance estimators will always underestimate the population sampling variance of RDS in empirical networks that do not conform to the FOM assumption. Analysis of 215 observed university and school networks from Facebook and Add Health indicates that the FOM assumption is violated in every empirical network we analyze, and that these violations lead to substantially biased RDS estimators of sampling variance. We propose and test two alternative variance estimators that show some promise for reducing biases, but which also illustrate the limits of estimating sampling variance with only partial information on the underlying population social network. PMID:26679927

  6. Budgeting and controllable cost variances. The case of multiple diagnoses, multiple services, and multiple resources.

    PubMed

    Broyles, R W; Lay, C M

    1982-12-01

    This paper examines an unfavorable cost variance in an institution which employs multiple resources to provide stay specific and ancillary services to patients presenting multiple diagnoses. It partitions the difference between actual and expected costs into components that are the responsibility of an identifiable individual or group of individuals. The analysis demonstrates that the components comprising an unfavorable cost variance are attributable to factor prices, the use of real resources, the mix of patients, and the composition of care provided by the institution. In addition, the interactive effects of these factors are also identified. PMID:7183731

  7. A NEW VARIANCE ESTIMATOR FOR PARAMETERS OF SEMI-PARAMETRIC GENERALIZED ADDITIVE MODELS. (R829213)

    EPA Science Inventory

    The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

  8. Modeling of genetic gain for single traits from marker-assisted seedling selection in clonally propagated crops

    PubMed Central

    Ru, Sushan; Hardner, Craig; Carter, Patrick A; Evans, Kate; Main, Dorrie; Peace, Cameron

    2016-01-01

    Seedling selection identifies superior seedlings as candidate cultivars based on predicted genetic potential for traits of interest. Traditionally, genetic potential is determined by phenotypic evaluation. With the availability of DNA tests for some agronomically important traits, breeders have the opportunity to include DNA information in their seedling selection operations—known as marker-assisted seedling selection. A major challenge in deploying marker-assisted seedling selection in clonally propagated crops is a lack of knowledge in genetic gain achievable from alternative strategies. Existing models based on additive effects considering seed-propagated crops are not directly relevant for seedling selection of clonally propagated crops, as clonal propagation captures all genetic effects, not just additive. This study modeled genetic gain from traditional and various marker-based seedling selection strategies on a single trait basis through analytical derivation and stochastic simulation, based on a generalized seedling selection scheme of clonally propagated crops. Various trait-test scenarios with a range of broad-sense heritability and proportion of genotypic variance explained by DNA markers were simulated for two populations with different segregation patterns. Both derived and simulated results indicated that marker-based strategies tended to achieve higher genetic gain than phenotypic seedling selection for a trait where the proportion of genotypic variance explained by marker information was greater than the broad-sense heritability. Results from this study provides guidance in optimizing genetic gain from seedling selection for single traits where DNA tests providing marker information are available. PMID:27148453

  9. On discrete stochastic processes with long-lasting time dependence in the variance

    NASA Astrophysics Data System (ADS)

    Queirós, S. M. D.

    2008-11-01

    In this manuscript, we analytically and numerically study statistical properties of an heteroskedastic process based on the celebrated ARCH generator of random variables whose variance is defined by a memory of qm-exponencial, form (eqm=1 x=ex). Specifically, we inspect the self-correlation function of squared random variables as well as the kurtosis. In addition, by numerical procedures, we infer the stationary probability density function of both of the heteroskedastic random variables and the variance, the multiscaling properties, the first-passage times distribution, and the dependence degree. Finally, we introduce an asymmetric variance version of the model that enables us to reproduce the so-called leverage effect in financial markets.

  10. Variance and bias confidence criteria for ERA modal parameter identification. [Eigensystem Realization Algorithm

    NASA Technical Reports Server (NTRS)

    Longman, Richard W.; Bergmann, Martin; Juang, Jer-Nan

    1988-01-01

    For the ERA system identification algorithm, perturbation methods are used to develop expressions for variance and bias of the identified modal parameters. Based on the statistics of the measurement noise, the variance results serve as confidence criteria by indicating how likely the true parameters are to lie within any chosen interval about their identified values. This replaces the use of expensive and time-consuming Monte Carlo computer runs to obtain similar information. The bias estimates help guide the ERA user in his choice of which data points to use and how much data to use in order to obtain the best results, performing the trade-off between the bias and scatter. Also, when the uncertainty in the bias is sufficiently small, the bias information can be used to correct the ERA results. In addition, expressions for the variance and bias of the singular values serve as tools to help the ERA user decide the proper modal order.

  11. Review of speckle and phase variance optical coherence tomography to visualize microvascular networks

    NASA Astrophysics Data System (ADS)

    Mahmud, Mohammad Sultan; Cadotte, David W.; Vuong, Barry; Sun, Carry; Luk, Timothy W. H.; Mariampillai, Adrian; Yang, Victor X. D.

    2013-05-01

    High-resolution mapping of microvasculature has been applied to diverse body systems, including the retinal and choroidal vasculature, cardiac vasculature, the central nervous system, and various tumor models. Many imaging techniques have been developed to address specific research questions, and each has its own merits and drawbacks. Understanding, optimization, and proper implementation of these imaging techniques can significantly improve the data obtained along the spectrum of unique research projects to obtain diagnostic clinical information. We describe the recently developed algorithms and applications of two general classes of microvascular imaging techniques: speckle-variance and phase-variance optical coherence tomography (OCT). We compare and contrast their performance with Doppler OCT and optical microangiography. In addition, we highlight ongoing work in the development of variance-based techniques to further refine the characterization of microvascular networks.

  12. Splitting the variance of statistical learning performance: A parametric investigation of exposure duration and transitional probabilities.

    PubMed

    Bogaerts, Louisa; Siegelman, Noam; Frost, Ram

    2016-08-01

    What determines individuals' efficacy in detecting regularities in visual statistical learning? Our theoretical starting point assumes that the variance in performance of statistical learning (SL) can be split into the variance related to efficiency in encoding representations within a modality and the variance related to the relative computational efficiency of detecting the distributional properties of the encoded representations. Using a novel methodology, we dissociated encoding from higher-order learning factors, by independently manipulating exposure duration and transitional probabilities in a stream of visual shapes. Our results show that the encoding of shapes and the retrieving of their transitional probabilities are not independent and additive processes, but interact to jointly determine SL performance. The theoretical implications of these findings for a mechanistic explanation of SL are discussed. PMID:26743060

  13. Image denoising via Bayesian estimation of local variance with Maxwell density prior

    NASA Astrophysics Data System (ADS)

    Kittisuwan, Pichid

    2015-10-01

    The need for efficient image denoising methods has grown with the massive production of digital images and movies of all kinds. The distortion of images by additive white Gaussian noise (AWGN) is common during its processing and transmission. This paper is concerned with dual-tree complex wavelet-based image denoising using Bayesian techniques. Indeed, one of the cruxes of the Bayesian image denoising algorithms is to estimate the local variance of the image. Here, we employ maximum a posteriori (MAP) estimation to calculate local observed variance with Maxwell density prior for local observed variance and Gaussian distribution for noisy wavelet coefficients. Evidently, our selection of prior distribution is motivated by analytical and computational tractability. The experimental results show that the proposed method yields good denoising results.

  14. Genetic counseling.

    PubMed

    Fraser, F C

    1974-09-01

    A workshop was sponsored by the National Genetics Foundation to evaluate and make recommendations about the status of genetic counseling, its goals, nature, achievements, and needs. The process of genetic workup and counseling is divided into 5 stages: validation of the diagnosis; obtaining family history; estimation of the risk of recurrence; helping the family make a decision and take appropriate action; and extending counseling to other members of the family. Counseling can be directed at individuals or at special groups with the potential of carrying such diseases as sickle cell amenia or Tay-Sachs. No consensus exists on an optimal counseling approach. Genetic counseling is regarded as a team effort, requiring, in addition to the counselor, laboratory facilities and a variety of specialists. The source of payment for genetic counseling services is regarded as a problem of increasing concern. Generally, the fee paid rarely covers the cost of the many procedures and it is suggested that the cost, like that of other public health services, should be subsidized by the state. Considerable argument exists over whether a genetic counselor must have a M.D. degree or whether a Ph. D. in medical genetics is suitable enough. The quality of much genetic counseling, which is often done in the office of doctors unskilled in the field, would be increased if better training in genetics were offered to medical students and if physicians were informed of the existence of counseling centers. Further, there is a growing feeling that some sort of accreditation of genetic counselors is desirable. PMID:4609197

  15. Variance and Covariance of Actual Relationships between Relatives at One Locus

    PubMed Central

    Garcia-Cortes, Luis Alberto; Legarra, Andres; Chevalet, Claude; Toro, Miguel Angel

    2013-01-01

    The relationship between pairs of individuals is an important topic in many areas of population and quantitative genetics. It is usually measured as the proportion of thegenome identical by descent shared by the pair and it can be inferred from pedigree information. But there is a variance in actual relationships as a consequence of Mendelian sampling, whose general formula has not been developed. The goal of this work is to develop this general formula for the one-locus situation,. We provide simple expressions for the variances and covariances of all actual relationships in an arbitrary complex pedigree. The proposed method relies on the use of the nine identity coefficients and the generalized relationship coefficients; formulas have been checked by computer simulation. Finally two examples for a short pedigree of dogs and a long pedigree of sheep are given. PMID:23451134

  16. 7 CFR 718.105 - Tolerances, variances, and adjustments.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 7 2014-01-01 2014-01-01 false Tolerances, variances, and adjustments. 718.105 Section 718.105 Agriculture Regulations of the Department of Agriculture (Continued) FARM SERVICE AGENCY... APPLICABLE TO MULTIPLE PROGRAMS Determination of Acreage and Compliance § 718.105 Tolerances, variances,...

  17. 7 CFR 718.105 - Tolerances, variances, and adjustments.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 7 Agriculture 7 2012-01-01 2012-01-01 false Tolerances, variances, and adjustments. 718.105 Section 718.105 Agriculture Regulations of the Department of Agriculture (Continued) FARM SERVICE AGENCY... APPLICABLE TO MULTIPLE PROGRAMS Determination of Acreage and Compliance § 718.105 Tolerances, variances,...

  18. 36 CFR 27.4 - Variances and exceptions.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 36 Parks, Forests, and Public Property 1 2013-07-01 2013-07-01 false Variances and exceptions. 27.4 Section 27.4 Parks, Forests, and Public Property NATIONAL PARK SERVICE, DEPARTMENT OF THE INTERIOR CAPE COD NATIONAL SEASHORE; ZONING STANDARDS § 27.4 Variances and exceptions. (a) Zoning bylaws...

  19. 36 CFR 27.4 - Variances and exceptions.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 36 Parks, Forests, and Public Property 1 2014-07-01 2014-07-01 false Variances and exceptions. 27.4 Section 27.4 Parks, Forests, and Public Property NATIONAL PARK SERVICE, DEPARTMENT OF THE INTERIOR CAPE COD NATIONAL SEASHORE; ZONING STANDARDS § 27.4 Variances and exceptions. (a) Zoning bylaws...

  20. 36 CFR 27.4 - Variances and exceptions.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 36 Parks, Forests, and Public Property 1 2011-07-01 2011-07-01 false Variances and exceptions. 27.4 Section 27.4 Parks, Forests, and Public Property NATIONAL PARK SERVICE, DEPARTMENT OF THE INTERIOR CAPE COD NATIONAL SEASHORE; ZONING STANDARDS § 27.4 Variances and exceptions. (a) Zoning bylaws...

  1. 36 CFR 27.4 - Variances and exceptions.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 36 Parks, Forests, and Public Property 1 2012-07-01 2012-07-01 false Variances and exceptions. 27.4 Section 27.4 Parks, Forests, and Public Property NATIONAL PARK SERVICE, DEPARTMENT OF THE INTERIOR CAPE COD NATIONAL SEASHORE; ZONING STANDARDS § 27.4 Variances and exceptions. (a) Zoning bylaws...

  2. Variances and Covariances of Kendall's Tau and Their Estimation.

    ERIC Educational Resources Information Center

    Cliff, Norman; Charlin, Ventura

    1991-01-01

    Variance formulas of H. E. Daniels and M. G. Kendall (1947) are generalized to allow for the presence of ties and variance of the sample tau correlation. Applications of these generalized formulas are discussed and illustrated using data from a 1965 study of contraceptive use in 15 developing countries. (SLD)

  3. 40 CFR 52.1390 - Missoula variance provision.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 4 2014-07-01 2014-07-01 false Missoula variance provision. 52.1390 Section 52.1390 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED) APPROVAL AND PROMULGATION OF IMPLEMENTATION PLANS (CONTINUED) Montana § 52.1390 Missoula variance provision. The Missoula City-County...

  4. 29 CFR 1904.38 - Variances from the recordkeeping rule.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... process your variance petition. (i) The Assistant Secretary will offer your employees and their authorized... the facts or conduct that may warrant revocation of your variance; and (ii) Provide you, your employees, and authorized employee representatives with an opportunity to participate in the...

  5. Productive Failure in Learning the Concept of Variance

    ERIC Educational Resources Information Center

    Kapur, Manu

    2012-01-01

    In a study with ninth-grade mathematics students on learning the concept of variance, students experienced either direct instruction (DI) or productive failure (PF), wherein they were first asked to generate a quantitative index for variance without any guidance before receiving DI on the concept. Whereas DI students relied only on the canonical…

  6. 10 CFR 52.93 - Exemptions and variances.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... CFR 52.7, and that the special circumstances outweigh any decrease in safety that may result from the... 10 Energy 2 2010-01-01 2010-01-01 false Exemptions and variances. 52.93 Section 52.93 Energy... Combined Licenses § 52.93 Exemptions and variances. (a) Applicants for a combined license under...

  7. Determining Sample Sizes for Precise Contrast Analysis with Heterogeneous Variances

    ERIC Educational Resources Information Center

    Jan, Show-Li; Shieh, Gwowen

    2014-01-01

    The analysis of variance (ANOVA) is one of the most frequently used statistical analyses in practical applications. Accordingly, the single and multiple comparison procedures are frequently applied to assess the differences among mean effects. However, the underlying assumption of homogeneous variances may not always be tenable. This study…

  8. A Study of Variance Estimation Methods. Working Paper Series.

    ERIC Educational Resources Information Center

    Zhang, Fan; Weng, Stanley; Salvucci, Sameena; Hu, Ming-xiu

    This working paper contains reports of five studies of variance estimation methods. The first, An Empirical Study of Poststratified Estimator, by Fan Zhang uses data from the National Household Education Survey to illustrate use of poststratified estimation. The second paper, BRR Variance Estimation Using BPLX Hadamard Procedure, by Stanley Weng…

  9. 21 CFR 821.2 - Exemptions and variances.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Exemptions and variances. 821.2 Section 821.2 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES MEDICAL DEVICE TRACKING REQUIREMENTS General Provisions § 821.2 Exemptions and variances. (a) A manufacturer, importer, or distributor...

  10. 40 CFR 142.40 - Requirements for a variance.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... Section 142.40 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) WATER PROGRAMS (CONTINUED) NATIONAL PRIMARY DRINKING WATER REGULATIONS IMPLEMENTATION Variances Issued by the Administrator... one or more variances to any public water system within a State that does not have primary...

  11. 40 CFR 142.43 - Disposition of a variance request.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ....43 Section 142.43 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) WATER PROGRAMS (CONTINUED) NATIONAL PRIMARY DRINKING WATER REGULATIONS IMPLEMENTATION Variances Issued by the... variance may be terminated at any time upon a finding that the nature of the raw water source is such...

  12. 40 CFR 142.43 - Disposition of a variance request.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ....43 Section 142.43 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) WATER PROGRAMS (CONTINUED) NATIONAL PRIMARY DRINKING WATER REGULATIONS IMPLEMENTATION Variances Issued by the... variance may be terminated at any time upon a finding that the nature of the raw water source is such...

  13. 40 CFR 142.43 - Disposition of a variance request.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ....43 Section 142.43 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) WATER PROGRAMS (CONTINUED) NATIONAL PRIMARY DRINKING WATER REGULATIONS IMPLEMENTATION Variances Issued by the... variance may be terminated at any time upon a finding that the nature of the raw water source is such...

  14. 40 CFR 142.43 - Disposition of a variance request.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ....43 Section 142.43 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) WATER PROGRAMS (CONTINUED) NATIONAL PRIMARY DRINKING WATER REGULATIONS IMPLEMENTATION Variances Issued by the... variance may be terminated at any time upon a finding that the nature of the raw water source is such...

  15. An efficient method to evaluate energy variances for extrapolation methods

    NASA Astrophysics Data System (ADS)

    Puddu, G.

    2012-08-01

    The energy variance extrapolation method consists of relating the approximate energies in many-body calculations to the corresponding energy variances and inferring eigenvalues by extrapolating to zero variance. The method needs a fast evaluation of the energy variances. For many-body methods that expand the nuclear wavefunctions in terms of deformed Slater determinants, the best available method for the evaluation of energy variances scales with the sixth power of the number of single-particle states. We propose a new method which depends on the number of single-particle orbits and the number of particles rather than the number of single-particle states. We discuss as an example the case of 4He using the chiral N3LO interaction in a basis consisting up to 184 single-particle states.

  16. Random regression test day models to estimate genetic parameters for milk yield and milk components in Philippine dairy buffaloes.

    PubMed

    Flores, E B; van der Werf, J

    2015-08-01

    Heritabilities and genetic correlations for milk production traits were estimated from first-parity test day records on 1022 Philippine dairy buffalo cows. Traits analysed included milk (MY), fat (FY) and protein (PY) yields, and fat (Fat%) and protein (Prot%) concentrations. Varying orders of Legendre polynomials (Leg(m)) as well as the Wilmink function (Wil) were used in random regression models. These various models were compared based on log likelihood, Akaike's information criterion, Bayesian information criterion and genetic variance estimates. Six residual variance classes were sufficient for MY, FY, PY and Fat%, while seven residual classes for Prot%. Multivariate analysis gave higher estimates of genetic variance and heritability compared with univariate analysis for all traits. Heritability estimates ranged from 0.25 to 0.44, 0.13 to 0.31 and 0.21 to 0.36 for MY, FY and PY, respectively. Wilmink's function was the better fitting function for additive genetic effects for all traits. It was also the preferred function for permanent environment effects for Fat% and Prot%, but for MY, FY and PY, the Legm was the appropriate function. Genetic correlations of MY with FY and PY were high and they were moderately negative with Fat% and Prot%. To prevent deterioration in Fat% and Prot% and improve milk quality, more weight should be applied to milk component traits. PMID:25727642

  17. Ant colony method to control variance reduction techniques in the Monte Carlo simulation of clinical electron linear accelerators

    NASA Astrophysics Data System (ADS)

    García-Pareja, S.; Vilches, M.; Lallena, A. M.

    2007-09-01

    The ant colony method is used to control the application of variance reduction techniques to the simulation of clinical electron linear accelerators of use in cancer therapy. In particular, splitting and Russian roulette, two standard variance reduction methods, are considered. The approach can be applied to any accelerator in a straightforward way and permits, in addition, to investigate the "hot" regions of the accelerator, an information which is basic to develop a source model for this therapy tool.

  18. Utility functions predict variance and skewness risk preferences in monkeys

    PubMed Central

    Genest, Wilfried; Stauffer, William R.; Schultz, Wolfram

    2016-01-01

    Utility is the fundamental variable thought to underlie economic choices. In particular, utility functions are believed to reflect preferences toward risk, a key decision variable in many real-life situations. To assess the validity of utility representations, it is therefore important to examine risk preferences. In turn, this approach requires formal definitions of risk. A standard approach is to focus on the variance of reward distributions (variance-risk). In this study, we also examined a form of risk related to the skewness of reward distributions (skewness-risk). Thus, we tested the extent to which empirically derived utility functions predicted preferences for variance-risk and skewness-risk in macaques. The expected utilities calculated for various symmetrical and skewed gambles served to define formally the direction of stochastic dominance between gambles. In direct choices, the animals’ preferences followed both second-order (variance) and third-order (skewness) stochastic dominance. Specifically, for gambles with different variance but identical expected values (EVs), the monkeys preferred high-variance gambles at low EVs and low-variance gambles at high EVs; in gambles with different skewness but identical EVs and variances, the animals preferred positively over symmetrical and negatively skewed gambles in a strongly transitive fashion. Thus, the utility functions predicted the animals’ preferences for variance-risk and skewness-risk. Using these well-defined forms of risk, this study shows that monkeys’ choices conform to the internal reward valuations suggested by their utility functions. This result implies a representation of utility in monkeys that accounts for both variance-risk and skewness-risk preferences. PMID:27402743

  19. Variance After-Effects Distort Risk Perception in Humans.

    PubMed

    Payzan-LeNestour, Elise; Balleine, Bernard W; Berrada, Tony; Pearson, Joel

    2016-06-01

    In many contexts, decision-making requires an accurate representation of outcome variance-otherwise known as "risk" in economics. Conventional economic theory assumes this representation to be perfect, thereby focusing on risk preferences rather than risk perception per se [1-3] (but see [4]). However, humans often misrepresent their physical environment. Perhaps the most striking of such misrepresentations are the many well-known sensory after-effects, which most commonly involve visual properties, such as color, contrast, size, and motion. For example, viewing downward motion of a waterfall induces the anomalous biased experience of upward motion during subsequent viewing of static rocks to the side [5]. Given that after-effects are pervasive, occurring across a wide range of time horizons [6] and stimulus dimensions (including properties such as face perception [7, 8], gender [9], and numerosity [10]), and that some evidence exists that neurons show adaptation to variance in the sole visual feature of motion [11], we were interested in assessing whether after-effects distort variance perception in humans. We found that perceived variance is decreased after prolonged exposure to high variance and increased after exposure to low variance within a number of different visual representations of variance. We demonstrate these after-effects occur across very different visual representations of variance, suggesting that these effects are not sensory, but operate at a high (cognitive) level of information processing. These results suggest, therefore, that variance constitutes an independent cognitive property and that prolonged exposure to extreme variance distorts risk perception-a fundamental challenge for economic theory and practice. PMID:27161500

  20. Food additives.

    PubMed

    Berglund, F

    1978-01-01

    The use of additives to food fulfils many purposes, as shown by the index issued by the Codex Committee on Food Additives: Acids, bases and salts; Preservatives, Antioxidants and antioxidant synergists; Anticaking agents; Colours; Emulfifiers; Thickening agents; Flour-treatment agents; Extraction solvents; Carrier solvents; Flavours (synthetic); Flavour enhancers; Non-nutritive sweeteners; Processing aids; Enzyme preparations. Many additives occur naturally in foods, but this does not exclude toxicity at higher levels. Some food additives are nutrients, or even essential nutritents, e.g. NaCl. Examples are known of food additives causing toxicity in man even when used according to regulations, e.g. cobalt in beer. In other instances, poisoning has been due to carry-over, e.g. by nitrate in cheese whey - when used for artificial feed for infants. Poisonings also occur as the result of the permitted substance being added at too high levels, by accident or carelessness, e.g. nitrite in fish. Finally, there are examples of hypersensitivity to food additives, e.g. to tartrazine and other food colours. The toxicological evaluation, based on animal feeding studies, may be complicated by impurities, e.g. orthotoluene-sulfonamide in saccharin; by transformation or disappearance of the additive in food processing in storage, e.g. bisulfite in raisins; by reaction products with food constituents, e.g. formation of ethylurethane from diethyl pyrocarbonate; by metabolic transformation products, e.g. formation in the gut of cyclohexylamine from cyclamate. Metabolic end products may differ in experimental animals and in man: guanylic acid and inosinic acid are metabolized to allantoin in the rat but to uric acid in man. The magnitude of the safety margin in man of the Acceptable Daily Intake (ADI) is not identical to the "safety factor" used when calculating the ADI. The symptoms of Chinese Restaurant Syndrome, although not hazardous, furthermore illustrate that the whole ADI

  1. 40 CFR 260.33 - Procedures for variances from classification as a solid waste, for variances to be classified as...

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... classification as a solid waste, for variances to be classified as a boiler, or for non-waste determinations. 260... from classification as a solid waste, for variances to be classified as a boiler, or for non-waste... as boilers, or applications for non-waste determinations. (a) The applicant must apply to...

  2. 40 CFR 260.33 - Procedures for variances from classification as a solid waste, for variances to be classified as...

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... classification as a solid waste, for variances to be classified as a boiler, or for non-waste determinations. 260... from classification as a solid waste, for variances to be classified as a boiler, or for non-waste... as boilers, or applications for non-waste determinations. (a) The applicant must apply to...

  3. 40 CFR 260.33 - Procedures for variances from classification as a solid waste, for variances to be classified as...

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... classification as a solid waste, for variances to be classified as a boiler, or for non-waste determinations. 260... from classification as a solid waste, for variances to be classified as a boiler, or for non-waste... as boilers, or applications for non-waste determinations. (a) The applicant must apply to...

  4. 40 CFR 260.33 - Procedures for variances from classification as a solid waste, for variances to be classified as...

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... classification as a solid waste, for variances to be classified as a boiler, or for non-waste determinations. 260... from classification as a solid waste, for variances to be classified as a boiler, or for non-waste... as boilers, or applications for non-waste determinations. (a) The applicant must apply to...

  5. 40 CFR 260.33 - Procedures for variances from classification as a solid waste, for variances to be classified as...

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... classification as a solid waste, for variances to be classified as a boiler, or for non-waste determinations. 260... from classification as a solid waste, for variances to be classified as a boiler, or for non-waste... as boilers, or applications for non-waste determinations. (a) The applicant must apply to...

  6. Genetic analysis of water-deficit response traits in maize.

    PubMed

    Ahmad, M; Saleem, M; Ahsan, M; Ahmad, A

    2016-01-01

    A set of sixty inbred lines of maize (Zea mays L.) were screened in the greenhouse at the seedling stage under both normal and water-deficit conditions. Six water deficit-tolerant inbred lines were selected based on root to shoot ratios. These selected lines were crossed in a diallel pattern. The parental, F1, and reciprocal cross plants were planted in a field under both normal and water-deficit conditions. Normal irrigation was applied to the control set, while the water-deficit set received 50% of normal irrigation levels. Analyses of variance of various morpho-physiological parameters identified significant differences among the selected lines under both conditions, indicating the presence of significant genetic variability. Variance components for general combining ability (GCA), specific combining ability (SCA), and reciprocal effects for all the parameters were estimated to determine the relative importance of additive and non-additive or dominance type of gene action. Variance components for GCA were larger than for SCA indicating the preponderance of additive types of gene action for all the traits under study. Hybrids developed from inbred lines W-10 and W-64SP proved to have the best grain yield under normal and water-deficit conditions. Under water-deficit conditions, the best performing cross was B-34 x W-10. Hence, these inbred lines and the hybrids might be of value in future breeding programs. PMID:27051012

  7. Genetic Structure in Dwarf Bamboo (Bashania fangiana) Clonal Populations with Different Genet Ages

    PubMed Central

    Ma, Qing-qing; Song, Hui-xing; Zhou, Shi-qiang; Yang, Wan-qin; Li, De-sheng; Chen, Jin-song

    2013-01-01

    Amplified fragment length polymorphism (AFLP) fingerprints were used to reveal genotypic diversity of dwarf bamboo (Bashania fangiana) clonal populations with two different genet ages (≤30 years versus >70 years) at Wolong National Natural Reserve, Sichuan province, China. We generated AFLP fingerprints for 96 leaf samples, collected at 30 m intervals in the two populations, using ten selective primer pairs. A total of 92 genotypes were identified from the both populations. The mean proportion of distinguishable genotypes (G/N) was 0.9583 (0.9375 to 0.9792) and Simpson's index of diversity (D) was 0.9982 (0.9973 to 0.9991). So, two B. fangiana populations were multiclonal and highly diverse. The largest single clone may occur over a distance of about 30 m. Our results demonstrated that the genotypic diversity and genet density of B. fangiana clonal population did not change significantly (47 versus 45) with genet aging and low partitioned genetic differentiation was between the two populations (Gst = 0.0571). The analysis of molecular variance consistently showed that a large proportion of the genetic variation (87.79%) existed among the individuals within populations, whereas only 12.21% were found among populations. In addition, the high level of genotypic diversity in the two populations implies that the further works were needed to investigate the reasons for the poor seed set in B. fangiana after flowering. PMID:24244360

  8. Quantitative Genetics of Transgenic Mice: Components of Phenotypic Variation in Body Weights and Weight Gains

    PubMed Central

    Clutter, A. C.; Pomp, D.; Murray, J. D.

    1996-01-01

    Transgenic mice possessing an ovine growth hormone gene were used to study the effects of elevated growth hormone on quantitative genetic variation. Males hemizygous for the transgene were mated to wild-type females to produce half- and full-sib families in which approximately half the progeny were transgenic and half were wild type. Analyses of body weights at 3-10 weeks, and weight gains from 3 to 6, and 6 to 10 weeks produced estimates of the proportion of total variance due to additive genetic effects (h(2)) and common litter effects (c(2)), and the genetic correlation between transgenic and wild-type expression of each trait. At 10 weeks, body weight of transgenics exceeded that of wild types by 26 and 49% in males and females, respectively. Estimated genetic variances in the transgenic group were significantly greater than zero for body weights at most ages and for both measurements of gain. Common litter effects accounted for a similar proportion of variation in the wild-type and transgenic groups. Additive genetic correlations between wild-type and transgenic expression of body weights tended to decline with age, indicating that a partially different array of genes may have begun to affect body weight in the transgenic group. PMID:8844161

  9. Genetic architecture of the pro-inflammatory state in an extended twin-family design.

    PubMed

    Neijts, Melanie; van Dongen, Jenny; Kluft, Cornelis; Boomsma, Dorret I; Willemsen, Gonneke; de Geus, Eco J C

    2013-10-01

    In this study we examined the genetic architecture of variation in the pro-inflammatory state, using an extended twin-family design. Within the Netherlands Twin Register Biobank, fasting Tumor Necrosis Factor-α (TNF-α), Interleukin-6 (IL-6), C-Reactive Protein (CRP), and fibrinogen levels were available for 3,534 twins, 1,568 of their non-twin siblings, and 2,227 parents from 3,095 families. Heritability analyses took into account the effects of current and recent illness, anti-inflammatory medication, female sex hormone status, age, sex, body mass index, smoking status, month of data collection, and batch processing. Moderate broad-sense heritability was found for all inflammatory parameters (39%, 21%, 45%, and 46% for TNF-α, IL-6, CRP and fibrinogen, respectively). For all parameters, the remaining variance was explained by unique environmental influences and not by environment shared by family members. There was no resemblance between spouses for any of the inflammatory parameters, except for fibrinogen. Also, there was no evidence for twin-specific effects. A considerable part of genetic variation was explained by non-additive genetic effects for TNF-α, CRP, and fibrinogen. For IL-6, all genetic variance was additive. This study may have implications for future genome-wide association studies by setting a clear numerical target for genome-wide screens that aim to find genetic variants regulating the levels of these pro-inflammatory markers. PMID:23953347

  10. The efficiency of close inbreeding to reduce genetic adaptation to captivity

    PubMed Central

    Theodorou, K; Couvet, D

    2015-01-01

    Although ex situ conservation is indispensable for thousands of species, captive breeding is associated with negative genetic changes: loss of genetic variance and genetic adaptation to captivity that is deleterious in the wild. We used quantitative genetic individual-based simulations to model the effect of genetic management on the evolution of a quantitative trait and the associated fitness of wild-born individuals that are brought to captivity. We also examined the feasibility of the breeding strategies under a scenario of a large number of loci subject to deleterious mutations. We compared two breeding strategies: repeated half-sib mating and a method of minimizing mean coancestry (referred to as gc/mc). Our major finding was that half-sib mating is more effective in reducing genetic adaptation to captivity than the gc/mc method. Moreover, half-sib mating retains larger allelic and adaptive genetic variance. Relative to initial standing variation, the additive variance of the quantitative trait increased under half-sib mating during the sojourn in captivity. Although fragmentation into smaller populations improves the efficiency of the gc/mc method, half-sib mating still performs better in the scenarios tested. Half-sib mating shows two caveats that could mitigate its beneficial effects: low heterozygosity and high risk of extinction when populations are of low fecundity and size and one of the following conditions are met: (i) the strength of selection in captivity is comparable with that in the wild, (ii) deleterious mutations are numerous and only slightly deleterious. Experimental validation of half-sib mating is therefore needed for the advancement of captive breeding programs. PMID:25052417

  11. The efficiency of close inbreeding to reduce genetic adaptation to captivity.

    PubMed

    Theodorou, K; Couvet, D

    2015-01-01

    Although ex situ conservation is indispensable for thousands of species, captive breeding is associated with negative genetic changes: loss of genetic variance and genetic adaptation to captivity that is deleterious in the wild. We used quantitative genetic individual-based simulations to model the effect of genetic management on the evolution of a quantitative trait and the associated fitness of wild-born individuals that are brought to captivity. We also examined the feasibility of the breeding strategies under a scenario of a large number of loci subject to deleterious mutations. We compared two breeding strategies: repeated half-sib mating and a method of minimizing mean coancestry (referred to as gc/mc). Our major finding was that half-sib mating is more effective in reducing genetic adaptation to captivity than the gc/mc method. Moreover, half-sib mating retains larger allelic and adaptive genetic variance. Relative to initial standing variation, the additive variance of the quantitative trait increased under half-sib mating during the sojourn in captivity. Although fragmentation into smaller populations improves the efficiency of the gc/mc method, half-sib mating still performs better in the scenarios tested. Half-sib mating shows two caveats that could mitigate its beneficial effects: low heterozygosity and high risk of extinction when populations are of low fecundity and size and one of the following conditions are met: (i) the strength of selection in captivity is comparable with that in the wild, (ii) deleterious mutations are numerous and only slightly deleterious. Experimental validation of half-sib mating is therefore needed for the advancement of captive breeding programs. PMID:25052417

  12. Random regression models to estimate genetic parameters for test-day milk yield in Brazilian Murrah buffaloes.

    PubMed

    Sesana, R C; Bignardi, A B; Borquis, R R A; El Faro, L; Baldi, F; Albuquerque, L G; Tonhati, H

    2010-10-01

    The objective of this work was to estimate covariance functions for additive genetic and permanent environmental effects and, subsequently, to obtain genetic parameters for buffalo's test-day milk production using random regression models on Legendre polynomials (LPs). A total of 17 935 test-day milk yield (TDMY) from 1433 first lactations of Murrah buffaloes, calving from 1985 to 2005 and belonging to 12 herds located in São Paulo state, Brazil, were analysed. Contemporary groups (CGs) were defined by herd, year and month of milk test. Residual variances were modelled through variance functions, from second to fourth order and also by a step function with 1, 4, 6, 22 and 42 classes. The model of analyses included the fixed effect of CGs, number of milking, age of cow at calving as a covariable (linear and quadratic) and the mean trend of the population. As random effects were included the additive genetic and permanent environmental effects. The additive genetic and permanent environmental random effects were modelled by LP of days in milk from quadratic to seventh degree polynomial functions. The model with additive genetic and animal permanent environmental effects adjusted by quintic and sixth order LP, respectively, and residual variance modelled through a step function with six classes was the most adequate model to describe the covariance structure of the data. Heritability estimates decreased from 0.44 (first week) to 0.18 (fourth week). Unexpected negative genetic correlation estimates were obtained between TDMY records at first weeks with records from middle to the end of lactation, being the values varied from -0.07 (second with eighth week) to -0.34 (1st with 42nd week). TDMY heritability estimates were moderate in the course of the lactation, suggesting that this trait could be applied as selection criteria in milking buffaloes. PMID:20831561

  13. Meta-analysis of ratios of sample variances.

    PubMed

    Prendergast, Luke A; Staudte, Robert G

    2016-05-20

    When conducting a meta-analysis of standardized mean differences (SMDs), it is common to use Cohen's d, or its variants, that require equal variances in the two arms of each study. While interpretation of these SMDs is simple, this alone should not be used as a justification for assuming equal variances. Until now, researchers have either used an F-test for each individual study or perhaps even conveniently ignored such tools altogether. In this paper, we propose a meta-analysis of ratios of sample variances to assess whether the equality of variances assumptions is justified prior to a meta-analysis of SMDs. Quantile-quantile plots, an omnibus test for equal variances or an overall meta-estimate of the ratio of variances can all be used to formally justify the use of less common methods when evidence of unequal variances is found. The methods in this paper are simple to implement and the validity of the approaches are reinforced by simulation studies and an application to a real data set. Copyright © 2016 John Wiley & Sons, Ltd. PMID:27062644

  14. A note on preliminary tests of equality of variances.

    PubMed

    Zimmerman, Donald W

    2004-05-01

    Preliminary tests of equality of variances used before a test of location are no longer widely recommended by statisticians, although they persist in some textbooks and software packages. The present study extends the findings of previous studies and provides further reasons for discontinuing the use of preliminary tests. The study found Type I error rates of a two-stage procedure, consisting of a preliminary Levene test on samples of different sizes with unequal variances, followed by either a Student pooled-variances t test or a Welch separate-variances t test. Simulations disclosed that the twostage procedure fails to protect the significance level and usually makes the situation worse. Earlier studies have shown that preliminary tests often adversely affect the size of the test, and also that the Welch test is superior to the t test when variances are unequal. The present simulations reveal that changes in Type I error rates are greater when sample sizes are smaller, when the difference in variances is slight rather than extreme, and when the significance level is more stringent. Furthermore, the validity of the Welch test deteriorates if it is used only on those occasions where a preliminary test indicates it is needed. Optimum protection is assured by using a separate-variances test unconditionally whenever sample sizes are unequal. PMID:15171807

  15. Environmental and genetic influences on early attachment

    PubMed Central

    Gervai, Judit

    2009-01-01

    Attachment theory predicts and subsequent empirical research has amply demonstrated that individual variations in patterns of early attachment behaviour are primarily influenced by differences in sensitive responsiveness of caregivers. However, meta-analyses have shown that parenting behaviour accounts for about one third of the variance in attachment security or disorganisation. The exclusively environmental explanation has been challenged by results demonstrating some, albeit inconclusive, evidence of the effect of infant temperament. In this paper, after reviewing briefly the well-demonstrated familial and wider environmental influences, the evidence is reviewed for genetic and gene-environment interaction effects on developing early attachment relationships. Studies investigating the interaction of genes of monoamine neurotransmission with parenting environment in the course of early relationship development suggest that children's differential susceptibility to the rearing environment depends partly on genetic differences. In addition to the overview of environmental and genetic contributions to infant attachment, and especially to disorganised attachment relevant to mental health issues, the few existing studies of gene-attachment interaction effects on development of childhood behavioural problems are also reviewed. A short account of the most important methodological problems to be overcome in molecular genetic studies of psychological and psychiatric phenotypes is also given. Finally, animal research focusing on brain-structural aspects related to early care and the new, conceptually important direction of studying environmental programming of early development through epigenetic modification of gene functioning is examined in brief. PMID:19732441

  16. Genetic control of inflorescence in common bean.

    PubMed

    Guilherme, S R; Ramalho, M A P; de F B Abreu, A; Pereira, L A

    2014-01-01

    The number of pods per common bean plant is a primary component of grain yield, which depends on the number of flowers produced and on the flower set. Thus, a larger number of flowers per plant would increase yield. Lines with inflorescences that had a large number of flowers compared to common bean plants now under cultivation were identified. We analyzed the genetic control of this trait and its association with grain yield. The cultivar BRSMG Talismã was crossed with 2 lines, L.59583 and L.59692, which have a large number of flowers. The F1, F2, and F3 generations were obtained. These generations were assessed together with the parents in a randomized block experimental design with 2 replications. The traits assessed included length of inflorescence, number of pods per inflorescence, number of pods per plant, number of grains per plant, 100-grain weight, and grain yield per plant. Mean genetic components and variance were estimated. The traits length of inflorescence and number of pods per inflorescence exhibited genetic control with predominance that showed an additive effect. In the 2 crosses, genetic control of grain yield and of its primary components showed that the allelic interaction of dominance was high. The wide variability in the traits assessed may be used to increase yield of the common bean plant by increasing the number of flowers on the plant. PMID:25501247

  17. Species interactions differ in their genetic robustness

    DOE PAGESBeta

    Chubiz, Lon M.; Granger, Brian R.; Segre, Daniel; Harcombe, William R.

    2015-04-14

    Conflict and cooperation between bacterial species drive the composition and function of microbial communities. Stability of these emergent properties will be influenced by the degree to which species' interactions are robust to genetic perturbations. We use genome-scale metabolic modeling to computationally analyze the impact of genetic changes when Escherichia coli and Salmonella enterica compete, or cooperate. We systematically knocked out in silico each reaction in the metabolic network of E. coli to construct all 2583 mutant stoichiometric models. Then, using a recently developed multi-scale computational framework, we simulated the growth of each mutant E. coli in the presence of S.more » enterica. The type of interaction between species was set by modulating the initial metabolites present in the environment. We found that the community was most robust to genetic perturbations when the organisms were cooperating. Species ratios were more stable in the cooperative community, and community biomass had equal variance in the two contexts. Additionally, the number of mutations that have a substantial effect is lower when the species cooperate than when they are competing. In contrast, when mutations were added to the S. enterica network the system was more robust when the bacteria were competing. These results highlight the utility of connecting metabolic mechanisms and studies of ecological stability. Cooperation and conflict alter the connection between genetic changes and properties that emerge at higher levels of biological organization.« less

  18. Variance Estimation for Myocardial Blood Flow by Dynamic PET.

    PubMed

    Moody, Jonathan B; Murthy, Venkatesh L; Lee, Benjamin C; Corbett, James R; Ficaro, Edward P

    2015-11-01

    The estimation of myocardial blood flow (MBF) by (13)N-ammonia or (82)Rb dynamic PET typically relies on an empirically determined generalized Renkin-Crone equation to relate the kinetic parameter K1 to MBF. Because the Renkin-Crone equation defines MBF as an implicit function of K1, the MBF variance cannot be determined using standard error propagation techniques. To overcome this limitation, we derived novel analytical approximations that provide first- and second-order estimates of MBF variance in terms of the mean and variance of K1 and the Renkin-Crone parameters. The accuracy of the analytical expressions was validated by comparison with Monte Carlo simulations, and MBF variance was evaluated in clinical (82)Rb dynamic PET scans. For both (82)Rb and (13)N-ammonia, good agreement was observed between both (first- and second-order) analytical variance expressions and Monte Carlo simulations, with moderately better agreement for second-order estimates. The contribution of the Renkin-Crone relation to overall MBF uncertainty was found to be as high as 68% for (82)Rb and 35% for (13)N-ammonia. For clinical (82)Rb PET data, the conventional practice of neglecting the statistical uncertainty in the Renkin-Crone parameters resulted in underestimation of the coefficient of variation of global MBF and coronary flow reserve by 14-49%. Knowledge of MBF variance is essential for assessing the precision and reliability of MBF estimates. The form and statistical uncertainty in the empirical Renkin-Crone relation can make substantial contributions to the variance of MBF. The novel analytical variance expressions derived in this work enable direct estimation of MBF variance which includes this previously neglected contribution. PMID:25974932

  19. Global Gravity Wave Variances from Aura MLS: Characteristics and Interpretation

    NASA Technical Reports Server (NTRS)

    Wu, Dong L.; Eckermann, Stephen D.

    2008-01-01

    The gravity wave (GW)-resolving capabilities of 118-GHz saturated thermal radiances acquired throughout the stratosphere by the Microwave Limb Sounder (MLS) on the Aura satellite are investigated and initial results presented. Because the saturated (optically thick) radiances resolve GW perturbations from a given altitude at different horizontal locations, variances are evaluated at 12 pressure altitudes between 21 and 51 km using the 40 saturated radiances found at the bottom of each limb scan. Forward modeling simulations show that these variances are controlled mostly by GWs with vertical wavelengths z 5 km and horizontal along-track wavelengths of y 100-200 km. The tilted cigar-shaped three-dimensional weighting functions yield highly selective responses to GWs of high intrinsic frequency that propagate toward the instrument. The latter property is used to infer the net meridional component of GW propagation by differencing the variances acquired from ascending (A) and descending (D) orbits. Because of improved vertical resolution and sensitivity, Aura MLS GW variances are 5?8 times larger than those from the Upper Atmosphere Research Satellite (UARS) MLS. Like UARS MLS variances, monthly-mean Aura MLS variances in January and July 2005 are enhanced when local background wind speeds are large, due largely to GW visibility effects. Zonal asymmetries in variance maps reveal enhanced GW activity at high latitudes due to forcing by flow over major mountain ranges and at tropical and subtropical latitudes due to enhanced deep convective generation as inferred from contemporaneous MLS cloud-ice data. At 21-28-km altitude (heights not measured by the UARS MLS), GW variance in the tropics is systematically enhanced and shows clear variations with the phase of the quasi-biennial oscillation, in general agreement with GW temperature variances derived from radiosonde, rocketsonde, and limb-scan vertical profiles.

  20. Time Variability of Quasars: the Structure Function Variance

    NASA Astrophysics Data System (ADS)

    MacLeod, C.; Ivezić, Ž.; de Vries, W.; Sesar, B.; Becker, A.

    2008-12-01

    Significant progress in the description of quasar variability has been recently made by employing SDSS and POSS data. Common to most studies is a fundamental assumption that photometric observations at two epochs for a large number of quasars will reveal the same statistical properties as well-sampled light curves for individual objects. We critically test this assumption using light curves for a sample of ~2,600 spectroscopically confirmed quasars observed about 50 times on average over 8 years by the SDSS stripe 82 survey. We find that the dependence of the mean structure function computed for individual quasars on luminosity, rest-frame wavelength and time is qualitatively and quantitatively similar to the behavior of the structure function derived from two-epoch observations of a much larger sample. We also reproduce the result that the variability properties of radio and X-ray selected subsamples are different. However, the scatter of the variability structure function for fixed values of luminosity, rest-frame wavelength and time is similar to the scatter induced by the variance of these quantities in the analyzed sample. Hence, our results suggest that, although the statistical properties of quasar variability inferred using two-epoch data capture some underlying physics, there is significant additional information that can be extracted from well-sampled light curves for individual objects.

  1. Genetic Screening

    PubMed Central

    Burke, Wylie; Tarini, Beth; Press, Nancy A.; Evans, James P.

    2011-01-01

    Current approaches to genetic screening include newborn screening to identify infants who would benefit from early treatment, reproductive genetic screening to assist reproductive decision making, and family history assessment to identify individuals who would benefit from additional prevention measures. Although the traditional goal of screening is to identify early disease or risk in order to implement preventive therapy, genetic screening has always included an atypical element—information relevant to reproductive decisions. New technologies offer increasingly comprehensive identification of genetic conditions and susceptibilities. Tests based on these technologies are generating a different approach to screening that seeks to inform individuals about all of their genetic traits and susceptibilities for purposes that incorporate rapid diagnosis, family planning, and expediting of research, as well as the traditional screening goal of improving prevention. Use of these tests in population screening will increase the challenges already encountered in genetic screening programs, including false-positive and ambiguous test results, overdiagnosis, and incidental findings. Whether this approach is desirable requires further empiric research, but it also requires careful deliberation on the part of all concerned, including genomic researchers, clinicians, public health officials, health care payers, and especially those who will be the recipients of this novel screening approach. PMID:21709145

  2. Mesoscale Gravity Wave Variances from AMSU-A Radiances

    NASA Technical Reports Server (NTRS)

    Wu, Dong L.

    2004-01-01

    A variance analysis technique is developed here to extract gravity wave (GW) induced temperature fluctuations from NOAA AMSU-A (Advanced Microwave Sounding Unit-A) radiance measurements. By carefully removing the instrument/measurement noise, the algorithm can produce reliable GW variances with the minimum detectable value as small as 0.1 K2. Preliminary analyses with AMSU-A data show GW variance maps in the stratosphere have very similar distributions to those found with the UARS MLS (Upper Atmosphere Research Satellite Microwave Limb Sounder). However, the AMSU-A offers better horizontal and temporal resolution for observing regional GW variability, such as activity over sub-Antarctic islands.

  3. Potlining Additives

    SciTech Connect

    Rudolf Keller

    2004-08-10

    In this project, a concept to improve the performance of aluminum production cells by introducing potlining additives was examined and tested. Boron oxide was added to cathode blocks, and titanium was dissolved in the metal pool; this resulted in the formation of titanium diboride and caused the molten aluminum to wet the carbonaceous cathode surface. Such wetting reportedly leads to operational improvements and extended cell life. In addition, boron oxide suppresses cyanide formation. This final report presents and discusses the results of this project. Substantial economic benefits for the practical implementation of the technology are projected, especially for modern cells with graphitized blocks. For example, with an energy savings of about 5% and an increase in pot life from 1500 to 2500 days, a cost savings of $ 0.023 per pound of aluminum produced is projected for a 200 kA pot.

  4. Phosphazene additives

    SciTech Connect

    Harrup, Mason K; Rollins, Harry W

    2013-11-26

    An additive comprising a phosphazene compound that has at least two reactive functional groups and at least one capping functional group bonded to phosphorus atoms of the phosphazene compound. One of the at least two reactive functional groups is configured to react with cellulose and the other of the at least two reactive functional groups is configured to react with a resin, such as an amine resin of a polycarboxylic acid resin. The at least one capping functional group is selected from the group consisting of a short chain ether group, an alkoxy group, or an aryloxy group. Also disclosed are an additive-resin admixture, a method of treating a wood product, and a wood product.

  5. Quantitative genetics of female choice in an ultrasonic pyralid moth, Achroia grisella: variation and evolvability of preference along multiple dimensions of the male advertisement signal.

    PubMed

    Jang, Y; Greenfield, M D

    2000-01-01

    The mating system of Achroia grisella (Lepidoptera: Pyralidae) is characterized by male ultrasonic advertisement signalling to which females orientate. Although males provide no direct, somatic benefits to their mates, females prefer males whose signal characters are more exaggerated than the population means. Previous studies showed that the signal characters influencing mate attraction are highly repeatable and heritable. We measured the phenotypic and additive genetic variances (heritability) of female preference in A. grisella, as this additive genetic variance is one of the genetic assumptions of indirect models of sexual selection. We determined the preference index of female A. grisella by repeated phonotaxis trials in which a choice of simulated male signals was presented. These playback experiments showed that female preference indices varied but were repeatable within individuals. Specifically, females differ in the relative importance of the several signal characters during mate assessment. A subsequent half-sib breeding design revealed an amount of additive genetic variance for the female preference index (h(s)2 = 0.212, SE = 0.1347, P = 0.0611; CVA = 0.1826). Our study highlights the importance of careful preparation of test signals and experimental design for quantifying individual variation in (female) preference along multiple signal dimensions. PMID:10692013

  6. Increased genetic risk for obesity in premature coronary artery disease

    PubMed Central

    Cole, Christopher B; Nikpay, Majid; Stewart, Alexandre FR; McPherson, Ruth

    2016-01-01

    There is ongoing controversy as to whether obesity confers risk for CAD independently of associated risk factors including diabetes mellitus. We have carried out a Mendelian randomization study using a genetic risk score (GRS) for body mass index (BMI) based on 35 risk alleles to investigate this question in a population of 5831 early onset CAD cases without diabetes mellitus and 3832 elderly healthy control subjects, all of strictly European ancestry, with adjustment for traditional risk factors (TRFs). We then estimated the genetic correlation between these BMI and CAD (rg) by relating the pairwise genetic similarity matrix to a phenotypic covariance matrix between these two traits. GRSBMI significantly (P=2.12 × 10−12) associated with CAD status in a multivariate model adjusted for TRFs, with a per allele odds ratio (OR) of 1.06 (95% CI 1.042–1.076). The addition of GRSBMI to TRFs explained 0.75% of CAD variance and yielded a continuous net recombination index of 16.54% (95% CI=11.82–21.26%, P<0.0001). To test whether GRSBMI explained CAD status when adjusted for measured BMI, separate models were constructed in which the score and BMI were either included as covariates or not. The addition of BMI explained ~1.9% of CAD variance and GRSBMI plus BMI explained 2.65% of CAD variance. Finally, using bivariate restricted maximum likelihood analysis, we provide strong evidence of genome-wide pleiotropy between obesity and CAD. This analysis supports the hypothesis that obesity is a causal risk factor for CAD. PMID:26220701

  7. Genetic landscapes GIS Toolbox: tools to map patterns of genetic divergence and diversity.

    USGS Publications Warehouse

    Vandergast, Amy G.; Perry, William M.; Lugo, Roberto V.; Hathaway, Stacie A.

    2011-01-01

    The Landscape Genetics GIS Toolbox contains tools that run in the Geographic Information System software, ArcGIS, to map genetic landscapes and to summarize multiple genetic landscapes as average and variance surfaces. These tools can be used to visualize the distribution of genetic diversity across geographic space and to study associations between patterns of genetic diversity and geographic features or other geo-referenced environmental data sets. Together, these tools create genetic landscape surfaces directly from tables containing genetic distance or diversity data and sample location coordinates, greatly reducing the complexity of building and analyzing these raster surfaces in a Geographic Information System.

  8. Estimating Genetic and Maternal Effects Determining Variation in Immune Function of a Mixed-Mating Snail

    PubMed Central

    Seppälä, Otto; Langeloh, Laura

    2016-01-01

    Evolution of host defenses such as immune function requires heritable genetic variation in them. However, also non-genetic maternal effects can contribute to phenotypic variation, thus being an alternative target for natural selection. We investigated the role of individuals’ genetic background and maternal effects in determining immune defense traits (phenoloxidase and antibacterial activity of hemolymph), as well as in survival and growth, in the simultaneously hermaphroditic snail Lymnaea stagnalis. We utilized the mixed mating system of this species by producing full-sib families in which each parental snail had produced offspring as both a dam and as a sire, and tested whether genetic background (family) and non-genetic maternal effects (dam nested within family) explain trait variation. Immune defense traits and growth were affected solely by individuals’ genetic background. Survival of snails did not show family-level variation. Additionally, some snails were produced through self-fertilization. They showed reduced growth and survival suggesting recessive load or overdominance. Immune defense traits did not respond to inbreeding. Our results suggest that the variation in snail immune function and growth was due to genetic differences. Since immune traits did not respond to inbreeding, this variation is most likely due to additive or epistatic genetic variance. PMID:27551822

  9. Estimating Genetic and Maternal Effects Determining Variation in Immune Function of a Mixed-Mating Snail.

    PubMed

    Seppälä, Otto; Langeloh, Laura

    2016-01-01

    Evolution of host defenses such as immune function requires heritable genetic variation in them. However, also non-genetic maternal effects can contribute to phenotypic variation, thus being an alternative target for natural selection. We investigated the role of individuals' genetic background and maternal effects in determining immune defense traits (phenoloxidase and antibacterial activity of hemolymph), as well as in survival and growth, in the simultaneously hermaphroditic snail Lymnaea stagnalis. We utilized the mixed mating system of this species by producing full-sib families in which each parental snail had produced offspring as both a dam and as a sire, and tested whether genetic background (family) and non-genetic maternal effects (dam nested within family) explain trait variation. Immune defense traits and growth were affected solely by individuals' genetic background. Survival of snails did not show family-level variation. Additionally, some snails were produced through self-fertilization. They showed reduced growth and survival suggesting recessive load or overdominance. Immune defense traits did not respond to inbreeding. Our results suggest that the variation in snail immune function and growth was due to genetic differences. Since immune traits did not respond to inbreeding, this variation is most likely due to additive or epistatic genetic variance. PMID:27551822

  10. A note on the asymptotic distribution of likelihood ratio tests to test variance components.

    PubMed

    Visscher, Peter M

    2006-08-01

    When using maximum likelihood methods to estimate genetic and environmental components of (co)variance, it is common to test hypotheses using likelihood ratio tests, since such tests have desirable asymptotic properties. In particular, the standard likelihood ratio test statistic is assumed asymptotically to follow a chi2 distribution with degrees of freedom equal to the number of parameters tested. Using the relationship between least squares and maximum likelihood estimators for balanced designs, it is shown why the asymptotic distribution of the likelihood ratio test for variance components does not follow a chi2 distribution with degrees of freedom equal to the number of parameters tested when the null hypothesis is true. Instead, the distribution of the likelihood ratio test is a mixture of chi2 distributions with different degrees of freedom. Implications for testing variance components in twin designs and for quantitative trait loci mapping are discussed. The appropriate distribution of the likelihood ratio test statistic should be used in hypothesis testing and model selection. PMID:16899155

  11. The genetic architecture of house fly mating behavior.

    PubMed

    Meffert, Lisa M; Hagenbuch, Kara L

    2005-01-01

    This chapter summarizes several experimental approaches used to identify the effects of dominance, epistasis, and genotype-by-environment interactions in the genetic architecture of the mating behavior of the common house fly (Musca domestica L.). Quantitative genetic investigations of mating behavior hold special intrigue for unraveling the complexities of fitness traits, with applications to theory on sexual selection and speciation. Besides being well suited to large-scale quantitative genetic protocols, the house fly has a remarkably complex courtship repertoire, affording special opportunities for studies on communication, social interactions, and learning. Increased additive genetic variances for the courtship repertoire of experimentally bottlenecked populations provided evidence for the presence of dominance and/or epistasis. Negative genetic variances in these populations suggested genotype-by-environment interactions, where the environment is the mating partner. Line cross assays of populations that had been subjected to selection for divergent courtship repertoire confirmed that both dominance and epistasis have significant effects. These crosses also showed more directly that the expression of the male's genotype is dependent upon the preferences of his mating partner. Repeatability studies also detailed how males alter their courtship performances with successive encounters within and across females, such that the males learn to improve their techniques in securing copulations. A review of 41 animal behavior studies found that a wide range of traits and taxa have dominance, epistasis, and genotype-y-environment interactions, although house fly courtship may remain a unique model where learning is an intersexually selected trait. Future development of more sophisticated molecular techniques for the M. domestica genome will help unravel the underlying biochemical and developmental pathways of these quantitative genetic interactions for a more complete

  12. Some variance reduction methods for numerical stochastic homogenization.

    PubMed

    Blanc, X; Le Bris, C; Legoll, F

    2016-04-28

    We give an overview of a series of recent studies devoted to variance reduction techniques for numerical stochastic homogenization. Numerical homogenization requires that a set of problems is solved at the microscale, the so-called corrector problems. In a random environment, these problems are stochastic and therefore need to be repeatedly solved, for several configurations of the medium considered. An empirical average over all configurations is then performed using the Monte Carlo approach, so as to approximate the effective coefficients necessary to determine the macroscopic behaviour. Variance severely affects the accuracy and the cost of such computations. Variance reduction approaches, borrowed from other contexts in the engineering sciences, can be useful. Some of these variance reduction techniques are presented, studied and tested here. PMID:27002065

  13. RISK ANALYSIS, ANALYSIS OF VARIANCE: GETTING MORE FROM OUR DATA

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Analysis of variance (ANOVA) and regression are common statistical techniques used to analyze agronomic experimental data and determine significant differences among yields due to treatments or other experimental factors. Risk analysis provides an alternate and complimentary examination of the same...

  14. 40 CFR 142.42 - Consideration of a variance request.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... contaminant level required by the national primary drinking water regulations because of the nature of the raw... effectiveness of treatment methods for the contaminant for which the variance is requested. (2) Cost and...

  15. 40 CFR 141.4 - Variances and exemptions.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... subparts H, P, S, T, W, and Y of this part. ... total coliforms and E. coli and variances from any of the treatment technique requirements of subpart H... Section 141.4 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) WATER...

  16. A multicomb variance reduction scheme for Monte Carlo semiconductor simulators

    SciTech Connect

    Gray, M.G.; Booth, T.E.; Kwan, T.J.T.; Snell, C.M.

    1998-04-01

    The authors adapt a multicomb variance reduction technique used in neutral particle transport to Monte Carlo microelectronic device modeling. They implement the method in a two-dimensional (2-D) MOSFET device simulator and demonstrate its effectiveness in the study of hot electron effects. The simulations show that the statistical variance of hot electrons is significantly reduced with minimal computational cost. The method is efficient, versatile, and easy to implement in existing device simulators.

  17. Variance-component analysis of obesity in type 2 diabetes confirms loci on chromosomes 1q and 11q.

    PubMed

    van Tilburg, Jonathan H O; Sandkuijl, Lodewijk A; Strengman, Eric; Pearson, Peter L; van Haeften, Timon W; Wijmenga, Cisca

    2003-11-01

    To study genetic loci influencing obesity in nuclear families with type 2 diabetes, we performed a genome-wide screen with 325 microsatellite markers that had an average spacing of 11 cM and a mean heterozygosity of approximately 75% covering all 22 autosomes. Genotype data were obtained from 562 individuals from 178 families from the Breda Study Cohort. These families were determined to have at least two members with type 2 diabetes. As a measure of obesity, the BMI of each diabetes patient was determined. The genotypes were analyzed using variance components (VCs) analysis implemented in GENEHUNTER 2 to determine quantitative trait loci influencing BMI. The VC analysis revealed two genomic regions showing VC logarithm of odds (LOD) scores > or =1.0 on chromosome 1 and chromosome 11. The regions of interest on both chromosomes were further investigated by fine-mapping with additional markers, resulting in a VC LOD score of 1.5 on chromosome 1q and a VC LOD of 2.4 on chromosome 11q. The locus on chromosome 1 has been implicated previously in diabetes. The locus on chromosome 11 has been implicated previously in diabetes and obesity. Our study to determine linkage for BMI confirms the presence of quantitative trait loci influencing obesity in subjects with type 2 diabetes on chromosomes 1q31-q42 and 11q14-q24. PMID:14627748

  18. Regional Variance in Novice Perceptions of Hurricanes

    NASA Astrophysics Data System (ADS)

    Arthurs, L.; Van Den Broeke, M.

    2013-12-01

    In order to assess novice understandings of hurricane formation prior to explicit instruction on the topic, a two-question open-ended survey was administered to 337 students enrolled in introductory college-level geoscience courses in Georgia (n=169) and Nebraska (n=168) . Respondents explained in their own words how they think hurricanes form and sketched diagrams that complimented their textual descriptions. The authors developed and iteratively refined a coding rubric for the non-segmented data (whole response). Two raters independently applied this rubric to the entire data set with an initial inter-rater reliability of 71%, and of 100% after discussion of the initially mismatched codes. In addition, responses were segmented and analyzed for common content features. Textual and diagrammatic analyses of responses indicated a broad range of student ideas about hurricane formation, from more novice-like to more expert-like. These findings can assist the design of instructional materials, such as lecture tutorials, that address student misconceptions and facilitate conceptual learning.

  19. Moderate genetic drift is driven by extreme recruitment events in the invasive mollusk Crepidula fornicata.

    PubMed

    Riquet, F; Le Cam, S; Fonteneau, E; Viard, F

    2016-07-01

    Effective population size (Ne) is a measure of genetic drift and is thus a central parameter in evolution, conservation genetics and invasion biology. Interestingly, in native marine species, Ne is typically several orders of magnitude lower than the census size. This pattern has often been explained by high fecundity, variation in reproductive success and pronounced early mortality, resulting in genetic drift across generations. Data documenting genetic drift and/or Ne in marine invasive species are, however, still scarce. We examined the importance of genetic drift in the invasive species Crepidula fornicata by genotyping 681 juveniles sampled during each annual recruitment peak over nine consecutive years in the Bay of Morlaix (Brittany, France). Observed variations in genetic diversity were partially explained by variation in recruitment intensity. In addition, substantial temporal genetic differentiation was documented (that is, genetic drift), and was attributed to nonrandom variance in the reproductive success of different breeding groups across years in the study species. Using a set of single-sample and temporal estimators for Ne, we estimated Ne to be three or four orders of magnitude smaller than the census size (Nc). On one hand, this reduction in Ne relative to Nc appeared congruent with, although slight higher than, values commonly observed in native marine species. Particular life-history traits of this invasive species may play an important role in buffering genetic drift. On the other hand, Ne still remained far below Nc, hence, possibly reducing the efficiency of selection effects. PMID:27118155

  20. Genetic Effects on Children’s Conversational Language Use

    PubMed Central

    DeThorne, Laura S.; Petrill, Stephen A.; Hart, Sara A.; Channell, Ron W.; Campbell, Rebecca J.; Deater-Deckard, Kirby; Thompson, Lee Anne; Vandenbergh, David J.

    2008-01-01

    Purpose The present study examined the extent of genetic and environmental influences on individual differences in children’s conversational language use. Method Behavioral genetic analyses focused on conversational measures and 2 standardized tests from 380 twins (M = 7.13 years) during the 2nd year of the Western Reserve Reading Project (S. A. Petrill, K. Deater-Deckard, L. A. Thompson, L. S. DeThorne, & C. Schatschneider, 2006). Multivariate analyses using latent factors were conducted to examine the extent of genetic overlap and specificity between conversational and formalized language. Results Multivariate analyses revealed a heritability of .70 for the conversational language factor and .45 for the formal language factor, with a significant genetic correlation of .37 between the two factors. Specific genetic effects were also significant for the conversational factor. Conclusions The current study indicated that over half of the variance in children’s conversational language skills can be accounted for by genetic effects with no evidence of significant shared environmental influence. This finding casts an alternative lens on past studies that have attributed differences in children’s spontaneous language use to differences in environmental language exposure. In addition, multivariate results generally support the context-dependent construction of language knowledge, as suggested by the theory of activity and situated cognition (J. S. Brown, A. Collins, & P. Duguid, 1989; T. A. Ukrainetz, 1998), but also indicate some degree of overlap between language use in conversational and formalized assessment contexts. PMID:18367687

  1. On variance estimate for covariate adjustment by propensity score analysis.

    PubMed

    Zou, Baiming; Zou, Fei; Shuster, Jonathan J; Tighe, Patrick J; Koch, Gary G; Zhou, Haibo

    2016-09-10

    Propensity score (PS) methods have been used extensively to adjust for confounding factors in the statistical analysis of observational data in comparative effectiveness research. There are four major PS-based adjustment approaches: PS matching, PS stratification, covariate adjustment by PS, and PS-based inverse probability weighting. Though covariate adjustment by PS is one of the most frequently used PS-based methods in clinical research, the conventional variance estimation of the treatment effects estimate under covariate adjustment by PS is biased. As Stampf et al. have shown, this bias in variance estimation is likely to lead to invalid statistical inference and could result in erroneous public health conclusions (e.g., food and drug safety and adverse events surveillance). To address this issue, we propose a two-stage analytic procedure to develop a valid variance estimator for the covariate adjustment by PS analysis strategy. We also carry out a simple empirical bootstrap resampling scheme. Both proposed procedures are implemented in an R function for public use. Extensive simulation results demonstrate the bias in the conventional variance estimator and show that both proposed variance estimators offer valid estimates for the true variance, and they are robust to complex confounding structures. The proposed methods are illustrated for a post-surgery pain study. Copyright © 2016 John Wiley & Sons, Ltd. PMID:26999553

  2. Analytic variance estimates of Swank and Fano factors

    SciTech Connect

    Gutierrez, Benjamin; Badano, Aldo; Samuelson, Frank

    2014-07-15

    Purpose: Variance estimates for detector energy resolution metrics can be used as stopping criteria in Monte Carlo simulations for the purpose of ensuring a small uncertainty of those metrics and for the design of variance reduction techniques. Methods: The authors derive an estimate for the variance of two energy resolution metrics, the Swank factor and the Fano factor, in terms of statistical moments that can be accumulated without significant computational overhead. The authors examine the accuracy of these two estimators and demonstrate how the estimates of the coefficient of variation of the Swank and Fano factors behave with data from a Monte Carlo simulation of an indirect x-ray imaging detector. Results: The authors' analyses suggest that the accuracy of their variance estimators is appropriate for estimating the actual variances of the Swank and Fano factors for a variety of distributions of detector outputs. Conclusions: The variance estimators derived in this work provide a computationally convenient way to estimate the error or coefficient of variation of the Swank and Fano factors during Monte Carlo simulations of radiation imaging systems.

  3. Variance estimation for systematic designs in spatial surveys.

    PubMed

    Fewster, R M

    2011-12-01

    In spatial surveys for estimating the density of objects in a survey region, systematic designs will generally yield lower variance than random designs. However, estimating the systematic variance is well known to be a difficult problem. Existing methods tend to overestimate the variance, so although the variance is genuinely reduced, it is over-reported, and the gain from the more efficient design is lost. The current approaches to estimating a systematic variance for spatial surveys are to approximate the systematic design by a random design, or approximate it by a stratified design. Previous work has shown that approximation by a random design can perform very poorly, while approximation by a stratified design is an improvement but can still be severely biased in some situations. We develop a new estimator based on modeling the encounter process over space. The new "striplet" estimator has negligible bias and excellent precision in a wide range of simulation scenarios, including strip-sampling, distance-sampling, and quadrat-sampling surveys, and including populations that are highly trended or have strong aggregation of objects. We apply the new estimator to survey data for the spotted hyena (Crocuta crocuta) in the Serengeti National Park, Tanzania, and find that the reported coefficient of variation for estimated density is 20% using approximation by a random design, 17% using approximation by a stratified design, and 11% using the new striplet estimator. This large reduction in reported variance is verified by simulation. PMID:21534940

  4. Analysis and application of minimum variance discrete time system identification. [for adaptive control system design

    NASA Technical Reports Server (NTRS)

    Kotob, S.; Kaufman, H.

    1976-01-01

    An on-line minimum variance parameter identifier is developed which embodies both accuracy and computational efficiency. The formulation results in a linear estimation problem with both additive and multiplicative noise. The resulting filter which utilizes both the covariance of the parameter vector itself and the covariance of the error in identification is proven to be mean square convergent and mean square consistent. The MV parameter identification scheme is then used to construct a stable state and parameter estimation algorithm.

  5. The genetic basis of female multiple mating in a polyandrous livebearing fish.

    PubMed

    Evans, Jonathan P; Gasparini, Clelia

    2012-01-01

    The widespread occurrence of female multiple mating (FMM) demands evolutionary explanation, particularly in the light of the costs of mating. One explanation encapsulated by "good sperm" and "sexy-sperm" (GS-SS) theoretical models is that FMM facilitates sperm competition, thus ensuring paternity by males that pass on genes for elevated sperm competitiveness to their male offspring. While support for this component of GS-SS theory is accumulating, a second but poorly tested assumption of these models is that there should be corresponding heritable genetic variation in FMM - the proposed mechanism of postcopulatory preferences underlying GS-SS models. Here, we conduct quantitative genetic analyses on paternal half-siblings to test this component of GS-SS theory in the guppy (Poecilia reticulata), a freshwater fish with some of the highest known rates of FMM in vertebrates. As with most previous quantitative genetic analyses of FMM in other species, our results reveal high levels of phenotypic variation in this trait and a correspondingly low narrow-sense heritability (h(2) = 0.11). Furthermore, although our analysis of additive genetic variance in FMM was not statistically significant (probably owing to limited statistical power), the ensuing estimate of mean-standardized additive genetic variance (I(A) = 0.7) was nevertheless relatively low compared with estimates published for life-history traits across a broad range of taxa. Our results therefore add to a growing body of evidence that FMM is characterized by relatively low additive genetic variation, thus apparently contradicting GS-SS theory. However, we qualify this conclusion by drawing attention to potential deficiencies in most designs (including ours) that have tested for genetic variation in FMM, particularly those that fail to account for intersexual interactions that underlie FMM in many systems. PMID:23403856

  6. Recent developments in alcoholism:genetic transmission.

    PubMed

    Goldman, D

    1993-01-01

    This chapter is an overview of developments in the study of genetic factors in vulnerability in alcoholism. The focus is on recent developments, including heritability studies in twins and transmission studies in families, both of which have continued to reveal evidence for a substantial role for genetic factors but also for etiologic complexity and variation in vulnerability across generations and across cultures. Studies are discussed which utilized psychophysiological and neurochemical markers for alcoholism for analysis of genetic association, transmission, and linkage. These markers include the low P300 event-related potential, sensitivity to ethanol's intoxicating and euphoric effects, platelet adenylate cyclase, and neurotransmitter metabolite concentrations. Although it is highly likely that many alcoholism-associated physiologic phenotypes are secondary traits, these approaches have increased the specificity of genetic analyses and genetic analyses are clarifying their relationship to alcoholism. For example, early efforts to study, in families, the co-occurrence of the P300 marker and alcoholism have yielded results indicating that the P300 abnormality precedes significant exposure to alcohol and that relatives of alcoholics are more likely to have this trait. In the area of animal models, two nonhuman primate species, the vervet monkey and the rhesus macaque, were shown to willingly consume alcohol to intoxicating blood levels. Also, linkage studies using the quantitative trait locus (QTL) mapping strategy were attempted for phenotypes relevant for alcoholism. The QTL strategy is theoretically capable of identifying determinant genes which contribute only a small portion of the variance. In human linkage studies, a genetic association was found to the DRD2 dopamine receptor. The DRD2 finding generated controversy, as a number of other groups failed to replicate it, and also focused attention on the advantages and pitfalls of the population association

  7. Variance in male lifetime reproductive success and estimation of the degree of polygyny in a primate

    PubMed Central

    Ruiz-Lambides, Angelina; Widdig, Anja

    2014-01-01

    The degree of polygyny is predicted to influence the strength of direct male–male competition, leading to a high variance in male lifetime reproductive success and to reproduction limited to the prime period of adulthood. Here, we explore the variance in male lifetime reproductive success and reproductive time in an anthropoid primate forming multimale–multifemale groups. Males of this species form dominance hierarchies, which are expected to skew reproduction toward few high-ranking males. At the same time, however, females mate with multiple males (polygynandry), which should limit the degree of polygyny. Using 20 years of genetic and demographic data, we calculated lifetime reproductive success for the free-ranging rhesus macaque (Macaca mulatta) population of Cayo Santiago for subjects that died naturally or reached senescence. Our results show that 1) male lifetime reproductive success was significantly skewed (range: 0–47 offspring; males reproducing below average: 62.8%; nonbreeders: 17.4%), 2) variance in male lifetime reproductive success was 5 times larger than in females, and 3) male lifetime reproductive success was more influenced by variation in fecundity (60%) than longevity (25%), suggesting that some direct male–male competition takes place. However, the opportunity for selection (i.e., standardized variance in male lifetime reproductive success) is low compared with that in other large mammal species characterized by a high degree of polygyny. Moreover, male reproductive life extended much beyond the prime period, showing that physical strength was not required to acquire mates. We conclude that rhesus macaques exhibit a moderate degree of polygyny and, therefore, low levels of direct male–male competition for fertile females, despite the fact that males form linear dominance hierarchies. PMID:25024637

  8. Modeling variation in early life mortality in the western lowland gorilla: Genetic, maternal and other effects.

    PubMed

    Ahsan, Monica H; Blomquist, Gregory E

    2015-06-01

    Uncovering sources of variation in gorilla infant mortality informs conservation and life history research efforts. The international studbook for the western lowland gorilla provides information on a sample of captive gorillas large enough for which to analyze genetic, maternal, and various other effects on early life mortality in this critically endangered species. We assess the importance of variables such as sex, maternal parity, paternal age, and hand rearing with regard to infant survival. We also quantify the proportions of variation in mortality influenced by heritable variation and maternal effects from these pedigree and survival data using variance component estimation. Markov chain Monte Carlo simulations of generalized linear mixed models produce variance component distributions in an animal model framework that employs all pedigree information. Two models, one with a maternal identity component and one with both additive genetic and maternal identity components, estimate variance components for different age classes during the first 2 years of life. This is informative of the extent to which mortality risk factors change over time during gorilla infancy. Our results indicate that gorilla mortality is moderately heritable with the strongest genetic influence just after birth. Maternal effects are most important during the first 6 months of life. Interestingly, hand-reared infants have lower mortality for the first 6 months of life. Aside from hand rearing, we found other predictors commonly used in studies of primate infant mortality to have little influence in these gorilla data. PMID:25809396

  9. Inter-vial Variance of the Sublimation Rate in Shelf Freeze-dryer

    NASA Astrophysics Data System (ADS)

    Kobayashi, Masakazu; Harashima, Konomi; Ariyama, Hiroichi; Yao, Ai-Ru

    Significant inter-vial variance in the sublimation rate has been pointed out by several authors in relation to the placement of the vials on a well controlled shelf. All the previous reports have described the phenomena observed in the experiments or the production processes, and have made some suggestive remarks, but have not clearly proposed a solution to the problem. In the shelf freeze-drying of pharmaceuticals, one of the major ploblems is how to achieve inter-vial uniformity and batch to batch uniformity or consistency. In this study, We have developed a new model of laboratory-scale freeze-dryer which has temperature-controllable chamber walls, and using this new model we have analyzed causes of inter-vial variance in the sublimation rate. The higher sublimation rate for the vials placed on the shelf edge is due to additional heat input from the wall and also due to further additional heat from the shelf surface on which no kissing vial is placed. It is possible to cancel out the additional heat input from the shelf by maintaining an optimum wall temperature, which must be lower than the material temperature. This paper discusses a method for eliminating the inter-vail variance in drying conditions and shortening the drying time by means of chamber wall temperature control.

  10. Seasonal time constraints reduce genetic variation in life-history traits along a latitudinal gradient.

    PubMed

    Sniegula, Szymon; Golab, Maria J; Drobniak, Szymon M; Johansson, Frank

    2016-01-01

    Time constraints cause strong selection on life-history traits, because populations need to complete their life cycles within a shorter time. We therefore expect lower genetic variation in these traits in high- than in low-latitude populations, since the former are more time-constrained. The aim was to estimate life-history traits and their genetic variation in an obligately univoltine damselfly along a latitudinal gradient of 2730 km. Populations were grown in the laboratory at temperatures and photoperiods simulating those at their place of origin. In a complementary experiment, individuals from the same families were grown in constant temperature and photoperiod that mimicked average conditions across the latitude. Development time and size was faster and smaller, respectively, and growth rate was higher at northern latitudes. Additive genetic variance was very low for life-history traits, and estimates for egg development time and larval growth rate showed significant decreases towards northern latitudes. The expression of genetic effects in life-history traits differed considerably when individuals were grown in constant rather than simulated and naturally variable conditions. Our results support strong selection by time constraints. They also highlight the importance of growing organisms in their native environment for correct estimates of genetic variance at their place of origin. Our results also suggest that the evolutionary potential of life-history traits is very low at northern compared to southern latitudes, but that changes in climate could alter this pattern. PMID:26333659

  11. Influence of mom and dad: quantitative genetic models for maternal effects and genomic imprinting.

    PubMed

    Santure, Anna W; Spencer, Hamish G

    2006-08-01

    The expression of an imprinted gene is dependent on the sex of the parent it was inherited from, and as a result reciprocal heterozygotes may display different phenotypes. In contrast, maternal genetic terms arise when the phenotype of an offspring is influenced by the phenotype of its mother beyond the direct inheritance of alleles. Both maternal effects and imprinting may contribute to resemblance between offspring of the same mother. We demonstrate that two standard quantitative genetic models for deriving breeding values, population variances and covariances between relatives, are not equivalent when maternal genetic effects and imprinting are acting. Maternal and imprinting effects introduce both sex-dependent and generation-dependent effects that result in differences in the way additive and dominance effects are defined for the two approaches. We use a simple example to demonstrate that both imprinting and maternal genetic effects add extra terms to covariances between relatives and that model misspecification may over- or underestimate true covariances or lead to extremely variable parameter estimation. Thus, an understanding of various forms of parental effects is essential in correctly estimating quantitative genetic variance components. PMID:16751674

  12. Genetic determination of head-size-related anthropometric traits in an ethnically homogeneous sample of 373 Indian pedigrees of West Bengal.

    PubMed

    Karmakar, B; Ermakov, S; Yakovenko, K; Kobyliansky, E

    2007-10-01

    The substantial involvement of genetic factors in the determination of head-size and head-shape traits has been firmly established. However, there has been a lack of agreement on a number of specific issues concerning the pattern of inheritance of craniofacial features. In this study we examined some of these issues in a large, ethnically homogeneous sample of Indian pedigrees. The data included 1,263 individuals belonging to 373 nuclear families. Eleven raw head-size traits and two synthetic phenotypes, interpreted as horizontal and vertical head-size components (HOC and VEC, respectively), were used in the analysis. To establish the pattern of inheritance of head traits, we carried out univariate and bivariate analyses. Maximum heritability estimates ranged from 0.41 to 0.83 for the studied head-size phenotypes. The portion of the total residual variance attributable to putative additive genetic factors was 68.3% and 70.3% for HOC and VEC, respectively, and common familial factor effects were found to be nonsignificant. The extent of genetic influences did not differ significantly with respect to sex or between HOC and VEC. The results of bivariate variance decomposition analysis strongly suggest the existence of common genetic factors simultaneously affecting HOC and VEC; 41.8% of the two traits' total residual variance was attributable to the effect of these common genetic factors. PMID:18478966

  13. Genetic and non-genetic parameters of replacement rate component traits in Holstein Friesian cattle.

    PubMed

    Goshu, Gebeyehu; Singh, Harpal

    2013-01-01

    Records on 3092 pregnancies distributed over a period of 24 years (1986 to 2010) were used to estimate genetic and non genetic parameters of threshold traits in Holstein Friesian. Parity, season and year of calving were included in the model to estimate their effect on replacement traits. A total of 105 sires' records were used to study the genetic component of the characters. The overall averages for abnormal and normal births, male-female sex ratios, mortality and culling rate in females up to age at first calving and female replacement rates based on female births and total pregnancies were estimated as 12.0% and 88.0%, 52.5% and 47.5%, 23.0% and 7.0% and 70.0% and 29.0% respectively. The effects of parity and year of calving on above traits were found to be significant, except parity effects on culling rate and replacement rate based on total pregnancies, which were non-significant. The season effects for all traits were non-significant. Average 3.45 pregnancies were required to produce one heifer that becomes replacement of the old and low producer cow. The heritability culling and replacement rate from total pregnancy were 0.71 and 0.66 suggesting sufficient additive genetic variance for selecting sires in these traits. Better feeding and health management could reduce mortality and force culling female calves. PMID:25674410

  14. Global genetic variation at nine short tandem repeat loci and implications on forensic genetics.

    PubMed

    Sun, Guangyun; McGarvey, Stephen T; Bayoumi, Riad; Mulligan, Connie J; Barrantes, Ramiro; Raskin, Salmo; Zhong, Yixi; Akey, Joshua; Chakraborty, Ranajit; Deka, Ranjan

    2003-01-01

    We have studied genetic variation at nine autosomal short tandem repeat loci in 20 globally distributed human populations defined by geographic and ethnic origins, viz., African, Caucasian, Asian, Native American and Oceanic. The purpose of this study is to evaluate the utility and applicability of these nine loci in forensic analysis in worldwide populations. The levels of genetic variation measured by number of alleles, allele size variance and heterozygosity are high in all populations irrespective of their effective sizes. Single- as well as multi-locus genotype frequencies are in conformity with the assumptions of Hardy-Weinberg equilibrium. Further, alleles across the entire set of nine loci are mutually independent in all populations. Gene diversity analysis shows that pooling of population data by major geographic groupings does not introduce substructure effects beyond the levels recommended by the National Research Council, validating the establishment of population databases based on major geographic and ethnic groupings. A network tree based on genetic distances further supports this assertion, in which populations of common ancestry cluster together. With respect to the power of discrimination and exclusion probabilities, even the relatively reduced levels of genetic variation at these nine STR loci in smaller and isolated populations provide an exclusionary power over 99%. However, in paternity testing with unknown genotype of the mother, the power of exclusion could fall below 80% in some isolated populations, and in such cases use of additional loci supplementing the battery of the nine loci is recommended. PMID:12529704

  15. A generalized approach and computer tool for quantitative genetics study

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Quantitative genetics is one of the most important components to provide valuable genetic information for improving production and quality of plants and animals. The research history of quantitative genetics study could be traced back more than one hundred years. Since the Analysis of Variance (ANOV...

  16. Nature vs nurture: are leaders born or made? A behavior genetic investigation of leadership style.

    PubMed

    Johnson, A M; Vernon, P A; McCarthy, J M; Molson, M; Harris, J A; Jang, K L

    1998-12-01

    With the recent resurgence in popularity of trait theories of leadership, it is timely to consider the genetic determination of the multiple factors comprising the leadership construct. Individual differences in personality traits have been found to be moderately to highly heritable, and so it follows that if there are reliable personality trait differences between leaders and non-leaders, then there may be a heritable component to these individual differences. Despite this connection between leadership and personality traits, however, there are no studies of the genetic basis of leadership using modern behavior genetic methodology. The present study proposes to address the lack of research in this area by examining the heritability of leadership style, as measured by self-report psychometric inventories. The Multifactor Leadership Questionnaire (MLQ), the Leadership Ability Evaluation, and the Adjective Checklist were completed by 247 adult twin pairs (183 monozygotic and 64 same-sex dizygotic). Results indicated that most of the leadership dimensions examined in this study are heritable, as are two higher level factors (resembling transactional and transformational leadership) derived from an obliquely rotated principal components factors analysis of the MLQ. Univariate analyses suggested that 48% of the variance in transactional leadership may be explained by additive heritability, and 59% of the variance in transformational leadership may be explained by non-additive (dominance) heritability. Multivariate analyses indicated that most of the variables studied shared substantial genetic covariance, suggesting a large overlap in the underlying genes responsible for the leadership dimensions. PMID:10100814

  17. Estimation of Model Error Variances During Data Assimilation

    NASA Technical Reports Server (NTRS)

    Dee, Dick

    2003-01-01

    Data assimilation is all about understanding the error characteristics of the data and models that are used in the assimilation process. Reliable error estimates are needed to implement observational quality control, bias correction of observations and model fields, and intelligent data selection. Meaningful covariance specifications are obviously required for the analysis as well, since the impact of any single observation strongly depends on the assumed structure of the background errors. Operational atmospheric data assimilation systems still rely primarily on climatological background error covariances. To obtain error estimates that reflect both the character of the flow and the current state of the observing system, it is necessary to solve three problems: (1) how to account for the short-term evolution of errors in the initial conditions; (2) how to estimate the additional component of error caused by model defects; and (3) how to compute the error reduction in the analysis due to observational information. Various approaches are now available that provide approximate solutions to the first and third of these problems. However, the useful accuracy of these solutions very much depends on the size and character of the model errors and the ability to account for them. Model errors represent the real-world forcing of the error evolution in a data assimilation system. Clearly, meaningful model error estimates and/or statistics must be based on information external to the model itself. The most obvious information source is observational, and since the volume of available geophysical data is growing rapidly, there is some hope that a purely statistical approach to model error estimation can be viable. This requires that the observation errors themselves are well understood and quantifiable. We will discuss some of these challenges and present a new sequential scheme for estimating model error variances from observations in the context of an atmospheric data

  18. A Danish Twin Study of Schizophrenia Liability: Investigation from Interviewed Twins for Genetic Links to Affective Psychoses and for Cross-Cohort Comparisons.

    PubMed

    Kläning, Ulla; Trumbetta, Susan L; Gottesman, Irving I; Skytthe, Axel; Kyvik, Kirsten O; Bertelsen, Aksel

    2016-03-01

    We studied schizophrenia liability in a Danish population-based sample of 44 twin pairs (13 MZ, 31 DZ, SS plus OS) in order to replicate previous twin study findings using contemporary diagnostic criteria, to examine genetic liability shared between schizophrenia and other disorders, and to explore whether variance in schizophrenia liability attributable to environmental factors may have decreased with successive cohorts exposed to improvements in public health. ICD-10 diagnoses were determined by clinical interview. Although the best-fitting, most parsimonious biometric model of schizophrenia liability specified variance attributable to additive genetic and non-shared environmental factors, this model did not differ significantly from a model that also included non-additive genetic factors, consistent with recent interview-based twin studies. Schizophrenia showed strong genetic links to other psychotic disorders but much less so for the broader category of psychiatric disorders in general. We also observed a marginally significant decline in schizophrenia variance attributable to environmental factors over successive Western European cohorts, consistent perhaps with improvements in diagnosis and in prenatal and perinatal care and with a secular decline in the prevalence of schizophrenia in that region. PMID:26538243

  19. Practice reduces task relevant variance modulation and forms nominal trajectory

    NASA Astrophysics Data System (ADS)

    Osu, Rieko; Morishige, Ken-Ichi; Nakanishi, Jun; Miyamoto, Hiroyuki; Kawato, Mitsuo

    2015-12-01

    Humans are capable of achieving complex tasks with redundant degrees of freedom. Much attention has been paid to task relevant variance modulation as an indication of online feedback control strategies to cope with motor variability. Meanwhile, it has been discussed that the brain learns internal models of environments to realize feedforward control with nominal trajectories. Here we examined trajectory variance in both spatial and temporal domains to elucidate the relative contribution of these control schemas. We asked subjects to learn reaching movements with multiple via-points, and found that hand trajectories converged to stereotyped trajectories with the reduction of task relevant variance modulation as learning proceeded. Furthermore, variance reduction was not always associated with task constraints but was highly correlated with the velocity profile. A model assuming noise both on the nominal trajectory and motor command was able to reproduce the observed variance modulation, supporting an expression of nominal trajectories in the brain. The learning-related decrease in task-relevant modulation revealed a reduction in the influence of optimal feedback around the task constraints. After practice, the major part of computation seems to be taken over by the feedforward controller around the nominal trajectory with feedback added only when it becomes necessary.

  20. Practice reduces task relevant variance modulation and forms nominal trajectory.

    PubMed

    Osu, Rieko; Morishige, Ken-ichi; Nakanishi, Jun; Miyamoto, Hiroyuki; Kawato, Mitsuo

    2015-01-01

    Humans are capable of achieving complex tasks with redundant degrees of freedom. Much attention has been paid to task relevant variance modulation as an indication of online feedback control strategies to cope with motor variability. Meanwhile, it has been discussed that the brain learns internal models of environments to realize feedforward control with nominal trajectories. Here we examined trajectory variance in both spatial and temporal domains to elucidate the relative contribution of these control schemas. We asked subjects to learn reaching movements with multiple via-points, and found that hand trajectories converged to stereotyped trajectories with the reduction of task relevant variance modulation as learning proceeded. Furthermore, variance reduction was not always associated with task constraints but was highly correlated with the velocity profile. A model assuming noise both on the nominal trajectory and motor command was able to reproduce the observed variance modulation, supporting an expression of nominal trajectories in the brain. The learning-related decrease in task-relevant modulation revealed a reduction in the influence of optimal feedback around the task constraints. After practice, the major part of computation seems to be taken over by the feedforward controller around the nominal trajectory with feedback added only when it becomes necessary. PMID:26639942