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Sample records for dominance genetic variance

  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. Bottleneck effect on genetic variance. A theoretical investigation of the role of dominance.

    PubMed Central

    Wang, J; Caballero, A; Keightley, P D; Hill, W G

    1998-01-01

    The phenomenon that the genetic variance of fitness components increase following a bottleneck or inbreeding is supported by a growing number of experiments and is explained theoretically by either dominance or epistasis. In this article, diffusion approximations under the infinite sites model are used to quantify the effect of dominance, using data on viability in Drosophila melanogaster. The model is based on mutation parameters from mutation accumulation experiments involving balancer chromosomes (set I) or inbred lines (set II). In essence, set I assumes many mutations of small effect, whereas set II assumes fewer mutations of large effect. Compared to empirical estimates from large outbred populations, set I predicts reasonable genetic variances but too low mean viability. In contrast, set II predicts a reasonable mean viability but a low genetic variance. Both sets of parameters predict the changes in mean viability (depression), additive variance, between-line variance and heritability following bottlenecks generally compatible with empirical results, and these changes are mainly caused by lethals and deleterious mutants of large effect. This article suggests that dominance is the main cause for increased genetic variances for fitness components and fitness-related traits after bottlenecks observed in various experiments. PMID:9725859

  3. Expected influence of linkage disequilibrium on genetic variance caused by dominance and epistasis on quantitative traits.

    PubMed

    Hill, W G; Mäki-Tanila, A

    2015-04-01

    Linkage disequilibrium (LD) influences the genetic variation in a quantitative trait contributed by two or more loci, with positive LD increasing the variance. The magnitude of LD also affects the relative magnitude of dominance and epistatic variation. We quantify the extent of the non-additive variance expected within populations, deriving analytical expressions for simple models and using numerical simulation in finite population more generally. As LD generates non-independence among loci, a simple partition into additive, dominance and epistatic components is not possible, so we merely distinguish between additive and non-additive components based on comparing covariances among close relatives, such as full sibs, half sibs and offspring-parent. As tight linkage is needed to yield substantial LD in outbred populations, we ignore recombination in the generation used to estimate components and it is analogous to a multi-allelic model. The expected magnitude of the non-additive variance is generally increased but not greatly so by the LD in outbred populations. Thus, as found in previous studies for unlinked loci, independent of the type and strength of gene interaction, the epistatic variance contributes little to the total.

  4. 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

  5. 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

  6. Genetic Dominance & Cellular Processes

    ERIC Educational Resources Information Center

    Seager, Robert D.

    2014-01-01

    In learning genetics, many students misunderstand and misinterpret what "dominance" means. Understanding is easier if students realize that dominance is not a mechanism, but rather a consequence of underlying cellular processes. For example, metabolic pathways are often little affected by changes in enzyme concentration. This means that…

  7. Dominance, Information, and Hierarchical Scaling of Variance Space.

    ERIC Educational Resources Information Center

    Ceurvorst, Robert W.; Krus, David J.

    1979-01-01

    A method for computation of dominance relations and for construction of their corresponding hierarchical structures is presented. The link between dominance and variance allows integration of the mathematical theory of information with least squares statistical procedures without recourse to logarithmic transformations of the data. (Author/CTM)

  8. 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.

  9. Variance in the reproductive success of dominant male mountain gorillas.

    PubMed

    Robbins, Andrew M; Gray, Maryke; Uwingeli, Prosper; Mburanumwe, Innocent; Kagoda, Edwin; Robbins, Martha M

    2014-10-01

    Using 30 years of demographic data from 15 groups, this study estimates how harem size, female fertility, and offspring survival may contribute to variance in the siring rates of dominant male mountain gorillas throughout the Virunga Volcano Region. As predicted for polygynous species, differences in harem size were the greatest source of variance in the siring rate, whereas differences in female fertility and offspring survival were relatively minor. Harem size was positively correlated with offspring survival, even after removing all known and suspected cases of infanticide, so the correlation does not seem to reflect differences in the ability of males to protect their offspring. Harem size was not significantly correlated with female fertility, which is consistent with the hypothesis that mountain gorillas have minimal feeding competition. Harem size, offspring survival, and siring rates were not significantly correlated with the proportion of dominant tenures that occurred in multimale groups versus one-male groups; even though infanticide is less likely when those tenures end in multimale groups than one-male groups. In contrast with the relatively small contribution of offspring survival to variance in the siring rates of this study, offspring survival is a major source of variance in the male reproductive success of western gorillas, which have greater predation risks and significantly higher rates of infanticide. If differences in offspring protection are less important among male mountain gorillas than western gorillas, then the relative importance of other factors may be greater for mountain gorillas. Thus, our study illustrates how variance in male reproductive success and its components can differ between closely related species.

  10. Maximization of total genetic variance in breed conservation programmes.

    PubMed

    Cervantes, I; Meuwissen, T H E

    2011-12-01

    The preservation of the maximum genetic diversity in a population is one of the main objectives within a breed conservation programme. We applied the maximum variance total (MVT) method to a unique population in order to maximize the total genetic variance. The function maximization was performed by the annealing algorithm. We have selected the parents and the mating scheme at the same time simply maximizing the total genetic variance (a mate selection problem). The scenario was compared with a scenario of full-sib lines, a MVT scenario with a rate of inbreeding restriction, and with a minimum coancestry selection scenario. The MVT method produces sublines in a population attaining a similar scheme as the full-sib sublining that agrees with other authors that the maximum genetic diversity in a population (the lowest overall coancestry) is attained in the long term by subdividing it in as many isolated groups as possible. The application of a restriction on the rate of inbreeding jointly with the MVT method avoids the consequences of inbreeding depression and maintains the effective size at an acceptable minimum. The scenario of minimum coancestry selection gave higher effective size values, but a lower total genetic variance. A maximization of the total genetic variance ensures more genetic variation for extreme traits, which could be useful in case the population needs to adapt to a new environment/production system.

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

    PubMed

    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.

  12. 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)

  13. Additive and nonadditive genetic variances for milk yield, fertility, and lifetime performance traits of dairy cattle.

    PubMed

    Fuerst, C; Sölkner, J

    1994-04-01

    Additive and nonadditive genetic variances were estimated for yield traits and fertility for three subsequent lactations and for lifetime performance traits of purebred and crossbred dairy cattle populations. Traits were milk yield, energy-corrected milk yield, fat percentage, protein percentage, calving interval, length of productive life, and lifetime FCM of purebred Simmental, Simmental including crossbreds, and Braunvieh crossed with Brown Swiss. Data files ranged from 66,740 to 375,093 records. An approach based on pedigree information for sire and maternal grandsire was used and included additive, dominance, and additive by additive genetic effects. Variances were estimated using the tildehat approximation to REML. Heritability estimated without nonadditive effects in the model was overestimated, particularly in presence of additive by additive variance. Dominance variance was important for most traits; for the lifetime performance traits, dominance was clearly higher than additive variance. Additive by additive variance was very high for milk yield and energy-corrected milk yield, especially for data including crossbreds. Effect of inbreeding was low in most cases. Inclusion of nonadditive effects in genetic evaluation models might improve estimation of additive effects and may require consideration for dairy cattle breeding programs.

  14. Mixed model methods for genomic prediction and variance component estimation of additive and dominance effects using SNP markers.

    PubMed

    Da, Yang; Wang, Chunkao; Wang, Shengwen; Hu, Guo

    2014-01-01

    We established a genomic model of quantitative trait with genomic additive and dominance relationships that parallels the traditional quantitative genetics model, which partitions a genotypic value as breeding value plus dominance deviation and calculates additive and dominance relationships using pedigree information. Based on this genomic model, two sets of computationally complementary but mathematically identical mixed model methods were developed for genomic best linear unbiased prediction (GBLUP) and genomic restricted maximum likelihood estimation (GREML) of additive and dominance effects using SNP markers. These two sets are referred to as the CE and QM sets, where the CE set was designed for large numbers of markers and the QM set was designed for large numbers of individuals. GBLUP and associated accuracy formulations for individuals in training and validation data sets were derived for breeding values, dominance deviations and genotypic values. Simulation study showed that GREML and GBLUP generally were able to capture small additive and dominance effects that each accounted for 0.00005-0.0003 of the phenotypic variance and GREML was able to differentiate true additive and dominance heritability levels. GBLUP of the total genetic value as the summation of additive and dominance effects had higher prediction accuracy than either additive or dominance GBLUP, causal variants had the highest accuracy of GREML and GBLUP, and predicted accuracies were in agreement with observed accuracies. Genomic additive and dominance relationship matrices using SNP markers were consistent with theoretical expectations. The GREML and GBLUP methods can be an effective tool for assessing the type and magnitude of genetic effects affecting a phenotype and for predicting the total genetic value at the whole genome level.

  15. 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.

  16. Genetic variance of tolerance and the toxicant threshold model.

    PubMed

    Tanaka, Yoshinari; Mano, Hiroyuki; Tatsuta, Haruki

    2012-04-01

    A statistical genetics method is presented for estimating the genetic variance (heritability) of tolerance to pollutants on the basis of a standard acute toxicity test conducted on several isofemale lines of cladoceran species. To analyze the genetic variance of tolerance in the case when the response is measured as a few discrete states (quantal endpoints), the authors attempted to apply the threshold character model in quantitative genetics to the threshold model separately developed in ecotoxicology. The integrated threshold model (toxicant threshold model) assumes that the response of a particular individual occurs at a threshold toxicant concentration and that the individual tolerance characterized by the individual's threshold value is determined by genetic and environmental factors. As a case study, the heritability of tolerance to p-nonylphenol in the cladoceran species Daphnia galeata was estimated by using the maximum likelihood method and nested analysis of variance (ANOVA). Broad-sense heritability was estimated to be 0.199 ± 0.112 by the maximum likelihood method and 0.184 ± 0.089 by ANOVA; both results implied that the species examined had the potential to acquire tolerance to this substance by evolutionary change.

  17. The genetic and environmental variance underlying elementary cognitive tasks.

    PubMed

    Petrill, S A; Thompson, L A; Detterman, D K

    1995-05-01

    Although previous studies have examined the genetic and environmental influences upon general intelligence and specific cognitive abilities in school-age children, few studies have examined elementary cognitive tasks in this population. The current study included 149 MZ and 138 same-sex DZ twin pairs who participated in the Western Reserve Twin Project. Thirty measures from the Cognitive Abilities Test (CAT; Detterman, 1986) were studied. Results indicate that (1) these measures are reliable indicators of general intelligence in children and (2) the structure of genetic and environmental influences varies across measures. These results not only indicate that elementary cognitive tasks display heterogeneous genetic and environmental effects, but also may demonstrate that individual differences in biologically based processes are not necessarily due to genetic variance.

  18. 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

  19. The molecular basis of genetic dominance.

    PubMed Central

    Wilkie, A O

    1994-01-01

    Studies of mutagenesis in many organisms indicate that the majority (over 90%) of mutations are recessive to wild type. If recessiveness represents the 'default' state, what are the distinguishing features that make a minority of mutations give rise to dominant or semidominant characters? This review draws on the rapid expansion in knowledge of molecular and cellular biology to classify the molecular mechanisms of dominant mutation. The categories discussed include (1) reduced gene dosage, expression, or protein activity (haploinsufficiency); (2) increased gene dosage; (3) ectopic or temporally altered mRNA expression; (4) increased or constitutive protein activity; (5) dominant negative effects; (6) altered structural proteins; (7) toxic protein alterations; and (8) new protein functions. This provides a framework for understanding the basis of dominant genetic phenomena in humans and other organisms. Images PMID:8182727

  20. Quantitative genetic divergence and standing genetic (co)variance in thermal reaction norms along latitude.

    PubMed

    Berger, David; Postma, Erik; Blanckenhorn, Wolf U; Walters, Richard J

    2013-08-01

    Although the potential to adapt to warmer climate is constrained by genetic trade-offs, our understanding of how selection and mutation shape genetic (co)variances in thermal reaction norms is poor. Using 71 isofemale lines of the fly Sepsis punctum, originating from northern, central, and southern European climates, we tested for divergence in juvenile development rate across latitude at five experimental temperatures. To investigate effects of evolutionary history in different climates on standing genetic variation in reaction norms, we further compared genetic (co)variances between regions. Flies were reared on either high or low food resources to explore the role of energy acquisition in determining genetic trade-offs between different temperatures. Although the latter had only weak effects on the strength and sign of genetic correlations, genetic architecture differed significantly between climatic regions, implying that evolution of reaction norms proceeds via different trajectories at high latitude versus low latitude in this system. Accordingly, regional genetic architecture was correlated to region-specific differentiation. Moreover, hot development temperatures were associated with low genetic variance and stronger genetic correlations compared to cooler temperatures. We discuss the evolutionary potential of thermal reaction norms in light of their underlying genetic architectures, evolutionary histories, and the materialization of trade-offs in natural environments.

  1. Dominant takeover regimes for genetic algorithms

    NASA Technical Reports Server (NTRS)

    Noever, David; Baskaran, Subbiah

    1995-01-01

    The genetic algorithm (GA) is a machine-based optimization routine which connects evolutionary learning to natural genetic laws. The present work addresses the problem of obtaining the dominant takeover regimes in the GA dynamics. Estimated GA run times are computed for slow and fast convergence in the limits of high and low fitness ratios. Using Euler's device for obtaining partial sums in closed forms, the result relaxes the previously held requirements for long time limits. Analytical solution reveal that appropriately accelerated regimes can mark the ascendancy of the most fit solution. In virtually all cases, the weak (logarithmic) dependence of convergence time on problem size demonstrates the potential for the GA to solve large N-P complete problems.

  2. Detecting epistatic genetic variance with a clonally replicated design: models for lowvs high-order nonallelic interaction.

    PubMed

    Wu, R L

    1996-07-01

    A quantitative genetic model, that uses known family structure with clonal replicates to separate genetic variance into its additive, dominance and epistatic components, is available in the current literature. Making use of offspring testing, this model is based on the theory that components of variance from the linear model of an experimental design may be expressed in terms of expected covariances among relatives. However, if interactions between a pair of quantitative trait loci (QTLs) explain a large proportion of the total epistasis, it will seriously overestimate the additive and dominance variances but underestimate the epistatic variance. In the present paper, a new model is developed to manipulate this problem by combining parental and offspring material into the same test. Under the condition described above, the new model can provide an accurate estimate for additive x additive variances. Also, its accuracy in estimating dominance and total epistatic variances is much greater than the accuracy of the previous model. However, if there is obvious evidence showing the major contribution of high-order interactions, especially among ≥ 4QTLs, to the total epistasis, the previous model is more appropriate to partition the genetic variance for a quantitative trait. The re-analysis of an example from a factorial mating design in poplar shows large differences in estimating variance components between the new and previous models when two different assumptions (lowvs high-order epistatic interactions) are used. The new model will be an alternative to estimating the mode of quantitative inheritance for species, especially for longlived, predominantly outcrossing forest trees, that can be clonally replicated.

  3. 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

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

    2015-11-01

    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.

  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. Estimating Additive and Non-Additive Genetic Variances and Predicting Genetic Merits Using Genome-Wide Dense Single Nucleotide Polymorphism Markers

    PubMed Central

    Su, Guosheng; Christensen, Ole F.; Ostersen, Tage; Henryon, Mark; Lund, Mogens S.

    2012-01-01

    Non-additive genetic variation is usually ignored when genome-wide markers are used to study the genetic architecture and genomic prediction of complex traits in human, wild life, model organisms or farm animals. However, non-additive genetic effects may have an important contribution to total genetic variation of complex traits. This study presented a genomic BLUP model including additive and non-additive genetic effects, in which additive and non-additive genetic relation matrices were constructed from information of genome-wide dense single nucleotide polymorphism (SNP) markers. In addition, this study for the first time proposed a method to construct dominance relationship matrix using SNP markers and demonstrated it in detail. The proposed model was implemented to investigate the amounts of additive genetic, dominance and epistatic variations, and assessed the accuracy and unbiasedness of genomic predictions for daily gain in pigs. In the analysis of daily gain, four linear models were used: 1) a simple additive genetic model (MA), 2) a model including both additive and additive by additive epistatic genetic effects (MAE), 3) a model including both additive and dominance genetic effects (MAD), and 4) a full model including all three genetic components (MAED). Estimates of narrow-sense heritability were 0.397, 0.373, 0.379 and 0.357 for models MA, MAE, MAD and MAED, respectively. Estimated dominance variance and additive by additive epistatic variance accounted for 5.6% and 9.5% of the total phenotypic variance, respectively. Based on model MAED, the estimate of broad-sense heritability was 0.506. Reliabilities of genomic predicted breeding values for the animals without performance records were 28.5%, 28.8%, 29.2% and 29.5% for models MA, MAE, MAD and MAED, respectively. In addition, models including non-additive genetic effects improved unbiasedness of genomic predictions. PMID:23028912

  6. Comparison of multiplicative heterogeneous variance adjustment models for genetic evaluations.

    PubMed

    Márkus, Sz; Mäntysaari, E A; Strandén, I; Eriksson, J-Å; Lidauer, M H

    2014-06-01

    Two heterogeneous variance adjustment methods and two variance models were compared in a simulation study. The method used for heterogeneous variance adjustment in the Nordic test-day model, which is a multiplicative method based on Meuwissen (J. Dairy Sci., 79, 1996, 310), was compared with a restricted multiplicative method where the fixed effects were not scaled. Both methods were tested with two different variance models, one with a herd-year and the other with a herd-year-month random effect. The simulation study was built on two field data sets from Swedish Red dairy cattle herds. For both data sets, 200 herds with test-day observations over a 12-year period were sampled. For one data set, herds were sampled randomly, while for the other, each herd was required to have at least 10 first-calving cows per year. The simulations supported the applicability of both methods and models, but the multiplicative mixed model was more sensitive in the case of small strata sizes. Estimation of variance components for the variance models resulted in different parameter estimates, depending on the applied heterogeneous variance adjustment method and variance model combination. Our analyses showed that the assumption of a first-order autoregressive correlation structure between random-effect levels is reasonable when within-herd heterogeneity is modelled by year classes, but less appropriate for within-herd heterogeneity by month classes. Of the studied alternatives, the multiplicative method and a variance model with a random herd-year effect were found most suitable for the Nordic test-day model for dairy cattle evaluation.

  7. 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.

  8. 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

  9. Genetic Variance for Body Size in a Natural Population of Drosophila Buzzatii

    PubMed Central

    Ruiz, A.; Santos, M.; Barbadilla, A.; Quezada-Diaz, J. E.; Hasson, E.; Fontdevila, A.

    1991-01-01

    Previous work has shown thorax length to be under directional selection in the Drosophila buzzatii population of Carboneras. In order to predict the genetic consequences of natural selection, genetic variation for this trait was investigated in two ways. First, narrow sense heritability was estimated in the laboratory F(2) generation of a sample of wild flies by means of the offspring-parent regression. A relatively high value, 0.59, was obtained. Because the phenotypic variance of wild flies was 7-9 times that of the flies raised in the laboratory, ``natural'' heritability may be estimated as one-seventh to one-ninth that value. Second, the contribution of the second and fourth chromosomes, which are polymorphic for paracentric inversions, to the genetic variance of thorax length was estimated in the field and in the laboratory. This was done with the assistance of a simple genetic model which shows that the variance among chromosome arrangements and the variance among karyotypes provide minimum estimates of the chromosome's contribution to the additive and genetic variances of the triat, respectively. In males raised under optimal conditions in the laboratory, the variance among second-chromosome karyotypes accounted for 11.43% of the total phenotypic variance and most of this variance was additive; by contrast, the contribution of the fourth chromosome was nonsignificant. The variance among second-chromosome karyotypes accounted for 1.56-1.78% of the total phenotypic variance in wild males and was nonsignificant in wild females. The variance among fourth chromosome karyotypes accounted for 0.14-3.48% of the total phenotypic variance in wild flies. At both chromosomes, the proportion of additive variance was higher in mating flies than in nonmating flies. PMID:1916242

  10. 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

  11. Genetics Home Reference: autosomal dominant partial epilepsy with auditory features

    MedlinePlus

    ... Genetics Home Health Conditions ADPEAF autosomal dominant partial epilepsy with auditory features Enable Javascript to view the ... Open All Close All Description Autosomal dominant partial epilepsy with auditory features ( ADPEAF ) is an uncommon form ...

  12. Epistasis Is a Major Determinant of the Additive Genetic Variance in Mimulus guttatus

    PubMed Central

    Monnahan, Patrick J.; Kelly, John K.

    2015-01-01

    The influence of genetic interactions (epistasis) on the genetic variance of quantitative traits is a major unresolved problem relevant to medical, agricultural, and evolutionary genetics. The additive genetic component is typically a high proportion of the total genetic variance in quantitative traits, despite that underlying genes must interact to determine phenotype. This study estimates direct and interaction effects for 11 pairs of Quantitative Trait Loci (QTLs) affecting floral traits within a single population of Mimulus guttatus. With estimates of all 9 genotypes for each QTL pair, we are able to map from QTL effects to variance components as a function of population allele frequencies, and thus predict changes in variance components as allele frequencies change. This mapping requires an analytical framework that properly accounts for bias introduced by estimation errors. We find that even with abundant interactions between QTLs, most of the genetic variance is likely to be additive. However, the strong dependency of allelic average effects on genetic background implies that epistasis is a major determinant of the additive genetic variance, and thus, the population’s ability to respond to selection. PMID:25946702

  13. 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

  14. Genetics Home Reference: autosomal dominant vitreoretinochoroidopathy

    MedlinePlus

    ... autosomal dominant vitreoretinochoroidopathy: a degenerative disease with a range of developmental ocular anomalies. Eye (Lond). 2011 Jan;25(1):113-8. doi: 10.1038/eye.2010.165. Epub 2010 Nov 12. Citation on PubMed or Free article on PubMed Central Yardley J, Leroy BP, ...

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

    PubMed

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

    2015-12-01

    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.

  16. 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

  17. A new explained-variance based genetic risk score for predictive modeling of disease risk.

    PubMed

    Che, Ronglin; Motsinger-Reif, Alison A

    2012-09-25

    The goal of association mapping is to identify genetic variants that predict disease, and as the field of human genetics matures, the number of successful association studies is increasing. Many such studies have shown that for many diseases, risk is explained by a reasonably large number of variants that each explains a very small amount of disease risk. This is prompting the use of genetic risk scores in building predictive models, where information across several variants is combined for predictive modeling. In the current study, we compare the performance of four previously proposed genetic risk score methods and present a new method for constructing genetic risk score that incorporates explained variance information. The methods compared include: a simple count Genetic Risk Score, an odds ratio weighted Genetic Risk Score, a direct logistic regression Genetic Risk Score, a polygenic Genetic Risk Score, and the new explained variance weighted Genetic Risk Score. We compare the methods using a wide range of simulations in two steps, with a range of the number of deleterious single nucleotide polymorphisms (SNPs) explaining disease risk, genetic modes, baseline penetrances, sample sizes, relative risks (RR) and minor allele frequencies (MAF). Several measures of model performance were compared including overall power, C-statistic and Akaike's Information Criterion. Our results show the relative performance of methods differs significantly, with the new explained variance weighted GRS (EV-GRS) generally performing favorably to the other methods.

  18. 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

  19. 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...

  20. Environmental and Genetic Variance in Children's Observed and Reported Maladaptive Behavior.

    ERIC Educational Resources Information Center

    Leve, Leslie D.; Winebarger, Allen A.; Fagot, Beverly I.; Reid, John B.; Goldsmith, H. Hill

    1998-01-01

    Used behavioral genetic methods and environmental assessment techniques to assess maladaptive behavior in 6- to 11-year-old twin pairs. Found that genetic variation accounts for majority of variance in parent-reported child maladaptive behavior; in contrast, observational coding and global impressions of parent-twin interactive behavior suggest…

  1. 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…

  2. The contribution of quantitative trait loci and neutral marker loci to the genetic variances and covariances among quantitative traits in random mating populations

    SciTech Connect

    Ruiz, A.; Barbadilla, A.

    1995-01-01

    Using Cockerham`s approach of orthogonal scales, we develop genetic models for the effect of an arbitrary number of multiallelic quantitative trait loci (QTLs) or neutral marker loci (NMLs) upon any number of quantitative traits. These models allow the unbiased estimation of the contributions of a set of marker loci to the additive and dominance variances and covariances among traits in a random mating population. The method has been applied to an analysis of allozyme and quantitative data from the European oyster. The contribution of a set of marker loci may either be real, when the markers are actually QTLs, or apparent, when they are NMLs that are in linkage disequilibrium with hidden QTLs. Our results show that the additive and dominance variances contributed by a set of NMLs are always minimum estimates of the corresponding variances contributed by the associated QTLs. In contrast, the apparent contribution of the NMLs to the additive and dominance covariances between two traits may be larger than, equal to or lower than the actual contributions of the QTLs. We also derive an expression for the expected variance explained by the correlation between a quantitative trait and multilocus heterozygosity. This correlation explains only a part of the genetic variance contributed by the markers, i.e., in general, a combination of additive and dominance variances and, thus, provides only very limited information relative to the method supplied here. 94 refs., 2 figs., 5 tabs.

  3. 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

  4. 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

  5. Complex sources of variance in female dominance rank in a nepotistic society

    PubMed Central

    Lea, Amanda J.; Learn, Niki H.; Theus, Marcus J.; Altmann, Jeanne; Alberts, Susan C.

    2016-01-01

    Many mammalian societies are structured by dominance hierarchies, and an individual’s position within this hierarchy can influence reproduction, behaviour, physiology and health. In nepotistic hierarchies, which are common in cercopithecine primates and also seen in spotted hyaenas, Crocuta crocuta, adult daughters are expected to rank immediately below their mother, and in reverse age order (a phenomenon known as ‘youngest ascendancy’). This pattern is well described, but few studies have systematically examined the frequency or causes of departures from the expected pattern. Using a longitudinal data set from a natural population of yellow baboons, Papio cynocephalus, we measured the influence of maternal kin, paternal kin and group size on female rank positions at two life history milestones, menarche and first live birth. At menarche, most females (73%) ranked adjacent to their family members (i.e. the female held an ordinal rank in consecutive order with other members of her maternal family); however, only 33% of females showed youngest ascendancy within their matriline at menarche. By the time they experienced their first live birth, many females had improved their dominance rank: 78% ranked adjacent to their family members and 49% showed youngest ascendancy within their matriline. The presence of mothers and maternal sisters exerted a powerful influence on rank outcomes. However, the presence of fathers, brothers and paternal siblings did not produce a clear effect on female dominance rank in our analyses, perhaps because females in our data set co-resided with variable numbers and types of paternal and male relatives. Our results also raise the possibility that female body size or competitive ability may influence dominance rank, even in this classically nepotistic species. In total, our analyses reveal that the predictors of dominance rank in nepotistic rank systems are much more complex than previously thought. PMID:26997663

  6. Estimating Modifying Effect of Age on Genetic and Environmental Variance Components in Twin Models.

    PubMed

    He, Liang; Sillanpää, Mikko J; Silventoinen, Karri; Kaprio, Jaakko; Pitkäniemi, Janne

    2016-04-01

    Twin studies have been adopted for decades to disentangle the relative genetic and environmental contributions for a wide range of traits. However, heritability estimation based on the classical twin models does not take into account dynamic behavior of the variance components over age. Varying variance of the genetic component over age can imply the existence of gene-environment (G×E) interactions that general genome-wide association studies (GWAS) fail to capture, which may lead to the inconsistency of heritability estimates between twin design and GWAS. Existing parametricG×Einteraction models for twin studies are limited by assuming a linear or quadratic form of the variance curves with respect to a moderator that can, however, be overly restricted in reality. Here we propose spline-based approaches to explore the variance curves of the genetic and environmental components. We choose the additive genetic, common, and unique environmental variance components (ACE) model as the starting point. We treat the component variances as variance functions with respect to age modeled by B-splines or P-splines. We develop an empirical Bayes method to estimate the variance curves together with their confidence bands and provide an R package for public use. Our simulations demonstrate that the proposed methods accurately capture dynamic behavior of the component variances in terms of mean square errors with a data set of >10,000 twin pairs. Using the proposed methods as an alternative and major extension to the classical twin models, our analyses with a large-scale Finnish twin data set (19,510 MZ twins and 27,312 DZ same-sex twins) discover that the variances of the A, C, and E components for body mass index (BMI) change substantially across life span in different patterns and the heritability of BMI drops to ∼50% after middle age. The results further indicate that the decline of heritability is due to increasing unique environmental variance, which provides more

  7. Quantitative genetics of genomic imprinting: a comparison of simple variance derivations, the effects of inbreeding, and response to selection.

    PubMed

    Santure, Anna W; Spencer, Hamish G

    2011-07-01

    The level of expression of an imprinted gene is dependent on the sex of the parent from which it was inherited. As a result, reciprocal heterozygotes in a population may have different mean phenotypes for quantitative traits. Using standard quantitative genetic methods for deriving breeding values, population variances, and covariances between relatives, we demonstrate that although these approaches are equivalent under Mendelian expression, this equivalence is lost when genomic imprinting is acting. Imprinting introduces both parent-of-origin-dependent and generation-dependent effects that result in differences in the way additive and dominance effects are defined for the various approaches. Further, imprinting creates a covariance between additive and dominance terms absent under Mendelian expression, but the expression for this covariance cannot be derived using a number of the standard approaches for defining additive and dominance terms. Inbreeding also generates such a covariance, and we demonstrate that a modified method for partitioning variances can easily accommodate both inbreeding and imprinting. As with inbreeding, the concept of breeding values has no useful meaning for an imprinted trait. Finally, we derive the expression for the response to selection under imprinting, and conclude that the response to selection for an imprinted trait cannot be predicted from the breeder's equation, even when there is no dominance. PMID:22384325

  8. 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

  9. [Genetic variance in Vicia cracca cenopopulation inhabiting site with enhanced level of natural radioactivity].

    PubMed

    Evseeva, T I; Maĭstrenko, T A; Geras'kin, S A; Belykh, E S

    2007-01-01

    The contribution of low dose rate ionizing radiation into genetic variance in Vicia cracca L. cenopopulation inhabiting high natural background territories more then 40 years quantity estimation was made. Incorporated in the aboveground parts of Vicia cracca 230Th determine both the level of intrapopulation genetic variance and the adaptive possibility. Significantly increased frequency of double fragments was revealed in root tips of plants inhabiting all experimental plots. This type of damages depends on 226Ra concentrations accumulated in the aboveground parts of Vicia cracca. External irradiation influences the embryonic lethals. It was found that the relative contribution on mutagenesis induced by ionizing radiation was significant and was about 3-5% of the total variance.

  10. 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.

  11. 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

  12. 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

  13. Multiplicative random regression model for heterogeneous variance adjustment in genetic evaluation for milk yield in Simmental.

    PubMed

    Lidauer, M H; Emmerling, R; Mäntysaari, E A

    2008-06-01

    A multiplicative random regression (M-RRM) test-day (TD) model was used to analyse daily milk yields from all available parities of German and Austrian Simmental dairy cattle. The method to account for heterogeneous variance (HV) was based on the multiplicative mixed model approach of Meuwissen. The variance model for the heterogeneity parameters included a fixed region x year x month x parity effect and a random herd x test-month effect with a within-herd first-order autocorrelation between test-months. Acceleration of variance model solutions after each multiplicative model cycle enabled fast convergence of adjustment factors and reduced total computing time significantly. Maximum Likelihood estimation of within-strata residual variances was enhanced by inclusion of approximated information on loss in degrees of freedom due to estimation of location parameters. This improved heterogeneity estimates for very small herds. The multiplicative model was compared with a model that assumed homogeneous variance. Re-estimated genetic variances, based on Mendelian sampling deviations, were homogeneous for the M-RRM TD model but heterogeneous for the homogeneous random regression TD model. Accounting for HV had large effect on cow ranking but moderate effect on bull ranking.

  14. Sex Modifies Genetic Effects on Residual Variance in Urinary Calcium Excretion in Rat (Rattus norvegicus)

    PubMed Central

    Perry, Guy M. L.; Nehrke, Keith W.; Bushinsky, David A.; Reid, Robert; Lewandowski, Krista L.; Hueber, Paul; Scheinman, Steven J.

    2012-01-01

    Conventional genetics assumes common variance among alleles or genetic groups. However, evidence from vertebrate and invertebrate models suggests that residual genotypic variance may itself be under partial genetic control. Such a phenomenon would have great significance: high-variability alleles might confound the detection of “classically” acting genes or scatter predicted evolutionary outcomes among unpredicted trajectories. Of the few works on this phenomenon, many implicate sex in some aspect of its control. We found that female genetic hypercalciuric stone-forming (GHS) rats (Rattus norvegicus) had higher coefficients of variation (CVs) for urinary calcium (CV = 0.14) than GHS males (CV = 0.06), and the reverse in normocalciuric Wistar–Kyoto rats (WKY) (CV♂ = 0.14; CV♀ = 0.09), suggesting sex-by-genotype interaction on residual variance. We therefore investigated the effect of sex on absolute-transformed residuals in urinary calcium in an F2 GHS × WKY mapping cohort. Absolute residuals were associated with genotype at two microsatellites, D3Rat46 (RNO3, 33.9 Mb) and D4Mgh1 (RNO4, 84.8 MB) at Bonferroni thresholds across the entire cohort, and with the microsatellites D3Rat46, D9Mgh2 (RNO9, 84.4 Mb), and D12Rat25 (RNO12, 40.4 Mb) in females (P < 0.05) but not males. In GHS chromosome 1 congenic lines bred onto a WKY genomic background, we found that congenic males had significantly (P < 0.0001) higher CVs for urinary calcium (CV = 0.25) than females (CV = 0.15), supporting the hypothesis of the inheritance of sex-by-genotype interaction on this effect. Our findings suggest that genetic effects on residual variance are sex linked; heritable, sex-specific residuals might have great potential implications for evolution, adaptation, and genetic analysis. PMID:22554889

  15. Genetic variance and genotype-by-environment interaction of immune response in Aedes aegypti (Diptera: Culicidae).

    PubMed

    Moreno-García, Miguel; Lanz-Mendoza, Humberto; Córdoba-Aguilar, Alex

    2010-03-01

    Immune response can be negatively affected by resource limitation, so it is expected that organisms evolve strategies to minimize the impact of this environmental outcome. Phenotypic plasticity in immune response could represent a genetic response to face such situations. We investigated the effects of high and low quality and quantity of food at the larval stage on two important immune components, phenoloxidase activity (PO) and nitric oxide production (NO) measured in adults of the Dengue vector, Aedes aegypti. We reared families to determine the magnitude and pattern of expression of genetic variance, environmental variance and genotype-by-environment interaction (GEI). In addition, we quantified whether there were differences in plastic immune responses in both sexes. Our results indicated additive variance for PO and NO, but rearing environment did not produce differences among individuals. For NO and PO in males, there were large differences among families in plasticity, as indicated by the different slopes produced by each reaction norm. Therefore, there is additive genetic variation in plasticity for NO production and PO activity. One possible interpretation of these results is that different genotypes may be favored to fight pathogens under the different food quality situations. Males and females showed similar overall GEI strategies but there were differences in PO and NO. Males showed a phenotypic correlation between PO and NO, but we did not find genetic correlations between immune parameters in both sexes.

  16. 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...

  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. Genetic impact dominates over environmental effects in development of carotid artery stiffness: a twin study.

    PubMed

    Horváth, Tamás; Osztovits, János; Pintér, Alexandra; Littvay, Levente; Cseh, Domonkos; Tárnoki, Adám D; Tárnoki, Dávid L; Jermendy, Adám L; Steinbach, Rita; Métneki, Júlia; Schillaci, Giuseppe; Kollai, Márk; Jermendy, György

    2014-01-01

    Arterial stiffness is an independent predictor of cardiovascular, cerebrovascular and all-cause mortality. Quantifying the genetic influence on the stiff arterial phenotype allows us to better predict the development of arterial stiffness. In this study, we aimed to determine the heritability of carotid artery stiffness in healthy twins. We studied 98 twin pairs of both sexes. We determined carotid artery stiffness locally using echo tracking and applanation tonometry. We estimated the heritability of stiffness parameters using structural equation modeling. The carotid distensibility coefficient showed the highest heritability (64%, 95% confidence interval 45-77%). The incremental elastic modulus, compliance and stiffness index β also showed substantial heritability (62%, 61% and 58%, respectively). The remaining 36-42% phenotypic variance was attributed to unshared environmental effects. Genetic influence appears to dominate over environmental factors in the development of carotid artery stiffness. Environmental factors may have an important role in favorably influencing the genetic predisposition for accelerated arterial stiffening.

  19. 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.

  20. 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

  1. 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.

  2. 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

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

    PubMed

    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

  4. 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

  5. The apportionment of total genetic variation by categorical analysis of variance.

    PubMed

    Khang, Tsung Fei; Yap, Von Bing

    2010-01-01

    We wish to suggest the categorical analysis of variance as a means of quantifying the proportion of total genetic variation attributed to different sources of variation. This method potentially challenges researchers to rethink conclusions derived from a well-known method known as the analysis of molecular variance (AMOVA). The CATANOVA framework allows explicit definition, and estimation, of two measures of genetic differentiation. These parameters form the subject of interest in many research programmes, but are often confused with the correlation measures defined in AMOVA, which cannot be interpreted as relative contributions of particular sources of variation. Through a simulation approach, we show that under certain conditions, researchers who use AMOVA to estimate these measures of genetic differentiation may attribute more than justified amounts of total variation to population labels. Moreover, the two measures can also lead to incongruent conclusions regarding the genetic structure of the populations of interest. Fortunately, one of the two measures seems robust to variations in relative sample sizes used. Its merits are illustrated in this paper using mitochondrial haplotype and amplified fragment length polymorphism (AFLP) data.

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

    PubMed

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

    2016-04-07

    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.

  7. Linear score tests for variance components in linear mixed models and applications to genetic association studies.

    PubMed

    Qu, Long; Guennel, Tobias; Marshall, Scott L

    2013-12-01

    Following the rapid development of genome-scale genotyping technologies, genetic association mapping has become a popular tool to detect genomic regions responsible for certain (disease) phenotypes, especially in early-phase pharmacogenomic studies with limited sample size. In response to such applications, a good association test needs to be (1) applicable to a wide range of possible genetic models, including, but not limited to, the presence of gene-by-environment or gene-by-gene interactions and non-linearity of a group of marker effects, (2) accurate in small samples, fast to compute on the genomic scale, and amenable to large scale multiple testing corrections, and (3) reasonably powerful to locate causal genomic regions. The kernel machine method represented in linear mixed models provides a viable solution by transforming the problem into testing the nullity of variance components. In this study, we consider score-based tests by choosing a statistic linear in the score function. When the model under the null hypothesis has only one error variance parameter, our test is exact in finite samples. When the null model has more than one variance parameter, we develop a new moment-based approximation that performs well in simulations. Through simulations and analysis of real data, we demonstrate that the new test possesses most of the aforementioned characteristics, especially when compared to existing quadratic score tests or restricted likelihood ratio tests. PMID:24328714

  8. 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

  9. 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.

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

    PubMed

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

    2014-05-01

    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.

  11. 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

  12. The Dominance Concept Inventory: A Tool for Assessing Undergraduate Student Alternative Conceptions about Dominance in Mendelian and Population Genetics

    ERIC Educational Resources Information Center

    Abraham, Joel K.; Perez, Kathryn E.; Price, Rebecca M.

    2014-01-01

    Despite the impact of genetics on daily life, biology undergraduates understand some key genetics concepts poorly. One concept requiring attention is dominance, which many students understand as a fixed property of an allele or trait and regularly conflate with frequency in a population or selective advantage. We present the Dominance Concept…

  13. Clinical features, molecular genetics, and pathophysiology of dominant optic atrophy.

    PubMed

    Votruba, M; Moore, A T; Bhattacharya, S S

    1998-10-01

    Inherited optic neuropathies are a significant cause of childhood and adult blindness and dominant optic atrophy (DOA) is the most common form of autosomally inherited (non-glaucomatous) optic neuropathy. Patients with DOA present with an insidious onset of bilateral visual loss and they characteristically have temporal optic nerve pallor, centrocaecal visual field scotoma, and a colour vision deficit, which is frequently blue-yellow. Evidence from histological and electrophysiological studies suggests that the pathology is confined to the retinal ganglion cell. A gene for dominant optic atrophy (OPA1) has been mapped to chromosome 3q28-qter, and studies are under way to refine the genetic interval in which the gene lies, to map the region physically, and hence to clone the gene. A second locus for dominant optic atrophy has recently been shown to map to chromosome 18q12.2-12.3 near the Kidd blood group locus. The cloning of genes for dominant optic atrophy will provide important insights into the pathophysiology of the retinal ganglion cell in health and disease. These insights may prove to be of great value in the understanding of other primary ganglion cell diseases, such as the mitochondrially inherited Leber's hereditary optic neuropathy and other diseases associated with ganglion cell loss, such as glaucoma.

  14. The genetic variance for multiple linked quantitative trait loci conditional on marker information in a crossed population.

    PubMed

    Matsuda, H; Iwaisaki, H

    2002-01-01

    In the prediction of genetic values and quantitative trait loci (QTLs) mapping via the mixed model method incorporating marker information in animal populations, it is important to model the genetic variance for individuals with an arbitrary pedigree structure. In this study, for a crossed population originated from different genetic groups such as breeds or outbred strains, the variance of additive genetic values for multiple linked QTLs that are contained in a chromosome segment, especially the segregation variance, is investigated assuming the use of marker data. The variance for a finite number of QTLs in one chromosomal segment is first examined for the crossed population with the general pedigree. Then, applying the concept of the expectation of identity-by-descent proportion, an approximation to the mean of the conditional probabilities for the linked QTLs over all loci is obtained, and using it an expression for the variance in the case of an infinite number of linked QTLs marked by flanking markers is derived. It appears that the approach presented can be useful in the segment mapping using, and in the genetic evaluation of, crosses with general pedigrees in the population of concern. The calculation of the segregation variance through the current approach is illustrated numerically, using a small data-set.

  15. 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.

  16. 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

  17. Evolvability of individual traits in a multivariate context: partitioning the additive genetic variance into common and specific components.

    PubMed

    McGuigan, Katrina; Blows, Mark W

    2010-07-01

    Genetic covariation among multiple traits will bias the direction of evolution. Although a trait's phenotypic context is crucial for understanding evolutionary constraints, the evolutionary potential of one (focal) trait, rather than the whole phenotype, is often of interest. The extent to which a focal trait can evolve independently depends on how much of the genetic variance in that trait is unique. Here, we present a hypothesis-testing framework for estimating the genetic variance in a focal trait that is independent of variance in other traits. We illustrate our analytical approach using two Drosophila bunnanda trait sets: a contact pheromone system comprised of cuticular hydrocarbons (CHCs), and wing shape, characterized by relative warps of vein position coordinates. Only 9% of the additive genetic variation in CHCs was trait specific, suggesting individual traits are unlikely to evolve independently. In contrast, most (72%) of the additive genetic variance in wing shape was trait specific, suggesting relative warp representations of wing shape could evolve independently. The identification of genetic variance in focal traits that is independent of other traits provides a way of studying the evolvability of individual traits within the broader context of the multivariate phenotype.

  18. Population divergence along lines of genetic variance and covariance in the invasive plant Lythrum salicaria in eastern North America.

    PubMed

    Colautti, Robert I; Barrett, Spencer C H

    2011-09-01

    Evolution during biological invasion may occur over contemporary timescales, but the rate of evolutionary change may be inhibited by a lack of standing genetic variation for ecologically relevant traits and by fitness trade-offs among them. The extent to which these genetic constraints limit the evolution of local adaptation during biological invasion has rarely been examined. To investigate genetic constraints on life-history traits, we measured standing genetic variance and covariance in 20 populations of the invasive plant purple loosestrife (Lythrum salicaria) sampled along a latitudinal climatic gradient in eastern North America and grown under uniform conditions in a glasshouse. Genetic variances within and among populations were significant for all traits; however, strong intercorrelations among measurements of seedling growth rate, time to reproductive maturity and adult size suggested that fitness trade-offs have constrained population divergence. Evidence to support this hypothesis was obtained from the genetic variance-covariance matrix (G) and the matrix of (co)variance among population means (D), which were 79.8% (95% C.I. 77.7-82.9%) similar. These results suggest that population divergence during invasive spread of L. salicaria in eastern North America has been constrained by strong genetic correlations among life-history traits, despite large amounts of standing genetic variation for individual traits.

  19. 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.

  20. 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

  1. 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

  2. Influence of dominance, leptokurtosis and pleiotropy of deleterious mutations on quantitative genetic variation at mutation-selection balance.

    PubMed Central

    Zhang, Xu-Sheng; Wang, Jinliang; Hill, William G

    2004-01-01

    In models of maintenance of genetic variance (V (G)) it has often been assumed that mutant alleles act additively. However, experimental data show that the dominance coefficient varies among mutant alleles and those of large effect tend to be recessive. On the basis of empirical knowledge of mutations, a joint-effect model of pleiotropic and real stabilizing selection that includes dominance is constructed and analyzed. It is shown that dominance can dramatically alter the prediction of equilibrium V (G). Analysis indicates that for the situations where mutations are more recessive for fitness than for a quantitative trait, as supported by the available data, the joint-effect model predicts a significantly higher V (G) than does an additive model. Importantly, for what seem to be realistic distributions of mutational effects (i.e., many mutants may not affect the quantitative trait substantially but are likely to affect fitness), the observed high levels of genetic variation in the quantitative trait under strong apparent stabilizing selection can be generated. This investigation supports the hypothesis that most V (G) comes from the alleles nearly neutral for fitness in heterozygotes while apparent stabilizing selection is contributed mainly by the alleles of large effect on the quantitative trait. Thus considerations of dominance coefficients of mutations lend further support to our previous conclusion that mutation-selection balance is a plausible mechanism of the maintenance of the genetic variance in natural populations. PMID:15020447

  3. Estimating the genetic variance of major depressive disorder due to all single nucleotide polymorphisms.

    PubMed

    Lubke, Gitta H; Hottenga, Jouke Jan; Walters, Raymond; Laurin, Charles; de Geus, Eco J C; Willemsen, Gonneke; Smit, Jan H; Middeldorp, Christel M; Penninx, Brenda W J H; Vink, Jacqueline M; Boomsma, Dorret I

    2012-10-15

    Genome-wide association studies of psychiatric disorders have been criticized for their lack of explaining a considerable proportion of the heritability established in twin and family studies. Genome-wide association studies of major depressive disorder in particular have so far been unsuccessful in detecting genome-wide significant single nucleotide polymorphisms (SNPs). Using two recently proposed methods designed to estimate the heritability of a phenotype that is attributable to genome-wide SNPs, we show that SNPs on current platforms contain substantial information concerning the additive genetic variance of major depressive disorder. To assess the consistency of these two methods, we analyzed four other complex phenotypes from different domains. The pattern of results is consistent with estimates of heritability obtained in twin studies carried out in the same population.

  4. The ARMC5 gene shows extensive genetic variance in primary macronodular adrenocortical hyperplasia

    PubMed Central

    Correa, Ricardo; Zilbermint, Mihail; Berthon, Annabel; Espiard, Stephanie; Batsis, Maria; Papadakis, Georgios Z.; Xekouki, Paraskevi; Lodish, Maya B.; Bertherat, Jerome; Faucz, Fabio R.; Stratakis, Constantine A.

    2015-01-01

    Objective Primary macronodular adrenal hyperplasia (PMAH) is a rare type of Cushing’s syndrome (CS) that results in increased cortisol production and bilateral enlargement of the adrenal glands. Recent work showed that the disease may be caused by germline and somatic mutations in the ARMC5 gene, a likely tumor-suppressor gene (TSG). We investigated 20 different adrenal nodules from one patient with PMAH for ARMC5 somatic sequence changes. Design All of the nodules where obtained from a single patient who underwent bilateral adrenalectomy. DNA was extracted by standard protocols and the ARMC5 sequence was determined by the Sanger method. Results Sixteen of 20 adrenocortical nodules harbored, in addition to what appeared to be the germline mutation, a second somatic variant. The p.Trp476* sequence change was present in all 20 nodules, as well as in normal tissue from the adrenal capsule, identifying it as the germline defect; each of the 16 other variants were found in different nodules: 6 were frame shift, 4 were missense, 3 were nonsense, and 1 was a splice site variation. Allelic losses were confirmed in 2 of the nodules. Conclusion This is the most genetic variance of the ARMC5 gene ever described in a single patient with PMAH: each of 16 adrenocortical nodules had a second new, “private”, and -in most cases- completely inactivating ARMC5 defect, in addition to the germline mutation. The data support the notion that ARMC5 is a TSG that needs a second, somatic hit, to mediate tumorigenesis leading to polyclonal nodularity; however, the driver of this extensive genetic variance of the second ARMC5 allele in adrenocortical tissue in the context of a germline defect and PMAH remains a mystery. PMID:26162405

  5. Autosomal dominant cyclic hematopoiesis: Genetics, phenotype, and natural history

    SciTech Connect

    Palmer, S.E.; Stephens, K.; Dale, D.C.

    1994-09-01

    Autosomal dominant cyclic hematopoiesis (ADCH; cyclic neutropenia) is a rare disorder manifested by transient neutropenia that recurs every three weeks. To facilitate mapping the ADCH gene by genetic linkage analysis, we studied 9 ADCH families with 42 affected individuals. Pedigrees revealed AD inheritance with no evidence for decreased penetrance. Similar intra- and interfamilial variable expression was observed, with no evidence to support heterogeneity. At least 3 families displayed apparent new mutations. Many adults developed chronic neutropenia, while offspring always cycled during childhood. Children displayed recurrent oral ulcers, gingivitis, lymphadenopathy, fever, and skin and other infections with additional symptoms. Interestingly, there were no cases of neonatal infection. Some children required multiple hospitalizations for treatment. Four males under age 18 died of Clostridium sepsis following necrotizing enterocolitis; all had affected mothers. No other deaths due to ADCH were found; most had improvement of symptoms and infections as adults. Adults experienced increased tooth loss prior to age 30 (16 out of 27 adults, with 9 edentulous). No increase in myelodysplasia, malignancy, or congenital anomalies was observed. Recombinant G-CSF treatment resulted in dramatic improvement of symptoms and infections. The results suggest that ADCH is not a benign disorder, especially in childhood, and abdominal pain requires immediate evaluation. Diagnosis of ADCH requires serial blood counts in the proband and at least one CBC in relatives to exclude similar disorders. Genetic counseling requires specific histories as well as CBCs of each family member at risk to determine status regardless of symptom history, especially to assess apparent new mutations.

  6. fullfact: an R package for the analysis of genetic and maternal variance components from full factorial mating designs.

    PubMed

    Houde, Aimee Lee S; Pitcher, Trevor E

    2016-03-01

    Full factorial breeding designs are useful for quantifying the amount of additive genetic, nonadditive genetic, and maternal variance that explain phenotypic traits. Such variance estimates are important for examining evolutionary potential. Traditionally, full factorial mating designs have been analyzed using a two-way analysis of variance, which may produce negative variance values and is not suited for unbalanced designs. Mixed-effects models do not produce negative variance values and are suited for unbalanced designs. However, extracting the variance components, calculating significance values, and estimating confidence intervals and/or power values for the components are not straightforward using traditional analytic methods. We introduce fullfact - an R package that addresses these issues and facilitates the analysis of full factorial mating designs with mixed-effects models. Here, we summarize the functions of the fullfact package. The observed data functions extract the variance explained by random and fixed effects and provide their significance. We then calculate the additive genetic, nonadditive genetic, and maternal variance components explaining the phenotype. In particular, we integrate nonnormal error structures for estimating these components for nonnormal data types. The resampled data functions are used to produce bootstrap-t confidence intervals, which can then be plotted using a simple function. We explore the fullfact package through a worked example. This package will facilitate the analyses of full factorial mating designs in R, especially for the analysis of binary, proportion, and/or count data types and for the ability to incorporate additional random and fixed effects and power analyses.

  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. Genetic Sorting of Subordinate Species in Grassland Modulated by Intraspecific Variation in Dominant Species

    PubMed Central

    Gustafson, Danny J.; Major, Charles; Jones, Dewitt; Synovec, John; Baer, Sara G.; Gibson, David J.

    2014-01-01

    Genetic variation in a single species can have predictable and heritable effects on associated communities and ecosystem processes, however little is known about how genetic variation of a dominant species affects plant community assembly. We characterized the genetic structure of a dominant grass (Sorghastrum nutans) and two subordinate species (Chamaecrista fasciculata, Silphium integrifolium), during the third growing season in grassland communities established with genetically distinct (cultivated varieties or local ecotypes) seed sources of the dominant grasses. There were genetic differences between subordinate species growing in the cultivar versus local ecotype communities, indicating that intraspecific genetic variation in the dominant grasses affected the genetic composition of subordinate species during community assembly. A positive association between genetic diversity of S. nutans, C. fasciculata, and S. integrifolium and species diversity established the role of an intraspecific biotic filter during community assembly. Our results show that intraspecific variation in dominant species can significantly modulate the genetic composition of subordinate species. PMID:24637462

  9. Genetics, phenotype, and natural history of autosomal dominant cyclic hematopoiesis

    SciTech Connect

    Palmer, S.E. |; Dale, D.C.

    1996-12-30

    Cyclic hematopoiesis (CH, or cyclic neutropenia) is a rare disease manifested by transient severe neutropenia that recurs approximately every 21 days. The hematologic profile of families with the autosomal dominant form (ADCH) has not been well characterized, and it is unknown if the phenotype is distinct from the more common sporadic congenital or acquired forms of CH. We studied nine ADCH families whose children displayed typical CH blood patterns. Pedigrees confirmed dominant inheritance without evidence of heterogeneity or decreased penetrance; three pedigrees suggested new mutations. Families were Caucasian with exception of one with a Cherokee Native American founder. A wide spectrum of symptom severity, ranging from asymptomatic to life-threatening illness, was observed within families. The phenotype changed with age. Children displayed typical neutrophil cycles with symptoms of mucosal ulceration, lymphadenopathy, and infections. Adults often had fewer and milder symptoms, sometimes accompanied by mild chronic neutropenia without distinct cycles. While CH is commonly described as {open_quotes}benign{close_quotes}, four children in three of the nine families died of Clostridium or E. coli colitis, documenting the need for urgent evaluation of abdominal pain. Misdiagnosis with other neutropenias was common but can be avoided by serial blood counts in index cases. Genetic counseling requires specific histories and complete blood counts in relatives at risk to assess status regardless of symptoms, especially to determine individuals with new mutations. We propose diagnostic criteria for ADCH in affected children and adults. Recombinant human granulocyte colony-stimulating factor treatment resulted in dramatic improvement of neutropenia and morbidity. The differential diagnosis from other forms of familial neutropenia is reviewed. 45 refs., 4 figs., 1 tab.

  10. A Genome-Wide Association Analysis Reveals Epistatic Cancellation of Additive Genetic Variance for Root Length in Arabidopsis thaliana.

    PubMed

    Lachowiec, Jennifer; Shen, Xia; Queitsch, Christine; Carlborg, Örjan

    2015-01-01

    Efforts to identify loci underlying complex traits generally assume that most genetic variance is additive. Here, we examined the genetics of Arabidopsis thaliana root length and found that the genomic narrow-sense heritability for this trait in the examined population was statistically zero. The low amount of additive genetic variance that could be captured by the genome-wide genotypes likely explains why no associations to root length could be found using standard additive-model-based genome-wide association (GWA) approaches. However, as the broad-sense heritability for root length was significantly larger, and primarily due to epistasis, we also performed an epistatic GWA analysis to map loci contributing to the epistatic genetic variance. Four interacting pairs of loci were revealed, involving seven chromosomal loci that passed a standard multiple-testing corrected significance threshold. The genotype-phenotype maps for these pairs revealed epistasis that cancelled out the additive genetic variance, explaining why these loci were not detected in the additive GWA analysis. Small population sizes, such as in our experiment, increase the risk of identifying false epistatic interactions due to testing for associations with very large numbers of multi-marker genotypes in few phenotyped individuals. Therefore, we estimated the false-positive risk using a new statistical approach that suggested half of the associated pairs to be true positive associations. Our experimental evaluation of candidate genes within the seven associated loci suggests that this estimate is conservative; we identified functional candidate genes that affected root development in four loci that were part of three of the pairs. The statistical epistatic analyses were thus indispensable for confirming known, and identifying new, candidate genes for root length in this population of wild-collected A. thaliana accessions. We also illustrate how epistatic cancellation of the additive genetic variance

  11. A Genome-Wide Association Analysis Reveals Epistatic Cancellation of Additive Genetic Variance for Root Length in Arabidopsis thaliana

    PubMed Central

    Lachowiec, Jennifer; Shen, Xia; Queitsch, Christine; Carlborg, Örjan

    2015-01-01

    Efforts to identify loci underlying complex traits generally assume that most genetic variance is additive. Here, we examined the genetics of Arabidopsis thaliana root length and found that the genomic narrow-sense heritability for this trait in the examined population was statistically zero. The low amount of additive genetic variance that could be captured by the genome-wide genotypes likely explains why no associations to root length could be found using standard additive-model-based genome-wide association (GWA) approaches. However, as the broad-sense heritability for root length was significantly larger, and primarily due to epistasis, we also performed an epistatic GWA analysis to map loci contributing to the epistatic genetic variance. Four interacting pairs of loci were revealed, involving seven chromosomal loci that passed a standard multiple-testing corrected significance threshold. The genotype-phenotype maps for these pairs revealed epistasis that cancelled out the additive genetic variance, explaining why these loci were not detected in the additive GWA analysis. Small population sizes, such as in our experiment, increase the risk of identifying false epistatic interactions due to testing for associations with very large numbers of multi-marker genotypes in few phenotyped individuals. Therefore, we estimated the false-positive risk using a new statistical approach that suggested half of the associated pairs to be true positive associations. Our experimental evaluation of candidate genes within the seven associated loci suggests that this estimate is conservative; we identified functional candidate genes that affected root development in four loci that were part of three of the pairs. The statistical epistatic analyses were thus indispensable for confirming known, and identifying new, candidate genes for root length in this population of wild-collected A. thaliana accessions. We also illustrate how epistatic cancellation of the additive genetic variance

  12. Genetic variance in the composition of two functional groups (diazotrophs and cyanobacteria) from a hypersaline microbial mat.

    PubMed

    Yannarell, Anthony C; Steppe, Timothy F; Paerl, Hans W

    2006-02-01

    Examination of variation in ecological communities can lead to an understanding of the forces that structure communities, the consequences of change at the ecosystem level, and the relevant scales involved. This study details spatial and seasonal variability in the composition of nitrogen-fixing and cyanobacterial (i.e., oxygenic photosynthetic) functional groups of a benthic, hypersaline microbial mat from Salt Pond, San Salvador Island, Bahamas. This system shows extreme annual variability in the salinity of the overlying water and the extent of water coverage. Analysis of molecular variance and F(ST) tests of genetic differentiation of nifH and cyanobacterial 16S rRNA gene clone libraries allowed for changes at multiple taxonomic levels (i.e., above, below, and at the species level) to inform the conclusions regarding these functional groups. Composition of the nitrogen-fixing community showed significant seasonal changes related to salinity, while cyanobacterial composition showed no consistent seasonal pattern. Both functional groups exhibited significant spatial variation, changing with depth in the mat and horizontally with distance from the shoreline. The patterns of change suggest that cyanobacterial composition was more insensitive to water stress, and consequently, cyanobacteria dominated the nitrogen-fixing community during dry months but gave way to a more diverse community of diazotrophs in wet months. This seasonal pattern may allow the mat community to respond quickly to water-freshening events after prolonged dry conditions (system recovery) and maintain ecosystem function in the face of disturbance during the wet season (system resilience).

  13. Genetics Home Reference: autosomal dominant congenital stationary night blindness

    MedlinePlus

    ... stationary night blindness autosomal dominant congenital stationary night blindness Enable Javascript to view the expand/collapse boxes. ... Close All Description Autosomal dominant congenital stationary night blindness is a disorder of the retina , which is ...

  14. How many marker loci are necessary? Analysis of dominant marker data sets using two popular population genetic algorithms.

    PubMed

    Nelson, Michael F; Anderson, Neil O

    2013-09-01

    The number of marker loci required to answer a given research question satisfactorily is especially important for dominant markers since they have a lower information content than co-dominant marker systems. In this study, we used simulated dominant marker data sets to determine the number of dominant marker loci needed to obtain satisfactory results from two popular population genetic analyses: STRUCTURE and AMOVA (analysis of molecular variance). Factors such as migration, level of population differentiation, and unequal sampling were varied in the data sets to mirror a range of realistic research scenarios. AMOVA performed well under all scenarios with a modest quantity of markers while STRUCTURE required a greater number, especially when populations were closely related. The popular ΔK method of determining the number of genetically distinct groups worked well when sampling was balanced, but underestimated the true number of groups with unbalanced sampling. These results provide a window through which to interpret previous work with dominant markers and we provide a protocol for determining the number of markers needed for future dominant marker studies.

  15. Genetics Home Reference: cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy

    MedlinePlus

    Skip to main content Your Guide to Understanding Genetic Conditions Enable Javascript for addthis links to activate. ... Conditions Genes Chromosomes & mtDNA Resources Help Me Understand Genetics Home Health Conditions CADASIL cerebral autosomal dominant arteriopathy ...

  16. Knowledge extraction algorithm for variances handling of CP using integrated hybrid genetic double multi-group cooperative PSO and DPSO.

    PubMed

    Du, Gang; Jiang, Zhibin; Diao, Xiaodi; Yao, Yang

    2012-04-01

    Although the clinical pathway (CP) predefines predictable standardized care process for a particular diagnosis or procedure, many variances may still unavoidably occur. Some key index parameters have strong relationship with variances handling measures of CP. In real world, these problems are highly nonlinear in nature so that it's hard to develop a comprehensive mathematic model. In this paper, a rule extraction approach based on combing hybrid genetic double multi-group cooperative particle swarm optimization algorithm (PSO) and discrete PSO algorithm (named HGDMCPSO/DPSO) is developed to discovery the previously unknown and potentially complicated nonlinear relationship between key parameters and variances handling measures of CP. Then these extracted rules can provide abnormal variances handling warning for medical professionals. Three numerical experiments on Iris of UCI data sets, Wisconsin breast cancer data sets and CP variances data sets of osteosarcoma preoperative chemotherapy are used to validate the proposed method. When compared with the previous researches, the proposed rule extraction algorithm can obtain the high prediction accuracy, less computing time, more stability and easily comprehended by users, thus it is an effective knowledge extraction tool for CP variances handling.

  17. 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 ...

  18. 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.

  19. Genetics Home Reference: autosomal dominant hyper-IgE syndrome

    MedlinePlus

    ... movement ( hyperextensibility ), an abnormal curvature of the spine ( scoliosis ), reduced bone density (osteopenia), and a tendency for ... health conditions: Diagnostic Tests Drug Therapy Surgery and Rehabilitation Genetic Counseling Palliative Care Related Information How are ...

  20. 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

  1. 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

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

    2014-08-01

    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.

  2. Variance Decomposition of MRI-Based Covariance Maps Using Genetically-Informative Samples and Structural Equation Modeling

    PubMed Central

    Schmitt, J. Eric; Lenroot, Rhoshel; Ordaz, Sarah E.; Wallace, Gregory L.; Lerch, Jason P.; Evans, Alan C.; Prom, Elizabeth C.; Kendler, Kenneth S.; Neale, Michael C.; Giedd, Jay N.

    2010-01-01

    The role of genetics in driving intracortical relationships is an important question that has rarely been studied in humans. In particular, there are no extant high-resolution imaging studies on genetic covariance. In this article, we describe a novel method that combines classical quantitative genetic methodologies for variance decomposition with recently-developed semi-multivariate algorithms for high-resolution measurement of phenotypic covariance. Using these tools, we produced correlational maps of genetic and environmental (i.e. nongenetic) relationships between several regions of interest and the cortical surface in a large pediatric sample of 600 twins, siblings, and singletons. These analyses demonstrated high, fairly uniform, statistically significant genetic correlations between the entire cortex and global mean cortical thickness. In agreement with prior reports on phenotypic covariance using similar methods, we found mean cortical thickness was most strongly correlated with association cortices. However, the present study suggests that genetics plays a large role in global brain patterning of cortical thickness in this manner. Further, using specific gyri with known high heritabilities as seed regions, we found a consistent pattern of high bilateral genetic correlations between structural homologues, with environmental correlations more restricted to the same hemisphere as the seed region, suggesting that interhemispheric covariance is largely genetically mediated. These findings are consistent with the limited existing knowledge on the genetics of cortical variability as well as our prior multivariate studies on cortical gyri. PMID:18672072

  3. Good genes and sexual selection in dung beetles (Onthophagus taurus): genetic variance in egg-to-adult and adult viability.

    PubMed

    Garcia-Gonzalez, Francisco; Simmons, Leigh W

    2011-01-18

    Whether species exhibit significant heritable variation in fitness is central for sexual selection. According to good genes models there must be genetic variation in males leading to variation in offspring fitness if females are to obtain genetic benefits from exercising mate preferences, or by mating multiply. However, sexual selection based on genetic benefits is controversial, and there is limited unambiguous support for the notion that choosy or polyandrous females can increase the chances of producing offspring with high viability. Here we examine the levels of additive genetic variance in two fitness components in the dung beetle Onthophagus taurus. We found significant sire effects on egg-to-adult viability and on son, but not daughter, survival to sexual maturity, as well as moderate coefficients of additive variance in these traits. Moreover, we do not find evidence for sexual antagonism influencing genetic variation for fitness. Our results are consistent with good genes sexual selection, and suggest that both pre- and postcopulatory mate choice, and male competition could provide indirect benefits to females.

  4. Power graph compression reveals dominant relationships in genetic transcription networks.

    PubMed

    Ahnert, Sebastian E

    2013-11-01

    We introduce a framework for the discovery of dominant relationship patterns in transcription networks, by compressing the network into a power graph with overlapping power nodes. Our application of this approach to the transcription networks of S. cerevisiae and E. coli, paired with GO term enrichment analysis, provides a highly informative overview of the most prominent relationships in the gene regulatory networks of these two organisms.

  5. Stability of genetic variance and covariance for reproductive characters in the face of climate change in a wild bird population.

    PubMed

    Garant, Dany; Hadfield, Jarrod D; Kruuk, Loeske E B; Sheldon, Ben C

    2008-01-01

    Global warming has had numerous effects on populations of animals and plants, with many species in temperate regions experiencing environmental change at unprecedented rates. Populations with low potential for adaptive evolutionary change and plasticity will have little chance of persistence in the face of environmental change. Assessment of the potential for adaptive evolution requires the estimation of quantitative genetic parameters, but it is as yet unclear what impact, if any, global warming will have on the expression of genetic variances and covariances. Here we assess the impact of a changing climate on the genetic architecture underlying three reproductive traits in a wild bird population. We use a large, long-term, data set collected on great tits (Parus major) in Wytham Woods, Oxford, and an 'animal model' approach to quantify the heritability of, and genetic correlations among, laying date, clutch size and egg mass during two periods with contrasting temperature conditions over a 40-year period (1965-1988 [cooler] vs. 1989-2004 [warmer]). We found significant additive genetic variance and heritability for all traits under both temperature regimes. We also found significant negative genetic covariances and correlations between clutch size and egg weight during both periods, and among laying date and clutch size in the colder years only. The overall G matrix comparison among periods, however, showed only a minor difference among periods, thus suggesting that genotype by environment interactions are negligible in this context. Our results therefore suggest that despite substantial changes in temperature and in mean laying date phenotype over the last decades, and despite the large sample sizes available, we are unable to detect any significant change in the genetic architecture of the reproductive traits studied.

  6. Model-specific tests on variance heterogeneity for detection of potentially interacting genetic loci

    PubMed Central

    2012-01-01

    Background Trait variances among genotype groups at a locus are expected to differ in the presence of an interaction between this locus and another locus or environment. A simple maximum test on variance heterogeneity can thus be used to identify potentially interacting single nucleotide polymorphisms (SNPs). Results We propose a multiple contrast test for variance heterogeneity that compares the mean of Levene residuals for each genotype group with their average as an alternative to a global Levene test. We applied this test to a Bogalusa Heart Study dataset to screen for potentially interacting SNPs across the whole genome that influence a number of quantitative traits. A user-friendly implementation of this method is available in the R statistical software package multcomp. Conclusions We show that the proposed multiple contrast test of model-specific variance heterogeneity can be used to test for potential interactions between SNPs and unknown alleles, loci or covariates and provide valuable additional information compared with traditional tests. Although the test is statistically valid for severely unbalanced designs, care is needed in interpreting the results at loci with low allele frequencies. PMID:22808950

  7. Genetic diversity and variance of Stentor coeruleus (Ciliophora: Heterotrichea) inferred from inter-simple sequence repeat (ISSR) fingerprinting.

    PubMed

    Zhang, Wen-Jing; Lin, Yuan-Shao; Cao, Wen-Qing; Yang, Jun

    2012-01-01

    We used inter-simple sequence repeat fingerprinting to analyze the genetic structure of 16 populations of Stentor coeruleus from three lakes and three ponds in China. Using 14 polymorphic primers, a total of 99 discernible DNA fragments were detected, among which 76 (76.77%) were polymorphic, indicating median genetic diversity in these populations. Further, both Nei's gene diversity (h) and Shannon's information index (I) between the different populations revealed a median genetic diversity. At the same time, gene flow was interpreted to be low. The main factors responsible for the median level of diversity and low gene flow within populations are probably due to a low frequency of sexual recombinations. Analysis of molecular variance showed that there was high genetic differentiation among the five water bodies. Both cluster analysis and a nonmetric multidimensional scaling analysis suggested that genotypes isolated from the same locations displayed a higher genetic similarity than those from different ones, separating populations into subgroups according to their geographical locations. However, there is a weak positive correlation between the genetic distance and geographical distance. PMID:22239713

  8. 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…

  9. Genetic Model Fitting in IQ, Assortative Mating & Components of IQ Variance.

    ERIC Educational Resources Information Center

    Capron, Christiane; Vetta, Adrian R.; Vetta, Atam

    1998-01-01

    The biometrical school of scientists who fit models to IQ data traces their intellectual ancestry to R. Fisher (1918), but their genetic models have no predictive value. Fisher himself was critical of the concept of heritability, because assortative mating, such as for IQ, introduces complexities into the study of a genetic trait. (SLD)

  10. Detection of novel genetic variation in autosomal dominant retinitis pigmentosa.

    PubMed

    Borràs, E; de Sousa Dias, M; Hernan, I; Pascual, B; Mañé, B; Gamundi, M J; Delás, B; Carballo, M

    2013-11-01

    We explored an approach to detect disease-causing sequence variants in 448 candidate genes from five index cases of autosomal dominant retinitis pigmentosa (adRP) by sequence DNA capture and next-generation DNA sequencing (NGS). Detection of sequence variants was carried out by sequence capture NimbleGen and NGS in a SOLiD platform. After filtering out variants previously reported in genomic databases, novel potential adRP-causing variants were validated by dideoxy capillary electrophoresis (Sanger) sequencing and co-segregation in the families. A total of 55 novel sequence variants in the coding or splicing regions of adRP candidate genes were detected, 49 of which were confirmed by Sanger sequencing. Segregation of these variants in the corresponding adRP families showed three variants present in all the RP-affected members of the family. A novel mutation, p.L270R in IMPDH1, was found to be disease causing in one family. In another family a variant, p.M96T in the NRL gene was detected; this variant was previously reported as probably causing adRP. However, the previously reported p.A76V mutation in NRL as a cause of RP was excluded by co-segregation in the family. We discuss the benefits and limitations of our approach in the context of mutation detection in adRP patients.

  11. Accuracy of whole-genome prediction using a genetic architecture-enhanced variance-covariance matrix.

    PubMed

    Zhang, Zhe; Erbe, Malena; He, Jinlong; Ober, Ulrike; Gao, Ning; Zhang, Hao; Simianer, Henner; Li, Jiaqi

    2015-02-09

    Obtaining accurate predictions of unobserved genetic or phenotypic values for complex traits in animal, plant, and human populations is possible through whole-genome prediction (WGP), a combined analysis of genotypic and phenotypic data. Because the underlying genetic architecture of the trait of interest is an important factor affecting model selection, we propose a new strategy, termed BLUP|GA (BLUP-given genetic architecture), which can use genetic architecture information within the dataset at hand rather than from public sources. This is achieved by using a trait-specific covariance matrix ( T: ), which is a weighted sum of a genetic architecture part ( S: matrix) and the realized relationship matrix ( G: ). The algorithm of BLUP|GA (BLUP-given genetic architecture) is provided and illustrated with real and simulated datasets. Predictive ability of BLUP|GA was validated with three model traits in a dairy cattle dataset and 11 traits in three public datasets with a variety of genetic architectures and compared with GBLUP and other approaches. Results show that BLUP|GA outperformed GBLUP in 20 of 21 scenarios in the dairy cattle dataset and outperformed GBLUP, BayesA, and BayesB in 12 of 13 traits in the analyzed public datasets. Further analyses showed that the difference of accuracies for BLUP|GA and GBLUP significantly correlate with the distance between the T: and G: matrices. The new strategy applied in BLUP|GA is a favorable and flexible alternative to the standard GBLUP model, allowing to account for the genetic architecture of the quantitative trait under consideration when necessary. This feature is mainly due to the increased similarity between the trait-specific relationship matrix ( T: matrix) and the genetic relationship matrix at unobserved causal loci. Applying BLUP|GA in WGP would ease the burden of model selection.

  12. Accuracy of Whole-Genome Prediction Using a Genetic Architecture-Enhanced Variance-Covariance Matrix

    PubMed Central

    Zhang, Zhe; Erbe, Malena; He, Jinlong; Ober, Ulrike; Gao, Ning; Zhang, Hao; Simianer, Henner; Li, Jiaqi

    2015-01-01

    Obtaining accurate predictions of unobserved genetic or phenotypic values for complex traits in animal, plant, and human populations is possible through whole-genome prediction (WGP), a combined analysis of genotypic and phenotypic data. Because the underlying genetic architecture of the trait of interest is an important factor affecting model selection, we propose a new strategy, termed BLUP|GA (BLUP-given genetic architecture), which can use genetic architecture information within the dataset at hand rather than from public sources. This is achieved by using a trait-specific covariance matrix (T), which is a weighted sum of a genetic architecture part (S matrix) and the realized relationship matrix (G). The algorithm of BLUP|GA (BLUP-given genetic architecture) is provided and illustrated with real and simulated datasets. Predictive ability of BLUP|GA was validated with three model traits in a dairy cattle dataset and 11 traits in three public datasets with a variety of genetic architectures and compared with GBLUP and other approaches. Results show that BLUP|GA outperformed GBLUP in 20 of 21 scenarios in the dairy cattle dataset and outperformed GBLUP, BayesA, and BayesB in 12 of 13 traits in the analyzed public datasets. Further analyses showed that the difference of accuracies for BLUP|GA and GBLUP significantly correlate with the distance between the T and G matrices. The new strategy applied in BLUP|GA is a favorable and flexible alternative to the standard GBLUP model, allowing to account for the genetic architecture of the quantitative trait under consideration when necessary. This feature is mainly due to the increased similarity between the trait-specific relationship matrix (T matrix) and the genetic relationship matrix at unobserved causal loci. Applying BLUP|GA in WGP would ease the burden of model selection. PMID:25670771

  13. Applications in genetic risk estimation of data on the induction of dominant skeletal mutations in mice

    SciTech Connect

    Selby, P.B.

    1982-01-01

    Studies on the induction of dominant skeleton mutations and of dominant cataract mutations provide means of estimating genetic hazard to humans from radiation. The breeding-test method of studying the induction of dominant skeletal mutations is slow and cumbersome. In an attempt to devise a more rapid method, three non-breeding-test methods have been developed which are likely to have wider application in mutagenicity testing. (ACR)

  14. Testing for Genetic Linkage in Families by a Variance-Components Approach in the Presence of Genomic Imprinting

    PubMed Central

    Shete, Sanjay; Amos, Christopher I.

    2002-01-01

    Some genes that affect development and behavior in mammals are known to be imprinted; and ⩾1% of all mammalian genes are imprinted. Hence, incorporating an imprinting parameter into linkage analysis may increase the power to detect linkage for these traits. Here we propose theoretical justifications for a recently developed model for testing of linkage, in the presence of genetic imprinting, between a quantitative-trait locus and a polymorphic marker; this is achieved in the variance-components framework. We also incorporate sex-specific recombination fractions into this model. We discuss the effects that imprinting and nonimprinting have on the power of the usual variance-components method and on the variance-components method that incorporates an imprinting parameter. We provide noncentrality parameters that can be used to determine the sample size necessary to attain a specified power for a given significance level, which is useful in the planning of a linkage study. Optimal strategies for a genome scan of potentially imprinted traits are discussed. PMID:11836650

  15. 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.

  16. Understanding the cellular and molecular mechanisms of dominant and recessive inheritance in genetics course.

    PubMed

    Wanjin, Xing; Morigen, Morigen

    2015-01-01

    In Mendellian genetics, the dominance and recessiveness are used to describe the functional relationship between two alleles of one gene in a heterozygote. The allele which constitutes a phenotypical character over the other is named dominant and the one functionally masked is called recessive. The definitions thereby led to the creation of Mendel's laws on segregation and independent assortment and subsequent classic genetics. The discrimination of dominance and recessiveness originally is a requirement for Mendel's logical reasoning, but now it should be explained by cellular and molecular principles in the modern genetics. To answer the question raised by students of how the dominance and recessiveness are controlled, we reviewed the recent articles and tried to summarize the cellular and molecular basis of dominant and recessive inheritance. Clearly, understanding the essences of dominant and recessive inheritance requires us to know the dissimilarity of the alleles and their products (RNA and/or proteins), and the way of their function in cells. The alleles spatio-temporally play different roles on offering cells, tissues or organs with discernible phenotypes, namely dominant or recessive. Here, we discuss the changes of allele dominance and recessiveness at the cellular and molecular levels based on the variation of gene structure, gene regulation, function and types of gene products, in order to make students understand gene mutation and function more comprehensively and concretely.

  17. 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...

  18. 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

  19. 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

  20. Genetic diversity within a dominant plant outweighs plant species diversity in structuring an arthropod community.

    PubMed

    Crawford, Kerri M; Rudgers, Jennifer A

    2013-05-01

    Plant biodiversity is being lost at a rapid rate. This has spurred much interest in elucidating the consequences of this loss for higher trophic levels. Experimental tests have shown that both plant species diversity and genetic diversity within a plant species can influence arthropod community structure. However, the majority of these studies have been conducted in separate systems, so their relative importance is currently unresolved. Furthermore, potential interactions between the two levels of diversity, which likely occur in natural systems, have not been investigated. To clarify these issues, we conducted three experiments in a freshwater sand dune ecosystem. We (1) independently manipulated plant species diversity, (2) independently manipulated genetic diversity within the dominant plant species, Ammophila breviligulata, and (3) jointly manipulated genetic diversity within the dominant plant and species diversity. We found that genetic diversity within the dominant plant species, Ammophila breviligulata, more strongly influenced arthropod communities than plant species diversity, but this effect was dependent on the presence of other species. In species mixtures, A. breviligulata genetic diversity altered overall arthropod community composition, and arthropod richness and abundance peaked at the highest level of genetic diversity. Positive nonadditive effects of diversity were detected, suggesting that arthropods respond to emergent properties of diverse plant communities. However, in the independent manipulations where A. breviligulata was alone, effects of genetic diversity were weaker, with only arthropod richness responding. In contrast, plant species diversity only influenced arthropods when A. breviligulata was absent, and then only influenced herbivore abundance. In addition to showing that genetic diversity within a dominant plant species can have large effects on arthropod community composition, these results suggest that understanding how species

  1. Molecular-genetic variance of RH blood group system within human population of Bosnia and Herzegovina.

    PubMed

    Lasić, Lejla; Lojo-Kadrić, Naida; Silajdžić, Elma; Pojskić, Lejla; Hadžiselimović, Rifat; Pojskić, Naris

    2013-02-01

    There are two major theories for inheritance of Rh blood group system: Fisher - Race theory and Wiener theory. Aim of this study was identifying frequency of RHDCE alleles in Bosnian - Herzegovinian population and introduction of this method in screening for Rh phenotype in B&H since this type of analysis was not used for blood typing in B&H before. Rh blood group was typed by Polymerase Chain Reaction, using the protocols and primers previously established by other authors, then carrying out electrophoresis in 2-3% agarose gel. Percentage of Rh positive individuals in our sample is 84.48%, while the percentage of Rh negative individuals is 15.52%. Inter-rater agreement statistic showed perfect agreement (K=1) between the results of Rh blood system detection based on serological and molecular-genetics methods. In conclusion, molecular - genetic methods are suitable for prenatal genotyping and specific cases while standard serological method is suitable for high-throughput of samples.

  2. 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

  3. 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

  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. 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.

  6. 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

  7. Genetics advances in autosomal dominant focal epilepsies: focus on DEPDC5.

    PubMed

    Baulac, Stéphanie

    2014-01-01

    Rare multiplex families with autosomal dominant focal epilepsies have been described with specific age-related and electroclinical syndromes: autosomal dominant nocturnal frontal lobe epilepsy (ADNFLE), familial temporal lobe epilepsy (FTLE), and familial focal epilepsy with variable foci (FFEVF). Molecular genetic advances in inherited focal epilepsies have pinpointed their genetic heterogeneity and the fact that they are mediated by different biological pathways: ion channel subunit genes have been linked to ADNFLE (CHRNA4, CHRNA2, CHRNB2, and KCNT1, encoding, respectively, the α4, α2, and β2 subunits of the neuronal nicotinic acetylcholine receptor, and a potassium channel subunit); neuronal secreted protein (LGI1-encoding epitempin) has been linked to autosomal dominant epilepsy with auditory features; and mTORC1-repressor DEPDC5 (DEP domain-containing protein 5) gene has recently been reported in a broad spectrum of inherited focal epilepsies (ADNFLE, FTLE, FFEVF). This chapter focuses on DEPDC5, a newly identified gene.

  8. Diversity and population structure of a dominant deciduous tree based on morphological and genetic data

    PubMed Central

    Zhang, Qin-di; Jia, Rui-Zhi; Meng, Chao; Ti, Chao-Wen; Wang, Yi-Ling

    2015-01-01

    Knowledge of the genetic diversity and structure of tree species across their geographic ranges is essential for sustainable use and management of forest ecosystems. Acer grosseri Pax., an economically and ecologically important maple species, is mainly distributed in North China. In this study, the genetic diversity and population differentiation of 24 natural populations of this species were evaluated using sequence-related amplified polymorphism markers and morphological characters. The results show that highly significant differences occurred in 32 morphological traits. The coefficient of variation of 34 characters was 18.19 %. Principal component analysis indicated that 18 of 34 traits explained 60.20 % of the total variance. The phenotypic differentiation coefficient (VST) was 36.06 % for all morphological traits. The Shannon–Wiener index of 34 morphological characters was 6.09, while at the population level, it was 1.77. The percentage of polymorphic bands of all studied A. grosseri populations was 82.14 %. Nei's gene diversity (He) and Shannon's information index (I) were 0.35 and 0.50, respectively. Less genetic differentiation was detected among the natural populations (GST = 0.20, ΦST = 0.10). Twenty-four populations of A. grosseri formed two main clusters, which is consistent with morphological cluster analysis. Principal coordinates analysis and STRUCTURE analysis supported the UPGMA-cluster dendrogram. There was no significant correlation between genetic and geographical distances among populations. Both molecular and morphological data suggested that A. grosseri is rich in genetic diversity. The high level of genetic variation within populations could be affected by the biological characters, mating system and lifespan of A. grosseri, whereas the lower genetic diversity among populations could be caused by effective gene exchange, selective pressure from environmental heterogeneity and the species' geographical range. PMID:26311734

  9. Diversity and population structure of a dominant deciduous tree based on morphological and genetic data.

    PubMed

    Zhang, Qin-di; Jia, Rui-Zhi; Meng, Chao; Ti, Chao-Wen; Wang, Yi-Ling

    2015-01-01

    Knowledge of the genetic diversity and structure of tree species across their geographic ranges is essential for sustainable use and management of forest ecosystems. Acer grosseri Pax., an economically and ecologically important maple species, is mainly distributed in North China. In this study, the genetic diversity and population differentiation of 24 natural populations of this species were evaluated using sequence-related amplified polymorphism markers and morphological characters. The results show that highly significant differences occurred in 32 morphological traits. The coefficient of variation of 34 characters was 18.19 %. Principal component analysis indicated that 18 of 34 traits explained 60.20 % of the total variance. The phenotypic differentiation coefficient (VST) was 36.06 % for all morphological traits. The Shannon-Wiener index of 34 morphological characters was 6.09, while at the population level, it was 1.77. The percentage of polymorphic bands of all studied A. grosseri populations was 82.14 %. Nei's gene diversity (He) and Shannon's information index (I) were 0.35 and 0.50, respectively. Less genetic differentiation was detected among the natural populations (GST = 0.20, ΦST = 0.10). Twenty-four populations of A. grosseri formed two main clusters, which is consistent with morphological cluster analysis. Principal coordinates analysis and STRUCTURE analysis supported the UPGMA-cluster dendrogram. There was no significant correlation between genetic and geographical distances among populations. Both molecular and morphological data suggested that A. grosseri is rich in genetic diversity. The high level of genetic variation within populations could be affected by the biological characters, mating system and lifespan of A. grosseri, whereas the lower genetic diversity among populations could be caused by effective gene exchange, selective pressure from environmental heterogeneity and the species' geographical range. PMID:26311734

  10. Diversity and population structure of a dominant deciduous tree based on morphological and genetic data.

    PubMed

    Zhang, Qin-di; Jia, Rui-Zhi; Meng, Chao; Ti, Chao-Wen; Wang, Yi-Ling

    2015-08-26

    Knowledge of the genetic diversity and structure of tree species across their geographic ranges is essential for sustainable use and management of forest ecosystems. Acer grosseri Pax., an economically and ecologically important maple species, is mainly distributed in North China. In this study, the genetic diversity and population differentiation of 24 natural populations of this species were evaluated using sequence-related amplified polymorphism markers and morphological characters. The results show that highly significant differences occurred in 32 morphological traits. The coefficient of variation of 34 characters was 18.19 %. Principal component analysis indicated that 18 of 34 traits explained 60.20 % of the total variance. The phenotypic differentiation coefficient (VST) was 36.06 % for all morphological traits. The Shannon-Wiener index of 34 morphological characters was 6.09, while at the population level, it was 1.77. The percentage of polymorphic bands of all studied A. grosseri populations was 82.14 %. Nei's gene diversity (He) and Shannon's information index (I) were 0.35 and 0.50, respectively. Less genetic differentiation was detected among the natural populations (GST = 0.20, ΦST = 0.10). Twenty-four populations of A. grosseri formed two main clusters, which is consistent with morphological cluster analysis. Principal coordinates analysis and STRUCTURE analysis supported the UPGMA-cluster dendrogram. There was no significant correlation between genetic and geographical distances among populations. Both molecular and morphological data suggested that A. grosseri is rich in genetic diversity. The high level of genetic variation within populations could be affected by the biological characters, mating system and lifespan of A. grosseri, whereas the lower genetic diversity among populations could be caused by effective gene exchange, selective pressure from environmental heterogeneity and the species' geographical range.

  11. Genetic (co)variances and breeding value estimation of Gompertz growth curve parameters in Finnish Yorkshire boars, gilts and barrows.

    PubMed

    Koivula, M; Sevón-Aimonen, M-L; Strandén, I; Matilainen, K; Serenius, T; Stalder, K J; Mäntysaari, E A

    2008-06-01

    This paper's objectives were to estimate the genetic (co)variance components of the Gompertz growth curve parameters and to evaluate the relationship of estimated breeding values (EBV) based on average daily gain (ADG) and Gompertz growth curves. Finnish Yorkshire central test station performance data was obtained from the Faba Breeding (Vantaa, Finland). The final data set included 121,488 weight records from 10,111 pigs. Heritability estimates for the Gompertz growth parameters mature weight (alpha), logarithm of mature weight to birth weight ratio (beta) and maturation rate (kappa) were 0.44, 0.55 and 0.31, respectively. Genotypic and phenotypic correlations between the growth curve parameters were high and mainly negative. The only positive relationship was found between alpha and beta. Pearson and Spearman rank correlation coefficients between EBV for ADG and daily gain calculated from Gompertz growth curves were 0.79. The Spearman rank correlation between the sire EBV for ADG and Gompertz growth curve parameter-based ADG for all sires with at least 15 progeny was 0.86. Growth curves differ significantly between individuals and this information could be utilized for selection purposes when improving growth rate in pigs.

  12. Detecting dominant resonant modes of rolling bearing faults using the niching genetic algorithm

    NASA Astrophysics Data System (ADS)

    Docekal, Adam; Smid, Radislav; Kreidl, Marcel; Krpata, Pavel

    2011-10-01

    In this paper we propose an improvement of methods for adaptive selection of frequency bands containing transients which indicate the presence of the dominant resonant modes of rolling bearing faults using niching genetic algorithm optimization. The main aim of this approach is to diagnose the condition of the bearings and to be able to recognize faults on various parts of bearings and possible combinations of faults. Because the vibration signals corresponding to faults on bearings are typically transients with a wide frequency range occurring around the excited mechanical resonant modes and drowned in the acquired vibration signals, it is necessary to emphasize these excited transients using a matched bank of filters. The dominant resonant modes of a bearing and the system modes produced from fault source are usually unknown, and so there is a need for robust global search methods able to deal with non-linear problems with multiple optima. Instead of applying an optimization method repeatedly for every optimum, non-dominated extensions of the genetic algorithm can be applied only one time to find and maintain multiple optimal solutions. The efficiency of the proposed approach - niching genetic algorithm with fitness sharing - was evaluated using vibration signals acquired on four tapered roller bearings with defined combinations of seeded faults.

  13. Solving multi-objective job shop scheduling problems using a non-dominated sorting genetic algorithm

    NASA Astrophysics Data System (ADS)

    Piroozfard, Hamed; Wong, Kuan Yew

    2015-05-01

    The efforts of finding optimal schedules for the job shop scheduling problems are highly important for many real-world industrial applications. In this paper, a multi-objective based job shop scheduling problem by simultaneously minimizing makespan and tardiness is taken into account. The problem is considered to be more complex due to the multiple business criteria that must be satisfied. To solve the problem more efficiently and to obtain a set of non-dominated solutions, a meta-heuristic based non-dominated sorting genetic algorithm is presented. In addition, task based representation is used for solution encoding, and tournament selection that is based on rank and crowding distance is applied for offspring selection. Swapping and insertion mutations are employed to increase diversity of population and to perform intensive search. To evaluate the modified non-dominated sorting genetic algorithm, a set of modified benchmarking job shop problems obtained from the OR-Library is used, and the results are considered based on the number of non-dominated solutions and quality of schedules obtained by the algorithm.

  14. Genetic (co)variances among birth weight, 200-day weight, and postweaning gain in composites and parental breeds of beef cattle.

    PubMed

    Bennett, G L; Gregory, K E

    1996-11-01

    Genetic and environmental (co)variances for birth weight, adjusted 200-d weight, and postweaning gain were estimated in nine parental and three composite populations of beef cattle. The parental breeds were Angus (A), Braunvieh (B), Charolais (C), Gelbvieh (G), Hereford (H), Limousin (L), Pinzgauer (P), Red Poll (R), and Simmental (S). The composites were MARC I (1/4 B, 1/4 C, 1/4 L, 1/8 H, 1/8 A), MARC II (1/4 G, 1/4 S, 1/4 H, 1/4 A), and MARC III (1/4 R, 1/4 P, 1/4 H, 1/4 A). Heritabilities of additive direct genetic effects for birth weight (.50) and postweaning gain (.49) were greater than for 200-d weight (.32). Heritabilities of additive maternal effects of .09 for birth weight and .10 for 200-d weight were much smaller than direct effect heritabilities. Heritabilities were larger in composites than in parental breeds for additive direct effects of all three traits but smaller for maternal 200-d weight. Correlations were high and positive for direct genetic effects of the three weight traits and higher in composites than in the parental breeds. Correlations between direct and maternal genetic effects for both birth weight and 200-d weight were near zero. Some differences in variances among populations were correlated with differences in weight and milk yield. Heavier populations had larger variances, supporting the use of logarithmic transformation of weights to stabilize variances among genetic groups. Increased average milk yield was correlated with decreased phenotypic variance of 200-d weight. Average milk yield was also implicated in the expression of direct and maternal genetic effects for 200-d weight and their covariance. Comparison of univariate and multivariate estimates of genetic variances suggested that it is important to include birth weight in multivariate analyses of all weight traits to account for increased preweaning mortality of calves with extremely heavy or light birth weights. Based on heritability estimates, within-herd selection in

  15. Genetic load in sexual and asexual diploids: segregation, dominance and genetic drift.

    PubMed

    Haag, Christoph R; Roze, Denis

    2007-07-01

    In diploid organisms, sexual reproduction rearranges allelic combinations between loci (recombination) as well as within loci (segregation). Several studies have analyzed the effect of segregation on the genetic load due to recurrent deleterious mutations, but considered infinite populations, thus neglecting the effects of genetic drift. Here, we use single-locus models to explore the combined effects of segregation, selection, and drift. We find that, for partly recessive deleterious alleles, segregation affects both the deterministic component of the change in allele frequencies and the stochastic component due to drift. As a result, we find that the mutation load may be far greater in asexuals than in sexuals in finite and/or subdivided populations. In finite populations, this effect arises primarily because, in the absence of segregation, heterozygotes may reach high frequencies due to drift, while homozygotes are still efficiently selected against; this is not possible with segregation, as matings between heterozygotes constantly produce new homozygotes. If deleterious alleles are partly, but not fully recessive, this causes an excess load in asexuals at intermediate population sizes. In subdivided populations without extinction, drift mostly occurs locally, which reduces the efficiency of selection in both sexuals and asexuals, but does not lead to global fixation. Yet, local drift is stronger in asexuals than in sexuals, leading to a higher mutation load in asexuals. In metapopulations with turnover, global drift becomes again important, leading to similar results as in finite, unstructured populations. Overall, the mutation load that arises through the absence of segregation in asexuals may greatly exceed previous predictions that ignored genetic drift.

  16. Bimodal expressivity in dominant retinitis pigmentosa genetically linked to chromosome 19q.

    PubMed Central

    Evans, K; al-Maghtheh, M; Fitzke, F W; Moore, A T; Jay, M; Inglehearn, C F; Arden, G B; Bird, A C

    1995-01-01

    A clinical, psychophysical, and electrophysiologic study was undertaken of two autosomal dominant retinitis pigmentosa pedigrees with a genetic mutation assigned to chromosome 19q by linkage analysis. Members with the abnormal haplotype were either symptomatic with adolescent onset nyctalopia, restricted visual fields, and non-detectable electroretinographic responses by 30 years of age, or asymptomatic with normal fundus appearance and minimal or no psychophysical or electroretinographic abnormalities. There was no correlation in the severity in parents and their offspring. Pedigree analysis suggested that although the offspring of parents with the genetic mutation were at 50% risk of having the genetic defect, the risk of being symptomatic during a working lifetime was only 31%. Such bimodal phenotypic expressivity in these particular pedigrees may be explained by a second, allelic genetic influence and may be a phenomenon unique to this genetic locus. Genetic counselling in families expressing this phenotype can only be based on haplotype analysis since clinical investigations, even in the most elderly, would not preclude the presence of the mutant gene. PMID:7488604

  17. Negative-dominance phenomenon with genetic variants of the cardiac sodium channel Nav1.5.

    PubMed

    Sottas, Valentin; Abriel, Hugues

    2016-07-01

    During the past two decades, many pathological genetic variants in SCN5A, the gene encoding the pore-forming subunit of the cardiac (monomeric) sodium channel Na(v)1.5, have been described. Negative dominance is a classical genetic concept involving a "poison" mutant peptide that negatively interferes with the co-expressed wild-type protein, thus reducing its cellular function. This phenomenon has been described for genetic variants of multimeric K(+) channels, which mechanisms are well understood. Unexpectedly, several pathologic SCN5A variants that are linked to Brugada syndrome also demonstrate such a dominant-negative (DN) effect. The molecular determinants of these observations, however, are not yet elucidated. This review article summarizes recent findings that describe the mechanisms underlying the DN phenomenon of genetic variants of K(+), Ca(2+), Cl(-) and Na(+) channels, and in particular Brugada syndrome variants of Na(v)1.5. This article is part of a Special Issue entitled: Cardiomyocyte Biology: Integration of Developmental and Environmental Cues in the Heart edited by Marcus Schaub and Hughes Abriel.

  18. 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

  19. Variance components of aggressive behavior in genetically highly connected Pietrain populations kept under two different housing conditions.

    PubMed

    Appel, Anne K; Voß, Barbara; Tönepöhl, Björn; König von Borstel, Uta; Gauly, Matthias

    2013-12-01

    Mixing of unfamiliar pigs is a standard management procedure in commercial pig production and is often associated with a period of intense and physically damaging aggression. Aggression is considered a problem for animal welfare and production. The objective of the present paper was to investigate the genetic background of aggressive behavior traits at mixing of unfamiliar gilts under 2 different housing conditions. Therefore, a total of 543 purebred Pietrain gilts, from 2 nucleus farms (farm A: n = 302; farm B: n = 241) of 1 breeding company, were tested at an average age of 214 d (SD 12.2 d) for aggressive behavior by 1 observer. Observations included the frequencies of aggressive attack and reciprocal fighting during mixing with unfamiliar gilts. On farm A 41% of the gilts were purebred Pietrains, whereas 59% were purebred Landrace or Duroc gilts. On the farm B 42% of the gilts were purebred Pietrains, and 58% purebred Large White gilts. The average size of the newly mixed groups of gilts was 28 animals on farm A and 18 animals on farm B. The Pietrain gilts from the 2 herds were genetically closely linked. They were the offspring of 96 sires, with 64% of these sires having tested progeny in both farms. There were clear differences in the housing of the animals between the 2 farms. The test pen on farm A had a solid concrete floor littered with wooden shavings and was equipped with a dry feeder. On farm B there was a partly slatted floor, and the gilts were fed by an electronic sow feeder. Mean space allowance was 2.6 m(2)/gilt on farm A and 3.9 m(2)/gilt on farm B. Although large interindividual differences existed, gilts from farm B performed numerically more aggressive attack (mean 1.12, SD 1.42 vs. mean 0.71, SD 1.20) and reciprocal fighting (mean 0.78, SD 0.98 vs. mean 0.44, SD 0.82) when compared with gilts from farm A. The heritabilities and additive genetic variances for behavioral traits were estimated with a linear animal model and were on a low level

  20. Including dominance effects in the genomic BLUP method for genomic evaluation.

    PubMed

    Nishio, Motohide; Satoh, Masahiro

    2014-01-01

    We evaluated the performance of GBLUP including dominance genetic effect (GBLUP-D) by estimating variances and predicting genetic merits in a computer simulation and 2 actual traits (T4 and T5) in pigs. In simulation data, GBLUP-D explained more than 50% of dominance genetic variance. Moreover, GBLUP-D yielded estimated total genetic effects over 1.2% more accurate than those yielded by GBLUP. In particular, when the dominance genetic variance was large, the accuracy could be substantially improved by increasing the number of markers. The dominance genetic variances in T4 and T5 accounted for 9.6% and 6.3% of the phenotypic variances, respectively. Estimates of such small dominance genetic variances contributed little to the improvement of the accuracies of estimated total genetic effects. In both simulation and pig data, there were nearly no differences in the estimates of additive genetic effects or their variance between GBLUP-D and GBLUP. Therefore, we conclude GBLUP-D is a feasible approach to improve genetic performance in crossbred populations with large dominance genetic variation and identify mating systems with good combining ability.

  1. Genetic linkage studies in autosomal dominant ataxia families with an MJD phenotype

    SciTech Connect

    Silveira, I.; Lopes-Cendes, I.; Paciel, P.

    1994-09-01

    Machado-Joseph disease (MJD) is an autosomal dominant spinocerebellar degeneration which was originally described in patients originating from the Portuguese islands of the Azores. The first non-Portuguese kindred was described in 1979 and was an American black family originating from North Carolina. Since then the number of pedigrees of non-Azorean, non-Portuguese origin has increased with families being reported from other European countries, as well as Brazil, Japan, India, The United States and Australia. The autosomal dominant ataxias are a clinically and genetically heterogeneous group of disorders. To date, genetic analysis of families with autosomal dominant ataxias has permitted the identification of four loci, the SCA1 (spinocerebellar ataxia type 1) locus on chromosome 6p, the SCA2 locus on chromosome 12q, a third locus on chromosome 14q, the MJD/SCA3 and, more recently, the DRPLA (Dentatorubral-pallidoluysian atrophy) locus on chromosome 12p. We ascertained a total of 181 individuals with 60 affected from eight Indian, two Brazilian and one Sicilian-American family; all of them have received the clinical diagnosis of MJD. Recently, we have begun molecular genetic studies in these families in order to test these four candidate regions. The SCA1 mutation and the DRPLA mutation has been found to be an expansion of a CAG repeat. Direct analysis of the SCA1 and DRPLA expansion has been performed in all families and no expansion was found in the affected individuals. We are now running flanking markers for the SCA2 and MJD/SCA3 loci. These results will also be presented.

  2. Machado-Joseph disease is genetically different from Holguin dominant ataxia (SCA2)

    SciTech Connect

    Silveria, I.; Manaia, A. Hopital Necker-Enfants Malades, Paris ); Melki, J.; Burlet, P.; Rozet, J.M.; Munnich, A. ); Magarino, C.; Gispert, S. Centro Nacional Genetica Medica, Havana ); Lunkes, A.; Auburger, G. )

    1993-09-01

    Machado-Joseph disease (MJD) and Holguin ataxia (SCA2) are autosomal dominant multisystem degenerations with spinocerebellar involvement that are predominant among people of Portuguese-Azorean and of Cuban descent, respectively. Their clinical distinction may at times be difficult to make in individual patients, due to significant phenotypic overlapping (similar overall age-of-onset and duration of cerebellar ataxia, eye movement, and, often, other common problems). The recent mapping of SCA2 to chromosome 12q provided another candidate region for linkage studies of MJD. Original data on 10 families with Holguin ataxia show that the locus of phenylalanine hydroxylase (PAH) on chromosome 12q is linked to SCA2 at 4 cM and is thus far its closest marker. The exclusion of linkage 15 cM on each side of PAH in 16 families with MJD shows that these two forms of dominant ataxia are genetically distinct and at different chromosomal locations (nonallelic). 20 refs., 2 tabs.

  3. Bilateral cataract and high serum ferritin: a new dominant genetic disorder?

    PubMed Central

    Bonneau, Dominique; Winter-Fuseau, Isabelle; Loiseau, Marie-Noëlle; Amati, Patrizia; Berthier, Michel; Oriot, Denis; Beaumont, Carole

    1995-01-01

    This paper reports the cosegregation in a three generation pedigree of dominantly inherited cataract with an abnormally high level of serum ferritin. In this family, circulating L ferritin was raised in all subjects affected by cataract independently of iron overload. We suggest that a disorder of ferritin metabolism could be a new genetic disorder leading to lens opacity. Cataract-hyperferritaemia syndrome could also be a new contiguous gene syndrome involving the L ferritin gene and the gene coding for the lens membrane protein (MP19), which both map to the same region of chromosome 19q. PMID:8558554

  4. Dominant, non-MHC genetic control of food allergy in an adjuvant-free mouse model.

    PubMed

    Parvataneni, S; Birmingham, N P; Gonipeta, B; Gangur, V

    2009-10-01

    Food allergy is a potentially fatal immune-mediated disorder with incompletely understood mechanisms. We studied the genetic control of food allergy using major histocompatibility complex-identical mice (H2(s)) and an adjuvant-free method of sensitization. Whereas, transdermal exposure to hazelnut - a model allergenic food, elicited robust IgG1 response in both strains, an IgE response was evident only in A.SW mice. Following oral challenge, only A.SW but not SJL mice exhibited signs of systemic anaphylaxis and hypothermia. In addition, (A.SW x SJL) F1 hybrids exhibited IgE responsiveness, systemic anaphylaxis and hypothermia similar to A.SW, indicating dominant inheritance of these traits. Furthermore, whereas A.SW and F1 mice but not SJL elicited robust interleukin (IL)-4 response, all three strains elicited IL-5 and IL-13 responses by spleen cells. These data demonstrate for the first time, dominant non-MHC genetic control of food allergy and a critical role of IL-4 but not IL-5 or IL-13 in this model. PMID:19624800

  5. 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

  6. 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

  7. 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

  8. 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.

  9. Autosomal dominant retinitis pigmentosa with apparent incomplete penetrance: a clinical, electrophysiological, psychophysical, and molecular genetic study.

    PubMed Central

    Moore, A T; Fitzke, F; Jay, M; Arden, G B; Inglehearn, C F; Keen, T J; Bhattacharya, S S; Bird, A C

    1993-01-01

    Twenty five symptomatic individuals and six asymptomatic obligate gene carriers from four families with autosomal dominant retinitis pigmentosa (adRP) showing apparent incomplete penetrance have been studied. Symptomatic individuals from three families showed early onset of night blindness, non-recordable rod electroretinograms, and marked elevation of both rod and cone thresholds in all subjects tested. In the fourth family, there was more variation in the age of onset of night blindness and some symptomatic individuals showed well preserved rod and cone function in some retinal areas. All asymptomatic individuals tested had evidence of mild abnormalities of rod and cone function, indicating that these families show marked variation in expressivity rather than true non-penetrance of the adRP gene. No mutations of the rhodopsin or RDS genes were found in these families and the precise genetic mutation(s) remain to be identified. PMID:8025041

  10. Genetic transformation of Nannochloropsis oculata with a bacterial phleomycin resistance gene as dominant selective marker

    NASA Astrophysics Data System (ADS)

    Ma, Xiaolei; Pan, Kehou; Zhang, Lin; Zhu, Baohua; Yang, Guanpin; Zhang, Xiangyang

    2016-04-01

    The gene ble from Streptoalloteichus hindustanus is widely used as a selective antibiotic marker. It can control the phleomycin resistance, and significantly increase the tolerance of hosts to zeocin. The unicellular marine microalga Nannochloropsis oculata is extremely sensitive to zeocin. We selected ble as the selective marker for the genetic transformation of N. oculata. After the algal cells at a density of 2×107 cells mL-1 was digested with 4% hemicellulase and 2% driselase for 1 h, the protoplasts accounted for 90% of the total. The ble was placed at the downstream of promoter HSP70A-RUBS2 isolated from Chlamydomonas reinhardtii, yielding a recombinant expression construct pMS188. The construct was transferred into the protoplasts through electroporation (1 kV, 15 μS). The transformed protoplasts were cultured in fresh f/2 liquid medium, and selected on solid f/2 medium supplemented with 500 ng mL-1 zeocin. The PCR result proved that ble existed in the transformants. Three transformants had been cultured for at least 5 generations without losing ble. Southern blotting analysis showed that the ble has been integrated into the genome of N. oculata. The ble will serve as a new dominant selective marker in genetic engineering N. oculata.

  11. Genetic analysis of Iranian autosomal dominant polycystic kidney disease: new insight to haplotype analysis.

    PubMed

    Entezam, M; Khatami, M R; Saddadi, F; Ayati, M; Roozbeh, J; Saghafi, H; Keramatipour, M

    2016-01-01

    Autosomal Dominant Polycystic Kidney Disease (ADPKD) caused by mutations in two PKD1 and PKD2 genes. Due to the complexity of the PKD1 gene, its direct mutation screening is an expensive and time-consuming procedure. Pedigree-based haplotype analysis is a useful indirect approach to identify the responsible gene in families with multiple affected individuals, before direct mutation analysis. Here, we applied this approach to investigate 15 appropriate unrelated ADPKD families, selected from 25 families, who referred for genetic counseling. Four polymorphic microsatellite markers were selected around each PKD1 and PKD2 loci. In addition, by investigating the genomic regions, two novel flanking tetranucleotide STR markers were identified. Haplotype analysis and calculating Lod score confirmed linkage to PKD1 in 9 families (60%) and to PKD2 in 2 families (13%). Linkage to both loci was excluded in one family (6.6%). In 2 families (13%) the Lod scores were inconclusive. Causative mutation was identified successfully by direct analysis in two families with confirmed linkage, one to PKD1 and another to PKD2 locus. The study showed that determining the causative locus prior to direct mutation analysis is an efficient strategy to reduce the resources required for genetic analysis of ADPKD families. This is more prominent in PKD2-linked families. Selection of suitable markers, and appropriate PCR multiplexing strategy, using fluorescent labeled primers and 3 primer system, will also add value to this approach. PMID:26950445

  12. Molecular genetics of autosomal-dominant demyelinating Charcot-Marie-Tooth disease.

    PubMed

    Houlden, Henry; Reilly, Mary M

    2006-01-01

    Charcot-Marie-Tooth disease (CMT) is a clinically and genetically heterogeneous group of disorders and is the most common inherited neuromuscular disorder, with an estimated overall prevalence of 17-40/10,000. Although there has been major advances in the understanding of the genetic basis of CMT in recent years, the most useful classification is still a neurophysiological classification that divides CMT into type 1 (demyelinating; median motor conduction velocity < 38 m/s) and type 2 (axonal; median motor conduction velocity > 38 m/s). An intermediate type is also increasingly being described. Inheritance can be autosomal-dominant (AD), X-linked, or autosomal-recessive (AR). AD CMT1 is the most common type of CMT and was the first form of CMT in which a causative gene was described. This review provides an up-to-date overview of AD CMT1 concentrating on the molecular genetics as the clinical, neurophysiological, and pathological features have been covered elsewhere. Four genes (PMP22, MPZ, LITAF, and EGR2) have been described in the last 15 yr associated with AD CMTI and a further gene (NEFL), originally described as causing AD CMT2 can also cause AD CMT1 (by neurophysiological criteria). Studies have shown many of these genes, when mutated, can cause a wide range of CMT phenotypes from the relatively mild CMT1 to the more severe Dejerine-Sottas disease and congenital hypomyelinating neuropathy, and even in some cases axonal CMT2. This review discusses what is known about these genes and in particular how they cause a peripheral neuropathy, when mutated. PMID:16775366

  13. Variance Components and Genetic Parameters Estimated for Fat and Protein Content in Individual Months of Lactation: The Case of Tsigai Sheep.

    PubMed

    Oravcová, Marta

    2016-02-01

    The objective of this study was to assess variance components and genetic parameters for fat and protein content in Tsigai sheep using multivariate animal models in which fat and protein content in individual months of lactation were treated as different traits, and univariate models in which fat and protein content were treated as repeated measures of the same traits. Test day measurements were taken between the second and the seventh month of lactation. The fixed effects were lactation number, litter size and days in milk. The random effects were animal genetic effect and permanent environmental effect of ewe. The effect of flock-year-month of test day measurement was fitted either as a fixed (FYM) or random (fym) effect. Heritabilities for fat content were estimated between 0.06 and 0.17 (FYM fitted) and between 0.06 and 0.11 (fym fitted). Heritabilities for protein content were estimated between 0.15 and 0.23 (FYM fitted) and between 0.10 and 0.18 (fym fitted). For fat content, variance ratios of permanent environmental effect of ewe were estimated between 0.04 and 0.11 (FYM fitted) and between 0.02 and 0.06 (fym fitted). For protein content, variance ratios of permanent environmental effect of ewe were estimated between 0.13 and 0.20 (FYM fitted) and between 0.08 and 0.12 (fym fitted). The proportion of phenotypic variance explained by fym effect ranged from 0.39 to 0.43 for fat content and from 0.25 to 0.36 for protein content. Genetic correlations between individual months of lactation ranged from 0.74 to 0.99 (fat content) and from 0.64 to 0.99 (protein content). Fat content heritabilities estimated with univariate animal models roughly corresponded with heritability estimates from multivariate models: 0.13 (FYM fitted) and 0.07 (fym fitted). Protein content heritabilities estimated with univariate animal models also corresponded with heritability estimates from multivariate models: 0.18 (FYM fitted) and 0.13 (fym fitted).

  14. AIMilano apoprotein identification of the complete kindred and evidence of a dominant genetic transmission.

    PubMed Central

    Gualandri, V; Franceschini, G; Sirtori, C R; Gianfranceschi, G; Orsini, G B; Cerrone, A; Menotti, A

    1985-01-01

    The AIMilano apoprotein variant is associated with a marked reduction of high density lipoprotein (HDL) cholesterol levels and with increased triglyceridemia. In spite of the low HDL-cholesterol (HDL-Ch), carriers do not generally show clinical signs of atherosclerosis. The biochemical disorder is linked to a molecular change in apoprotein AI, that is, an arg----cys substitution in the 173 position, thus allowing the formation of AIMilano-AIMilano dimers and AIMilano-AII complexes. The origin of the variant gene has been located in Limone sul Garda, a small community in Northern Italy (about 1,000 individuals). This community has a genetic, biochemical, and clinical individuality, consequent to its isolation up to a few years ago; the citizens show highly uniform alimentary habits and elevated consanguinity. The complete population of the small village was sampled, and, by the use of an analytical isoelectric focusing technique for the detection of the mutant, a total of 33 living carriers, ranging in age from 2 to 81 yrs, were identified. Analysis of the genealogic tree of the complete family groups showed that the apoprotein (apo) AIMilano is transmitted as an autosomal dominant trait, all carriers coming from a single mating couple, living in the eighteenth century. The carriers are heterozygous for the apoprotein variant. Images Fig. 1 Fig. 3 PMID:3936350

  15. Analyzing the control of mosquito-borne diseases by a dominant lethal genetic system.

    PubMed

    Atkinson, Michael P; Su, Zheng; Alphey, Nina; Alphey, Luke S; Coleman, Paul G; Wein, Lawrence M

    2007-05-29

    Motivated by the failure of current methods to control dengue fever, we formulate a mathematical model to assess the impact on the spread of a mosquito-borne viral disease of a strategy that releases adult male insects homozygous for a dominant, repressible, lethal genetic trait. A dynamic model for the female adult mosquito population, which incorporates the competition for female mating between released mosquitoes and wild mosquitoes, density-dependent competition during the larval stage, and realization of the lethal trait either before or after the larval stage, is embedded into a susceptible-exposed-infectious-susceptible human-vector epidemic model for the spread of the disease. For the special case in which the number of released mosquitoes is maintained in a fixed proportion to the number of adult female mosquitoes at each point in time, we derive mathematical formulas for the disease eradication condition and the approximate number of released mosquitoes necessary for eradication. Numerical results using data for dengue fever suggest that the proportional policy outperforms a release policy in which the released mosquito population is held constant, and that eradication in approximately 1 year is feasible for affected human populations on the order of 10(5) to 10(6), although the logistical considerations are daunting. We also construct a policy that achieves an exponential decay in the female mosquito population; this policy releases approximately the same number of mosquitoes as the proportional policy but achieves eradication nearly twice as fast.

  16. 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

  17. Why is genetic screening for autosomal dominant disorders underutilized in families? The case of hereditary hemorrhagic telangiectasia (HHT)

    PubMed Central

    Bernhardt, Barbara A.; Zayac, Cara; Pyeritz, Reed E.

    2011-01-01

    Purpose Appropriate management of autosomal dominant disorders reduces morbidity and mortality, but relies on identifying which family members are affected. Genetic testing may identify relatives needing follow-up, but is underutilized. We conducted this study to identify barriers to genetic testing for one disorder, hereditary hemorrhagic telangiectasia (HHT). Methods Surveys and on-line discussion groups with people from HHT families. Results Multiple barriers to HHT genetic testing were identified including lack of knowledge about genetic testing, problems with access, and emotional barriers. Many participants: did not understand the rationale for HHT testing or benefits of early detection; believed that genetic testing is expensive and not covered by insurance; believed that primary care providers don’t know how to order genetic testing. Access to HHT testing is limited by distance from an HHT Center or a genetics clinic. Emotional barriers include fear of insurance discrimination; denial of having HHT or being at risk; guilt and stigma. Conclusion Voluntary disease organizations should develop and disseminate brief educational materials that describe the rationale for genetic testing, and emphasize the benefits of early detection and treatment. In addition, laboratories offering genetic testing should provide support for primary care physicians to order and interpret genetic tests. PMID:21637104

  18. 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

  19. 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.

  20. 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

  1. 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.

  2. 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

  3. Genomic analysis of dominance effects on milk production and conformation traits in Fleckvieh cattle

    PubMed Central

    2014-01-01

    Background Estimates of dominance variance in dairy cattle based on pedigree data vary considerably across traits and amount to up to 50% of the total genetic variance for conformation traits and up to 43% for milk production traits. Using bovine SNP (single nucleotide polymorphism) genotypes, dominance variance can be estimated both at the marker level and at the animal level using genomic dominance effect relationship matrices. Yield deviations of high-density genotyped Fleckvieh cows were used to assess cross-validation accuracy of genomic predictions with additive and dominance models. The potential use of dominance variance in planned matings was also investigated. Results Variance components of nine milk production and conformation traits were estimated with additive and dominance models using yield deviations of 1996 Fleckvieh cows and ranged from 3.3% to 50.5% of the total genetic variance. REML and Gibbs sampling estimates showed good concordance. Although standard errors of estimates of dominance variance were rather large, estimates of dominance variance for milk, fat and protein yields, somatic cell score and milkability were significantly different from 0. Cross-validation accuracy of predicted breeding values was higher with genomic models than with the pedigree model. Inclusion of dominance effects did not increase the accuracy of the predicted breeding and total genetic values. Additive and dominance SNP effects for milk yield and protein yield were estimated with a BLUP (best linear unbiased prediction) model and used to calculate expectations of breeding values and total genetic values for putative offspring. Selection on total genetic value instead of breeding value would result in a larger expected total genetic superiority in progeny, i.e. 14.8% for milk yield and 27.8% for protein yield and reduce the expected additive genetic gain only by 4.5% for milk yield and 2.6% for protein yield. Conclusions Estimated dominance variance was substantial

  4. Mating strategies in dominant meerkats: evidence for extra-pair paternity in relation to genetic relatedness between pair mates.

    PubMed

    Leclaire, S; Nielsen, J F; Sharp, S P; Clutton-Brock, T H

    2013-07-01

    Rates of extra-pair paternity (EPP) have frequently been associated with genetic relatedness between social mates in socially monogamous birds. However, evidence is limited in mammals. Here, we investigate whether dominant females use divorce or extra-pair paternity as a strategy to avoid the negative effects of inbreeding when paired with a related male in meerkats Suricata suricatta, a species where inbreeding depression is evident for several traits. We show that dominant breeding pairs seldom divorce, but that rates of EPP are associated with genetic similarity between mates. Although extra-pair males are no more distantly related to the female than social males, they are more heterozygous. Nevertheless, extra-pair pups are not more heterozygous than within-pair pups. Whether females benefit from EPP in terms of increased fitness of the offspring, such as enhanced survival or growth, requires further investigations.

  5. Mating strategies in dominant meerkats: evidence for extra-pair paternity in relation to genetic relatedness between pair mates.

    PubMed

    Leclaire, S; Nielsen, J F; Sharp, S P; Clutton-Brock, T H

    2013-07-01

    Rates of extra-pair paternity (EPP) have frequently been associated with genetic relatedness between social mates in socially monogamous birds. However, evidence is limited in mammals. Here, we investigate whether dominant females use divorce or extra-pair paternity as a strategy to avoid the negative effects of inbreeding when paired with a related male in meerkats Suricata suricatta, a species where inbreeding depression is evident for several traits. We show that dominant breeding pairs seldom divorce, but that rates of EPP are associated with genetic similarity between mates. Although extra-pair males are no more distantly related to the female than social males, they are more heterozygous. Nevertheless, extra-pair pups are not more heterozygous than within-pair pups. Whether females benefit from EPP in terms of increased fitness of the offspring, such as enhanced survival or growth, requires further investigations. PMID:23675879

  6. 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

  7. Geographic Variation in Genetic Dominance of the Color Morphs of the Red-Backed Salamander, PLETHODON CINEREUS.

    PubMed

    Highton, R

    1975-06-01

    Female parent-offspring phenotypic data on color morph frequencies in the red-backed salamander, Plethodon cinereus, were obtained from two Virginia localities (164 broods from Greene County and 97 broods from Giles County). The color morph data indicate that the striped morph is genetically dominant in Giles County and recessive in Greene County. It is suggested that epistatic interaction of two or more loci is responsible for the difference between the localities.

  8. Sex-linked dominant

    MedlinePlus

    Inheritance - sex-linked dominant; Genetics - sex-linked dominant; X-linked dominant; Y-linked dominant ... can be either an autosomal chromosome or a sex chromosome. It also depends on whether the trait ...

  9. Partial Dominance, Overdominance and Epistasis as the Genetic Basis of Heterosis in Upland Cotton (Gossypium hirsutum L.).

    PubMed

    Liang, Qingzhi; Shang, Lianguang; Wang, Yumei; Hua, Jinping

    2015-01-01

    Determination of genetic basis of heterosis may promote hybrid production in Upland cotton (Gossypium hirsutum L.). This study was designed to explore the genetic mechanism of heterosis for yield and yield components in F2: 3 and F2: 4 populations derived from a hybrid 'Xinza No. 1'. Replicated yield field trials of the progenies were conducted in 2008 and 2009. Phenotypic data analyses indicated overdominance in F1 for yield and yield components. Additive and dominance effects at single-locus level and digenic epistatic interactions at two-locus level were analyzed by 421 marker loci spanning 3814 cM of the genome. A total of 38 and 49 QTLs controlling yield and yield components were identified in F2: 3 and F2: 4 populations, respectively. Analyses of these QTLs indicated that the effects of partial dominance and overdominance contributed to heterosis in Upland cotton simultaneously. Most of the QTLs showed partial dominance whereas 13 QTLs showing overdominance in F2:3 population, and 19 QTLs showed overdominance in F2:4. Among them, 21 QTLs were common in both F2: 3 and F2: 4 populations. A large number of two-locus interactions for yield and yield components were detected in both generations. AA (additive × additive) epistasis accounted for majority portion of epistatic effects. Thirty three complementary two-locus homozygotes (11/22 and 22/11) were the best genotypes for AA interactions in terms of bolls per plant. Genotypes of double homozygotes, 11/22, 22/11 and 22/22, performed best for AD/DA interactions, while genotype of 11/12 performed best for DD interactions. These results indicated that (1) partial dominance and overdominance effects at single-locus level and (2) epistasis at two-locus level elucidated the genetic basis of heterosis in Upland cotton.

  10. Partial Dominance, Overdominance and Epistasis as the Genetic Basis of Heterosis in Upland Cotton (Gossypium hirsutum L.)

    PubMed Central

    Wang, Yumei; Hua, Jinping

    2015-01-01

    Determination of genetic basis of heterosis may promote hybrid production in Upland cotton (Gossypium hirsutum L.). This study was designed to explore the genetic mechanism of heterosis for yield and yield components in F2: 3 and F2: 4 populations derived from a hybrid ‘Xinza No. 1’. Replicated yield field trials of the progenies were conducted in 2008 and 2009. Phenotypic data analyses indicated overdominance in F1 for yield and yield components. Additive and dominance effects at single-locus level and digenic epistatic interactions at two-locus level were analyzed by 421 marker loci spanning 3814 cM of the genome. A total of 38 and 49 QTLs controlling yield and yield components were identified in F2: 3 and F2: 4 populations, respectively. Analyses of these QTLs indicated that the effects of partial dominance and overdominance contributed to heterosis in Upland cotton simultaneously. Most of the QTLs showed partial dominance whereas 13 QTLs showing overdominance in F2:3 population, and 19 QTLs showed overdominance in F2:4. Among them, 21 QTLs were common in both F2: 3 and F2: 4 populations. A large number of two-locus interactions for yield and yield components were detected in both generations. AA (additive × additive) epistasis accounted for majority portion of epistatic effects. Thirty three complementary two-locus homozygotes (11/22 and 22/11) were the best genotypes for AA interactions in terms of bolls per plant. Genotypes of double homozygotes, 11/22, 22/11 and 22/22, performed best for AD/DA interactions, while genotype of 11/12 performed best for DD interactions. These results indicated that (1) partial dominance and overdominance effects at single-locus level and (2) epistasis at two-locus level elucidated the genetic basis of heterosis in Upland cotton. PMID:26618635

  11. 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

  12. Previous estimates of mitochondrial DNA mutation level variance did not account for sampling error: comparing the mtDNA genetic bottleneck in mice and humans.

    PubMed

    Wonnapinij, Passorn; Chinnery, Patrick F; Samuels, David C

    2010-04-01

    In cases of inherited pathogenic mitochondrial DNA (mtDNA) mutations, a mother and her offspring generally have large and seemingly random differences in the amount of mutated mtDNA that they carry. Comparisons of measured mtDNA mutation level variance values have become an important issue in determining the mechanisms that cause these large random shifts in mutation level. These variance measurements have been made with samples of quite modest size, which should be a source of concern because higher-order statistics, such as variance, are poorly estimated from small sample sizes. We have developed an analysis of the standard error of variance from a sample of size n, and we have defined error bars for variance measurements based on this standard error. We calculate variance error bars for several published sets of measurements of mtDNA mutation level variance and show how the addition of the error bars alters the interpretation of these experimental results. We compare variance measurements from human clinical data and from mouse models and show that the mutation level variance is clearly higher in the human data than it is in the mouse models at both the primary oocyte and offspring stages of inheritance. We discuss how the standard error of variance can be used in the design of experiments measuring mtDNA mutation level variance. Our results show that variance measurements based on fewer than 20 measurements are generally unreliable and ideally more than 50 measurements are required to reliably compare variances with less than a 2-fold difference.

  13. Genetic linkage analysis of 14 candidate gene loci in a family with autosomal dominant osteoarthritis without dysplasia.

    PubMed Central

    Meulenbelt, I; Bijkerk, C; Breedveld, F C; Slagboom, P E

    1997-01-01

    The role of various gene loci was investigated in a family in which familial osteoarthritis (FOA), with onset at an early age, is transmitted as an autosomal dominant mendelian trait. The absence of clinical and radiographic signs of dysplasia and calcium pyrophosphate deposition disease (CPDD) indicates that the basic disease process in this family is osteoarthritis (OA). Genetic linkage analysis of 14 candidate genes resulted in the exclusion of 10 important genes (COL2A1, COL9A1, COL9A2, COL11A1, COL11A2, COMP, the CPDD region, CRTL-1, CRTM, and MMP3). Other relevant genes were not informative in this family. The candidate loci previously identified in FOA and heritable skeletal disorders associated with OA are clearly not involved in the development of the primary FOA phenotype in the family investigated, indicating genetic heterogeneity. Images PMID:9429149

  14. Genetic differentiation and genetic diversity of Castanopsis (Fagaceae), the dominant tree species in Japanese broadleaved evergreen forests, revealed by analysis of EST-associated microsatellites.

    PubMed

    Aoki, Kyoko; Ueno, Saneyoshi; Kamijo, Takashi; Setoguchi, Hiroaki; Murakami, Noriaki; Kato, Makoto; Tsumura, Yoshihiko

    2014-01-01

    The broadleaved evergreen forests of the East Asian warm temperate zone are characterised by their high biodiversity and endemism, and there is therefore a need to extend our understanding of its genetic diversity and phylogeographic patterns. Castanopsis (Fagaceae) is one of the dominant tree species in the broadleaved evergreen forests of Japan. In this study we investigate the genetic diversity, genetic structure and leaf epidermal morphology of 63 natural populations of C. sieboldii and C. cuspidata, using 32 Expressed Sequence Tag associated microsatellites. The overall genetic differentiation between populations was low (GST = 0.069 in C. sieboldii and GST = 0.057 in C. cuspidata). Neighbor-joining tree and Bayesian clustering analyses revealed that the populations of C. sieboldii and C. cuspidata were genetically clearly differentiated, a result which is consistent with the morphology of their epidermal cell layers. This suggests that C. sieboldii and C. cuspidata should be treated as independent species, although intermediate morphologies are often observed, especially at sites where the two species coexist. The higher level of genetic diversity observed in the Kyushu region (for both species) and the Ryukyu Islands (for C. sieboldii) is consistent with the available fossil pollen data for Castanopsis-type broadleaved evergreen trees during the Last Glacial Maximum and suggests the existence of refugia for Castanopsis forests in southern Japan. Within the C. sieboldii populations, Bayesian clustering analyses detected three clusters, in the western and eastern parts of the main islands and in the Ryukyu Islands. The west-east genetic differentiation observed for this species in the main islands, a pattern which is also found in several plant and animal species inhabiting Castanopsis forests in Japan, suggests that they have been isolated from each other in the western and eastern populations for an extended period of time, and may imply the

  15. Genetic Differentiation and Genetic Diversity of Castanopsis (Fagaceae), the Dominant Tree Species in Japanese Broadleaved Evergreen Forests, Revealed by Analysis of EST-Associated Microsatellites

    PubMed Central

    Aoki, Kyoko; Ueno, Saneyoshi; Kamijo, Takashi; Setoguchi, Hiroaki; Murakami, Noriaki; Kato, Makoto; Tsumura, Yoshihiko

    2014-01-01

    The broadleaved evergreen forests of the East Asian warm temperate zone are characterised by their high biodiversity and endemism, and there is therefore a need to extend our understanding of its genetic diversity and phylogeographic patterns. Castanopsis (Fagaceae) is one of the dominant tree species in the broadleaved evergreen forests of Japan. In this study we investigate the genetic diversity, genetic structure and leaf epidermal morphology of 63 natural populations of C. sieboldii and C. cuspidata, using 32 Expressed Sequence Tag associated microsatellites. The overall genetic differentiation between populations was low (GST = 0.069 in C. sieboldii and GST = 0.057 in C. cuspidata). Neighbor-joining tree and Bayesian clustering analyses revealed that the populations of C. sieboldii and C. cuspidata were genetically clearly differentiated, a result which is consistent with the morphology of their epidermal cell layers. This suggests that C. sieboldii and C. cuspidata should be treated as independent species, although intermediate morphologies are often observed, especially at sites where the two species coexist. The higher level of genetic diversity observed in the Kyushu region (for both species) and the Ryukyu Islands (for C. sieboldii) is consistent with the available fossil pollen data for Castanopsis-type broadleaved evergreen trees during the Last Glacial Maximum and suggests the existence of refugia for Castanopsis forests in southern Japan. Within the C. sieboldii populations, Bayesian clustering analyses detected three clusters, in the western and eastern parts of the main islands and in the Ryukyu Islands. The west-east genetic differentiation observed for this species in the main islands, a pattern which is also found in several plant and animal species inhabiting Castanopsis forests in Japan, suggests that they have been isolated from each other in the western and eastern populations for an extended period of time, and may imply the

  16. Early-onset autosomal dominant Alzheimer disease: prevalence, genetic heterogeneity, and mutation spectrum.

    PubMed Central

    Campion, D; Dumanchin, C; Hannequin, D; Dubois, B; Belliard, S; Puel, M; Thomas-Anterion, C; Michon, A; Martin, C; Charbonnier, F; Raux, G; Camuzat, A; Penet, C; Mesnage, V; Martinez, M; Clerget-Darpoux, F; Brice, A; Frebourg, T

    1999-01-01

    To determine the prevalence of early-onset Alzheimer disease (EOAD) and of autosomal dominant forms of EOAD (ADEOAD), we performed a population-based study in the city of Rouen (426,710 residents). EOAD was defined as onset of disease at age <61 years, and ADEOAD was defined as the occurrence of at least three EOAD cases in three generations. Using these stringent criteria, we calculated that the EOAD and ADEOAD prevalences per 100,000 persons at risk were 41.2 and 5.3, respectively. We then performed a mutational analysis of the genes for amyloid precursor protein (APP), presenilin 1 (PSEN1), and presenilin 2 (PSEN2) in 34 families with ADEOAD ascertained in France. In 19 (56%) of these families, we identified 16 distinct PSEN1 missense mutations, including 4 (Thr147Ile, Trp165Cys, Leu173Trp, and Ser390Ile) not reported elsewhere. APP mutations, including a novel mutation located at codon 715, were identified in 5 (15%) of the families. In the 10 remaining ADEOAD families and in 9 additional autosomal dominant Alzheimer disease families that did not fulfill the strict criteria for ADEOAD, no PSEN1, PSEN2, or APP mutation was identified. These results show that (1) PSEN1 and APP mutations account for 71% of ADEOAD families and (2) nonpenetrance at age <61 years is probably infrequent for PSEN1 or APP mutations. PMID:10441572

  17. Dominant Enhancers of Egfr in Drosophila Melanogaster: Genetic Links between the Notch and Egfr Signaling Pathways

    PubMed Central

    Price, J. V.; Savenye, E. D.; Lum, D.; Breitkreutz, A.

    1997-01-01

    The Drosophila epidermal growth factor receptor (EGFR) is a key component of a complex signaling pathway that participates in multiple developmental processes. We have performed an F(1) screen for mutations that cause dominant enhancement of wing vein phenotypes associated with mutations in Egfr. With this screen, we have recovered mutations in Hairless (H), vein, groucho (gro), and three apparently novel loci. All of the E(Egfr)s we have identified show dominant interactions in transheterozygous combinations with each other and with alleles of N or Su(H), suggesting that they are involved in cross-talk between the N and EGFR signaling pathways. Further examination of the phenotypic interactions between Egfr, H, and gro revealed that reductions in Egfr activity enhanced both the bristle loss associated with H mutations, and the bristle hyperplasia and ocellar hypertrophy associated with gro mutations. Double mutant combinations of Egfr and gro hypomorphic alleles led to the formation of ectopic compound eyes in a dosage sensitive manner. Our findings suggest that these E(Egfr)s represent links between the Egfr and Notch signaling pathways, and that Egfr activity can either promote or suppress Notch signaling, depending on its developmental context. PMID:9383058

  18. Further evidence for a locus for autosomal dominant juvenile glaucoma on chromosome 1q and evidence for genetic heterogeneity

    SciTech Connect

    Wiggs, J.; Paglinauan, C.; Stawski, S.

    1994-09-01

    Glaucoma is a term used to describe a group of disorders which have in common a characteristic degeneration of the optic nerve associated with typical visual field defects and usually associated with elevated intraocular pressure. Two percent of white Americans and 6-10% of black Americans are affected by the disease. Compelling data indicate that susceptibility to many types of glaucoma is inherited. Hereditary juvenile glaucoma is one form of glaucoma that develops in children and is inherited as an autosomal dominant trait with high penetrance. Using a single large Caucasian pedigree affected with autosomal dominant juvenile glaucoma, Sheffield discovered positive linkage to a group of markers that map to a 30 cM region on the long arm of chromosome 1 (1q21-q31). We have subsequently identified three unrelated Caucasian pedigrees affected with autosomal dominant juvenile glaucoma that also demonstrate linkage to this region on chromosome 1, with the highest combined lod score of 5.12 at theta = .05 for marker D1S218. The identification of critical recombinant individuals in our three pedigrees has allowed us to further localize the disease gene to a 12 cM region between markers D1S242 and D1S431. In addition, we have identified several pedigrees which do not demonstrate linkage to chromosome 1q, including a black family affected with autosomal dominant juvenile glaucoma that is indistinguishable clinically from the disorder affecting the caucasian pedigrees and three pedigrees affected with pigmentary dispersion syndrome, a form of glaucoma that also affects the juvenile population and is also inherited as an autosomal dominant trait. These findings provide evidence for genetic heterogeneity in juvenile glaucoma.

  19. Genetic differentiation in spite of high gene flow in the dominant rainforest tree of southeastern Australia, Nothofagus cunninghamii.

    PubMed

    Duncan, C J; Worth, J R P; Jordan, G J; Jones, R C; Vaillancourt, R E

    2016-01-01

    Nothofagus cunninghamii is a long-lived, wind-pollinated tree species that dominates the cool temperate rainforests of southeastern Australia. The species' distribution is more or less continuous in western Tasmania but is fragmented elsewhere. However, it is unknown whether this fragmentation has affected the species' genetic architecture. Thus, we examined N. cunninghamii using 12 nuclear microsatellites and 633 individuals from 18 populations spanning the species' natural range. Typical of wind-pollinated trees, there was low range-wide genetic structure (FST=0.04) consistent with significant gene flow across most of the species' range. However, gene flow was not high enough to overcome the effects of drift across some disjunctions. Victorian populations (separated from Tasmania by the 240 km wide Bass Strait) formed a genetic group distinct from Tasmanian populations, had lower diversity (mean allelic richness (Ar)=5.4 in Victoria versus 6.9 in Tasmania) and were significantly more differentiated from one another than those in Tasmania (FST=0.045 in Victoria versus 0.012 in Tasmania). Evidence for bottlenecking was found in small populations that were at least 20 km from other populations. Interestingly, we found little divergence in microsatellite markers between the extremes of genetically based morphological and physiological altitudinal clines suggesting adaptive differentiation is strongly driven by selection because it is likely to be occurring in the presence of gene flow. Even though the cool temperate rainforests of Australia are highly relictual, the species is relatively robust to population fragmentation due to high levels of genetic diversity and gene flow, especially in Tasmania.

  20. The effects of locus number, genetic divergence, and genotyping error on the utility of dominant markers for hybrid identification

    PubMed Central

    Sovic, Michael G; Kubatko, Laura S; Fuerst, Paul A

    2014-01-01

    In surveys of hybrid zones, dominant genetic markers are often used to identify individuals of hybrid origin and assign these individuals to one of several potential hybrid classes. Quantitative analyses that address the statistical power of dominant markers in such inference are scarce. In this study, dominant genotype data were simulated to evaluate the effects of, first, the number of loci analyzed, second, the magnitude of differentiation between the markers scored in the groups that are hybridizing, and third, the level of genotyping error associated with the data when assigning individuals to various parental and hybrid categories. The overall performance of the assignment methods was relatively modest at the lowest level of divergence examined (Fst ˜ 0.4), but improved substantially at higher levels of differentiation (Fst ˜ 0.67 or 0.8). The effect of genotyping error was dependent on the level of divergence between parental taxa, with larger divergences tempering the effects of genotyping error. These results highlight the importance of considering the effects of each of the variables when assigning individuals to various parental and hybrid categories, and can help guide decisions regarding the number of loci employed in future hybridization studies to achieve the power and level of resolution desired. PMID:24634730

  1. One Group of Genetically Similar Listeria monocytogenes Strains Frequently Dominates and Persists in Several Fish Slaughter- and Smokehouses

    PubMed Central

    Wulff, Gitte; Gram, Lone; Ahrens, Peter; Vogel, Birte Fonnesbech

    2006-01-01

    Contamination of foods with the human pathogen Listeria monocytogenes may occur during processing, and the purpose of this study was to determine whether genetically similar strains colonize different processing plants or whether specific persistent strains are unique to each processing plant. We hypothesized that specific L. monocytogenes strains may be better adapted to specific environmental niches in the processing environment. L. monocytogenes contamination patterns were identified by the collection of 686 and 267 samples from the processing environments: raw fish and products of four fish smokehouses and four fish slaughterhouses, respectively. Samples were collected both during production and after cleaning and disinfection. Typically, these samplings were separated by 1 to 3 months. Sampling sites were targeted toward areas likely to harbor the bacterium. L. monocytogenes was isolated from 213 samples, and one strain from each positive sample was typed by RAPD (random amplified polymorphic DNA) analysis with four different primers. The 213 strains were divided into 37 RAPD types. One RAPD type was predominant; 86 of 213 strains belonged to this type. This type was found in three smokehouses and two slaughterhouses and was predominant in three of these plants. A subset of 35 strains was also analyzed by amplified fragment length polymorphism typing, which confirmed the genetic similarity of the groups. Moreover, strains of the dominant RAPD type were indistinguishable from strains isolated frequently from smoked fish products 10 years ago. One smokehouse was surveyed for a year and a half, and the dominant RAPD type persisted throughout the survey period and accounted for 94 of 118 isolates. Our study indicates that strains of L. monocytogenes that are genetically very closely related may be especially adapted to colonizing the processing equipment or especially resistant to cleaning and disinfection. PMID:16751546

  2. Statistics of Scientific Procedures on Living Animals 2012: another increase in experimentation - genetically-altered animals dominate again.

    PubMed

    Hudson-Shore, Michelle

    2013-09-01

    The Annual Statistics of Scientific Procedures on Living Animals Great Britain 2012 reveal that the level of animal experimentation in Great Britain continues to rise, with just over 4.1 million procedures being started in that year. Despite the previous year's indication that the dominance of the production and use of genetically-altered (GA, i.e. genetically-modified animals plus animals with harmful genetic defects) animal might be abating, it returned with a vengeance in 2012. Breeding increased from 43% to 48% of all procedures, and GA animals were involved in 59% of all the procedures. Indeed, if the breeding of these animals were removed from the statistics, the total number of procedures would actually decline by 2%. In order to honour their pledge to reduce animal use in science, the Coalition Government will have to address this issue. The general trends in the species used, and the numbers and types of procedures, are also reviewed. Finally, forthcoming changes to the statistics are discussed.

  3. Genetic linkage of autosomal dominant progressive supranuclear palsy to 1q31.1.

    PubMed

    Ros, Raquel; Gómez Garre, Pilar; Hirano, Michio; Tai, Yen F; Ampuero, Israel; Vidal, Lídice; Rojo, Ana; Fontan, Aurora; Vazquez, Ana; Fanjul, Samira; Hernandez, Jaime; Cantarero, Susana; Hoenicka, Janet; Jones, Alison; Ahsan, R Laila; Pavese, Nicola; Piccini, Paola; Brooks, David J; Perez-Tur, Jordi; Nyggard, Torbjorn; de Yébenes, Justo G

    2005-05-01

    Progressive supranuclear palsy (PSP) is a disorder of unknown pathogenesis. Familial clusters of PSP have been reported related to mutations of protein tau. We report the linkage of a large Spanish family with typical autosomal dominant PSP to a new locus in chromosome 1. Four members of this family had typical PSP, confirmed by neuropathology in one case. At least five ancestors had similar disease. Other members of the family have incomplete phenotypes. The power of the linkage analysis was increased by detecting presymptomatic individuals with 18F-fluoro-dopa and 18F-deoxyglucose positron emission tomography. We screened the human genome with 340 polymorphic markers and we enriched the areas of interest with additional markers. The disease status was defined according to the clinical and positron emission tomography data. We excluded linkage to the tau gene in chromosome 17. PSP was linked, in this family, to one area of 3.4 cM in chromosome 1q31.1, with a maximal multipoint < OD score of +3.53. This area contains at least three genes, whose relevance in PSP is unknown. We expect to further define the gene responsible for PSP, which could help to understand the pathogenesis of this disease and to design effective treatment.

  4. Autosomal dominant retinitis pigmentosa: no evidence for nonallelic genetic heterogeneity on 3q.

    PubMed Central

    Kumar-Singh, R; Wang, H; Humphries, P; Farrar, G J

    1993-01-01

    Since the initial report of linkage of autosomal dominant retinitis pigmentosa (adRP) to the long arm of chromosome 3, several mutations in the gene encoding rhodopsin, which also maps to 3q, have been reported in adRP pedigrees. However, there has been some discussion as to the possibility of a second adRP locus on 3q. This suggestion has important diagnostic and research implications and must raise doubts about the usefulness of linked markers for reliable diagnosis of RP patients. In order to address this issue we have performed an admixture test (A-test) on 10 D3S47-linked adRP pedigrees and have found a likelihood ratio of heterogeneity versus homogeneity of 4.90. We performed a second A-test, combining the data from all families with known rhodopsin mutations. In this test we obtained a reduced likelihood ratio of heterogeneity versus homogeneity, of 1.0. On the basis of these statistical analyses we have found no significant support for two adRP loci on chromosome 3q. Furthermore, using 40 CEPH families, we have localized the rhodopsin gene to the D3S47-D3S20 interval, with a maximum lod score (Zm) of 20 and have found that the order qter-D3S47-rhodopsin-D3S20-cen is significantly more likely than any other order. In addition, we have mapped (Zm = 30) the microsatellite marker D3S621 relative to other loci in this region of the genome. PMID:8430695

  5. Hyperkalaemic periodic paralysis in homozygous and heterozygous horses: a co-dominant genetic condition.

    PubMed

    Naylor, J M; Nickel, D D; Trimino, G; Card, C; Lightfoot, K; Adams, G

    1999-03-01

    Historical, clinical and experimental data were collected from 9 horses homozygous for HYPP (H/H). All showed episodes of respiratory stertor, described as a rattling or honking sound, usually within the first week post partum. Five horses had one or more episodes of dysphagia, in 3 horses this was accompanied by drooling and in 3 by weight loss. In comparison, only one of 35 contemporaneous half siblings (of which approximately half would be expected to be of the H/N genotype and half N/N) was observed to have respiratory stertor prior to weaning and none had problems with dysphagia. One mature homozygous stallion was infertile secondary to urospermia. Six homozygous horses died or were subjected to euthanasia; 4 age less than a year, one age 20 months and one age 5 years. The remaining 3 cases were still alive at the end of the study. A comparison of homozygous and heterozygous horses using standardised potassium chloride challenge testing indicated that during attacks homozygotes showed significantly more frequent signs of drooling, prolapse of the third eyelid, respiratory stridor and weakness than heterozygous horses. Homozygotes also had significantly more total abnormalities (including myotonic discharges, high frequency repetitive discharges, and spontaneous activity) on electromyographic examination than heterozygotes. These data imply that HYPP is inherited as a codominant genetic defect, because the homozygotes showed more severe clinical signs of disease than heterozygotes. Homozygous foals would be expected to be produced in 25% of matings in which both parents are heterozygous. Owners and veterinarians should be aware of the risks of this mating. PMID:10213428

  6. 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

  7. Evolutionary dynamics analysis of human metapneumovirus subtype A2: genetic evidence for its dominant epidemic.

    PubMed

    Li, Jianguo; Ren, Lili; Guo, Li; Xiang, Zichun; Paranhos-Baccalà, Gláucia; Vernet, Guy; Wang, Jianwei

    2012-01-01

    Human metapneumovirus (hMPV) is a respiratory viral pathogen in children worldwide. hMPV is divided into four subtypes: hMPV_A1, hMPV_A2, hMPV_B1, and hMPV_B2. hMPV_A2 can be further divided into hMPV_A2a and A2b based on phylogenetic analysis. The typical prevalence pattern of hMPV involves a shift of the predominant subtype within one or two years. However, hMPV_A2, in particular hMPV_A2b, has circulated worldwide with a several years long term high epidemic. To study this distinct epidemic behavior of hMPV_A2, we analyzed 294 sequences of partial G genes of the virus from different countries. Molecular evolutionary data indicates that hMPV_A2 evolved toward heterogeneity faster than the other subtypes. Specifically, a bayesian skyline plot analysis revealed that hMPV_A2 has undergone a generally upward fluctuation since 1997, whereas the other subtypes experienced only one upward fluctuation. Although hMPV_A2 showed a lower value of mean dN/dS than the other subtypes, it had the largest number of positive selection sites. Meanwhile, various styles of mutation were observed in the mutation hotspots of hMPV_A2b. Bayesian phylogeography analysis also revealed two fusions of diffusion routes of hMPV_A2b in India (June 2006) and Beijing, China (June 2008). Sequences of hMPV_A2b retrieved from GenBank boosted simultaneously with the two fusions respectively, indicating that fusion of genetic transmission routes from different regions improved survival of hMPV_A2. Epidemic and evolutionary dynamics of hMPV_A2b were similar to those of hMPV_A2. Overall, our findings provide important molecular insights into hMPV epidemics and viral variation, and explain the occurrence of an atypical epidemic of hMPV_A2, particularly hMPV_A2b.

  8. Evolutionary Dynamics Analysis of Human Metapneumovirus Subtype A2: Genetic Evidence for Its Dominant Epidemic

    PubMed Central

    Li, Jianguo; Ren, Lili; Guo, Li; Xiang, Zichun; Paranhos-Baccalà, Gláucia; Vernet, Guy; Wang, Jianwei

    2012-01-01

    Human metapneumovirus (hMPV) is a respiratory viral pathogen in children worldwide. hMPV is divided into four subtypes: hMPV_A1, hMPV_A2, hMPV_B1, and hMPV_B2. hMPV_A2 can be further divided into hMPV_A2a and A2b based on phylogenetic analysis. The typical prevalence pattern of hMPV involves a shift of the predominant subtype within one or two years. However, hMPV_A2, in particular hMPV_A2b, has circulated worldwide with a several years long term high epidemic. To study this distinct epidemic behavior of hMPV_A2, we analyzed 294 sequences of partial G genes of the virus from different countries. Molecular evolutionary data indicates that hMPV_A2 evolved toward heterogeneity faster than the other subtypes. Specifically, a Bayesian skyline plot analysis revealed that hMPV_A2 has undergone a generally upward fluctuation since 1997, whereas the other subtypes experienced only one upward fluctuation. Although hMPV_A2 showed a lower value of mean dN/dS than the other subtypes, it had the largest number of positive selection sites. Meanwhile, various styles of mutation were observed in the mutation hotspots of hMPV_A2b. Bayesian phylogeography analysis also revealed two fusions of diffusion routes of hMPV_A2b in India (June 2006) and Beijing, China (June 2008). Sequences of hMPV_A2b retrieved from GenBank boosted simultaneously with the two fusions respectively, indicating that fusion of genetic transmission routes from different regions improved survival of hMPV_A2. Epidemic and evolutionary dynamics of hMPV_A2b were similar to those of hMPV_A2. Overall, our findings provide important molecular insights into hMPV epidemics and viral variation, and explain the occurrence of an atypical epidemic of hMPV_A2, particularly hMPV_A2b. PMID:22479641

  9. Genetic linkage of autosomal dominant juvenile glaucoma to 1q21-q31 in three affected pedigrees

    SciTech Connect

    Wiggs, J.L.; Paglinauan, C.; Fine, A.; Sporn, C.; Lou, D. ); Haines, J.L. )

    1994-05-15

    Glaucoma is a common disorder that results in irreversible damage to the optic nerve, causing absolute blindness. In most cases, the optic nerve is damaged by an elevation of the intraocular pressure that is the result of an abnormality in the normal drainage function of the trabecular meshwork. A family history of glaucoma is an important risk factor for the disease, suggesting that genetic defects predisposing to this condition are likely. Three pedigrees segregating an autosomal dominant juvenile glaucoma demonstrated significant linkage to a group of closely spaced markers on chromosome 1. These results confirm the initial mapping of this disease and suggest that this region on chromosome 1 contains an important locus for juvenile glaucoma. The authors describe recombination events that improve the localization of the responsible gene, reducing the size of the candidate region from 30 to 12 cM. 27 refs., 2 figs., 1 tab.

  10. A non-dominated sorting genetic algorithm for a bi-objective pick-up and delivery problem

    NASA Astrophysics Data System (ADS)

    Velasco, N.; Dejax, P.; Guéret, C.; Prins, C.

    2012-03-01

    Some companies must transport their personnel within facilities. This is especially the case for oil companies that use helicopters to transport engineers, technicians and assistant personnel from platform to platform. This operation has the potential to become expensive if the transportation routes are not correctly planned and provide a bad quality of service. Here this issue is modelled as a pick-up and delivery problem where a set of transportation requests should be scheduled in routes, minimizing the total transportation cost while the most urgent requests are satisfied by priority. To solve the problem, a method based on a Non-dominated Sorting Genetic Algorithm (NSGA-II) is proposed. This algorithm is tested on both randomly generated and real instances provided by a petroleum company. The results show that the proposed algorithm improves the best-known solutions.

  11. Multi-objective optimal design of magnetorheological engine mount based on an improved non-dominated sorting genetic algorithm

    NASA Astrophysics Data System (ADS)

    Zheng, Ling; Duan, Xuwei; Deng, Zhaoxue; Li, Yinong

    2014-03-01

    A novel flow-mode magneto-rheological (MR) engine mount integrated a diaphragm de-coupler and the spoiler plate is designed and developed to isolate engine and the transmission from the chassis in a wide frequency range and overcome the stiffness in high frequency. A lumped parameter model of the MR engine mount in single degree of freedom system is further developed based on bond graph method to predict the performance of the MR engine mount accurately. The optimization mathematical model is established to minimize the total of force transmissibility over several frequency ranges addressed. In this mathematical model, the lumped parameters are considered as design variables. The maximum of force transmissibility and the corresponding frequency in low frequency range as well as individual lumped parameter are limited as constraints. The multiple interval sensitivity analysis method is developed to select the optimized variables and improve the efficiency of optimization process. An improved non-dominated sorting genetic algorithm (NSGA-II) is used to solve the multi-objective optimization problem. The synthesized distance between the individual in Pareto set and the individual in possible set in engineering is defined and calculated. A set of real design parameters is thus obtained by the internal relationship between the optimal lumped parameters and practical design parameters for the MR engine mount. The program flowchart for the improved non-dominated sorting genetic algorithm (NSGA-II) is given. The obtained results demonstrate the effectiveness of the proposed optimization approach in minimizing the total of force transmissibility over several frequency ranges addressed.

  12. Eco-geographical diversity of cowpea bradyrhizobia in Senegal is marked by dominance of two genetic types.

    PubMed

    Wade, Tatiana Krasova; Le Quéré, Antoine; Laguerre, Gisèle; N'zoué, Angèle; Ndione, Jacques-André; Dorego, Francis; Sadio, Omar; Ndoye, Ibrahima; Neyra, Marc

    2014-03-01

    The genetic diversity of native cowpea rhizobia originating from 60 sites across four eco-geographic zones in Senegal was studied. More than 300 cowpea nodules were analyzed by PCR-RFLP of the 16S-23S rDNA InterGenic Spacer region (IGS). Alignments of IGS sequences indicated that all genotypes were grouping within the Bradyrhizobium genus. The geographical distribution showed that apart from five IGS types, the others were specifically found in only one region. The diversity was significantly higher in the Senegal River valley zone, which presents lower mean annual rainfalls and slightly alkaline soils. Interestingly, two IGS types dominated the Senegalese rhizobial collection, one IGS type (VI) was found on more than half of the nodules collected in the northern Senegal River valley while another IGS type (I) was recovered from the great majority of nodules in the three other regions sampled. Two representative strains from each of these two dominant types were isolated and further analyzed. Multi Locus Sequence Analyses using 6 housekeeping genes indicate that they belong to a new Bradyrhizobium species closely related to B. yuanmingense. Phylogenetic analyses of 2 symbiotic genes nodC and nifH show that they are clustered with B. arachidis. Physiological tests on these strains have shown that under laboratory conditions, the growth of the IGS type VI strains was slightly less affected by a higher osmotic strength in the medium and to alkaline pH, which corroborates the soil physico-chemical parameters. PMID:24373721

  13. Genetic linkage of autosomal dominant primary open angle glaucoma to chromosome 3q in a Greek pedigree.

    PubMed

    Kitsos, G; Eiberg, H; Economou-Petersen, E; Wirtz, M K; Kramer, P L; Aspiotis, M; Tommerup, N; Petersen, M B; Psilas, K

    2001-06-01

    A locus for juvenile onset open angle glaucoma (OAG) has been assigned to chromosome 1q in families with autosomal dominant inheritance (GLC1A), due to mutations in the TIGR/MYOC gene. For adult onset OAG, called primary open angle glaucoma or POAG, five loci have so far been mapped to different chromosomes (GLC1B-GLC1F). Except for the GLC1B locus, the other POAG loci have so far been reported only in single large pedigrees. We studied a large family identified in Epirus, Greece, segregating POAG in an autosomal dominant fashion. Clinical findings included increased cup to disc ratio (mean 0.7), characteristic glaucomatous changes in the visual field, and intraocular pressure before treatment more than 21 mmHg (mean 31 mmHg), with age at diagnosis 33 years and older. Linkage analysis was performed between the disease phenotype and microsatellite DNA polymorphisms. Linkage was established with a group of DNA markers located on chromosome 3q, where the GLC1C locus has previously been described in one large Oregon pedigree. A maximal multipoint lod score of 3.88 was obtained at marker D3S1763 (penetrance 80%). This represents the second POAG family linked to the GLC1C locus on chromosome 3q, and haplotype analysis in the two families suggests an independent origin of the genetic defect.

  14. Horka, a dominant mutation of Drosophila, induces nondisjunction and, through paternal effect, chromosome loss and genetic mosaics

    SciTech Connect

    Szabad, J.; Mathe, E.; Puro, J.

    1995-04-01

    Fs(3) Horka (Horka) was described as a dominant female-sterile mutation of Drosophila melanogaster. Genetic and cytological data show that Horka induces mostly equational nondisjunction during spermatogenesis but not chromosome loss and possesses a predominant paternal effect: the X, second, third and the fourth chromosomes, but not the Y, are rendered unstable while undergoing spermatogenesis and may be lost in the descending zygotes. The frequency of Horka-induced chromosome loss is usually 2-4% but varies with the genetic background and can be over 20%. The X chromosome loss occurs during the gonomeric and the initial cleavage divisions. Loss of the X and fourth chromosomes shows no correlation. We propose, based on similarities in the mutant phenotypes with the chromosome destabilizing mutations nonclaret disjunctional and paternal loss, that the normal Horka{sup +} product is required for function of the centromeres and/or nearby regions. Horka is a convenient tool for the generation of gynandromorphs, autosome mosaics and for the study of gene expression in mosaics. 55 refs., 6 figs., 8 tabs.

  15. Immunological loss-of-function due to genetic gain-of-function in humans: autosomal dominance of the third kind

    PubMed Central

    Quartier, Pierre

    2015-01-01

    All the human primary immunodeficiencies (PIDs) recognized as such in the 1950s were Mendelian traits and, whether autosomal or X-linked, displayed recessive inheritance. The first autosomal dominant (AD) PID, hereditary angioedema, was recognized in 1963. However, since the first identification of autosomal recessive (AR), X-linked recessive (XR) and AD PID-causing genes in 1985 (ADA; severe combined immunodeficiency), 1986 (CYBB, chronic granulomatous disease) and 1989 (SERPING1; hereditary angioedema), respectively, the number of genetically defined AD PIDs has increased more rapidly than that of any other type of PID. AD PIDs now account for 61 of the 260 known conditions (23%). All known AR PIDs are caused by alleles with some loss-of-function (LOF). A single XR PID is caused by gain-of-function (GOF) mutations (WASP-related neutropenia, 2001). In contrast, only 44 of 61 AD defects are caused by LOF alleles, which exert dominance by haploinsufficiency or negative dominance. Since 2003, up to 17 AD disorders of the third kind, due to GOF alleles, have been described. Remarkably, six of the 17 genes concerned also harbor monoallelic (STAT3), biallelic (C3, CFB, CARD11, PIK3R1) or both monoallelic and biallelic (STAT1) LOF alleles in patients with other clinical phenotypes. Most heterozygous GOF alleles result in auto-inflammation, auto-immunity, or both, with a wide range of immunological and clinical forms. Some also underlie infections and, fewer, allergies, by impairing or enhancing immunity to non-self. Malignancies are also rare. The enormous diversity of immunological and clinical phenotypes is thought provoking and mirrors the diversity and pleiotropy of the underlying genotypes. These experiments of nature provide a unique insight into the quantitative regulation of human immunity. PMID:25645939

  16. Immunological loss-of-function due to genetic gain-of-function in humans: autosomal dominance of the third kind.

    PubMed

    Boisson, Bertrand; Quartier, Pierre; Casanova, Jean-Laurent

    2015-02-01

    All the human primary immunodeficiencies (PIDs) recognized as such in the 1950s were Mendelian traits and, whether autosomal or X-linked, displayed recessive inheritance. The first autosomal dominant (AD) PID, hereditary angioedema, was recognized in 1963. However, since the first identification of autosomal recessive (AR), X-linked recessive (XR) and AD PID-causing genes in 1985 (ADA; severe combined immunodeficiency), 1986 (CYBB, chronic granulomatous disease) and 1989 (SERPING1; hereditary angioedema), respectively, the number of genetically defined AD PIDs has increased more rapidly than that of any other type of PID. AD PIDs now account for 61 of the 260 known conditions (23%). All known AR PIDs are caused by alleles with some loss-of-function (LOF). A single XR PID is caused by gain-of-function (GOF) mutations (WASP-related neutropenia, 2001). In contrast, only 44 of 61 AD defects are caused by LOF alleles, which exert dominance by haploinsufficiency or negative dominance. Since 2003, up to 17 AD disorders of the third kind, due to GOF alleles, have been described. Remarkably, six of the 17 genes concerned also harbor monoallelic (STAT3), biallelic (C3, CFB, CARD11, PIK3R1) or both monoallelic and biallelic (STAT1) LOF alleles in patients with other clinical phenotypes. Most heterozygous GOF alleles result in auto-inflammation, auto-immunity, or both, with a wide range of immunological and clinical forms. Some also underlie infections and, fewer, allergies, by impairing or enhancing immunity to non-self. Malignancies are also rare. The enormous diversity of immunological and clinical phenotypes is thought provoking and mirrors the diversity and pleiotropy of the underlying genotypes. These experiments of nature provide a unique insight into the quantitative regulation of human immunity. PMID:25645939

  17. Improvement of Prediction Ability for Genomic Selection of Dairy Cattle by Including Dominance Effects

    PubMed Central

    Sun, Chuanyu; VanRaden, Paul M.; Cole, John B.; O'Connell, Jeffrey R.

    2014-01-01

    Dominance may be an important source of non-additive genetic variance for many traits of dairy cattle. However, nearly all prediction models for dairy cattle have included only additive effects because of the limited number of cows with both genotypes and phenotypes. The role of dominance in the Holstein and Jersey breeds was investigated for eight traits: milk, fat, and protein yields; productive life; daughter pregnancy rate; somatic cell score; fat percent and protein percent. Additive and dominance variance components were estimated and then used to estimate additive and dominance effects of single nucleotide polymorphisms (SNPs). The predictive abilities of three models with both additive and dominance effects and a model with additive effects only were assessed using ten-fold cross-validation. One procedure estimated dominance values, and another estimated dominance deviations; calculation of the dominance relationship matrix was different for the two methods. The third approach enlarged the dataset by including cows with genotype probabilities derived using genotyped ancestors. For yield traits, dominance variance accounted for 5 and 7% of total variance for Holsteins and Jerseys, respectively; using dominance deviations resulted in smaller dominance and larger additive variance estimates. For non-yield traits, dominance variances were very small for both breeds. For yield traits, including additive and dominance effects fit the data better than including only additive effects; average correlations between estimated genetic effects and phenotypes showed that prediction accuracy increased when both effects rather than just additive effects were included. No corresponding gains in prediction ability were found for non-yield traits. Including cows with derived genotype probabilities from genotyped ancestors did not improve prediction accuracy. The largest additive effects were located on chromosome 14 near DGAT1 for yield traits for both breeds; those SNPs also

  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. MCNP variance reduction overview

    SciTech Connect

    Hendricks, J.S.; Booth, T.E.

    1985-01-01

    The MCNP code is rich in variance reduction features. Standard variance reduction methods found in most Monte Carlo codes are available as well as a number of methods unique to MCNP. We discuss the variance reduction features presently in MCNP as well as new ones under study for possible inclusion in future versions of the code.

  20. Pervasive effects of a dominant foliar endophytic fungus on host genetic and phenotypic expression in a tropical tree

    PubMed Central

    Mejía, Luis C.; Herre, Edward A.; Sparks, Jed P.; Winter, Klaus; García, Milton N.; Van Bael, Sunshine A.; Stitt, Joseph; Shi, Zi; Zhang, Yufan; Guiltinan, Mark J.; Maximova, Siela N.

    2014-01-01

    It is increasingly recognized that macro-organisms (corals, insects, plants, vertebrates) consist of both host tissues and multiple microbial symbionts that play essential roles in their host's ecological and evolutionary success. Consequently, identifying benefits and costs of symbioses, as well as mechanisms underlying them are research priorities. All plants surveyed under natural conditions harbor foliar endophytic fungi (FEF) in their leaf tissues, often at high densities. Despite producing no visible effects on their hosts, experiments have nonetheless shown that FEF reduce pathogen and herbivore damage. Here, combining results from three genomic, and two physiological experiments, we demonstrate pervasive genetic and phenotypic effects of the apparently asymptomatic endophytes on their hosts. Specifically, inoculation of endophyte-free (E−) Theobroma cacao leaves with Colletotrichum tropicale (E+), the dominant FEF species in healthy T. cacao, induces consistent changes in the expression of hundreds of host genes, including many with known defensive functions. Further, E+ plants exhibited increased lignin and cellulose content, reduced maximum rates of photosynthesis (Amax), and enrichment of nitrogen-15 and carbon-13 isotopes. These phenotypic changes observed in E+ plants correspond to changes in expression of specific functional genes in related pathways. Moreover, a cacao gene (Tc00g04254) highly up-regulated by C. tropicale also confers resistance to pathogen damage in the absence of endophytes or their products in host tissues. Thus, the benefits of increased pathogen resistance in E+ plants are derived in part from up-regulation of intrinsic host defense responses, and appear to be offset by potential costs including reduced photosynthesis, altered host nitrogen metabolism, and endophyte heterotrophy of host tissues. Similar effects are likely in most plant-endophyte interactions, and should be recognized in the design and interpretation of genetic

  1. Dominance Is the Major Genetic Basis of Heterosis in Rice as Revealed by Qtl Analysis Using Molecular Markers

    PubMed Central

    Xiao, J.; Li, J.; Yuan, L.; Tanksley, S. D.

    1995-01-01

    A set of 194 F(7) lines derived from a subspecific rice cross showing strong F(1) heterosis was backcrossed to the two parents. The materials (388 BC(1)F(7) lines, 194 F(8) lines, two parents, F(1)) were phenotyped for 12 quantitative traits. A total of 37 significant QTLs (LOD >/= 2.0) was detected through 141 RFLP markers in the BC(1)F(7) populations. Twenty-seven (73%) quantitative trait loci (QTLs) were detected in only one of the BC(1)F(7) populations. In 82% of these cases, the heterozygotes were superior to the respective homozygotes. The remaining 10 (27%) QTLs were detected in both BC(1)F(7) populations, and the heterozygote had a phenotype falling between those of the two homozygotes and in no instances were the heterozygotes found to be superior to both homozygotes. These results suggest that dominance complementation is the major genetic basis of heterosis in rice. This conclusion was strengthened by the finding that there was no correlation between most traits and overall genome heterozygosity and that there were some recombinant inbred lines in the F(8) population having phenotypic values superior to the F(1) for all of the traits evaluated--a result not expected if overdominance was a major contributor to heterosis. Digenic epistasis was not evident. PMID:7498751

  2. Genetic diagnosis of autosomal dominant polycystic kidney disease by targeted capture and next-generation sequencing: utility and limitations.

    PubMed

    Qi, Xiao-Ping; Du, Zhen-Fang; Ma, Ju-Ming; Chen, Xiao-Ling; Zhang, Qing; Fei, Jun; Wei, Xiao-Ming; Chen, Dong; Ke, Hai-Ping; Liu, Xuan-Zhu; Li, Feng; Chen, Zhen-Guang; Su, Zheng; Jin, Hang-Yang; Liu, Wen-Ting; Zhao, Yan; Jiang, Hu-Ling; Lan, Zhang-Zhang; Li, Peng-Fei; Fang, Ming-Yan; Dong, Wei; Zhang, Xian-Ning

    2013-03-01

    Mutation-based molecular diagnostics of autosomal dominant polycystic kidney disease (ADPKD) is complicated by genetic and allelic heterogeneity, large multi-exon genes, and duplication sequences of PKD1. Recently, targeted resequencing by pooling long-range polymerase chain reaction (LR-PCR) amplicons has been used in the identification of mutations in ADPKD. Despite its high sensitivity, specificity and accuracy, LR-PCR is still complicated. We performed whole-exome sequencing on two unrelated typical Chinese ADPKD probands and evaluated the effectiveness of this approach compared with Sanger sequencing. Meanwhile, we performed targeted gene and next-generation sequencing (targeted DNA-HiSeq) on 8 individuals (1 patient from one family, 5 patients and 2 normal individuals from another family). Both whole-exome sequencing and targeted DNA-HiSeq confirmed c.11364delC (p.H3788QfsX37) within the unduplicated region of PKD1 in one proband; in the other family, targeted DNA-HiSeq identified a small insertion, c.401_402insG (p.V134VfsX79), in PKD2. These methods do not overcome the screening complexity of homology. However, the true positives of variants confirmed by targeted gene and next-generation sequencing were 69.4%, 50% and 100% without a false positive in the whole coding region and the duplicated and unduplicated regions, which indicated that the screening accuracy of PKD1 and PKD2 can be largely improved by using a greater sequencing depth and elaborate design of the capture probe.

  3. Reporting explained variance

    NASA Astrophysics Data System (ADS)

    Good, Ron; Fletcher, Harold J.

    The importance of reporting explained variance (sometimes referred to as magnitude of effects) in ANOVA designs is discussed in this paper. Explained variance is an estimate of the strength of the relationship between treatment (or other factors such as sex, grade level, etc.) and dependent variables of interest to the researcher(s). Three methods that can be used to obtain estimates of explained variance in ANOVA designs are described and applied to 16 studies that were reported in recent volumes of this journal. The results show that, while in most studies the treatment accounts for a relatively small proportion of the variance in dependent variable scores., in., some studies the magnitude of the treatment effect is respectable. The authors recommend that researchers in science education report explained variance in addition to the commonly reported tests of significance, since the latter are inadequate as the sole basis for making decisions about the practical importance of factors of interest to science education researchers.

  4. Multicomponent pre-stack seismic waveform inversion in transversely isotropic media using a non-dominated sorting genetic algorithm

    NASA Astrophysics Data System (ADS)

    Padhi, Amit; Mallick, Subhashis

    2014-03-01

    Inversion of band- and offset-limited single component (P wave) seismic data does not provide robust estimates of subsurface elastic parameters and density. Multicomponent seismic data can, in principle, circumvent this limitation but adds to the complexity of the inversion algorithm because it requires simultaneous optimization of multiple objective functions, one for each data component. In seismology, these multiple objectives are typically handled by constructing a single objective given as a weighted sum of the objectives of individual data components and sometimes with additional regularization terms reflecting their interdependence; which is then followed by a single objective optimization. Multi-objective problems, inclusive of the multicomponent seismic inversion are however non-linear. They have non-unique solutions, known as the Pareto-optimal solutions. Therefore, casting such problems as a single objective optimization provides one out of the entire set of the Pareto-optimal solutions, which in turn, may be biased by the choice of the weights. To handle multiple objectives, it is thus appropriate to treat the objective as a vector and simultaneously optimize each of its components so that the entire Pareto-optimal set of solutions could be estimated. This paper proposes such a novel multi-objective methodology using a non-dominated sorting genetic algorithm for waveform inversion of multicomponent seismic data. The applicability of the method is demonstrated using synthetic data generated from multilayer models based on a real well log. We document that the proposed method can reliably extract subsurface elastic parameters and density from multicomponent seismic data both when the subsurface is considered isotropic and transversely isotropic with a vertical symmetry axis. We also compute approximate uncertainty values in the derived parameters. Although we restrict our inversion applications to horizontally stratified models, we outline a practical

  5. Testing for beneficial reversal of dominance during salinity shifts in the invasive copepod Eurytemora affinis, and implications for the maintenance of genetic variation.

    PubMed

    Posavi, Marijan; Gelembiuk, Gregory William; Larget, Bret; Lee, Carol Eunmi

    2014-11-01

    Maintenance of genetic variation at loci under selection has profound implications for adaptation under environmental change. In temporally and spatially varying habitats, non-neutral polymorphism could be maintained by heterozygote advantage across environments (marginal overdominance), which could be greatly increased by beneficial reversal of dominance across conditions. We tested for reversal of dominance and marginal overdominance in salinity tolerance in the saltwater-to-freshwater invading copepod Eurytemora affinis. We compared survival of F1 offspring generated by crossing saline and freshwater inbred lines (between-salinity F1 crosses) relative to within-salinity F1 crosses, across three salinities. We found evidence for both beneficial reversal of dominance and marginal overdominance in salinity tolerance. In support of reversal of dominance, survival of between-salinity F1 crosses was not different from that of freshwater F1 crosses under freshwater conditions and saltwater F1 crosses under saltwater conditions. In support of marginal overdominance, between-salinity F1 crosses exhibited significantly higher survival across salinities relative to both freshwater and saltwater F1 crosses. Our study provides a rare empirical example of complete beneficial reversal of dominance associated with environmental change. This mechanism might be crucial for maintaining genetic variation in salinity tolerance in E. affinis populations, allowing rapid adaptation to salinity changes during habitat invasions. PMID:25135455

  6. 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.

  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. Autosomal dominant spinocerebellar ataxia with sensory axonal neuropathy (SCA4): clinical description and genetic localization to chromosome 16q22.1.

    PubMed Central

    Flanigan, K.; Gardner, K.; Alderson, K.; Galster, B.; Otterud, B.; Leppert, M. F.; Kaplan, C.; Ptácek, L. J.

    1996-01-01

    The hereditary ataxias represent a clinically and genetically heterogeneous group of neurodegenerative disorders. Various classification schemes based on clinical criteria are being replaced as molecular characterization of the ataxias proceeds; so far, seven distinct autosomal dominant hereditary ataxias have been genetically mapped in the human genome. We report linkage to chromosome 16q22.1 for one of these genes (SCA4) in a five-generation family with an autosomal dominant, late-onset spinocerebellar ataxia; the gene is tightly linked to the microsatellite marker D16S397 (LOD score = 5.93 at theta = .00). In addition, we present clinical and electrophysiological data regarding the distinct and previously unreported phenotype consisting of ataxia with the invariant presence of a prominent axonal sensory neuropathy. PMID:8755926

  10. U1 small nuclear ribonucleoproteins (snRNPs) aggregate in Alzheimer’s disease due to autosomal dominant genetic mutations and trisomy 21

    PubMed Central

    2014-01-01

    Background We recently identified U1 small nuclear ribonucleoprotein (snRNP) tangle-like aggregates and RNA splicing abnormalities in sporadic Alzheimer’s disease (AD). However little is known about snRNP biology in early onset AD due to autosomal dominant genetic mutations or trisomy 21 in Down syndrome. Therefore we investigated snRNP biochemical and pathologic features in these disorders. Findings We performed quantitative proteomics and immunohistochemistry in postmortem brain from genetic AD cases. Electron microscopy was used to characterize ultrastructural features of pathologic aggregates. U1-70k and other snRNPs were biochemically enriched in the insoluble fraction of human brain from subjects with presenilin 1 (PS1) mutations. Aggregates of U1 snRNP-immunoreactivity formed cytoplasmic tangle-like structures in cortex of AD subjects with PS1 and amyloid precursor protein (APP) mutations as well as trisomy 21. Ultrastructural analysis with electron microscopy in an APP mutation case demonstrated snRNP immunogold labeling of paired helical filaments (PHF). Conclusions These studies identify U1 snRNP pathologic changes in brain of early onset genetic forms of AD. Since dominant genetic mutations and trisomy 21 result in dysfunctional amyloid processing, the findings suggest that aberrant β-amyloid processing may influence U1 snRNP aggregate formation. PMID:24773620

  11. Ecotypes of an ecologically dominant prairie grass (Andropogon gerardii) exhibit genetic divergence across the U.S. Midwest grasslands' environmental gradient.

    PubMed

    Gray, Miranda M; St Amand, Paul; Bello, Nora M; Galliart, Matthew B; Knapp, Mary; Garrett, Karen A; Morgan, Theodore J; Baer, Sara G; Maricle, Brian R; Akhunov, Eduard D; Johnson, Loretta C

    2014-12-01

    Big bluestem (Andropogon gerardii) is an ecologically dominant grass with wide distribution across the environmental gradient of U.S. Midwest grasslands. This system offers an ideal natural laboratory to study population divergence and adaptation in spatially varying climates. Objectives were to: (i) characterize neutral genetic diversity and structure within and among three regional ecotypes derived from 11 prairies across the U.S. Midwest environmental gradient, (ii) distinguish between the relative roles of isolation by distance (IBD) vs. isolation by environment (IBE) on ecotype divergence, (iii) identify outlier loci under selection and (iv) assess the association between outlier loci and climate. Using two primer sets, we genotyped 378 plants at 384 polymorphic AFLP loci across regional ecotypes from central and eastern Kansas and Illinois. Neighbour-joining tree and PCoA revealed strong genetic differentiation between Kansas and Illinois ecotypes, which was better explained by IBE than IBD. We found high genetic variability within prairies (80%) and even fragmented Illinois prairies, surprisingly, contained high within-prairie genetic diversity (92%). Using Bayenv2, 14 top-ranked outlier loci among ecotypes were associated with temperature and precipitation variables. Six of seven BayeScanFST outliers were in common with Bayenv2 outliers. High genetic diversity may enable big bluestem populations to better withstand changing climates; however, population divergence supports the use of local ecotypes in grassland restoration. Knowledge of genetic variation in this ecological dominant and other grassland species will be critical to understanding grassland response and restoration challenges in the face of a changing climate.

  12. The quantum Allan variance

    NASA Astrophysics Data System (ADS)

    Chabuda, Krzysztof; Leroux, Ian D.; Demkowicz-Dobrzański, Rafał

    2016-08-01

    The instability of an atomic clock is characterized by the Allan variance, a measure widely used to describe the noise of frequency standards. We provide an explicit method to find the ultimate bound on the Allan variance of an atomic clock in the most general scenario where N atoms are prepared in an arbitrarily entangled state and arbitrary measurement and feedback are allowed, including those exploiting coherences between succeeding interrogation steps. While the method is rigorous and general, it becomes numerically challenging for large N and long averaging times.

  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. The Rules of Aggression: How Genetic, Chemical and Spatial Factors Affect Intercolony Fights in a Dominant Species, the Mediterranean Acrobat Ant Crematogaster scutellaris.

    PubMed

    Frizzi, Filippo; Ciofi, Claudio; Dapporto, Leonardo; Natali, Chiara; Chelazzi, Guido; Turillazzi, Stefano; Santini, Giacomo

    2015-01-01

    Nest-mate recognition plays a key role in the biology of ants. Although individuals coming from a foreign nest are, in most cases, promptly rejected, the degree of aggressiveness towards non nest-mates may be highly variable among species and relies on genetic, chemical and environmental factors. We analyzed intraspecific relationships among neighboring colonies of the dominant Mediterranean acrobat ant Crematogaster scutellaris integrating genetic, chemical and behavioral analyses. Colony structure, parental relationships between nests, cuticular hydrocarbons profiles (CHCs) and aggressive behavior against non nest-mates were studied in 34 nests located in olive tree trunks. Bayesian clustering analysis of allelic variation at nine species-specific microsatellite DNA markers pooled nests into 14 distinct clusters, each representing a single colony, confirming a polydomous arrangement of nests in this species. A marked genetic separation among colonies was also detected, probably due to long distance dispersion of queens and males during nuptial flights. CHCs profiles varied significantly among colonies and between nests of the same colony. No relationship between CHCs profiles and genetic distances was detected. The level of aggressiveness between colonies was inversely related to chemical and spatial distance, suggesting a 'nasty neighbor' effect. Our findings also suggest that CHCs profiles in C. scutellaris may be linked to external environmental factors rather than genetic relationships. PMID:26445245

  15. The Rules of Aggression: How Genetic, Chemical and Spatial Factors Affect Intercolony Fights in a Dominant Species, the Mediterranean Acrobat Ant Crematogaster scutellaris

    PubMed Central

    Frizzi, Filippo; Ciofi, Claudio; Dapporto, Leonardo; Natali, Chiara; Chelazzi, Guido; Turillazzi, Stefano; Santini, Giacomo

    2015-01-01

    Nest-mate recognition plays a key role in the biology of ants. Although individuals coming from a foreign nest are, in most cases, promptly rejected, the degree of aggressiveness towards non nest-mates may be highly variable among species and relies on genetic, chemical and environmental factors. We analyzed intraspecific relationships among neighboring colonies of the dominant Mediterranean acrobat ant Crematogaster scutellaris integrating genetic, chemical and behavioral analyses. Colony structure, parental relationships between nests, cuticular hydrocarbons profiles (CHCs) and aggressive behavior against non nest-mates were studied in 34 nests located in olive tree trunks. Bayesian clustering analysis of allelic variation at nine species-specific microsatellite DNA markers pooled nests into 14 distinct clusters, each representing a single colony, confirming a polydomous arrangement of nests in this species. A marked genetic separation among colonies was also detected, probably due to long distance dispersion of queens and males during nuptial flights. CHCs profiles varied significantly among colonies and between nests of the same colony. No relationship between CHCs profiles and genetic distances was detected. The level of aggressiveness between colonies was inversely related to chemical and spatial distance, suggesting a ‘nasty neighbor’ effect. Our findings also suggest that CHCs profiles in C. scutellaris may be linked to external environmental factors rather than genetic relationships. PMID:26445245

  16. 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…

  17. 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…

  18. 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.

  19. Multi-objective optimization in spatial planning: Improving the effectiveness of multi-objective evolutionary algorithms (non-dominated sorting genetic algorithm II)

    NASA Astrophysics Data System (ADS)

    Karakostas, Spiros

    2015-05-01

    The multi-objective nature of most spatial planning initiatives and the numerous constraints that are introduced in the planning process by decision makers, stakeholders, etc., synthesize a complex spatial planning context in which the concept of solid and meaningful optimization is a unique challenge. This article investigates new approaches to enhance the effectiveness of multi-objective evolutionary algorithms (MOEAs) via the adoption of a well-known metaheuristic: the non-dominated sorting genetic algorithm II (NSGA-II). In particular, the contribution of a sophisticated crossover operator coupled with an enhanced initialization heuristic is evaluated against a series of metrics measuring the effectiveness of MOEAs. Encouraging results emerge for both the convergence rate of the evolutionary optimization process and the occupation of valuable regions of the objective space by non-dominated solutions, facilitating the work of spatial planners and decision makers. Based on the promising behaviour of both heuristics, topics for further research are proposed to improve their effectiveness.

  20. Factors affecting the reproductive success of dominant male meerkats.

    PubMed

    Spong, Göran F; Hodge, Sarah J; Young, Andrew J; Clutton-Brock, Tim H

    2008-05-01

    Identifying traits that affect the reproductive success of individuals is fundamental for our understanding of evolutionary processes. In cooperative breeders, a dominant male typically restricts mating access to the dominant female for extended periods, resulting in pronounced variation in reproductive success among males. This may result in strong selection for traits that increase the likelihood of dominance acquisition, dominance retention and reproductive rates while dominant. However, despite considerable research on reproductive skew, few studies have explored the factors that influence these three processes among males in cooperative species. Here we use genetic, behavioural and demographic data to investigate the factors affecting reproductive success in dominant male meerkats (Suricata suricatta). Our data show that dominant males sire the majority of all offspring surviving to 1 year. A male's likelihood of becoming dominant is strongly influenced by age, but not by weight. Tenure length and reproductive rate, both important components of dominant male reproductive success, are largely affected by group size and composition, rather than individual traits. Dominant males in large groups have longer tenures, but after this effect is controlled, male tenure length also correlates negatively to the number of adult females in the group. Male reproductive rate also declines as the number of intra- and extra-group competitors increases. As the time spent in the dominant position and reproductive rate while dominant explain > 80% of the total variance in reproductive success, group composition thus has major implications for male reproductive success.

  1. Factors affecting the reproductive success of dominant male meerkats.

    PubMed

    Spong, Göran F; Hodge, Sarah J; Young, Andrew J; Clutton-Brock, Tim H

    2008-05-01

    Identifying traits that affect the reproductive success of individuals is fundamental for our understanding of evolutionary processes. In cooperative breeders, a dominant male typically restricts mating access to the dominant female for extended periods, resulting in pronounced variation in reproductive success among males. This may result in strong selection for traits that increase the likelihood of dominance acquisition, dominance retention and reproductive rates while dominant. However, despite considerable research on reproductive skew, few studies have explored the factors that influence these three processes among males in cooperative species. Here we use genetic, behavioural and demographic data to investigate the factors affecting reproductive success in dominant male meerkats (Suricata suricatta). Our data show that dominant males sire the majority of all offspring surviving to 1 year. A male's likelihood of becoming dominant is strongly influenced by age, but not by weight. Tenure length and reproductive rate, both important components of dominant male reproductive success, are largely affected by group size and composition, rather than individual traits. Dominant males in large groups have longer tenures, but after this effect is controlled, male tenure length also correlates negatively to the number of adult females in the group. Male reproductive rate also declines as the number of intra- and extra-group competitors increases. As the time spent in the dominant position and reproductive rate while dominant explain > 80% of the total variance in reproductive success, group composition thus has major implications for male reproductive success. PMID:18410290

  2. Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy, genetic homogeneity, and mapping of the locus within a 2-cM interval

    SciTech Connect

    Ducros, A.; Alamowitch, S.; Nagy, T.

    1996-01-01

    Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) is a recently identified autosomal dominant cerebral arteriopathy characterized by the recurrence of subcortical infarcts leading to dementia. A genetic linkage analysis conducted in two large families recently allowed us to map the affected gene on chromosome 19 in a 12-cM interval bracketed by D19S221 and D19S215. In the present study, these first 2 families and 13 additional ones, including a total of 199 potentially informative meiosis, have been genotyped with eight polymorphic markers located between D19S221 and D19S215. All families were linked to chromosome 19. The highest combined lod score (Z{sub max} = 37.24 at {theta} = .01) was obtained with marker D19S841, a new CA{sub n} microsatellite marker that we isolated from chromosome 19 cosmids. The recombinant events observed within these families were used to refine the genetic mapping of CADASIL within a 2-cM interval that is now bracketed by D19S226 and D19S199 on 19p13.1. These data strongly suggest the genetic homogeneity of this recently identified condition and establish the value of its clinical and neuroimaging diagnostic criteria. Besides their importance for the ongoing positional cloning of the CADASIL gene, these data help to refine the genetic mapping of CADASIL relative to familial hemiplegic migraine and hereditary paroxysmal cerebellar ataxia, conditions that we both mapped within the same chromosome 19 region. 35 refs., 5 figs., 2 tabs.

  3. 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

  4. A novel genetic system to isolate a dominant negative effector on DNA-binding activity of Oct-2.

    PubMed Central

    Terunuma, A; Shiba, K; Noda, T

    1997-01-01

    Recent studies have revealed that interactions between transcription factors play an important role in regulation of gene expression in eukaryotic cells. To isolate cDNA clones that dominantly inhibit the DNA-binding activity of Oct-2, chosen as a representative factor, we have developed a novel screening system. This employs an Escherichia coli tester strain carrying a modified lac operon as a reporter gene, with the lac operator sequence replaced by an octamer sequence. Oct-2 expressed in this tester strain represses the expression of the reporter gene and changes the phenotype of the cell from Lac+to Lac-. Introduction of a cDNA expression library prepared from a human T-cell line into the Oct-2-harboring tester strain allowed selection of three Lac+clones out of 1 x 10(5) transformants. One of them, hT86, encoding a putative zinc finger protein was found to derepress beta-galactosidase activity in the Oct-2-harboring tester strain at the transcriptional level. In gel mobility shift assays, hT86 attenuated the intensity of the retarded band composed of the octamer probe and Oct-2, suggesting a dominant negative effect on the DNA-binding activity of Oct-2. The strategy described here provides a new approach for studying protein-protein interactions that govern the complex regulation of gene expression. PMID:9115366

  5. Testing the genetic predictions of a biogeographical model in a dominant endemic Eastern Pacific coral (Porites panamensis) using a genetic seascape approach.

    PubMed

    Saavedra-Sotelo, Nancy C; Calderon-Aguilera, Luis E; Reyes-Bonilla, Héctor; Paz-García, David A; López-Pérez, Ramón A; Cupul-Magaña, Amilcar; Cruz-Barraza, José A; Rocha-Olivares, Axayácatl

    2013-10-01

    The coral fauna of the Eastern Tropical Pacific (ETP) is depauperate and peripheral; hence, it has drawn attention to the factors allowing its survival. Here, we use a genetic seascape approach and ecological niche modeling to unravel the environmental factors correlating with the genetic variation of Porites panamensis, a hermatypic coral endemic to the ETP. Specifically, we test if levels of diversity and connectivity are higher among abundant than among depauperate populations, as expected by a geographically relaxed version of the Abundant Center Hypothesis (rel-ACH). Unlike the original ACH, referring to a geographical center of distribution of maximal abundance, the rel-ACH refers only to a center of maximum abundance, irrespective of its geographic position. The patterns of relative abundance of P. panamensis in the Mexican Pacific revealed that northern populations from Baja California represent its center of abundance; and southern depauperate populations along the continental margin are peripheral relative to it. Genetic patterns of diversity and structure of nuclear DNA sequences (ribosomal DNA and a single copy open reading frame) and five alloenzymatic loci partially agreed with rel-ACH predictions. We found higher diversity levels in peninsular populations and significant differentiation between peninsular and continental colonies. In addition, continental populations showed higher levels of differentiation and lower connectivity than peninsular populations in the absence of isolation by distance in each region. Some discrepancies with model expectations may relate to the influence of significant habitat discontinuities in the face of limited dispersal potential. Environmental data analyses and niche modeling allowed us to identify temperature, water clarity, and substrate availability as the main factors correlating with patterns of abundance, genetic diversity, and structure, which may hold the key to the survival of P. panamensis in the face of

  6. Testing the genetic predictions of a biogeographical model in a dominant endemic Eastern Pacific coral (Porites panamensis) using a genetic seascape approach.

    PubMed

    Saavedra-Sotelo, Nancy C; Calderon-Aguilera, Luis E; Reyes-Bonilla, Héctor; Paz-García, David A; López-Pérez, Ramón A; Cupul-Magaña, Amilcar; Cruz-Barraza, José A; Rocha-Olivares, Axayácatl

    2013-10-01

    The coral fauna of the Eastern Tropical Pacific (ETP) is depauperate and peripheral; hence, it has drawn attention to the factors allowing its survival. Here, we use a genetic seascape approach and ecological niche modeling to unravel the environmental factors correlating with the genetic variation of Porites panamensis, a hermatypic coral endemic to the ETP. Specifically, we test if levels of diversity and connectivity are higher among abundant than among depauperate populations, as expected by a geographically relaxed version of the Abundant Center Hypothesis (rel-ACH). Unlike the original ACH, referring to a geographical center of distribution of maximal abundance, the rel-ACH refers only to a center of maximum abundance, irrespective of its geographic position. The patterns of relative abundance of P. panamensis in the Mexican Pacific revealed that northern populations from Baja California represent its center of abundance; and southern depauperate populations along the continental margin are peripheral relative to it. Genetic patterns of diversity and structure of nuclear DNA sequences (ribosomal DNA and a single copy open reading frame) and five alloenzymatic loci partially agreed with rel-ACH predictions. We found higher diversity levels in peninsular populations and significant differentiation between peninsular and continental colonies. In addition, continental populations showed higher levels of differentiation and lower connectivity than peninsular populations in the absence of isolation by distance in each region. Some discrepancies with model expectations may relate to the influence of significant habitat discontinuities in the face of limited dispersal potential. Environmental data analyses and niche modeling allowed us to identify temperature, water clarity, and substrate availability as the main factors correlating with patterns of abundance, genetic diversity, and structure, which may hold the key to the survival of P. panamensis in the face of

  7. Testing the genetic predictions of a biogeographical model in a dominant endemic Eastern Pacific coral (Porites panamensis) using a genetic seascape approach

    PubMed Central

    Saavedra-Sotelo, Nancy C; Calderon-Aguilera, Luis E; Reyes-Bonilla, Héctor; Paz-García, David A; López-Pérez, Ramón A; Cupul-Magaña, Amilcar; Cruz-Barraza, José A; Rocha-Olivares, Axayácatl

    2013-01-01

    The coral fauna of the Eastern Tropical Pacific (ETP) is depauperate and peripheral; hence, it has drawn attention to the factors allowing its survival. Here, we use a genetic seascape approach and ecological niche modeling to unravel the environmental factors correlating with the genetic variation of Porites panamensis, a hermatypic coral endemic to the ETP. Specifically, we test if levels of diversity and connectivity are higher among abundant than among depauperate populations, as expected by a geographically relaxed version of the Abundant Center Hypothesis (rel-ACH). Unlike the original ACH, referring to a geographical center of distribution of maximal abundance, the rel-ACH refers only to a center of maximum abundance, irrespective of its geographic position. The patterns of relative abundance of P. panamensis in the Mexican Pacific revealed that northern populations from Baja California represent its center of abundance; and southern depauperate populations along the continental margin are peripheral relative to it. Genetic patterns of diversity and structure of nuclear DNA sequences (ribosomal DNA and a single copy open reading frame) and five alloenzymatic loci partially agreed with rel-ACH predictions. We found higher diversity levels in peninsular populations and significant differentiation between peninsular and continental colonies. In addition, continental populations showed higher levels of differentiation and lower connectivity than peninsular populations in the absence of isolation by distance in each region. Some discrepancies with model expectations may relate to the influence of significant habitat discontinuities in the face of limited dispersal potential. Environmental data analyses and niche modeling allowed us to identify temperature, water clarity, and substrate availability as the main factors correlating with patterns of abundance, genetic diversity, and structure, which may hold the key to the survival of P. panamensis in the face of

  8. Genetic forms of nephrogenic diabetes insipidus (NDI): Vasopressin receptor defect (X-linked) and aquaporin defect (autosomal recessive and dominant).

    PubMed

    Bichet, Daniel G; Bockenhauer, Detlef

    2016-03-01

    Nephrogenic diabetes insipidus (NDI), which can be inherited or acquired, is characterized by an inability to concentrate urine despite normal or elevated plasma concentrations of the antidiuretic hormone, arginine vasopressin (AVP). Polyuria with hyposthenuria and polydipsia are the cardinal clinical manifestations of the disease. About 90% of patients with congenital NDI are males with X-linked NDI who have mutations in the vasopressin V2 receptor (AVPR2) gene encoding the vasopressin V2 receptor. In less than 10% of the families studied, congenital NDI has an autosomal recessive or autosomal dominant mode of inheritance with mutations in the aquaporin-2 (AQP2) gene. When studied in vitro, most AVPR2 and AQP2 mutations lead to proteins trapped in the endoplasmic reticulum and are unable to reach the plasma membrane. Prior knowledge of AVPR2 or AQP2 mutations in NDI families and perinatal mutation testing is of direct clinical value and can avert the physical and mental retardation associated with repeated episodes of dehydration.

  9. Genetic forms of nephrogenic diabetes insipidus (NDI): Vasopressin receptor defect (X-linked) and aquaporin defect (autosomal recessive and dominant).

    PubMed

    Bichet, Daniel G; Bockenhauer, Detlef

    2016-03-01

    Nephrogenic diabetes insipidus (NDI), which can be inherited or acquired, is characterized by an inability to concentrate urine despite normal or elevated plasma concentrations of the antidiuretic hormone, arginine vasopressin (AVP). Polyuria with hyposthenuria and polydipsia are the cardinal clinical manifestations of the disease. About 90% of patients with congenital NDI are males with X-linked NDI who have mutations in the vasopressin V2 receptor (AVPR2) gene encoding the vasopressin V2 receptor. In less than 10% of the families studied, congenital NDI has an autosomal recessive or autosomal dominant mode of inheritance with mutations in the aquaporin-2 (AQP2) gene. When studied in vitro, most AVPR2 and AQP2 mutations lead to proteins trapped in the endoplasmic reticulum and are unable to reach the plasma membrane. Prior knowledge of AVPR2 or AQP2 mutations in NDI families and perinatal mutation testing is of direct clinical value and can avert the physical and mental retardation associated with repeated episodes of dehydration. PMID:27156763

  10. Nominal analysis of "variance".

    PubMed

    Weiss, David J

    2009-08-01

    Nominal responses are the natural way for people to report actions or opinions. Because nominal responses do not generate numerical data, they have been underutilized in behavioral research. On those occasions in which nominal responses are elicited, the responses are customarily aggregated over people or trials so that large-sample statistics can be employed. A new analysis is proposed that directly associates differences among responses with particular sources in factorial designs. A pair of nominal responses either matches or does not; when responses do not match, they vary. That analogue to variance is incorporated in the nominal analysis of "variance" (NANOVA) procedure, wherein the proportions of matches associated with sources play the same role as do sums of squares in an ANOVA. The NANOVA table is structured like an ANOVA table. The significance levels of the N ratios formed by comparing proportions are determined by resampling. Fictitious behavioral examples featuring independent groups and repeated measures designs are presented. A Windows program for the analysis is available.

  11. The Genetics of Canadian Type 3 von Willebrand Disease (VWD): Further Evidence for Co-dominant Inheritance of Mutant Alleles

    PubMed Central

    Bowman, M.; Tuttle, A.; Notley, C.; Brown, C.; Tinlin, S.; Deforest, M.; Leggo, J.; Blanchette, V.S.; Lillicrap, D.; James, P.

    2014-01-01

    Summary Background Type 3 von Willebrand disease (VWD) is the most severe form of the disease and is classically inherited in an autosomal recessive fashion. Objectives The aim of the current study was to investigate the molecular pathogenesis of a Canadian cohort of type 3 VWD patients. Patients/Methods 34 families comprised of 100 individuals were investigated. Phenotypic data, including bleeding scores (BS), von Willebrand factor (VWF) laboratory values, and anti-VWF inhibitor status were included as well as sequence analysis. Results We identified 31 different mutations (20 novel): 8 frameshift, 5 splice site, 9 nonsense, 1 gene conversion, 6 missense, and 2 partial gene deletion mutations. The majority of mutations identified were in the propeptide (42%); index cases (IC) with these mutations exhibited more severe bleeding (BS=22) than those with mutations elsewhere in VWF (BS=13). 62 of 68 (91%) mutant alleles were identified. Twenty-nine IC (85%) had a VWF null genotype identified; 17 homozygous, 12 compound heterozygous. In five IC (15%), two mutant VWF alleles were not identified to explain the type 3 VWD phenotype. In four ICs only one mutant VWF allele was identified and in one IC no mutant VWF alleles were identified. Conclusions We have investigated the molecular pathogenesis of a Canadian cohort of type 3 VWD patients. Obligate carriers are not phenotypically silent in the Canadian population; 48% have been diagnosed with type 1 VWD. In ~50% of families in this study the inheritance pattern for type 3 VWD is co-dominant and not recessive. PMID:23311757

  12. Uncovering hidden variance: pair-wise SNP analysis accounts for additional variance in nicotine dependence

    PubMed Central

    Culverhouse, Robert C.; Saccone, Nancy L.; Stitzel, Jerry A.; Wang, Jen C.; Steinbach, Joseph H.; Goate, Alison M.; Schwantes-An, Tae-Hwi; Grucza, Richard A.; Stevens, Victoria L.; Bierut, Laura J.

    2010-01-01

    Results from genome-wide association studies of complex traits account for only a modest proportion of the trait variance predicted to be due to genetics. We hypothesize that joint analysis of polymorphisms may account for more variance. We evaluated this hypothesis on a case–control smoking phenotype by examining pairs of nicotinic receptor single-nucleotide polymorphisms (SNPs) using the Restricted Partition Method (RPM) on data from the Collaborative Genetic Study of Nicotine Dependence (COGEND). We found evidence of joint effects that increase explained variance. Four signals identified in COGEND were testable in independent American Cancer Society (ACS) data, and three of the four signals replicated. Our results highlight two important lessons: joint effects that increase the explained variance are not limited to loci displaying substantial main effects, and joint effects need not display a significant interaction term in a logistic regression model. These results suggest that the joint analyses of variants may indeed account for part of the genetic variance left unexplained by single SNP analyses. Methodologies that limit analyses of joint effects to variants that demonstrate association in single SNP analyses, or require a significant interaction term, will likely miss important joint effects. PMID:21079997

  13. 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

  14. Optimization of an ammonia-cooled rectangular microchannel heat sink using multi-objective non-dominated sorting genetic algorithm (NSGA2)

    NASA Astrophysics Data System (ADS)

    Adham, Ahmed Mohammed; Mohd-Ghazali, Normah; Ahmad, Robiah

    2012-10-01

    The ever decreasing size of modern electronic packaging has induced researchers to search for an effective and efficient heat removal system to handle the continuously increasing power density. Investigations have involved different geometry, material and coolant to address the thermal management issues. This paper reports the potential improvement in the overall performance of a rectangular microchannel heat sink using a new gaseous coolant namely ammonia gas. Using a multi-objective general optimization scheme with the thermal resistance model as an analysis method in combination with a non-dominated sorting genetic algorithm as an optimization technique, it was found that significant reduction in the total thermal resistance up to 34 % for ammonia-cooled compared to air-cooled microchannel heat sink under the same operating conditions is achievable. In addition, a considerable decrease in the microchannel heat sink's mass up to 30 % was achieved due to the different heat sink's material used.

  15. Genetic linkage of type VII collagen (COL7A1) to dominant dystrophic epidermolysis bullosa in families with abnormal anchoring fibrils.

    PubMed Central

    Ryynänen, M; Ryynänen, J; Sollberg, S; Iozzo, R V; Knowlton, R G; Uitto, J

    1992-01-01

    Epidermolysis bullosa (EB) in a group of genodermatoses characterized by the fragility of skin. Previous studies on the dystrophic (scarring) forms of EB have suggested abnormalities in anchoring fibrils, morphologically recognizable attachment structures that provide stability to the association of the cutaneous basement membrane to the underlying dermis. Since type VII collagen is the major component of the anchoring fibrils, we examined the genetic linkage of dominant dystrophic EB (EBDD) and the type VII collagen gene (COL7A1) locus, which we have recently mapped to chromosome 3p, in three large kindreds with abnormal anchoring fibrils. Strong genetic linkage of EBDD and COL7A1 loci was demonstrated with the maximum logarithm of odds (LOD) score of 8.77 at theta = 0. This linkage was further confirmed with two additional markers in this region of the short arm of chromosome 3, and these analyses allowed further refinement of the map locus of COL7A1. Since there were no recombinants between the COL7A1 and EBDD loci, our findings suggest that type VII collagen is the candidate gene that may harbor the mutations responsible for the EB phenotype in these three families. Images PMID:1347297

  16. 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.

  17. Cosmology without cosmic variance

    DOE PAGES

    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

  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. 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

  20. Identifying Source Populations and Genetic Structure for Savannah Elephants in Human-Dominated Landscapes and Protected Areas in the Kenya-Tanzania Borderlands

    PubMed Central

    Ahlering, Marissa A.; Eggert, Lori S.; Western, David; Estes, Anna; Munishi, Linus; Fleischer, Robert; Roberts, Melissa; Maldonado, Jesus E.

    2012-01-01

    We investigated the genetic metapopulation structure of elephants across the trans Rift Valley region of Kenya and Tanzania, one of the remaining strongholds for savannah elephants (Loxodonata africana) in East Africa, using microsatellite and mitochondrial DNA (mtDNA) markers. We then examined this population structure to determine the source population for a recent colonization event of savannah elephants on community-owned land within the trans rift valley region. Four of the five sampled populations showed significant genetic differentiation (p<0.05) as measured with both mtDNA haplotypes and microsatellites. Only the samples from the adjacent Maasai Mara and Serengeti ecosystems showed no significant differentiation. A phylogenetic neighbour-joining tree constructed from mtDNA haplotypes detected four clades. Clade four corresponds to the F clade of previous mtDNA studies that reported to have originated in forest elephants (Loxodonta cyclotis) but to also be present in some savannah elephant populations. The split between clade four and the other three clades corresponded strongly to the geographic distribution of mtDNA haplotypes across the rift valley in the study area. Clade four was the dominant clade detected on the west side of the rift valley with rare occurrences on the east side. Finally, the strong patterns of population differentiation clearly indicated that the recent colonists to the community-owned land in Kenya came from the west side of the rift valley. Our results indicate strong female philopatry within the isolated populations of the trans rift valley region, with gene flow primarily mediated via male movements. The recent colonization event from Maasai Mara or Serengeti suggests there is hope for maintaining connectivity and population viability outside formal protected areas in the region. PMID:23300634

  1. The genetic basis of political sophistication.

    PubMed

    Arceneaux, Kevin; Johnson, Martine; Maes, Hermine H

    2012-02-01

    Political sophistication is a concept that encompasses political reasoning, the coherence of people's issue attitudes, and their knowledge of political processes. To what extent is political sophistication affected by genes and environments? Do these distinct but related measures of sophistication share a common genetic structure? We analyze survey data collected from participants in the Minnesota Twin Registry to estimate influences of genes and environments on variables used to measure political sophistication. Additive genetic factors explain 48-76% of the variation in educational attainment, political interest, and political knowledge, while dominance genetics influence 28% of the variance of ideological consistency. Multivariate analyses show that, although these measures share common genetic and unique environmental factors to a modest extent, much of the variance is explained by specific genetic and unique environmental factors. Ideological consistency appears to be mostly distinct from the other measures, as it is strongly accounted for by unique environmental influences.

  2. Sampling Errors of Variance Components.

    ERIC Educational Resources Information Center

    Sanders, Piet F.

    A study on sampling errors of variance components was conducted within the framework of generalizability theory by P. L. Smith (1978). The study used an intuitive approach for solving the problem of how to allocate the number of conditions to different facets in order to produce the most stable estimate of the universe score variance. Optimization…

  3. Linkage to D3S47 (C17) in one large autosomal dominant retinitis pigmentosa family and exclusion in another: confirmation of genetic heterogeneity.

    PubMed Central

    Lester, D H; Inglehearn, C F; Bashir, R; Ackford, H; Esakowitz, L; Jay, M; Bird, A C; Wright, A F; Papiha, S S; Bhattacharya, S S

    1990-01-01

    Recently Dryja and his co-workers observed a mutation in the 23d codon of the rhodopsin gene in a proportion of autosomal dominant retinitis pigmentosa (ADRP) patients. Linkage analysis with a rhodopsin-linked probe C17 (D3S47) was carried out in two large British ADRP families, one with diffuse-type (D-type) RP and the other with regional-type (R-type) RP. Significantly positive lod scores (lod score maximum [Zmax] = +5.58 at recombination fraction [theta] = .0) were obtained between C17 and our D-type ADRP family showing complete penetrance. Sequence and oligonucleotide analysis has, however, shown that no point mutation at the 23d codon exists in affected individuals in our complete-penetrance pedigree, indicating that another rhodopsin mutation is probably responsible for ADRP in this family. Significantly negative lod scores (Z less than -2 at theta = .045) were, however, obtained between C17 and our R-type family which showed incomplete penetrance. Previous results presented by this laboratory also showed no linkage between C17 and another large British R-type ADRP family with incomplete penetrance. This confirms genetic heterogeneity. Some types of ADRP are being caused by different mutations in the rhodopsin locus (3q21-24) or another tightly linked gene in this region, while other types of ADRP are the result of mutations elsewhere in the genome. Images Figure 2 Figure 3 Figure 4 PMID:2393026

  4. Utility functions predict variance and skewness risk preferences in monkeys.

    PubMed

    Genest, Wilfried; Stauffer, William R; Schultz, Wolfram

    2016-07-26

    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

  5. 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

  6. Utility functions predict variance and skewness risk preferences in monkeys.

    PubMed

    Genest, Wilfried; Stauffer, William R; Schultz, Wolfram

    2016-07-26

    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.

  7. The dominant Australian community-acquired methicillin-resistant Staphylococcus aureus clone ST93-IV [2B] is highly virulent and genetically distinct.

    PubMed

    Chua, Kyra Y L; Seemann, Torsten; Harrison, Paul F; Monagle, Shaun; Korman, Tony M; Johnson, Paul D R; Coombs, Geoffrey W; Howden, Brian O; Davies, John K; Howden, Benjamin P; Stinear, Timothy P

    2011-01-01

    Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) USA300 has spread rapidly across North America, and CA-MRSA is also increasing in Australia. However, the dominant Australian CA-MRSA strain, ST93-IV [2B] appears distantly related to USA300 despite strikingly similar clinical and epidemiological profiles. Here, we compared the virulence of a recent Australian ST93 isolate (JKD6159) to other MRSA, including USA300, and found that JKD6159 was the most virulent in a mouse skin infection model. We fully sequenced the genome of JKD6159 and confirmed that JKD6159 is a distinct clone with 7616 single nucleotide polymorphisms (SNPs) distinguishing this strain from all other S. aureus genomes. Despite its high virulence there were surprisingly few virulence determinants. However, genes encoding α-hemolysin, Panton-Valentine leukocidin (PVL) and α-type phenol soluble modulins were present. Genome comparisons revealed 32 additional CDS in JKD6159 but none appeared to encode new virulence factors, suggesting that this clone's enhanced pathogenicity could lie within subtler genome changes, such as SNPs within regulatory genes. To investigate the role of accessory genome elements in CA-MRSA epidemiology, we next sequenced three additional Australian non-ST93 CA-MRSA strains and compared them with JKD6159, 19 completed S. aureus genomes and 59 additional S. aureus genomes for which unassembled genome sequence data was publicly available (82 genomes in total). These comparisons showed that despite its distinctive genotype, JKD6159 and other CA-MRSA clones (including USA300) share a conserved repertoire of three notable accessory elements (SSCmecIV, PVL prophage, and pMW2). This study demonstrates that the genetically distinct ST93 CA-MRSA from Australia is highly virulent. Our comparisons of geographically and genetically diverse CA-MRSA genomes suggest that apparent convergent evolution in CA-MRSA may be better explained by the rapid dissemination of a

  8. 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 ...

  9. Variance and covariance estimates for weaning weight of Senepol cattle.

    PubMed

    Wright, D W; Johnson, Z B; Brown, C J; Wildeus, S

    1991-10-01

    Variance and covariance components were estimated for weaning weight from Senepol field data for use in the reduced animal model for a maternally influenced trait. The 4,634 weaning records were used to evaluate 113 sires and 1,406 dams on the island of St. Croix. Estimates of direct additive genetic variance (sigma 2A), maternal additive genetic variance (sigma 2M), covariance between direct and maternal additive genetic effects (sigma AM), permanent maternal environmental variance (sigma 2PE), and residual variance (sigma 2 epsilon) were calculated by equating variances estimated from a sire-dam model and a sire-maternal grandsire model, with and without the inverse of the numerator relationship matrix (A-1), to their expectations. Estimates were sigma 2A, 139.05 and 138.14 kg2; sigma 2M, 307.04 and 288.90 kg2; sigma AM, -117.57 and -103.76 kg2; sigma 2PE, -258.35 and -243.40 kg2; and sigma 2 epsilon, 588.18 and 577.72 kg2 with and without A-1, respectively. Heritability estimates for direct additive (h2A) were .211 and .210 with and without A-1, respectively. Heritability estimates for maternal additive (h2M) were .47 and .44 with and without A-1, respectively. Correlations between direct and maternal (IAM) effects were -.57 and -.52 with and without A-1, respectively. PMID:1778806

  10. 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

  11. A Bayesian framework for comparative quantitative genetics

    PubMed Central

    Ovaskainen, Otso; Cano, José Manuel; Merilä, Juha

    2008-01-01

    Bayesian approaches have been extensively used in animal breeding sciences, but similar approaches in the context of evolutionary quantitative genetics have been rare. We compared the performance of Bayesian and frequentist approaches in estimation of quantitative genetic parameters (viz. matrices of additive and dominance variances) in datasets typical of evolutionary studies and traits differing in their genetic architecture. Our results illustrate that it is difficult to disentangle the relative roles of different genetic components from small datasets, and that ignoring, e.g. dominance is likely to lead to biased estimates of additive variance. We suggest that a natural summary statistic for G-matrix comparisons can be obtained by examining how different the underlying multinormal probability distributions are, and illustrate our approach with data on the common frog (Rana temporaria). Furthermore, we derive a simple Monte Carlo method for computation of fraternity coefficients needed for the estimation of dominance variance, and use the pedigree of a natural Siberian jay (Perisoreus infaustus) population to illustrate that the commonly used approximate values can be substantially biased. PMID:18211881

  12. Multicomponent, multi-azimuth pre-stack seismic waveform inversion for azimuthally anisotropic media using a parallel and computationally efficient non-dominated sorting genetic algorithm

    NASA Astrophysics Data System (ADS)

    Li, Tao; Mallick, Subhashis

    2015-02-01

    Consideration of azimuthal anisotropy, at least to an orthorhombic symmetry is important in exploring the naturally fractured and unconventional hydrocarbon reservoirs. Full waveform inversion of multicomponent seismic data can, in principle, provide more robust estimates of subsurface elastic parameters and density than the inversion of single component (P wave) seismic data. In addition, azimuthally dependent anisotropy can only be resolved by carefully studying the multicomponent seismic displacement data acquired and processed along different azimuths. Such an analysis needs an inversion algorithm capable of simultaneously optimizing multiple objectives, one for each data component along each azimuth. These multicomponent and multi-azimuthal seismic inversions are non-linear with non-unique solutions; it is therefore appropriate to treat the objectives as a vector and simultaneously optimize each of its components such that the optimal set of solutions could be obtained. The fast non-dominated sorting genetic algorithm (NSGA II) is a robust stochastic global search method capable of handling multiple objectives, but its computational expense increases with increasing number of objectives and the number of model parameters to be inverted for. In addition, an accurate extraction of subsurface azimuthal anisotropy requires multicomponent seismic data acquired at a fine spatial resolution along many source-to-receiver azimuths. Because routine acquisition of such data is prohibitively expensive, they are typically available along two or at most three azimuthal orientations at a spatial resolution where such an inversion could be applied. This paper proposes a novel multi-objective methodology using a parallelized version of NSGA II for waveform inversion of multicomponent seismic displacement data along two azimuths. By scaling the objectives prior to ranking, redefining the crowding distance as functions of the scaled objective and the model spaces, and varying

  13. 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.

  14. Inclusion of Dominance Effects in the Multivariate GBLUP Model.

    PubMed

    dos Santos, Jhonathan Pedroso Rigal; Vasconcellos, Renato Coelho de Castro; Pires, Luiz Paulo Miranda; Balestre, Marcio; Von Pinho, Renzo Garcia

    2016-01-01

    New proposals for models and applications of prediction processes with data on molecular markers may help reduce the financial costs of and identify superior genotypes in maize breeding programs. Studies evaluating Genomic Best Linear Unbiased Prediction (GBLUP) models including dominance effects have not been performed in the univariate and multivariate context in the data analysis of this crop. A single cross hybrid construction procedure was performed in this study using phenotypic data and actual molecular markers of 4,091 maize lines from the public database Panzea. A total of 400 simple hybrids resulting from this process were analyzed using the univariate and multivariate GBLUP model considering only additive effects additive plus dominance effects. Historic heritability scenarios of five traits and other genetic architecture settings were used to compare models, evaluating the predictive ability and estimation of variance components. Marginal differences were detected between the multivariate and univariate models. The main explanation for the small discrepancy between models is the low- to moderate-magnitude correlations between the traits studied and moderate heritabilities. These conditions do not favor the advantages of multivariate analysis. The inclusion of dominance effects in the models was an efficient strategy to improve the predictive ability and estimation quality of variance components. PMID:27074056

  15. 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…

  16. 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…

  17. Familial Resemblance of Borderline Personality Disorder Features: Genetic or Cultural Transmission?

    PubMed Central

    Distel, Marijn A.; Rebollo-Mesa, Irene; Willemsen, Gonneke; Derom, Catherine A.; Trull, Timothy J.; Martin, Nicholas G.; Boomsma, Dorret I.

    2009-01-01

    Borderline personality disorder is a severe personality disorder for which genetic research has been limited to family studies and classical twin studies. These studies indicate that genetic effects explain 35 to 45% of the variance in borderline personality disorder and borderline personality features. However, effects of non-additive (dominance) genetic factors, non-random mating and cultural transmission have generally not been explored. In the present study an extended twin-family design was applied to self-report data of twins (N = 5,017) and their siblings (N = 1,266), parents (N = 3,064) and spouses (N = 939) from 4,015 families, to estimate the effects of additive and non-additive genetic and environmental factors, cultural transmission and non-random mating on individual differences in borderline personality features. Results showed that resemblance among biological relatives could completely be attributed to genetic effects. Variation in borderline personality features was explained by additive genetic (21%; 95% CI 17–26%) and dominant genetic (24%; 95% CI 17–31%) factors. Environmental influences (55%; 95% CI 51–60%) explained the remaining variance. Significant resemblance between spouses was observed, which was best explained by phenotypic assortative mating, but it had only a small effect on the genetic variance (1% of the total variance). There was no effect of cultural transmission from parents to offspring. PMID:19390632

  18. Understanding the influence of watershed storage caused by human interferences on ET variance

    NASA Astrophysics Data System (ADS)

    Zeng, R.; Cai, X.

    2014-12-01

    Understanding the temporal variance of evapotranspiration (ET) at the watershed scale remains a challenging task, because it is affected by complex climate conditions, soil properties, vegetation, groundwater and human activities. In a changing environment with extensive and intensive human interferences, understanding ET variance and its factors is important for sustainable water resources management. This study presents an analysis of the effect of storage change caused by human activities on ET variance Irrigation usually filters ET variance through the use of surface and groundwater; however, over-amount irrigation may cause the depletion of watershed storage, which changes the coincidence of water availability and energy supply for ET. This study develops a framework by incorporating the water balance and the Budyko Hypothesis. It decomposes the ET variance to the variances of precipitation, potential ET, catchment storage change, and their covariances. The contributions of ET variance from the various components are scaled by some weighting functions, expressed as long-term climate conditions and catchment properties. ET variance is assessed by records from 32 major river basins across the world. It is found that ET variance is dominated by precipitation variance under hot-dry condition and by evaporative demand variance under cool-wet condition; while the coincidence of water and energy supply controls ET variance under moderate climate condition. Watershed storage change plays an increasing important role in determining ET variance with relatively shorter time scale. By incorporating storage change caused by human interferences, this framework corrects the over-estimation of ET variance in hot-dry climate and under-estimation of ET variance in cool-wet climate. Furthermore, classification of dominant factors on ET variance shows similar patterns as geographic zonation.

  19. Functional analysis of variance for association studies.

    PubMed

    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.

  20. Functional analysis of variance for association studies.

    PubMed

    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

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. The evolution and consequences of sex-specific reproductive variance.

    PubMed

    Mullon, Charles; Reuter, Max; Lehmann, Laurent

    2014-01-01

    Natural selection favors alleles that increase the number of offspring produced by their carriers. But in a world that is inherently uncertain within generations, selection also favors alleles that reduce the variance in the number of offspring produced. If previous studies have established this principle, they have largely ignored fundamental aspects of sexual reproduction and therefore how selection on sex-specific reproductive variance operates. To study the evolution and consequences of sex-specific reproductive variance, we present a population-genetic model of phenotypic evolution in a dioecious population that incorporates previously neglected components of reproductive variance. First, we derive the probability of fixation for mutations that affect male and/or female reproductive phenotypes under sex-specific selection. We find that even in the simplest scenarios, the direction of selection is altered when reproductive variance is taken into account. In particular, previously unaccounted for covariances between the reproductive outputs of different individuals are expected to play a significant role in determining the direction of selection. Then, the probability of fixation is used to develop a stochastic model of joint male and female phenotypic evolution. We find that sex-specific reproductive variance can be responsible for changes in the course of long-term evolution. Finally, the model is applied to an example of parental-care evolution. Overall, our model allows for the evolutionary analysis of social traits in finite and dioecious populations, where interactions can occur within and between sexes under a realistic scenario of reproduction.

  6. 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...

  7. trans-dominant mutants of E1A provide genetic evidence that the zinc finger of the trans-activating domain binds a transcription factor.

    PubMed Central

    Webster, L C; Ricciardi, R P

    1991-01-01

    The 289R E1A protein of adenovirus stimulates transcription of early viral and certain cellular genes. trans-Activation requires residues 140 to 188, which encompass a zinc finger. Several studies have indicated that trans-activation by E1A is mediated through cellular transcription factors. In particular, the ability of the trans-dominant E1A point mutant hr5 (Ser-185 to Asn) to inhibit wild-type E1A trans-activation was proposed to result from the sequestration of a cellular factor. Using site-directed mutagenesis, we individually replaced every residue within and flanking the trans-activating domain with a conservative amino acid, revealing 16 critical residues. Six of the individual substitutions lying in a contiguous stretch C terminal to the zinc finger (carboxyl region183-188) imparted a trans-dominant phenotype. trans-Dominance was even produced by deletion of the entire carboxyl region183-188. Conversely, an intact finger region147-177 was absolutely required for trans-dominance, since second-site substitution of every critical residue in this region abrogated the trans-dominant phenotype of the hr5 protein. These data indicate that the finger region147-177 bind a limiting cellular transcription factor and that the carboxyl region183-188 provides a separate and essential function. In addition, we show that four negatively charged residues within the trans-activating domain do not comprise a distinct acidic activating region. We present a model in which the trans-activating domain of E1A binds to two different cellular protein targets through the finger and carboxyl regions. Images PMID:1831535

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

    PubMed

    Crews, D H; Franke, D E

    1998-07-01

    considered as a source of heterogeneity of variance. Genetic covariances estimated from the model accounting for heterogeneous variances resulted in genetic correlations of or near unity. These results suggest that different genetic values be considered for genetic evaluation of carcass yield and shear force traits from steers with different degrees of Brahman inheritance. PMID:9690635

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

    PubMed

    Crews, D H; Franke, D E

    1998-07-01

    considered as a source of heterogeneity of variance. Genetic covariances estimated from the model accounting for heterogeneous variances resulted in genetic correlations of or near unity. These results suggest that different genetic values be considered for genetic evaluation of carcass yield and shear force traits from steers with different degrees of Brahman inheritance.

  10. Additive, dominance, and epistatic loss effects on preweaning weight gain of crossbred beef cattle from different Bos taurus breeds.

    PubMed

    Roso, V M; Schenkel, F S; Miller, S P; Wilton, J W

    2005-08-01

    (Co)variance components, direct and maternal breed additive, dominance, and epistatic loss effects on preweaning weight gain of beef cattle were estimated. Data were from 478,466 animals in Ontario, Canada, from 1986 to 1999, including records of both purebred and crossbred animals from Angus, Blonde d'Aquitaine, Charolais, Gelbvieh, Hereford, Limousin, Maine-Anjou, Salers, Shorthorn, and Simmental breeds. The genetic model included fixed direct and maternal breed additive, dominance, and epistatic loss effects, fixed environmental effects of age of the calf, contemporary group, and age of the dam x sex of the calf, random additive direct and maternal genetic effects, and random maternal permanent environment effects. Estimates of direct and maternal additive genetic, maternal permanent environmental and residual variances, expressed as proportions of the phenotypic variance, were 0.32, 0.20, 0.12, and 0.52, respectively. Correlation between direct and maternal additive genetic effects was -0.63. Breed ranking was similar to previous studies, but estimates showed large SE. The favorable effects of direct and maternal dominance (P < 0.05) on preweaning gain were equivalent to 1.3 and 2.3% of the phenotypic mean of purebred calves, respectively. The same features for direct and maternal epistatic loss effects were -2.2% (P < 0.05) and -0.1% (P > 0.05). The large SE of breed effects were likely due to multicollinearity among predictor variables and deficiencies in the dataset to separate direct and maternal effects and may result in a less reliable ranking of the animals for across breed comparisons. Further research to identify the causes of the instability of estimates of breed additive, dominance, and epistatic loss genetic effects, and application of alternative statistical methods is recommended.

  11. The contribution of dominance to phenotype prediction in a pine breeding and simulated population.

    PubMed

    de Almeida Filho, J E; Guimarães, J F R; E Silva, F F; de Resende, M D V; Muñoz, P; Kirst, M; Resende, M F R

    2016-07-01

    Pedigrees and dense marker panels have been used to predict the genetic merit of individuals in plant and animal breeding, accounting primarily for the contribution of additive effects. However, nonadditive effects may also affect trait variation in many breeding systems, particularly when specific combining ability is explored. Here we used models with different priors, and including additive-only and additive plus dominance effects, to predict polygenic (height) and oligogenic (fusiform rust resistance) traits in a structured breeding population of loblolly pine (Pinus taeda L.). Models were largely similar in predictive ability, and the inclusion of dominance only improved modestly the predictions for tree height. Next, we simulated a genetically similar population to assess the ability of predicting polygenic and oligogenic traits controlled by different levels of dominance. The simulation showed an overall decrease in the accuracy of total genomic predictions as dominance increases, regardless of the method used for prediction. Thus, dominance effects may not be accounted for as effectively in prediction models compared with traits controlled by additive alleles only. When the ratio of dominance to total phenotypic variance reached 0.2, the additive-dominance prediction models were significantly better than the additive-only models. However, in the prediction of the subsequent progeny population, this accuracy increase was only observed for the oligogenic trait. PMID:27118156

  12. The contribution of dominance to phenotype prediction in a pine breeding and simulated population

    PubMed Central

    de Almeida Filho, J E; Guimarães, J F R; e Silva, F F; de Resende, M D V; Muñoz, P; Kirst, M; Resende, M F R

    2016-01-01

    Pedigrees and dense marker panels have been used to predict the genetic merit of individuals in plant and animal breeding, accounting primarily for the contribution of additive effects. However, nonadditive effects may also affect trait variation in many breeding systems, particularly when specific combining ability is explored. Here we used models with different priors, and including additive-only and additive plus dominance effects, to predict polygenic (height) and oligogenic (fusiform rust resistance) traits in a structured breeding population of loblolly pine (Pinus taeda L.). Models were largely similar in predictive ability, and the inclusion of dominance only improved modestly the predictions for tree height. Next, we simulated a genetically similar population to assess the ability of predicting polygenic and oligogenic traits controlled by different levels of dominance. The simulation showed an overall decrease in the accuracy of total genomic predictions as dominance increases, regardless of the method used for prediction. Thus, dominance effects may not be accounted for as effectively in prediction models compared with traits controlled by additive alleles only. When the ratio of dominance to total phenotypic variance reached 0.2, the additive–dominance prediction models were significantly better than the additive-only models. However, in the prediction of the subsequent progeny population, this accuracy increase was only observed for the oligogenic trait. PMID:27118156

  13. Bayesian models with dominance effects for genomic evaluation of quantitative traits.

    PubMed

    Wellmann, Robin; Bennewitz, Jörn

    2012-02-01

    Genomic selection refers to the use of dense, genome-wide markers for the prediction of breeding values (BV) and subsequent selection of breeding individuals. It has become a standard tool in livestock and plant breeding for accelerating genetic gain. The core of genomic selection is the prediction of a large number of marker effects from a limited number of observations. Various Bayesian methods that successfully cope with this challenge are known. Until now, the main research emphasis has been on additive genetic effects. Dominance coefficients of quantitative trait loci (QTLs), however, can also be large, even if dominance variance and inbreeding depression are relatively small. Considering dominance might contribute to the accuracy of genomic selection and serve as a guide for choosing mating pairs with good combining abilities. A general hierarchical Bayesian model for genomic selection that can realistically account for dominance is introduced. Several submodels are proposed and compared with respect to their ability to predict genomic BV, dominance deviations and genotypic values (GV) by stochastic simulation. These submodels differ in the way the dependency between additive and dominance effects is modelled. Depending on the marker panel, the inclusion of dominance effects increased the accuracy of GV by about 17% and the accuracy of genomic BV by 2% in the offspring. Furthermore, it slowed down the decrease of the accuracies in subsequent generations. It was possible to obtain accurate estimates of GV, which enables mate selection programmes.

  14. The ethics of contacting family members of a subject in a genetic research study to return results for an autosomal dominant syndrome.

    PubMed

    Taylor, Holly A; Wilfond, Benjamin S

    2013-01-01

    This case explores the ethical landscape around recontacting a subject's relatives to return genetic research results when the informed consent form signed by the original cohort of subjects is silent on whether investigators may share new information with the research subject's family. As a result of rapid advances in genetic technology, methods to identify genetic markers can mature during the life course of a study. In this case, the investigators identified the genetic mutation responsible for the disorder after a number of their original subjects had died. The researchers now have the ability to inform relatives of the subject about their risk of developing the same disease. Mark Rothstein, JD, from the University of Louisville School of Medicine, provides an overview of the medical/scientific, legal, and ethical issues underlying this case. Lauren Milner, PhD, and colleagues at Stanford University explore how the relationship between researcher and subject affect this debate. Seema Shah, JD, and colleagues at the National Institutes of Health and University of California, Los Angeles (UCLA) discuss whether and how requirements of the duty to warn are applicable in this case.

  15. The genetics of hybrid male sterility between the allopatric species pair Drosophila persimilis and D. pseudoobscura bogotana: dominant sterility alleles in collinear autosomal regions.

    PubMed

    Chang, Audrey S; Noor, Mohamed A F

    2007-05-01

    F(1) hybrid male sterility is thought to result from interactions between loci on the X chromosome and dominant-acting loci on the autosomes. While X-linked loci that contribute to hybrid male sterility have been precisely localized in many animal taxa, their dominant autosomal interactors have been more difficult to localize precisely and/or have been shown to be of relatively smaller effect. Here, we identified and mapped at least four dominant autosomal factors contributing to hybrid male sterility in the allopatric species pair Drosophila persimilis and D. pseudoobscura bogotana. Using these results, we tested predictions of reduced recombination models of speciation. Consistent with these models, three of the four QTL associated with hybrid male sterility occur in collinear (uninverted) regions of these genomes. Furthermore, these QTL do not contribute significantly to hybrid male sterility in crosses between the sympatric species D. persimilis and D. pseudoobscura pseudoobscura. The autosomal loci identified in this study provide the basis for introgression mapping and, ultimately, for molecular cloning of interacting genes that contribute to F(1) hybrid sterility.

  16. Population Genetic Structure, Abundance, and Health Status of Two Dominant Benthic Species in the Saba Bank National Park, Caribbean Netherlands: Montastraea cavernosa and Xestospongia muta.

    PubMed

    de Bakker, Didier M; Meesters, Erik H W G; van Bleijswijk, Judith D L; Luttikhuizen, Pieternella C; Breeuwer, Hans J A J; Becking, Leontine E

    2016-01-01

    Saba Bank, a submerged atoll in the Caribbean Sea with an area of 2,200 km2, has attained international conservation status due to the rich diversity of species that reside on the bank. In order to assess the role of Saba Bank as a potential reservoir of diversity for the surrounding reefs, we examined the population genetic structure, abundance and health status of two prominent benthic species, the coral Montastraea cavernosa and the sponge Xestospongia muta. Sequence data were collected from 34 colonies of M. cavernosa (nDNA ITS1-5.8S-ITS2; 892 bp) and 68 X. muta sponges (mtDNA I3-M11 partition of COI; 544 bp) on Saba Bank and around Saba Island, and compared with published data across the wider Caribbean. Our data indicate that there is genetic connectivity between populations on Saba Bank and the nearby Saba Island as well as multiple locations in the wider Caribbean, ranging in distance from 100s-1000s km. The genetic diversity of Saba Bank populations of M. cavernosa (π = 0.055) and X. muta (π = 0.0010) was comparable to those in other regions in the western Atlantic. Densities and health status were determined along 11 transects of 50 m2 along the south-eastern rim of Saba Bank. The densities of M. cavernosa (0.27 ind. m-2, 95% CI: 0.12-0.52) were average, while the densities of X. muta (0.09 ind. m-2, 95% CI: 0.02-0.32) were generally higher with respect to other Caribbean locations. No disease or bleaching was present in any of the specimens of the coral M. cavernosa, however, we did observe partial tissue loss (77.9% of samples) as well as overgrowth (48.1%), predominantly by cyanobacteria. In contrast, the majority of observed X. muta (83.5%) showed signs of presumed bleaching. The combined results of apparent gene flow among populations on Saba Bank and surrounding reefs, the high abundance and unique genetic diversity, indicate that Saba Bank could function as an important buffer for the region. Either as a natural source of larvae to replenish

  17. Population Genetic Structure, Abundance, and Health Status of Two Dominant Benthic Species in the Saba Bank National Park, Caribbean Netherlands: Montastraea cavernosa and Xestospongia muta

    PubMed Central

    de Bakker, Didier M.; Meesters, Erik H. W. G.; van Bleijswijk, Judith D. L.; Luttikhuizen, Pieternella C.; Breeuwer, Hans J. A. J.; Becking, Leontine E.

    2016-01-01

    Saba Bank, a submerged atoll in the Caribbean Sea with an area of 2,200 km2, has attained international conservation status due to the rich diversity of species that reside on the bank. In order to assess the role of Saba Bank as a potential reservoir of diversity for the surrounding reefs, we examined the population genetic structure, abundance and health status of two prominent benthic species, the coral Montastraea cavernosa and the sponge Xestospongia muta. Sequence data were collected from 34 colonies of M. cavernosa (nDNA ITS1-5.8S-ITS2; 892 bp) and 68 X. muta sponges (mtDNA I3-M11 partition of COI; 544 bp) on Saba Bank and around Saba Island, and compared with published data across the wider Caribbean. Our data indicate that there is genetic connectivity between populations on Saba Bank and the nearby Saba Island as well as multiple locations in the wider Caribbean, ranging in distance from 100s–1000s km. The genetic diversity of Saba Bank populations of M. cavernosa (π = 0.055) and X. muta (π = 0.0010) was comparable to those in other regions in the western Atlantic. Densities and health status were determined along 11 transects of 50 m2 along the south-eastern rim of Saba Bank. The densities of M. cavernosa (0.27 ind. m-2, 95% CI: 0.12–0.52) were average, while the densities of X. muta (0.09 ind. m-2, 95% CI: 0.02–0.32) were generally higher with respect to other Caribbean locations. No disease or bleaching was present in any of the specimens of the coral M. cavernosa, however, we did observe partial tissue loss (77.9% of samples) as well as overgrowth (48.1%), predominantly by cyanobacteria. In contrast, the majority of observed X. muta (83.5%) showed signs of presumed bleaching. The combined results of apparent gene flow among populations on Saba Bank and surrounding reefs, the high abundance and unique genetic diversity, indicate that Saba Bank could function as an important buffer for the region. Either as a natural source of larvae to

  18. Population Genetic Structure, Abundance, and Health Status of Two Dominant Benthic Species in the Saba Bank National Park, Caribbean Netherlands: Montastraea cavernosa and Xestospongia muta.

    PubMed

    de Bakker, Didier M; Meesters, Erik H W G; van Bleijswijk, Judith D L; Luttikhuizen, Pieternella C; Breeuwer, Hans J A J; Becking, Leontine E

    2016-01-01

    Saba Bank, a submerged atoll in the Caribbean Sea with an area of 2,200 km2, has attained international conservation status due to the rich diversity of species that reside on the bank. In order to assess the role of Saba Bank as a potential reservoir of diversity for the surrounding reefs, we examined the population genetic structure, abundance and health status of two prominent benthic species, the coral Montastraea cavernosa and the sponge Xestospongia muta. Sequence data were collected from 34 colonies of M. cavernosa (nDNA ITS1-5.8S-ITS2; 892 bp) and 68 X. muta sponges (mtDNA I3-M11 partition of COI; 544 bp) on Saba Bank and around Saba Island, and compared with published data across the wider Caribbean. Our data indicate that there is genetic connectivity between populations on Saba Bank and the nearby Saba Island as well as multiple locations in the wider Caribbean, ranging in distance from 100s-1000s km. The genetic diversity of Saba Bank populations of M. cavernosa (π = 0.055) and X. muta (π = 0.0010) was comparable to those in other regions in the western Atlantic. Densities and health status were determined along 11 transects of 50 m2 along the south-eastern rim of Saba Bank. The densities of M. cavernosa (0.27 ind. m-2, 95% CI: 0.12-0.52) were average, while the densities of X. muta (0.09 ind. m-2, 95% CI: 0.02-0.32) were generally higher with respect to other Caribbean locations. No disease or bleaching was present in any of the specimens of the coral M. cavernosa, however, we did observe partial tissue loss (77.9% of samples) as well as overgrowth (48.1%), predominantly by cyanobacteria. In contrast, the majority of observed X. muta (83.5%) showed signs of presumed bleaching. The combined results of apparent gene flow among populations on Saba Bank and surrounding reefs, the high abundance and unique genetic diversity, indicate that Saba Bank could function as an important buffer for the region. Either as a natural source of larvae to replenish

  19. 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

  20. Medical genetics

    SciTech Connect

    Jorde, L.B.; Carey, J.C.; White, R.L.

    1995-10-01

    This book on the subject of medical genetics is a textbook aimed at a very broad audience: principally, medical students, nursing students, graduate, and undergraduate students. The book is actually a primer of general genetics as applied to humans and provides a well-balanced introduction to the scientific and clinical basis of human genetics. The twelve chapters include: Introduction, Basic Cell Biology, Genetic Variation, Autosomal Dominant and Recessive Inheritance, Sex-linked and Mitochondrial Inheritance, Clinical Cytogenetics, Gene Mapping, Immunogenetics, Cancer Genetics, Multifactorial Inheritance and Common Disease, Genetic Screening, Genetic Diagnosis and Gene Therapy, and Clinical Genetics and Genetic Counseling.

  1. 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

  2. Genetic study of the loss and restoration of Mutator transposon activity in maize: evidence against dominant-negative regulator associated with loss of activity.

    PubMed

    Brown, J; Sundaresan, V

    1992-04-01

    The Mutator system of transposable elements is characterized by a family of transposons called Mu transposons that share common termini and are actively transposing in Robertson's Mutator (Mu) lines of maize. Mu lines lose transposition activity during propagation by either outcrossing or inbreeding. This loss of transposition activity, which can occur at non-Mendelian frequencies, is in the form of loss of forward transposition activity resulting in a decrease in the generation of new mutations, as well as the loss of mutability of Mu transposon induced mutations, and it has been correlated with hypermethylation of the Mu elements. Previous studies have concluded that restoration of Mutator transposon activity by crossing inactive lines back to active lines is incomplete or transient, and depends upon the sex of the inactive parent. Further, it has been proposed that the inactive system is dominant to the active system, with the dominance possibly mediated through a negative regulatory factor that is preferentially transmitted through the female. In this study, we have examined the frequencies of loss and restoration of Mu transposon activity using a Mu line carrying an insertion in the bronze 1 locus. We find that transmission of Mu transposon activity to non-Mu plants can occur at high rates through males and females, but individual cases of decreased transmission through the male were observed. We also find that in crosses between inactive-Mu and active-Mu plants, reactivation was efficient as well as heritable, regardless of the sex of the inactive parent. Similar results were obtained whether the inactivation occurred in an outcross or a self. In all cases examined, loss of Mu transposon activity was correlated with hypermethylation of Mu elements, and reactivation was correlated with their demethylation. Our results indicate that an inactive Mu system does not exhibit dominance over an active Mu system. We conclude that contrary to current models

  3. Warped functional analysis of variance.

    PubMed

    Gervini, Daniel; Carter, Patrick A

    2014-09-01

    This article presents an Analysis of Variance model for functional data that explicitly incorporates phase variability through a time-warping component, allowing for a unified approach to estimation and inference in presence of amplitude and time variability. The focus is on single-random-factor models but the approach can be easily generalized to more complex ANOVA models. The behavior of the estimators is studied by simulation, and an application to the analysis of growth curves of flour beetles is presented. Although the model assumes a smooth latent process behind the observed trajectories, smootheness of the observed data is not required; the method can be applied to irregular time grids, which are common in longitudinal studies.

  4. Pathogenic Potential, Genetic Diversity, and Population Structure of Escherichia coli Strains Isolated from a Forest-Dominated Watershed (Comox Lake) in British Columbia, Canada

    PubMed Central

    Mazumder, Asit

    2014-01-01

    Escherichia coli isolates (n = 658) obtained from drinking water intakes of Comox Lake (2011 to 2013) were screened for the following virulence genes (VGs): stx1 and stx2 (Shiga toxin-producing E. coli [STEC]), eae and the adherence factor (EAF) gene (enteropathogenic E. coli [EPEC]), heat-stable (ST) enterotoxin (variants STh and STp) and heat-labile enterotoxin (LT) genes (enterotoxigenic E. coli [ETEC]), and ipaH (enteroinvasive E. coli [EIEC]). The only genes detected were eae and stx2, which were carried by 37.69% (n = 248) of the isolates. Only eae was harbored by 26.74% (n = 176) of the isolates, representing potential atypical EPEC strains, while only stx2 was detected in 10.33% (n = 68) of the isolates, indicating potential STEC strains. Moreover, four isolates were positive for both the stx2 and eae genes, representing potential EHEC strains. The prevalence of VGs (eae or stx2) was significantly (P < 0.0001) higher in the fall season, and multiple genes (eae plus stx2) were detected only in fall. Repetitive element palindromic PCR (rep-PCR) fingerprint analysis of 658 E. coli isolates identified 335 unique fingerprints, with an overall Shannon diversity (H′) index of 3.653. Diversity varied among seasons over the years, with relatively higher diversity during fall. Multivariate analysis of variance (MANOVA) revealed that the majority of the fingerprints showed a tendency to cluster according to year, season, and month. Taken together, the results indicated that the diversity and population structure of E. coli fluctuate on a temporal scale, reflecting the presence of diverse host sources and their behavior over time in the watershed. Furthermore, the occurrence of potentially pathogenic E. coli strains in the drinking water intakes highlights the risk to human health associated with direct and indirect consumption of untreated surface water. PMID:25548059

  5. Pathogenic potential, genetic diversity, and population structure of Escherichia coli strains isolated from a forest-dominated watershed (Comox Lake) in British Columbia, Canada.

    PubMed

    Chandran, Abhirosh; Mazumder, Asit

    2015-03-01

    Escherichia coli isolates (n = 658) obtained from drinking water intakes of Comox Lake (2011 to 2013) were screened for the following virulence genes (VGs): stx1 and stx2 (Shiga toxin-producing E. coli [STEC]), eae and the adherence factor (EAF) gene (enteropathogenic E. coli [EPEC]), heat-stable (ST) enterotoxin (variants STh and STp) and heat-labile enterotoxin (LT) genes (enterotoxigenic E. coli [ETEC]), and ipaH (enteroinvasive E. coli [EIEC]). The only genes detected were eae and stx2, which were carried by 37.69% (n = 248) of the isolates. Only eae was harbored by 26.74% (n = 176) of the isolates, representing potential atypical EPEC strains, while only stx2 was detected in 10.33% (n = 68) of the isolates, indicating potential STEC strains. Moreover, four isolates were positive for both the stx2 and eae genes, representing potential EHEC strains. The prevalence of VGs (eae or stx2) was significantly (P < 0.0001) higher in the fall season, and multiple genes (eae plus stx2) were detected only in fall. Repetitive element palindromic PCR (rep-PCR) fingerprint analysis of 658 E. coli isolates identified 335 unique fingerprints, with an overall Shannon diversity (H') index of 3.653. Diversity varied among seasons over the years, with relatively higher diversity during fall. Multivariate analysis of variance (MANOVA) revealed that the majority of the fingerprints showed a tendency to cluster according to year, season, and month. Taken together, the results indicated that the diversity and population structure of E. coli fluctuate on a temporal scale, reflecting the presence of diverse host sources and their behavior over time in the watershed. Furthermore, the occurrence of potentially pathogenic E. coli strains in the drinking water intakes highlights the risk to human health associated with direct and indirect consumption of untreated surface water.

  6. 29 CFR 1920.2 - Variances.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 29 Labor 7 2011-07-01 2011-07-01 false Variances. 1920.2 Section 1920.2 Labor Regulations Relating to Labor (Continued) OCCUPATIONAL SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR (CONTINUED...' COMPENSATION ACT § 1920.2 Variances. (a) Variances from standards in parts 1915 through 1918 of this...

  7. Estimation of Variance Components Using Computer Packages.

    ERIC Educational Resources Information Center

    Chastain, Robert L.; Willson, Victor L.

    Generalizability theory is based upon analysis of variance (ANOVA) and requires estimation of variance components for the ANOVA design under consideration in order to compute either G (Generalizability) or D (Decision) coefficients. Estimation of variance components has a number of alternative methods available using SAS, BMDP, and ad hoc…

  8. 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...

  9. 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 ...

  10. 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...

  11. Increasing selection response by Bayesian modeling of heterogeneous environmental variances

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Heterogeneity of environmental variance among genotypes reduces selection response because genotypes with higher variance are more likely to be selected than low-variance genotypes. Modeling heterogeneous variances to obtain weighted means corrected for heterogeneous variances is difficult in likel...

  12. Cosmic Variance in the Nanohertz Gravitational Wave Background

    NASA Astrophysics Data System (ADS)

    Roebber, Elinore; Holder, Gilbert; Holz, Daniel E.; Warren, Michael

    2016-03-01

    We use large N-body simulations and empirical scaling relations between dark matter halos, galaxies, and supermassive black holes (SMBBHs) to estimate the formation rates of SMBBH binaries and the resulting low-frequency stochastic gravitational wave background (GWB). We find this GWB to be relatively insensitive (≲ 10%) to cosmological parameters, with only slight variation between wmap5 and Planck cosmologies. We find that uncertainty in the astrophysical scaling relations changes the amplitude of the GWB by a factor of ∼2. Current observational limits are already constraining this predicted range of models. We investigate the Poisson variance in the amplitude of the GWB for randomly generated populations of SMBBHs, finding a scatter of order unity per frequency bin below 10 nHz, and increasing to a factor of ∼10 near 100 nHz. This variance is a result of the rarity of the most massive binaries, which dominate the signal, and acts as a fundamental uncertainty on the amplitude of the underlying power law spectrum. This Poisson uncertainty dominates at ≳ 20 nHz, while at lower frequencies the dominant uncertainty is related to our poor understanding of the astrophysical scaling relations, although very low frequencies may be dominated by uncertainties related to the final parsec problem and the processes which drive binaries to the gravitational wave dominated regime. Cosmological effects are negligible at all frequencies.

  13. Genetic and Environmental Stability of Neuroticism From Adolescence to Adulthood.

    PubMed

    Nivard, Michel G; Middeldorp, Christel M; Dolan, Conor V; Boomsma, Dorret I

    2015-12-01

    Longitudinal studies of neuroticism have shown that, on average, neuroticism scores decrease from adolescence to adulthood. The heritability of neuroticism is estimated between 0.30 and 0.60 and does not seem to vary greatly as a function of age. Shared environmental effects are rarely reported. Less is known about the role of genetic and environmental influences on the rank order stability of neuroticism in the period from adolescence to adulthood. We studied the stability of neuroticism in a cohort sequential (classical) twin design, from adolescence (age 14 years) to young adulthood (age 32 years). A genetic simplex model that was fitted to the longitudinal neuroticism data showed that the genetic stability of neuroticism was relatively high (genetic correlations between adjacent age bins >0.9), and increased from adolescence to adulthood. Environmental stability was appreciably lower (environmental correlations between adjacent age bins were between 0.3 and 0.6). This low stability was largely due to age-specific environmental variance, which was dominated by measurement error. This attenuated the age-to-age environmental correlations. We constructed an environmental covariance matrix corrected for this error, under the strong assumption that all age-specific environmental variance is error variance. The environmental (co)variance matrix corrected for attenuation revealed highly stable environmental influences on neuroticism (correlations between adjacent age bins were between 0.7 and 0.9). Our results indicate that both genetic and environmental influences have enduring effects on individual differences in neuroticism.

  14. Restricted sample variance reduces generalizability.

    PubMed

    Lakes, Kimberley D

    2013-06-01

    One factor that affects the reliability of observed scores is restriction of range on the construct measured for a particular group of study participants. This study illustrates how researchers can use generalizability theory to evaluate the impact of restriction of range in particular sample characteristics on the generalizability of test scores and to estimate how changes in measurement design could improve the generalizability of the test scores. An observer-rated measure of child self-regulation (Response to Challenge Scale; Lakes, 2011) is used to examine scores for 198 children (Grades K through 5) within the generalizability theory (GT) framework. The generalizability of ratings within relatively developmentally homogeneous samples is examined and illustrates the effect of reduced variance among ratees on generalizability. Forecasts for g coefficients of various D study designs demonstrate how higher generalizability could be achieved by increasing the number of raters or items. In summary, the research presented illustrates the importance of and procedures for evaluating the generalizability of a set of scores in a particular research context. PMID:23205627

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

    PubMed

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

    2016-03-01

    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.

  16. 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

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

    PubMed

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

    2016-03-01

    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

  18. Multi-objective optimization of discrete time-cost tradeoff problem in project networks using non-dominated sorting genetic algorithm

    NASA Astrophysics Data System (ADS)

    Shahriari, Mohammadreza

    2016-03-01

    The time-cost tradeoff problem is one of the most important and applicable problems in project scheduling area. There are many factors that force the mangers to crash the time. This factor could be early utilization, early commissioning and operation, improving the project cash flow, avoiding unfavorable weather conditions, compensating the delays, and so on. Since there is a need to allocate extra resources to short the finishing time of project and the project managers are intended to spend the lowest possible amount of money and achieve the maximum crashing time, as a result, both direct and indirect costs will be influenced in the project, and here, we are facing into the time value of money. It means that when we crash the starting activities in a project, the extra investment will be tied in until the end date of the project; however, when we crash the final activities, the extra investment will be tied in for a much shorter period. This study is presenting a two-objective mathematical model for balancing compressing the project time with activities delay to prepare a suitable tool for decision makers caught in available facilities and due to the time of projects. Also drawing the scheduling problem to real world conditions by considering nonlinear objective function and the time value of money are considered. The presented problem was solved using NSGA-II, and the effect of time compressing reports on the non-dominant set.

  19. Combining Study Outcome Measures Using Dominance Adjusted Weights

    ERIC Educational Resources Information Center

    Makambi, Kepher H.; Lu, Wenxin

    2013-01-01

    Weighting of studies in meta-analysis is usually implemented by using the estimated inverse variances of treatment effect estimates. However, there is a possibility of one study dominating other studies in the estimation process by taking on a weight that is above some upper limit. We implement an estimator of the heterogeneity variance that takes…

  20. Multi-objective optimization of combustion, performance and emission parameters in a jatropha biodiesel engine using Non-dominated sorting genetic algorithm-II

    NASA Astrophysics Data System (ADS)

    Dhingra, Sunil; Bhushan, Gian; Dubey, Kashyap Kumar

    2014-03-01

    The present work studies and identifies the different variables that affect the output parameters involved in a single cylinder direct injection compression ignition (CI) engine using jatropha biodiesel. Response surface methodology based on Central composite design (CCD) is used to design the experiments. Mathematical models are developed for combustion parameters (Brake specific fuel consumption (BSFC) and peak cylinder pressure (Pmax)), performance parameter brake thermal efficiency (BTE) and emission parameters (CO, NO x , unburnt HC and smoke) using regression techniques. These regression equations are further utilized for simultaneous optimization of combustion (BSFC, Pmax), performance (BTE) and emission (CO, NO x , HC, smoke) parameters. As the objective is to maximize BTE and minimize BSFC, Pmax, CO, NO x , HC, smoke, a multiobjective optimization problem is formulated. Nondominated sorting genetic algorithm-II is used in predicting the Pareto optimal sets of solution. Experiments are performed at suitable optimal solutions for predicting the combustion, performance and emission parameters to check the adequacy of the proposed model. The Pareto optimal sets of solution can be used as guidelines for the end users to select optimal combination of engine output and emission parameters depending upon their own requirements.

  1. Coupling Genetic and Chemical Microbiome Profiling Reveals Heterogeneity of Archaeome and Bacteriome in Subsurface Biofilms That Are Dominated by the Same Archaeal Species

    PubMed Central

    Holman, Hoi-Ying N.; DeSantis, Todd Z.; Wanner, Gerhard; Andersen, Gary L.; Perras, Alexandra K.; Meck, Sandra; Völkel, Jörg; Bechtel, Hans A.; Wirth, Reinhard; Moissl-Eichinger, Christine

    2014-01-01

    Earth harbors an enormous portion of subsurface microbial life, whose microbiome flux across geographical locations remains mainly unexplored due to difficult access to samples. Here, we investigated the microbiome relatedness of subsurface biofilms of two sulfidic springs in southeast Germany that have similar physical and chemical parameters and are fed by one deep groundwater current. Due to their unique hydrogeological setting these springs provide accessible windows to subsurface biofilms dominated by the same uncultivated archaeal species, called SM1 Euryarchaeon. Comparative analysis of infrared imaging spectra demonstrated great variations in archaeal membrane composition between biofilms of the two springs, suggesting different SM1 euryarchaeal strains of the same species at both aquifer outlets. This strain variation was supported by ultrastructural and metagenomic analyses of the archaeal biofilms, which included intergenic spacer region sequencing of the rRNA gene operon. At 16S rRNA gene level, PhyloChip G3 DNA microarray detected similar biofilm communities for archaea, but site-specific communities for bacteria. Both biofilms showed an enrichment of different deltaproteobacterial operational taxonomic units, whose families were, however, congruent as were their lipid spectra. Consequently, the function of the major proportion of the bacteriome appeared to be conserved across the geographic locations studied, which was confirmed by dsrB-directed quantitative PCR. Consequently, microbiome differences of these subsurface biofilms exist at subtle nuances for archaea (strain level variation) and at higher taxonomic levels for predominant bacteria without a substantial perturbation in bacteriome function. The results of this communication provide deep insight into the dynamics of subsurface microbial life and warrant its future investigation with regard to metabolic and genomic analyses. PMID:24971452

  2. Coupling genetic and chemical microbiome profiling reveals heterogeneity of archaeome and bacteriome in subsurface biofilms that are dominated by the same archaeal species.

    PubMed

    Probst, Alexander J; Birarda, Giovanni; Holman, Hoi-Ying N; DeSantis, Todd Z; Wanner, Gerhard; Andersen, Gary L; Perras, Alexandra K; Meck, Sandra; Völkel, Jörg; Bechtel, Hans A; Wirth, Reinhard; Moissl-Eichinger, Christine

    2014-01-01

    Earth harbors an enormous portion of subsurface microbial life, whose microbiome flux across geographical locations remains mainly unexplored due to difficult access to samples. Here, we investigated the microbiome relatedness of subsurface biofilms of two sulfidic springs in southeast Germany that have similar physical and chemical parameters and are fed by one deep groundwater current. Due to their unique hydrogeological setting these springs provide accessible windows to subsurface biofilms dominated by the same uncultivated archaeal species, called SM1 Euryarchaeon. Comparative analysis of infrared imaging spectra demonstrated great variations in archaeal membrane composition between biofilms of the two springs, suggesting different SM1 euryarchaeal strains of the same species at both aquifer outlets. This strain variation was supported by ultrastructural and metagenomic analyses of the archaeal biofilms, which included intergenic spacer region sequencing of the rRNA gene operon. At 16S rRNA gene level, PhyloChip G3 DNA microarray detected similar biofilm communities for archaea, but site-specific communities for bacteria. Both biofilms showed an enrichment of different deltaproteobacterial operational taxonomic units, whose families were, however, congruent as were their lipid spectra. Consequently, the function of the major proportion of the bacteriome appeared to be conserved across the geographic locations studied, which was confirmed by dsrB-directed quantitative PCR. Consequently, microbiome differences of these subsurface biofilms exist at subtle nuances for archaea (strain level variation) and at higher taxonomic levels for predominant bacteria without a substantial perturbation in bacteriome function. The results of this communication provide deep insight into the dynamics of subsurface microbial life and warrant its future investigation with regard to metabolic and genomic analyses. PMID:24971452

  3. Coupling genetic and chemical microbiome profiling reveals heterogeneity of archaeome and bacteriome in subsurface biofilms that are dominated by the same archaeal species.

    PubMed

    Probst, Alexander J; Birarda, Giovanni; Holman, Hoi-Ying N; DeSantis, Todd Z; Wanner, Gerhard; Andersen, Gary L; Perras, Alexandra K; Meck, Sandra; Völkel, Jörg; Bechtel, Hans A; Wirth, Reinhard; Moissl-Eichinger, Christine

    2014-01-01

    Earth harbors an enormous portion of subsurface microbial life, whose microbiome flux across geographical locations remains mainly unexplored due to difficult access to samples. Here, we investigated the microbiome relatedness of subsurface biofilms of two sulfidic springs in southeast Germany that have similar physical and chemical parameters and are fed by one deep groundwater current. Due to their unique hydrogeological setting these springs provide accessible windows to subsurface biofilms dominated by the same uncultivated archaeal species, called SM1 Euryarchaeon. Comparative analysis of infrared imaging spectra demonstrated great variations in archaeal membrane composition between biofilms of the two springs, suggesting different SM1 euryarchaeal strains of the same species at both aquifer outlets. This strain variation was supported by ultrastructural and metagenomic analyses of the archaeal biofilms, which included intergenic spacer region sequencing of the rRNA gene operon. At 16S rRNA gene level, PhyloChip G3 DNA microarray detected similar biofilm communities for archaea, but site-specific communities for bacteria. Both biofilms showed an enrichment of different deltaproteobacterial operational taxonomic units, whose families were, however, congruent as were their lipid spectra. Consequently, the function of the major proportion of the bacteriome appeared to be conserved across the geographic locations studied, which was confirmed by dsrB-directed quantitative PCR. Consequently, microbiome differences of these subsurface biofilms exist at subtle nuances for archaea (strain level variation) and at higher taxonomic levels for predominant bacteria without a substantial perturbation in bacteriome function. The results of this communication provide deep insight into the dynamics of subsurface microbial life and warrant its future investigation with regard to metabolic and genomic analyses.

  4. Morphological and Genetic Variation along a North-to-South Transect in Stipa purpurea, a Dominant Grass on the Qinghai-Tibetan Plateau: Implications for Response to Climate Change

    PubMed Central

    You, Jianling; Qi, Danhui; Zhou, Yin; Chen, Jiakuan; Song, Zhiping

    2016-01-01

    Estimating the potential of species to cope with rapid environmental climatic modifications is of vital importance for determining their future viability and conservation. The variation between existing populations along a climatic gradient may predict how a species will respond to future climate change. Stipa purpurea is a dominant grass species in the alpine steppe and meadow of the Qinghai-Tibetan Plateau (QTP). Ecological niche modelling was applied to S. purpurea, and its distribution was found to be most strongly correlated with the annual precipitation and the mean temperature of the warmest quarter. We established a north-to-south transect over 2000 km long on the QTP reflecting the gradients of temperature and precipitation, and then we estimated the morphological by sampling fruited tussocks and genetic divergence by using 11 microsatellite markers between 20 populations along the transect. Reproductive traits (the number of seeds and reproductive shoots), the reproductive-vegetative growth ratio and the length of roots in the S. purpurea populations varied significantly with climate variables. S. purpurea has high genetic diversity (He = 0.585), a large effective population size (Ne >1,000), and a considerable level of gene flow between populations. The S. purpurea populations have a mosaic genetic structure: some distant populations (over 1000 km apart) clustered genetically, whereas closer populations (< 100 km apart) had diverged significantly, suggesting local adaptation. Asymmetrical long-distance inter-population gene flow occurs along the sampling transect and might be mediated by seed dispersal via migratory herbivores, such as the chiru (Pantholops hodgsonii). These findings suggest that population performance variation and gene flow both facilitate the response of S. purpurea to climate change. PMID:27580056

  5. Morphological and Genetic Variation along a North-to-South Transect in Stipa purpurea, a Dominant Grass on the Qinghai-Tibetan Plateau: Implications for Response to Climate Change.

    PubMed

    Liu, Wensheng; Zhao, Yao; You, Jianling; Qi, Danhui; Zhou, Yin; Chen, Jiakuan; Song, Zhiping

    2016-01-01

    Estimating the potential of species to cope with rapid environmental climatic modifications is of vital importance for determining their future viability and conservation. The variation between existing populations along a climatic gradient may predict how a species will respond to future climate change. Stipa purpurea is a dominant grass species in the alpine steppe and meadow of the Qinghai-Tibetan Plateau (QTP). Ecological niche modelling was applied to S. purpurea, and its distribution was found to be most strongly correlated with the annual precipitation and the mean temperature of the warmest quarter. We established a north-to-south transect over 2000 km long on the QTP reflecting the gradients of temperature and precipitation, and then we estimated the morphological by sampling fruited tussocks and genetic divergence by using 11 microsatellite markers between 20 populations along the transect. Reproductive traits (the number of seeds and reproductive shoots), the reproductive-vegetative growth ratio and the length of roots in the S. purpurea populations varied significantly with climate variables. S. purpurea has high genetic diversity (He = 0.585), a large effective population size (Ne >1,000), and a considerable level of gene flow between populations. The S. purpurea populations have a mosaic genetic structure: some distant populations (over 1000 km apart) clustered genetically, whereas closer populations (< 100 km apart) had diverged significantly, suggesting local adaptation. Asymmetrical long-distance inter-population gene flow occurs along the sampling transect and might be mediated by seed dispersal via migratory herbivores, such as the chiru (Pantholops hodgsonii). These findings suggest that population performance variation and gene flow both facilitate the response of S. purpurea to climate change. PMID:27580056

  6. Morphological and Genetic Variation along a North-to-South Transect in Stipa purpurea, a Dominant Grass on the Qinghai-Tibetan Plateau: Implications for Response to Climate Change.

    PubMed

    Liu, Wensheng; Zhao, Yao; You, Jianling; Qi, Danhui; Zhou, Yin; Chen, Jiakuan; Song, Zhiping

    2016-01-01

    Estimating the potential of species to cope with rapid environmental climatic modifications is of vital importance for determining their future viability and conservation. The variation between existing populations along a climatic gradient may predict how a species will respond to future climate change. Stipa purpurea is a dominant grass species in the alpine steppe and meadow of the Qinghai-Tibetan Plateau (QTP). Ecological niche modelling was applied to S. purpurea, and its distribution was found to be most strongly correlated with the annual precipitation and the mean temperature of the warmest quarter. We established a north-to-south transect over 2000 km long on the QTP reflecting the gradients of temperature and precipitation, and then we estimated the morphological by sampling fruited tussocks and genetic divergence by using 11 microsatellite markers between 20 populations along the transect. Reproductive traits (the number of seeds and reproductive shoots), the reproductive-vegetative growth ratio and the length of roots in the S. purpurea populations varied significantly with climate variables. S. purpurea has high genetic diversity (He = 0.585), a large effective population size (Ne >1,000), and a considerable level of gene flow between populations. The S. purpurea populations have a mosaic genetic structure: some distant populations (over 1000 km apart) clustered genetically, whereas closer populations (< 100 km apart) had diverged significantly, suggesting local adaptation. Asymmetrical long-distance inter-population gene flow occurs along the sampling transect and might be mediated by seed dispersal via migratory herbivores, such as the chiru (Pantholops hodgsonii). These findings suggest that population performance variation and gene flow both facilitate the response of S. purpurea to climate change.

  7. 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.

  8. 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...

  9. 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...

  10. Multireader multicase variance analysis for binary data.

    PubMed

    Gallas, Brandon D; Pennello, Gene A; Myers, Kyle J

    2007-12-01

    Multireader multicase (MRMC) variance analysis has become widely utilized to analyze observer studies for which the summary measure is the area under the receiver operating characteristic (ROC) curve. We extend MRMC variance analysis to binary data and also to generic study designs in which every reader may not interpret every case. A subset of the fundamental moments central to MRMC variance analysis of the area under the ROC curve (AUC) is found to be required. Through multiple simulation configurations, we compare our unbiased variance estimates to naïve estimates across a range of study designs, average percent correct, and numbers of readers and cases.

  11. 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...

  12. 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...

  13. 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...

  14. Inheritance of dermatoglyphic asymmetry and diversity traits in twins based on factor: variance decomposition analysis.

    PubMed

    Karmakar, Bibha; Malkin, Ida; Kobyliansky, Eugene

    2013-06-01

    Dermatoglyphic asymmetry and diversity traits from a large number of twins (MZ and DZ) were analyzed based on principal factors to evaluate genetic effects and common familial environmental influences on twin data by the use of maximum likelihood-based Variance decomposition analysis. Sample consists of monozygotic (MZ) twins of two sexes (102 male pairs and 138 female pairs) and 120 pairs of dizygotic (DZ) female twins. All asymmetry (DA and FA) and diversity of dermatoglyphic traits were clearly separated into factors. These are perfectly corroborated with the earlier studies in different ethnic populations, which indicate a common biological validity perhaps exists of the underlying component structures of dermatoglyphic characters. Our heritability result in twins clearly showed that DA_F2 is inherited mostly in dominant type (28.0%) and FA_F1 is additive (60.7%), but no significant difference in sexes was observed for these factors. Inheritance is also very prominent in diversity Factor 1, which is exactly corroborated with our previous findings. The present results are similar with the earlier results of finger ridge count diversity in twin data, which suggested that finger ridge count diversity is under genetic control.

  15. Genetic studies: dominant lethal study, sex linked recessive lethal, ames mutagenicity, and heritable translocation test of thermal processed, frozen, electron irradiated, and gamma irradiated chicken. Final report Jun 76-Aug 83

    SciTech Connect

    Sullivan, D.; Lusskin, R.M.; Thomson, G.M.; Kuzdas, C.D.; Ronning, D.C.

    1983-01-01

    Four samples of chicken meat identified as the frozen control, thermally processed, gamma sterilized (5.9 Mrad), and electron sterilized (5.9 MeV), along with negative and positive controls, were evaluated for genetic activity. The samples were evaluated for ability to induce dominant lethal mutations in spermatid and spermatozoan stages of spermatogenesis in mice fed 35 percent chicken meat. The test meat samples were not observed to have an effect on the incidence of the dominant lethal mutations. However, the positive control failed to give a positive response. The meat samples were investigated for mutagenic activity employing Drosophila melanogaster in the sex linked recessive lethal test. The samples were determined to be nonmutagenic in this test and the positive control gave a significant response. Reduced production of offspring in cultures of Drosophila reared on gamma irradiated chicken which could not be overcome by the addition of vitamins was observed. Pre-incubation tests with and without added mutagens revealed that in no case was a positive result observed in the Ames test from chicken meat without an added mutagen. The manner in which chicken meat was processed had no effect upon the response to the Ames test. A heritable translocation test in mice failed to reveal any cytological evidence of translocation heterozygosity in any of the chicken-containing diets.

  16. [Genetics and genetic counseling].

    PubMed

    Izzi, Claudia; Liut, Francesca; Dallera, Nadia; Mazza, Cinzia; Magistroni, Riccardo; Savoldi, Gianfranco; Scolari, Francesco

    2016-01-01

    Autosomal Dominant Polycystic Kidney Disease (ADPKD) is the most frequent genetic disease, characterized by progressive development of bilateral renal cysts. Two causative genes have been identified: PKD1 and PKD2. ADPKD phenotype is highly variable. Typically, ADPKD is an adult onset disease. However, occasionally, ADPKD manifests as very early onset disease. The phenotypic variability of ADPKD can be explained at three genetic levels: genic, allelic and gene modifier effects. Recent advances in molecular screening for PKD gene mutations and the introduction of the new next generation sequencing (NGS)- based genotyping approach have generated considerable improvement regarding the knowledge of genetic basis of ADPKD. The purpose of this article is to provide a comprehensive review of the genetics of ADPKD, focusing on new insights in genotype-phenotype correlation and exploring novel clinical approach to genetic testing. Evaluation of these new genetic information requires a multidisciplinary approach involving a nephrologist and a clinical geneticist. PMID:27067213

  17. 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...

  18. Variance Design and Air Pollution Control

    ERIC Educational Resources Information Center

    Ferrar, Terry A.; Brownstein, Alan B.

    1975-01-01

    Air pollution control authorities were forced to relax air quality standards during the winter of 1972 by granting variances. This paper examines the institutional characteristics of these variance policies from an economic incentive standpoint, sets up desirable structural criteria for institutional design and arrives at policy guidelines for…

  19. 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…

  20. Save money by understanding variance and tolerancing.

    PubMed

    Stuart, K

    2007-01-01

    Manufacturing processes are inherently variable, which results in component and assembly variance. Unless process capability, variance and tolerancing are fully understood, incorrect design tolerances may be applied, which will lead to more expensive tooling, inflated production costs, high reject rates, product recalls and excessive warranty costs. A methodology is described for correctly allocating tolerances and performing appropriate analyses.

  1. 10 CFR 851.31 - Variance process.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... OF ENERGY WORKER SAFETY AND HEALTH PROGRAM Variances § 851.31 Variance process. (a) Application... that the contractor has taken to inform the affected workers of the application, which must include... application and specifying where a copy may be examined at the place or places where notices to workers...

  2. 10 CFR 851.31 - Variance process.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... OF ENERGY WORKER SAFETY AND HEALTH PROGRAM Variances § 851.31 Variance process. (a) Application... that the contractor has taken to inform the affected workers of the application, which must include... application and specifying where a copy may be examined at the place or places where notices to workers...

  3. 10 CFR 851.31 - Variance process.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... OF ENERGY WORKER SAFETY AND HEALTH PROGRAM Variances § 851.31 Variance process. (a) Application... that the contractor has taken to inform the affected workers of the application, which must include... application and specifying where a copy may be examined at the place or places where notices to workers...

  4. 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.

  5. 42 CFR 456.525 - Request for renewal of variance.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ..., and Variances for Hospitals and Mental Hospitals Ur Plan: Remote Facility Variances from Time... variance to the Administrator at least 30 days before the variance expires. (b) The renewal request...

  6. Gravity Wave Variances and Propagation Derived from AIRS Radiances

    NASA Technical Reports Server (NTRS)

    Gong, Jie; Wu, Dong L.; Eckermann, S. D.

    2012-01-01

    As the first gravity wave (GW) climatology study using nadir-viewing infrared sounders, 50 Atmospheric Infrared Sounder (AIRS) radiance channels are selected to estimate GW variances at pressure levels between 2-100 hPa. The GW variance for each scan in the cross-track direction is derived from radiance perturbations in the scan, independently of adjacent scans along the orbit. Since the scanning swaths are perpendicular to the satellite orbits, which are inclined meridionally at most latitudes, the zonal component of GW propagation can be inferred by differencing the variances derived between the westmost and the eastmost viewing angles. Consistent with previous GW studies using various satellite instruments, monthly mean AIRS variance shows large enhancements over meridionally oriented mountain ranges as well as some islands at winter hemisphere high latitudes. Enhanced wave activities are also found above tropical deep convective regions. GWs prefer to propagate westward above mountain ranges, and eastward above deep convection. AIRS 90 field-of-views (FOVs), ranging from +48 deg. to -48 deg. off nadir, can detect large-amplitude GWs with a phase velocity propagating preferentially at steep angles (e.g., those from orographic and convective sources). The annual cycle dominates the GW variances and the preferred propagation directions for all latitudes. Indication of a weak two-year variation in the tropics is found, which is presumably related to the Quasi-biennial oscillation (QBO). AIRS geometry makes its out-tracks capable of detecting GWs with vertical wavelengths substantially shorter than the thickness of instrument weighting functions. The novel discovery of AIRS capability of observing shallow inertia GWs will expand the potential of satellite GW remote sensing and provide further constraints on the GW drag parameterization schemes in the general circulation models (GCMs).

  7. Variance in disease risk: rural populations and genetic diversity.

    PubMed

    Jenkins, W D; Lipka, A E; Fogleman, A J; Delfino, K R; Malhi, R S; Hendricks, B

    2016-07-01

    Over 19% of the US population resides in rural areas, where studies of disease risk and disease outcomes are difficult to assess due to smaller populations and lower incidence. While some studies suggest rural disparities for different chronic diseases, the data are inconsistent across geography and definitions of rurality. We reviewed the literature to examine if local variations in population genomic diversity may plausibly explain inconsistencies in estimating disease risk. Many rural communities were founded over 150 years ago by small groups of ethnically and ancestrally similar families. These have since endured relative geographical isolation, similar to groups in other industrialized nations, perhaps resulting in founder effects impacting local disease susceptibility. Studies in Europe and Asia have found that observably different phenotypes may appear in isolated communities within 100 years, and that genomic variation can significantly vary over small geographical scales. Epidemiological studies utilizing common "rural" definitions may miss significant disease differences due to assumptions of risk homogeneity and misinterpretation of administrative definitions of rurality. Local genomic heterogeneity should be an important aspect of chronic disease epidemiology in rural areas, and it is important to consider for designing studies and interpreting results, enabling a better understanding of the heritable components of complex diseases. PMID:27334395

  8. 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.

  9. Genetic and environmental contributions to individual differences: the three major dimensions of personality.

    PubMed

    Eysenck, H J

    1990-03-01

    This article deals with the contribution of genetic and environmental factors to individual differences in the three major dimensions of personality (Psychoticism, Extraversion, and Neuroticism). Twin studies indicate, and family studies confirm within limits, the strong genetic determination of these and many other personality factors, additive genetic variance accounting for roughly half the total phenotypic variance. On the environmental side, shared family environment plays little or no part, all environmental effects being within-family. Assortative mating, important in the formation of social attitudes, has little impact on personality. Dominance may be important for Extraversion. Epistasis (emergenesis) may account for the comparative low values of dizygotic (DZ) twins' correlations. Evidence for differential heritability of traits is present, but not very strong. It is concluded that behavioral genetics forms a vital part of the psychological understanding of the causes of individual differences in personality.

  10. Genetics Home Reference: autosomal dominant hypocalcemia

    MedlinePlus

    ... hormone (hypoparathyroidism). This hormone is involved in the regulation of calcium levels in the blood. Abnormal levels ... that increase calcium can also disrupt the normal regulation of other molecules, such as phosphate and magnesium, ...

  11. Behavior Genetics and the Within-Person Variability of Daily Interpersonal Styles: The Heritability of Flux, Spin and Pulse

    PubMed Central

    Markey, Patrick M.; Racine, Sarah E.; Markey, Charlotte N.; Hopwood, Christopher J.; Keel, Pamela K.; Burt, S. Alexandra; Neale, Michael C.; Sisk, Cheryl L.; Boker, Steven M.; Klump, Kelly L.

    2014-01-01

    A classical twin study was used to estimate the magnitude of genetic and environmental influences on four measurements of within-person variability: dominance flux, warmth flux, spin and pulse. Flux refers to the variability of an individual’s interpersonal dominance and warmth. Spin measures changes in the tone of interpersonal styles and pulse measures changes in the intensity of interpersonal styles. Daily reports of interpersonal styles were collected from 494 same-sex female twins (142 monozygotic pairs and 105 dizygotic pairs) over 45 days. For dominance flux, warmth flux, and spin, genetic effects accounted for a larger proportion of variance (37%, 24%, and 30%, respectively) than shared environmental effects (14%, 13%, 0%, respectively), with the remaining variance due to the non-shared environment (62%, 50%, 70% respectively). Pulse appeared to be primarily influenced by the non-shared environment, although conclusions about the contribution of familial influences were difficult to draw from this study. PMID:25977748

  12. 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)

  13. 40 CFR 142.41 - Variance request.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... and evidence of the best available treatment technology and techniques. (2) Economic and legal factors... water in the case of an excessive rise in the contaminant level for which the variance is requested....

  14. 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...

  15. 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...

  16. 7 CFR 205.290 - Temporary variances.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... Agriculture Regulations of the Department of Agriculture (Continued) AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing Practices), DEPARTMENT OF AGRICULTURE (CONTINUED) ORGANIC FOODS PRODUCTION ACT... notify each production or handling operation it certifies to which the temporary variance applies....

  17. 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.

  18. 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 Business Credit and Assistance ECONOMIC DEVELOPMENT ADMINISTRATION, DEPARTMENT OF COMMERCE ECONOMIC... Federal, State and local law....

  19. 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...

  20. 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...

  1. 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...

  2. Variance Components in Discrete Force Production Tasks

    PubMed Central

    SKM, Varadhan; Zatsiorsky, Vladimir M.; Latash, Mark L.

    2010-01-01

    The study addresses the relationships between task parameters and two components of variance, “good” and “bad”, during multi-finger accurate force production. The variance components are defined in the space of commands to the fingers (finger modes) and refer to variance that does (“bad”) and does not (“good”) affect total force. Based on an earlier study of cyclic force production, we hypothesized that speeding-up an accurate force production task would be accompanied by a drop in the regression coefficient linking the “bad” variance and force rate such that variance of the total force remains largely unaffected. We also explored changes in parameters of anticipatory synergy adjustments with speeding-up the task. The subjects produced accurate ramps of total force over different times and in different directions (force-up and force-down) while pressing with the four fingers of the right hand on individual force sensors. The two variance components were quantified, and their normalized difference was used as an index of a total force stabilizing synergy. “Good” variance scaled linearly with force magnitude and did not depend on force rate. “Bad” variance scaled linearly with force rate within each task, and the scaling coefficient did not change across tasks with different ramp times. As a result, a drop in force ramp time was associated with an increase in total force variance, unlike the results of the study of cyclic tasks. The synergy index dropped 100-200 ms prior to the first visible signs of force change. The timing and magnitude of these anticipatory synergy adjustments did not depend on the ramp time. Analysis of the data within an earlier model has shown adjustments in the variance of a timing parameter, although these adjustments were not as pronounced as in the earlier study of cyclic force production. Overall, we observed qualitative differences between the discrete and cyclic force production tasks: Speeding-up the cyclic

  3. Evidence for Fisher's dominance theory: how many 'special cases'?

    PubMed

    Billiard, Sylvain; Castric, Vincent

    2011-11-01

    Dominance, its genetic basis and evolution has been at the heart of one of the most intense controversies in the history of genetics. For more than eighty years the existence of dominance modifiers, genetic elements controlling dominance-recessivity interactions, has been suggested as a theoretical possibility, but the modifier elements themselves have remained elusive. A recent study of the self-incompatibility locus in flowering plants provided the first empirical evidence for such genetic elements: small non-coding RNAs that control dominance-recessivity by mediating methylation of the promoter of the recessive allele. Theory has shown that several biological situations are favorable for the evolution of dominance modifiers. We argue that the elucidation of this mechanism of dominance opens up new research avenues that could lead to uncovering dominance modifiers in other genetic systems, such as genes controlling Batesian and Müllerian mimicry or host-parasite interactions, thereby shedding light on the generality of the proposed mechanism.

  4. Fitted Hanbury-Brown-Twiss radii versus space-time variances in flow-dominated models

    SciTech Connect

    Frodermann, Evan; Heinz, Ulrich; Lisa, Michael Annan

    2006-04-15

    The inability of otherwise successful dynamical models to reproduce the Hanbury-Brown-Twiss (HBT) radii extracted from two-particle correlations measured at the Relativistic Heavy Ion Collider (RHIC) is known as the RHIC HBT Puzzle. Most comparisons between models and experiment exploit the fact that for Gaussian sources the HBT radii agree with certain combinations of the space-time widths of the source that can be directly computed from the emission function without having to evaluate, at significant expense, the two-particle correlation function. We here study the validity of this approach for realistic emission function models, some of which exhibit significant deviations from simple Gaussian behavior. By Fourier transforming the emission function, we compute the two-particle correlation function, and fit it with a Gaussian to partially mimic the procedure used for measured correlation functions. We describe a novel algorithm to perform this Gaussian fit analytically. We find that for realistic hydrodynamic models the HBT radii extracted from this procedure agree better with the data than the values previously extracted from the space-time widths of the emission function. Although serious discrepancies between the calculated and the measured HBT radii remain, we show that a more apples-to-apples comparison of models with data can play an important role in any eventually successful theoretical description of RHIC HBT data.

  5. Fitted Hanbury-Brown Twiss radii versus space-time variances in flow-dominated models

    NASA Astrophysics Data System (ADS)

    Frodermann, Evan; Heinz, Ulrich; Lisa, Michael Annan

    2006-04-01

    The inability of otherwise successful dynamical models to reproduce the Hanbury-Brown Twiss (HBT) radii extracted from two-particle correlations measured at the Relativistic Heavy Ion Collider (RHIC) is known as the RHIC HBT Puzzle. Most comparisons between models and experiment exploit the fact that for Gaussian sources the HBT radii agree with certain combinations of the space-time widths of the source that can be directly computed from the emission function without having to evaluate, at significant expense, the two-particle correlation function. We here study the validity of this approach for realistic emission function models, some of which exhibit significant deviations from simple Gaussian behavior. By Fourier transforming the emission function, we compute the two-particle correlation function, and fit it with a Gaussian to partially mimic the procedure used for measured correlation functions. We describe a novel algorithm to perform this Gaussian fit analytically. We find that for realistic hydrodynamic models the HBT radii extracted from this procedure agree better with the data than the values previously extracted from the space-time widths of the emission function. Although serious discrepancies between the calculated and the measured HBT radii remain, we show that a more apples-to-apples comparison of models with data can play an important role in any eventually successful theoretical description of RHIC HBT data.

  6. Variance estimation for nucleotide substitution models.

    PubMed

    Chen, Weishan; Wang, Hsiuying

    2015-09-01

    The current variance estimators for most evolutionary models were derived when a nucleotide substitution number estimator was approximated with a simple first order Taylor expansion. In this study, we derive three variance estimators for the F81, F84, HKY85 and TN93 nucleotide substitution models, respectively. They are obtained using the second order Taylor expansion of the substitution number estimator, the first order Taylor expansion of a squared deviation and the second order Taylor expansion of a squared deviation, respectively. These variance estimators are compared with the existing variance estimator in terms of a simulation study. It shows that the variance estimator, which is derived using the second order Taylor expansion of a squared deviation, is more accurate than the other three estimators. In addition, we also compare these estimators with an estimator derived by the bootstrap method. The simulation shows that the performance of this bootstrap estimator is similar to the estimator derived by the second order Taylor expansion of a squared deviation. Since the latter one has an explicit form, it is more efficient than the bootstrap estimator.

  7. A noise variance estimation approach for CT

    NASA Astrophysics Data System (ADS)

    Shen, Le; Jin, Xin; Xing, Yuxiang

    2012-10-01

    The Poisson-like noise model has been widely used for noise suppression and image reconstruction in low dose computed tomography. Various noise estimation and suppression approaches have been developed and studied to enhance the image quality. Among them, the recently proposed generalized Anscombe transform (GAT) has been utilized to stabilize the variance of Poisson-Gaussian noise. In this paper, we present a variance estimation approach using GAT. After the transform, the projection data is denoised conventionally with an assumption that the noise variance is uniformly equals to 1. The difference of the original and the denoised projection is treated as pure noise and the global variance σ2 can be estimated from the residual difference. Thus, the final denoising step with the estimated σ2 is performed. The proposed approach is verified on a cone-beam CT system and demonstrated to obtain a more accurate estimation of the actual parameter. We also examine FBP algorithm with the two-step noise suppression in the projection domain using the estimated noise variance. Reconstruction results with simulated and practical projection data suggest that the presented approach could be effective in practical imaging applications.

  8. Polyclonal IgE increase after HgCl2 injections in BN and LEW rats: a genetic analysis.

    PubMed

    Sapin, C; Hirsch, F; Delaporte, J P; Bazin, H; Druet, P

    1984-01-01

    An autoimmune disease and a dramatic increase in total serum IgE concentration are observed in BN rats that are chronically injected with HgCl2. In contrast, LEW rats do not develop the characteristic glomerulonephritis and are very "low IgE responders". In this study, we examined the genetic control of total serum IgE increase after HgCl2 injection in F1 and F2 hybrids, in both backcrosses between LEW and BN rats, and in LEW.1N congenic rats. Genetic analysis was performed using peak IgE concentrations expressed as log microgram/ml. A high IgE phenotype was found to be dominant. Eighty-five percent of F2 variance was due to genetic factors (VG) while only 15% of this variance was caused by environmental factors (VE). From observations in F2 hybrids and backcrosses, estimations of additive variance (VA) and dominance variance (VD) were made following three different methods. Genetic control by about four loci is demonstrated. One of these genes is RT1-linked. This gene contributes to 25% of the phenotypic difference observed between BN and LEW rats. No correlation was found between the peak total IgE level and autoimmune disease based on IgG deposition in spleen and/or kidney.

  9. Scaling of the mean and variance of population dynamics under fluctuating regimes.

    PubMed

    Pertoldi, Cino; Faurby, S; Reed, D H; Knape, J; Björklund, M; Lundberg, P; Kaitala, V; Loeschcke, V; Bach, L A

    2014-12-01

    Theoretical ecologists have long sought to understand how the persistence of populations depends on the interactions between exogenous (biotic and abiotic) and endogenous (e.g., demographic and genetic) drivers of population dynamics. Recent work focuses on the autocorrelation structure of environmental perturbations and its effects on the persistence of populations. Accurate estimation of extinction times and especially determination of the mechanisms affecting extinction times is important for biodiversity conservation. Here we examine the interaction between environmental fluctuations and the scaling effect of the mean population size with its variance. We investigate how interactions between environmental and demographic stochasticity can affect the mean time to extinction, change optimal patch size dynamics, and how it can alter the often-assumed linear relationship between the census size and the effective population size. The importance of the correlation between environmental and demographic variation depends on the relative importance of the two types of variation. We found the correlation to be important when the two types of variation were approximately equal; however, the importance of the correlation diminishes as one source of variation dominates. The implications of these findings are discussed from a conservation and eco-evolutionary point of view.

  10. 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

  11. 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

  12. The social dominance paradox.

    PubMed

    Cook, Jennifer Louise; den Ouden, Hanneke E M; Heyes, Cecilia M; Cools, Roshan

    2014-12-01

    Dominant individuals report high levels of self-sufficiency, self-esteem, and authoritarianism. The lay stereotype suggests that such individuals ignore information from others, preferring to make their own choices. However, the nonhuman animal literature presents a conflicting view, suggesting that dominant individuals are avid social learners, whereas subordinates focus on learning from private experience. Whether dominant humans are best characterized by the lay stereotype or the animal view is currently unknown. Here, we present a "social dominance paradox": using self-report scales and computerized tasks, we demonstrate that socially dominant people explicitly value independence, but, paradoxically, in a complex decision-making task, they show an enhanced reliance (relative to subordinate individuals) on social learning. More specifically, socially dominant people employed a strategy of copying other agents when the agents' responses had a history of being correct. However, in humans, two subtypes of dominance have been identified: aggressive and social. Aggressively dominant individuals, who are as likely to "get their own way" as socially dominant individuals but who do so through the use of aggressive or Machiavellian tactics, did not use social information, even when it was beneficial to do so. This paper presents the first study of dominance and social learning in humans and challenges the lay stereotype in which all dominant individuals ignore others' views. The more subtle perspective we offer could have important implications for decision making in both the boardroom and the classroom. PMID:25454588

  13. 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.

  14. 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

  15. PSYCHOPATHIC PERSONALITY TRAITS IN MIDDLE-AGED MALE TWINS:A BEHAVIOR GENETIC INVESTIGATION

    PubMed Central

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

    2015-01-01

    Psychopathic personality is characterized by Interpersonal dominance, Impulsivity, sensation seeking, poor planning, and aggressiveness. Studies have shown that the Multidimensional Personality Question-naire (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

  16. Genetic variation, climate models and the ecological genetics of Larix occidentalis

    SciTech Connect

    Rehfeldt, G.E.

    1995-12-31

    Provenance tests of 138 populations of Larix occidentalis revealed genetic differentiation for eight variables describing growth, phenology, tolerance to spring frosts, effects of Meria laricis needle cast, and survival. Geographic variables accounted for as much as 34% of the variance among Rocky Mountain populations. Patterns of genetic variation were dominated by the effects of latitude and elevation, with populations from the north and from high elevations having the lowest growth potential, the least tolerance to the needle cast, and the lowest survival. However, the slope of the geographic clines was relatively flat. Populations in the same geographic area, for instance, need to be separated by about 500 m in elevation before genetic differentiation can be expected.

  17. 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.

  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, 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...

  20. 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...

  1. 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...

  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. Regression Calibration with Heteroscedastic Error Variance

    PubMed Central

    Spiegelman, Donna; Logan, Roger; Grove, Douglas

    2011-01-01

    The problem of covariate measurement error with heteroscedastic measurement error variance is considered. Standard regression calibration assumes that the measurement error has a homoscedastic measurement error variance. An estimator is proposed to correct regression coefficients for covariate measurement error with heteroscedastic variance. Point and interval estimates are derived. Validation data containing the gold standard must be available. This estimator is a closed-form correction of the uncorrected primary regression coefficients, which may be of logistic or Cox proportional hazards model form, and is closely related to the version of regression calibration developed by Rosner et al. (1990). The primary regression model can include multiple covariates measured without error. The use of these estimators is illustrated in two data sets, one taken from occupational epidemiology (the ACE study) and one taken from nutritional epidemiology (the Nurses’ Health Study). In both cases, although there was evidence of moderate heteroscedasticity, there was little difference in estimation or inference using this new procedure compared to standard regression calibration. It is shown theoretically that unless the relative risk is large or measurement error severe, standard regression calibration approximations will typically be adequate, even with moderate heteroscedasticity in the measurement error model variance. In a detailed simulation study, standard regression calibration performed either as well as or better than the new estimator. When the disease is rare and the errors normally distributed, or when measurement error is moderate, standard regression calibration remains the method of choice. PMID:22848187

  4. 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... whether a proposed structure or other regulated activity would adversely impact navigation, flood...

  5. 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... whether a proposed structure or other regulated activity would adversely impact navigation, flood...

  6. 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…

  7. Understanding gender variance in children and adolescents.

    PubMed

    Simons, Lisa K; Leibowitz, Scott F; Hidalgo, Marco A

    2014-06-01

    Gender variance is an umbrella term used to describe gender identity, expression, or behavior that falls outside of culturally defined norms associated with a specific gender. In recent years, growing media coverage has heightened public awareness about gender variance in childhood and adolescence, and an increasing number of referrals to clinics specializing in care for gender-variant youth have been reported in the United States. Gender-variant expression, behavior, and identity may present in childhood and adolescence in a number of ways, and youth with gender variance have unique health needs. For those experiencing gender dysphoria, or distress encountered by the discordance between biological sex and gender identity, puberty is often an exceptionally challenging time. Pediatric primary care providers may be families' first resource for education and support, and they play a critical role in supporting the health of youth with gender variance by screening for psychosocial problems and health risks, referring for gender-specific mental health and medical care, and providing ongoing advocacy and support. PMID:24972420

  8. Understanding gender variance in children and adolescents.

    PubMed

    Simons, Lisa K; Leibowitz, Scott F; Hidalgo, Marco A

    2014-06-01

    Gender variance is an umbrella term used to describe gender identity, expression, or behavior that falls outside of culturally defined norms associated with a specific gender. In recent years, growing media coverage has heightened public awareness about gender variance in childhood and adolescence, and an increasing number of referrals to clinics specializing in care for gender-variant youth have been reported in the United States. Gender-variant expression, behavior, and identity may present in childhood and adolescence in a number of ways, and youth with gender variance have unique health needs. For those experiencing gender dysphoria, or distress encountered by the discordance between biological sex and gender identity, puberty is often an exceptionally challenging time. Pediatric primary care providers may be families' first resource for education and support, and they play a critical role in supporting the health of youth with gender variance by screening for psychosocial problems and health risks, referring for gender-specific mental health and medical care, and providing ongoing advocacy and support.

  9. 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…

  10. 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.

  11. 29 CFR 1920.2 - Variances.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ...) or 6(d) of the Williams-Steiger Occupational Safety and Health Act of 1970 (29 U.S.C. 655). The... under the Williams-Steiger Occupational Safety and Health Act of 1970, and any variance from §§ 1910.13... from the standard under both the Longshoremen's and Harbor Workers' Compensation Act and the...

  12. 7 CFR 205.290 - Temporary variances.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 3 2014-01-01 2014-01-01 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...

  13. Number variance for arithmetic hyperbolic surfaces

    NASA Astrophysics Data System (ADS)

    Luo, W.; Sarnak, P.

    1994-03-01

    We prove that the number variance for the spectrum of an arithmetic surface is highly nonrigid in part of the universal range. In fact it is close to having a Poisson behavior. This fact was discovered numerically by Schmit, Bogomolny, Georgeot and Giannoni. It has its origin in the high degeneracy of the length spectrum, first observed by Selberg.

  14. 7 CFR 205.290 - Temporary variances.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 7 Agriculture 3 2012-01-01 2012-01-01 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...

  15. 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…

  16. 20 CFR 654.402 - Variances.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ...' 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... employment service complaint procedures set forth at §§ 658.421 (i) and (j), 658.422 and 658.423 of...

  17. 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..., construction, and use of scaffolds (61 FR 46026). In the preamble to the final rule, OSHA stated that it was... for tank scaffolds under the general provisions of the final rule (see 61 FR 46033). In this...

  18. INTERPRETING MAGNETIC VARIANCE ANISOTROPY MEASUREMENTS IN THE SOLAR WIND

    SciTech Connect

    TenBarge, J. M.; Klein, K. G.; Howes, G. G.; Podesta, J. J.

    2012-07-10

    The magnetic variance anisotropy (A{sub m}) of the solar wind has been used widely as a method to identify the nature of solar wind turbulent fluctuations; however, a thorough discussion of the meaning and interpretation of the A{sub m} has not appeared in the literature. This paper explores the implications and limitations of using the A{sub m} as a method for constraining the solar wind fluctuation mode composition and presents a more informative method for interpreting spacecraft data. The paper also compares predictions of the A{sub m} from linear theory to nonlinear turbulence simulations and solar wind measurements. In both cases, linear theory compares well and suggests that the solar wind for the interval studied is dominantly Alfvenic in the inertial and dissipation ranges to scales of k{rho}{sub i} {approx_equal} 5.

  19. Variance in saccadic eye movements reflects stable traits.

    PubMed

    Meyhöfer, Inga; Bertsch, Katja; Esser, Moritz; Ettinger, Ulrich

    2016-04-01

    Saccadic tasks are widely used to study cognitive processes, effects of pharmacological treatments, and mechanisms underlying psychiatric disorders. In genetic studies, it is assumed that saccadic endophenotypes are traits. While internal consistency and temporal stability of saccadic performance is high for most of the measures, the magnitude of underlying trait components has not been estimated, and influences of situational aspects and person by situation interactions have not been investigated. To do so, 68 healthy participants performed prosaccades, antisaccades, and memory-guided saccades on three occasions at weekly intervals at the same time of day. Latent state-trait modeling was applied to estimate the proportions of variance reflecting stable trait components, situational influences, and Person × Situation interaction effects. Mean variables for all saccadic tasks showed high to excellent reliabilities. Intraindividual standard deviations were found to be slightly less reliable. Importantly, an average of 60% of variance of a single measurement was explained by trans-situationally stable person effects, while situation aspects and interactions between person and situation were found to play a negligible role. We conclude that saccadic variables, in standard laboratory settings, represent highly reliable measures that are largely unaffected by situational influences. Extending previous reliability studies, these findings clearly demonstrate the trait-like nature of these measures and support their role as endophenotypes.

  20. 42 CFR 456.521 - Conditions for granting variance requests.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ..., and Variances for Hospitals and Mental Hospitals Ur Plan: Remote Facility Variances from Time... submits concurrently— (1) A request for the variance that documents to his satisfaction that the facility is unable to meet the time requirements for which the variance is requested; and (2) A revised...

  1. Variance Reduction Factor of Nuclear Data for Integral Neutronics Parameters

    SciTech Connect

    Chiba, G. Tsuji, M.; Narabayashi, T.

    2015-01-15

    We propose a new quantity, a variance reduction factor, to identify nuclear data for which further improvements are required to reduce uncertainties of target integral neutronics parameters. Important energy ranges can be also identified with this variance reduction factor. Variance reduction factors are calculated for several integral neutronics parameters. The usefulness of the variance reduction factors is demonstrated.

  2. Variant evolutionary trees under phenotypic variance.

    PubMed

    Nishimura, Kinya; Isoda, Yutaka

    2004-01-01

    Evolutionary branching, which is a coevolutionary phenomenon of the development of two or more distinctive traits from a single trait in a population, is the issue of recent studies on adaptive dynamics. In previous studies, it was revealed that trait variance is a minimum requirement for evolutionary branching, and that it does not play an important role in the formation of an evolutionary pattern of branching. Here we demonstrate that the trait evolution exhibits various evolutionary branching paths starting from an identical initial trait to different evolutional terminus traits as determined by only changing the assumption of trait variance. The key feature of this phenomenon is the topological configuration of equilibria and the initial point in the manifold of dimorphism from which dimorphic branches develop. This suggests that the existing monomorphic or polymorphic set in a population is not an unique inevitable consequence of an identical initial phenotype.

  3. Analysis of Variance of Multiply Imputed Data.

    PubMed

    van Ginkel, Joost R; Kroonenberg, Pieter M

    2014-01-01

    As a procedure for handling missing data, Multiple imputation consists of estimating the missing data multiple times to create several complete versions of an incomplete data set. All these data sets are analyzed by the same statistical procedure, and the results are pooled for interpretation. So far, no explicit rules for pooling F-tests of (repeated-measures) analysis of variance have been defined. In this paper we outline the appropriate procedure for the results of analysis of variance for multiply imputed data sets. It involves both reformulation of the ANOVA model as a regression model using effect coding of the predictors and applying already existing combination rules for regression models. The proposed procedure is illustrated using three example data sets. The pooled results of these three examples provide plausible F- and p-values.

  4. 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.

  5. 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.

  6. On the Distribution of the Mean and Variance of a Quantitative Trait under Mutation-Selection-Drift Balance

    PubMed Central

    Burger, R.; Lande, R.

    1994-01-01

    The distributions of the mean phenotype and of the genetic variance of a polygenic trait under a balance between mutation, stabilizing selection and genetic drift are investigated. This is done by stochastic simulations in which each individual and each gene are represented. The results are compared with theoretical predictions. Some aspects of the existing theories for the evolution of quantitative traits are discussed. The maintenance of genetic variance and the average dynamics of phenotypic evolution in finite populations (with N(e) < 1000) are generally simpler than those suggested by some recent deterministic theories for infinite populations. PMID:7851784

  7. 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.

  8. 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.

  9. Uses and abuses of analysis of variance.

    PubMed Central

    Evans, S J

    1983-01-01

    Analysis of variance is a term often quoted to explain the analysis of data in experiments and clinical trials. The relevance of its methodology to clinical trials is shown and an explanation of the principles of the technique is given. The assumptions necessary are examined and the problems caused by their violation are discussed. The dangers of misuse are given with some suggestions for alternative approaches. PMID:6347228

  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. Double decomposition: decomposing the variance in subcomponents of male extra-pair reproductive success.

    PubMed

    Losdat, Sylvain; Arcese, Peter; Reid, Jane M

    2015-09-01

    1. Extra-pair reproductive success (EPRS) is a key component of male fitness in socially monogamous systems and could cause selection on female extra-pair reproduction if extra-pair offspring (EPO) inherit high value for EPRS from their successful extra-pair fathers. However, EPRS is itself a composite trait that can be fully decomposed into subcomponents of variation, each of which can be further decomposed into genetic and environmental variances. However, such decompositions have not been implemented in wild populations, impeding evolutionary inference. 2. We first show that EPRS can be decomposed into the product of three life-history subcomponents: the number of broods available to a focal male to sire EPO, the male's probability of siring an EPO in an available brood and the number of offspring in available broods. This decomposition of EPRS facilitates estimation from field data because all subcomponents can be quantified from paternity data without need to quantify extra-pair matings. Our decomposition also highlights that the number of available broods, and hence population structure and demography, might contribute substantially to variance in male EPRS and fitness. 3. We then used 20 years of complete genetic paternity and pedigree data from wild song sparrows (Melospiza melodia) to partition variance in each of the three subcomponents of EPRS, and thereby estimate their additive genetic variance and heritability conditioned on effects of male coefficient of inbreeding, age and social status. 4. All three subcomponents of EPRS showed some degree of within-male repeatability, reflecting combined permanent environmental and genetic effects. Number of available broods and offspring per brood showed low additive genetic variances. The estimated additive genetic variance in extra-pair siring probability was larger, although the 95% credible interval still converged towards zero. Siring probability also showed inbreeding depression and increased with male age

  12. 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

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

    PubMed

    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.

  14. 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

  15. 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

  16. Genetic and statistical analyses of strong selection on polygenic traits: What, me normal?

    SciTech Connect

    Turelli, M.; Barton, N.H.

    1994-11-01

    We develop a general population genetic framework for analyzing selection on many loci, and apply it to strong truncation and disruptive selection on an additive polygenic trait. We first present statistical methods for analyzing the infinitesimal model, in which offspring breeding values are normally distributed around the mean of the parents, with fixed variance. The usual assumption of a Gaussian distribution of breeding values in the population gives remarkably accurate predictions for the mean and the variance, even when disruptive selection generates substantial deviations from normality. We then set out a general genetic analysis of selection and recombination. The population is represented by multilocus cumulants describing the distribution of haploid genotypes, and selection is described by the relation between mean fitness and these cumulants. We provide exact recursions in terms of generating functions for the effects of selection on non-central moments. The new cumulants that describe the next generation are computed from the non-central moments. Numerical multilocus results show that the standard Gaussian approximation gives accurate predictions for the dynamics of the mean and genetic variance in this limit. Even with intense truncation selection, linkage disequilibria of order three and higher never cause much deviation from normality. Thus, the empirical deviations frequently found between predicted and observed responses to artificial selection are not caused by linkage-disequilibrium-induced departures from normality. Disruptive selection can generate substantial four-way disequilibria, and hence kurtosis; but even then, the Gaussian assumption predicts the variance accurately. In contrast to the apparent simplicity of the infinitesimal limit, data suggest that changes in genetic variance after 10 or more generations of selection are likely to be dominated by allele frequency dynamics that depend on genetic details. 51 refs., 11 figs., 3 tabs.

  17. Variation and Genetic Structure in Platanus mexicana (Platanaceae) along Riparian Altitudinal Gradient

    PubMed Central

    Galván-Hernández, Dulce M.; Lozada-García, J. Armando; Flores-Estévez, Norma; Galindo-González, Jorge; Vázquez-Torres, S. Mario

    2015-01-01

    Platanus mexicana is a dominant arboreal species of riparian ecosystems. These ecosystems are associated with altitudinal gradients that can generate genetic differences in the species, especially in the extremes of the distribution. However, studies on the altitudinal effect on genetic variation to riparian species are scarce. In Mexico, the population of P. mexicana along the Colipa River (Veracruz State) grows below its reported minimum altitude range, possibly the lowest where this tree grows. This suggests that altitude might be an important factor in population genetics differentiation. We examined the genetic variation and population structuring at four sites with different altitudes (70, 200, 600 and 1700 m a.s.l.) using ten inter-simple sequence repeats (ISSR) markers. The highest value for Shannon index and Nei’s gene diversity was obtained at 1700 m a.s.l. (He = 0.27, Ne = 1.47, I = 0.42) and polymorphism reached the top value at the middle altitude (% p = 88.57). Analysis of molecular variance (AMOVA) and STRUCTURE analysis indicated intrapopulation genetic differentiation. The arithmetic average (UPGMA) dendrogram identified 70 m a.s.l. as the most genetically distant site. The genetic structuring resulted from limited gene flow and genetic drift. This is the first report of genetic variation in populations of P. mexicana in Mexico. This research highlights its importance as a dominant species, and its ecological and evolutionary implications in altitudinal gradients of riparian ecosystems. PMID:25607732

  18. Decomposing variation in male reproductive success: age-specific variances and covariances through extra-pair and within-pair reproduction.

    PubMed

    Lebigre, Christophe; Arcese, Peter; Reid, Jane M

    2013-07-01

    Age-specific variances and covariances in reproductive success shape the total variance in lifetime reproductive success (LRS), age-specific opportunities for selection, and population demographic variance and effective size. Age-specific (co)variances in reproductive success achieved through different reproductive routes must therefore be quantified to predict population, phenotypic and evolutionary dynamics in age-structured populations. While numerous studies have quantified age-specific variation in mean reproductive success, age-specific variances and covariances in reproductive success, and the contributions of different reproductive routes to these (co)variances, have not been comprehensively quantified in natural populations. We applied 'additive' and 'independent' methods of variance decomposition to complete data describing apparent (social) and realised (genetic) age-specific reproductive success across 11 cohorts of socially monogamous but genetically polygynandrous song sparrows (Melospiza melodia). We thereby quantified age-specific (co)variances in male within-pair and extra-pair reproductive success (WPRS and EPRS) and the contributions of these (co)variances to the total variances in age-specific reproductive success and LRS. 'Additive' decomposition showed that within-age and among-age (co)variances in WPRS across males aged 2-4 years contributed most to the total variance in LRS. Age-specific (co)variances in EPRS contributed relatively little. However, extra-pair reproduction altered age-specific variances in reproductive success relative to the social mating system, and hence altered the relative contributions of age-specific reproductive success to the total variance in LRS. 'Independent' decomposition showed that the (co)variances in age-specific WPRS, EPRS and total reproductive success, and the resulting opportunities for selection, varied substantially across males that survived to each age. Furthermore, extra-pair reproduction increased

  19. Variance partitioning of stream diatom, fish, and invertebrate indicators of biological condition

    USGS Publications Warehouse

    Zuellig, Robert E.; Carlisle, Daren M.; Meador, Michael R.; Potapova, Marina

    2012-01-01

    Stream indicators used to make assessments of biological condition are influenced by many possible sources of variability. To examine this issue, we used multiple-year and multiple-reach diatom, fish, and invertebrate data collected from 20 least-disturbed and 46 developed stream segments between 1993 and 2004 as part of the US Geological Survey National Water Quality Assessment Program. We used a variance-component model to summarize the relative and absolute magnitude of 4 variance components (among-site, among-year, site × year interaction, and residual) in indicator values (observed/expected ratio [O/E] and regional multimetric indices [MMI]) among assemblages and between basin types (least-disturbed and developed). We used multiple-reach samples to evaluate discordance in site assessments of biological condition caused by sampling variability. Overall, patterns in variance partitioning were similar among assemblages and basin types with one exception. Among-site variance dominated the relative contribution to the total variance (64–80% of total variance), residual variance (sampling variance) accounted for more variability (8–26%) than interaction variance (5–12%), and among-year variance was always negligible (0–0.2%). The exception to this general pattern was for invertebrates at least-disturbed sites where variability in O/E indicators was partitioned between among-site and residual (sampling) variance (among-site  =  36%, residual  =  64%). This pattern was not observed for fish and diatom indicators (O/E and regional MMI). We suspect that unexplained sampling variability is what largely remained after the invertebrate indicators (O/E predictive models) had accounted for environmental differences among least-disturbed sites. The influence of sampling variability on discordance of within-site assessments was assemblage or basin-type specific. Discordance among assessments was nearly 2× greater in developed basins (29–31%) than in least

  20. Autosomal dominant vitreoretinochoroidopathy (ADVIRC).

    PubMed Central

    Blair, N P; Goldberg, M F; Fishman, G A; Salzano, T

    1984-01-01

    We report the second family recognised to have autosomal dominant vitreoretinochoroidopathy. The clinical features were (1) autosomal dominant inheritance; (2) peripheral, coarse pigmentary degeneration of the fundus for 360 degrees, with a relatively discrete posterior border in the equatorial region (this finding may be pathognomonic); (3) superficial punctate yellowish-white opacities in the retina; (4) various vascular abnormalities; (5) breakdown of the blood-retinal barrier; (6) retinal neovascularisation; (7) vitreous abnormalities; and (8) choroidal atrophy. Visual reduction was mainly due to macular oedema or vitreous haemorrhage. Images PMID:6689931

  1. The influence of mean climate trends and climate variance on beaver survival and recruitment dynamics.

    PubMed

    Campbell, Ruairidh D; Nouvellet, Pierre; Newman, Chris; Macdonald, David W; Rosell, Frank

    2012-09-01

    Ecologists are increasingly aware of the importance of environmental variability in natural systems. Climate change is affecting both the mean and the variability in weather and, in particular, the effect of changes in variability is poorly understood. Organisms are subject to selection imposed by both the mean and the range of environmental variation experienced by their ancestors. Changes in the variability in a critical environmental factor may therefore have consequences for vital rates and population dynamics. Here, we examine ≥90-year trends in different components of climate (precipitation mean and coefficient of variation (CV); temperature mean, seasonal amplitude and residual variance) and consider the effects of these components on survival and recruitment in a population of Eurasian beavers (n = 242) over 13 recent years. Within climatic data, no trends in precipitation were detected, but trends in all components of temperature were observed, with mean and residual variance increasing and seasonal amplitude decreasing over time. A higher survival rate was linked (in order of influence based on Akaike weights) to lower precipitation CV (kits, juveniles and dominant adults), lower residual variance of temperature (dominant adults) and lower mean precipitation (kits and juveniles). No significant effects were found on the survival of nondominant adults, although the sample size for this category was low. Greater recruitment was linked (in order of influence) to higher seasonal amplitude of temperature, lower mean precipitation, lower residual variance in temperature and higher precipitation CV. Both climate means and variance, thus proved significant to population dynamics; although, overall, components describing variance were more influential than those describing mean values. That environmental variation proves significant to a generalist, wide-ranging species, at the slow end of the slow-fast continuum of life histories, has broad implications for

  2. Boson dominance in nuclei

    SciTech Connect

    Palumbo, Fabrizio

    2005-07-01

    We present a new method of bosonization of fermion systems applicable when the partition function is dominated by composite bosons. By restricting the partition function to such states, we obtain a Euclidean bosonic action from which we derive the Hamiltonian. Such a procedure respects all the fermion symmetries, particularly the fermion number conservation, and provides a boson mapping of all fermion operators.

  3. Iron dominated magnets

    SciTech Connect

    Fischer, G.E.

    1985-07-01

    These two lectures on iron dominated magnets are meant for the student of accelerator science and contain general treatments of the subjects design and construction. The material is arranged in the categories: General Concepts and Cost Considerations, Profile Configuration and Harmonics, Magnetic Measurements, a few examples of ''special magnets'' and Materials and Practices. Extensive literature is provided.

  4. Apical Dominance in Plants

    ERIC Educational Resources Information Center

    Tucker, D. J.

    1974-01-01

    Describes a tentative hypothesis for the control of plant branching (apical dominance). Explores the mechanism by which apical buds inhibit the growth of axillary buds on the same shoot. Presents an up-to-date picture of the problem and gives economic implications of the study. (BR)

  5. Traditional Risk Factors are Not Major Contributors to the Variance in Carotid Intima-Media Thickness

    PubMed Central

    Rundek, Tatjana; Blanton, Susan H.; Bartels, Susanne; Dong, Chuanhui; Raval, Ami; Demmer, Ryan T.; Cabral, Digna; Elkind, Mitchell S.V.; Sacco, Ralph L.; Desvarieux, Moise

    2013-01-01

    Background and Purpose Carotid Intima-Media Thickness (cIMT) was a widely accepted ultrasound marker of subclinical atherosclerosis in the past. Although traditional risk factors may explain approximately 50% of the variance in plaque burden, they may not explain such a high proportion of the variance in IMT, especially when measured in plaque free-locations. We aimed this study to identify individuals with cIMT unexplained by traditional risk factors for future environmental and genetic research. Methods As part of the Northern Manhattan Study, 1,790 stroke-free individuals (mean age 69±9; 60% women; 61% Hispanic, 19% black, 18% white) were assessed for cIMT using B-mode carotid ultrasound. Multiple linear regression models were evaluated: (1) incorporating pre-specified traditional risk factors; and (2) including less traditional factors, such as inflammation biomarkers, adiponectin, homocysteine and kidney function. Standardized cIMT residual scores were constructed to select individuals with unexplained cIMT. Results Mean total cIMT was 0.92±0.09 mm. The traditional model explained 11% of the variance in cIMT. Age (7%), male sex (3%), glucose (<1%), pack years of smoking (<1%), and LDL-cholesterol (<1%) were significant contributing factors. The model including inflammatory biomarkers explained 16% of the variance in cIMT. Adiponectin was the only additional significant contributor to the variance in cIMT. We identified 358 (20%) individuals with cIMT unexplained by the investigated risk factors. Conclusions Vascular risk factors explain only a small proportion of variance in cIMT. Identification of novel genetic and environmental factors underlying unexplained subclinical atherosclerosis is of outmost importance for future effective prevention of vascular disease. PMID:23704105

  6. Modeling loblolly pine dominant height using airborne LiDAR

    NASA Astrophysics Data System (ADS)

    Maceyka, Andy

    The dominant height of 73 georeferenced field sample plots were modeled from various canopy height metrics derived by means of a small-footprint laser scanning technology, known as light detection and ranging (or just LiDAR), over young and mature forest stands using regression analysis. LiDAR plot metrics were regressed against field measured dominant height using Best Subsets Regression to reduce the number of models. From those models, regression assumptions were evaluated to determine which model was actually the best. The best model included the 1st and 90th height percentiles as predictors and explained 95% of the variance in average dominant height.

  7. 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

  8. 42 CFR 456.522 - Content of request for variance.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... travel time between the remote facility and each facility listed in paragraph (e) of this section; (f..., and Variances for Hospitals and Mental Hospitals Ur Plan: Remote Facility Variances from Time... perform UR within the time requirements for which the variance is requested and its good faith efforts...

  9. 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...

  10. 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

  11. 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.

  12. Evolution of dominance mechanisms at a butterfly mimicry supergene

    PubMed Central

    Le Poul, Yann; Whibley, Annabel; Chouteau, Mathieu; Prunier, Florence; Llaurens, Violaine; Joron, Mathieu

    2014-01-01

    Genetic dominance in polymorphic loci may respond to selection; however, the evolution of dominance in complex traits remains a puzzle. We analyse dominance at a wing-patterning supergene controlling local mimicry polymorphism in the butterfly Heliconius numata. Supergene alleles are associated with chromosomal inversion polymorphism, defining ancestral versus derived alleles. Using controlled crosses and the new procedure, Colour Pattern Modelling, allowing whole-wing pattern comparisons, we estimate dominance coefficients between alleles. Here we show strict dominance in sympatry favouring mimicry and inconsistent dominance throughout the wing between alleles from distant populations. Furthermore, dominance among derived alleles is uncoordinated across wing-pattern elements, producing mosaic heterozygous patterns determined by a hierarchy in colour expression. By contrast, heterozygotes with an ancestral allele show complete, coordinated dominance of the derived allele, independently of colours. Therefore, distinct dominance mechanisms have evolved in association with supergene inversions, in response to strong selection on mimicry polymorphism. PMID:25429605

  13. 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

  14. 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.

  15. Dominating Biological Networks

    PubMed Central

    Milenković, Tijana; Memišević, Vesna; Bonato, Anthony; Pržulj, Nataša

    2011-01-01

    Proteins are essential macromolecules of life that carry out most cellular processes. Since proteins aggregate to perform function, and since protein-protein interaction (PPI) networks model these aggregations, one would expect to uncover new biology from PPI network topology. Hence, using PPI networks to predict protein function and role of protein pathways in disease has received attention. A debate remains open about whether network properties of “biologically central (BC)” genes (i.e., their protein products), such as those involved in aging, cancer, infectious diseases, or signaling and drug-targeted pathways, exhibit some topological centrality compared to the rest of the proteins in the human PPI network. To help resolve this debate, we design new network-based approaches and apply them to get new insight into biological function and disease. We hypothesize that BC genes have a topologically central (TC) role in the human PPI network. We propose two different concepts of topological centrality. We design a new centrality measure to capture complex wirings of proteins in the network that identifies as TC those proteins that reside in dense extended network neighborhoods. Also, we use the notion of domination and find dominating sets (DSs) in the PPI network, i.e., sets of proteins such that every protein is either in the DS or is a neighbor of the DS. Clearly, a DS has a TC role, as it enables efficient communication between different network parts. We find statistically significant enrichment in BC genes of TC nodes and outperform the existing methods indicating that genes involved in key biological processes occupy topologically complex and dense regions of the network and correspond to its “spine” that connects all other network parts and can thus pass cellular signals efficiently throughout the network. To our knowledge, this is the first study that explores domination in the context of PPI networks. PMID:21887225

  16. Thermophoretically Dominated Aerosol Coagulation

    NASA Astrophysics Data System (ADS)

    Rosner, Daniel E.; Arias-Zugasti, Manuel

    2011-01-01

    A theory of aerosol coagulation due to size-dependent thermophoresis is presented. This previously overlooked effect is important when local temperature gradients are large, the sol population is composed of particles of much greater thermal conductivity than the carrier gas, with mean diameters much greater than the prevailing gas mean free path, and an adequate “spread” in sizes (as in metallurgical mists or fumes). We illustrate this via a population-balance analysis of the evolution of an initially log-normal distribution when this mechanism dominates ordinary Brownian diffusion.

  17. 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

  18. Divergent clonal selection dominates medulloblastoma at recurrence.

    PubMed

    Morrissy, A Sorana; Garzia, Livia; Shih, David J H; Zuyderduyn, Scott; Huang, Xi; Skowron, Patryk; Remke, Marc; Cavalli, Florence M G; Ramaswamy, Vijay; Lindsay, Patricia E; Jelveh, Salomeh; Donovan, Laura K; Wang, Xin; Luu, Betty; Zayne, Kory; Li, Yisu; Mayoh, Chelsea; Thiessen, Nina; Mercier, Eloi; Mungall, Karen L; Ma, Yusanne; Tse, Kane; Zeng, Thomas; Shumansky, Karey; Roth, Andrew J L; Shah, Sohrab; Farooq, Hamza; Kijima, Noriyuki; Holgado, Borja L; Lee, John J Y; Matan-Lithwick, Stuart; Liu, Jessica; Mack, Stephen C; Manno, Alex; Michealraj, K A; Nor, Carolina; Peacock, John; Qin, Lei; Reimand, Juri; Rolider, Adi; Thompson, Yuan Y; Wu, Xiaochong; Pugh, Trevor; Ally, Adrian; Bilenky, Mikhail; Butterfield, Yaron S N; Carlsen, Rebecca; Cheng, Young; Chuah, Eric; Corbett, Richard D; Dhalla, Noreen; He, An; Lee, Darlene; Li, Haiyan I; Long, William; Mayo, Michael; Plettner, Patrick; Qian, Jenny Q; Schein, Jacqueline E; Tam, Angela; Wong, Tina; Birol, Inanc; Zhao, Yongjun; Faria, Claudia C; Pimentel, José; Nunes, Sofia; Shalaby, Tarek; Grotzer, Michael; Pollack, Ian F; Hamilton, Ronald L; Li, Xiao-Nan; Bendel, Anne E; Fults, Daniel W; Walter, Andrew W; Kumabe, Toshihiro; Tominaga, Teiji; Collins, V Peter; Cho, Yoon-Jae; Hoffman, Caitlin; Lyden, David; Wisoff, Jeffrey H; Garvin, James H; Stearns, Duncan S; Massimi, Luca; Schüller, Ulrich; Sterba, Jaroslav; Zitterbart, Karel; Puget, Stephanie; Ayrault, Olivier; Dunn, Sandra E; Tirapelli, Daniela P C; Carlotti, Carlos G; Wheeler, Helen; Hallahan, Andrew R; Ingram, Wendy; MacDonald, Tobey J; Olson, Jeffrey J; Van Meir, Erwin G; Lee, Ji-Yeoun; Wang, Kyu-Chang; Kim, Seung-Ki; Cho, Byung-Kyu; Pietsch, Torsten; Fleischhack, Gudrun; Tippelt, Stephan; Ra, Young Shin; Bailey, Simon; Lindsey, Janet C; Clifford, Steven C; Eberhart, Charles G; Cooper, Michael K; Packer, Roger J; Massimino, Maura; Garre, Maria Luisa; Bartels, Ute; Tabori, Uri; Hawkins, Cynthia E; Dirks, Peter; Bouffet, Eric; Rutka, James T; Wechsler-Reya, Robert J; Weiss, William A; Collier, Lara S; Dupuy, Adam J; Korshunov, Andrey; Jones, David T W; Kool, Marcel; Northcott, Paul A; Pfister, Stefan M; Largaespada, David A; Mungall, Andrew J; Moore, Richard A; Jabado, Nada; Bader, Gary D; Jones, Steven J M; Malkin, David; Marra, Marco A; Taylor, Michael D

    2016-01-21

    The development of targeted anti-cancer therapies through the study of cancer genomes is intended to increase survival rates and decrease treatment-related toxicity. We treated a transposon-driven, functional genomic mouse model of medulloblastoma with 'humanized' in vivo therapy (microneurosurgical tumour resection followed by multi-fractionated, image-guided radiotherapy). Genetic events in recurrent murine medulloblastoma exhibit a very poor overlap with those in matched murine diagnostic samples (<5%). Whole-genome sequencing of 33 pairs of human diagnostic and post-therapy medulloblastomas demonstrated substantial genetic divergence of the dominant clone after therapy (<12% diagnostic events were retained at recurrence). In both mice and humans, the dominant clone at recurrence arose through clonal selection of a pre-existing minor clone present at diagnosis. Targeted therapy is unlikely to be effective in the absence of the target, therefore our results offer a simple, proximal, and remediable explanation for the failure of prior clinical trials of targeted therapy.

  19. 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.

  20. 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

  1. Correcting an analysis of variance for clustering.

    PubMed

    Hedges, Larry V; Rhoads, Christopher H

    2011-02-01

    A great deal of educational and social data arises from cluster sampling designs where clusters involve schools, classrooms, or communities. A mistake that is sometimes encountered in the analysis of such data is to ignore the effect of clustering and analyse the data as if it were based on a simple random sample. This typically leads to an overstatement of the precision of results and too liberal conclusions about precision and statistical significance of mean differences. This paper gives simple corrections to the test statistics that would be computed in an analysis of variance if clustering were (incorrectly) ignored. The corrections are multiplicative factors depending on the total sample size, the cluster size, and the intraclass correlation structure. For example, the corrected F statistic has Fisher's F distribution with reduced degrees of freedom. The corrected statistic reduces to the F statistic computed by ignoring clustering when the intraclass correlations are zero. It reduces to the F statistic computed using cluster means when the intraclass correlations are unity, and it is in between otherwise. A similar adjustment to the usual statistic for testing a linear contrast among group means is described.

  2. Accounting for Variance in Hyperspectral Data Coming from Limitations of the Imaging System

    NASA Astrophysics Data System (ADS)

    Shurygin, B.; Shestakova, M.; Nikolenko, A.; Badasen, E.; Strakhov, P.

    2016-06-01

    Over the course of the past few years, a number of methods was developed to incorporate hyperspectral imaging specifics into generic data mining techniques, traditionally used for hyperspectral data processing. Projection pursuit methods embody the largest class of methods empoyed for hyperspectral image data reduction, however, they all have certain drawbacks making them either hard to use or inefficient. It has been shown that hyperspectral image (HSI) statistics tend to display "heavy tails" (Manolakis2003)(Theiler2005), rendering most of the projection pursuit methods hard to use. Taking into consideration the magnitude of described deviations of observed data PDFs from normal distribution, it is apparent that a priori knowledge of variance in data caused by the imaging system is to be employed in order to efficiently classify objects on HSIs (Kerr, 2015), especially in cases of wildly varying SNR. A number of attempts to describe this variance and compensating techniques has been made (Aiazzi2006), however, new data quality standards are not yet set and accounting for the detector response is made under large set of assumptions. Current paper addresses the issue of hyperspectral image classification in the context of different variance sources based on the knowledge of calibration curves (both spectral and radiometric) obtained for each pixel of imaging camera. A camera produced by ZAO NPO Lepton (Russia) was calibrated and used to obtain a test image. A priori known values of SNR and spectral channel cross-correlation were incorporated into calculating test statistics used in dimensionality reduction and feature extraction. Expectation-Maximization classification algorithm modification for non-Gaussian model as described by (Veracini2010) was further employed. The impact of calibration data coarsening by ignoring non-uniformities on false alarm rate was studied. Case study shows both regions of scene-dominated variance and sensor-dominated variance, leading

  3. Sources of variance in personality facets: a multiple-rater twin study of self-peer, peer-peer, and self-self (dis)agreement.

    PubMed

    Kandler, Christian; Riemann, Rainer; Spinath, Frank M; Angleitner, Alois

    2010-10-01

    This study considered the validity of the personality structure based on the Five-Factor Model using both self- and peer reports on twins' NEO-PI-R facets. Separating common from specific genetic variance in self- and peer reports, this study examined genetic substance of different trait levels and rater-specific perspectives relating to personality judgments. Data of 919 twin pairs were analyzed using a multiple-rater twin model to disentangle genetic and environmental effects on domain-level trait, facet-specific trait, and rater-specific variance. About two thirds of both the domain-level trait variance and the facet-specific trait variance was attributable to genetic factors. This suggests that the more personality is measured accurately, the better these measures reflect the genetic structure. Specific variance in self- and peer reports also showed modest to substantial genetic influence. This may indicate not only genetically influenced self-rater biases but also substance components specific for self- and peer raters' perspectives on traits actually measured.

  4. Autosomal dominant polycystic kidney disease diagnosed in utero. Review.

    PubMed

    Nowak, Magdalena; Huras, Hubert; Wiecheć, Marcin; Jach, Robert; Radoń-Pokracka, Małgorzata; Górecka, Joanna

    2016-01-01

    Autosomal dominant polycystic kidney disease (ADPKD) is one of most common inherited renal diseases. It is estimated that very early onset ADPKD affects even 2% patients. The purpose of this article is to provide a comprehensive review of genetics, prenatal diagnosis and prognosis in very early onset autosomal dominant polycystic kidney disease. PMID:27629138

  5. Genetic control of inflorescence in common bean.

    PubMed

    Guilherme, S R; Ramalho, M A P; de F B Abreu, A; Pereira, L A

    2014-12-04

    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.

  6. Role of dominant visibles in mutagenicity testing

    SciTech Connect

    Searle, A.G.; Beechey, C.

    1986-01-01

    Our results suggest that inclusion of growth retardation as one of the components of the dominant visible category will make this a useful end-point for mutational studies in which it is important to gauge the extent to which transmissible genetic damage of a particularly relevant kind is induced in mammals. These visibles are easily scored and the use of an automated weighing device would lessen subjectivity. In the present experiment with 5Gy + 5Gy spermatogonial X-irradiation (24h interval) 7309 offspring have been examined at weaning age and 23 heritable dominant visibles identified. These included 12 with growth retardation, one of which was mutant at the steel (S1) locus, as were 3-4 others of normal size. However, only 46 out of 112 offspring recorded as small were actually kept for genetic tests, while only 30 (65%) of these could be fully tested because of death or infertility in the others. Thus this experiment throws some light on the induction of presumptive dominant sub-lethals which survive until weaning age, a little-studied category. Twelve out of the 30 fully tested small mice (40%) proved to carry dominant visible mutations. If this proportion is applied to the total recorded as small then we can derive an overall total of about 45 mutations for growth retardation. It is hoped to determine the actual rate of induction of these by further work.

  7. Rings dominate western Gulf

    NASA Astrophysics Data System (ADS)

    Vidal L., Francisco V.; Vidal L., Victor M. V.; Molero, José María Pérez

    Surface and deep circulation of the central and western Gulf of Mexico is controlled by interactions of rings of water pinched from the gulf's Loop Current. The discovery was made by Mexican oceanographers who are preparing a full-color, 8-volume oceanographic atlas of the gulf.Anticyclonic warm-core rings pinch off the Loop Current at a rate of about one to two per year, the scientists of the Grupo de Estudios Oceanográficos of the Instituto de Investigaciones Eléctricas (GEO-IIE) found. The rings migrate west until they collide with the continental shelf break of the western gulf, almost always between 22° and 23°N latitude. On their westward travel they transfer angular momentum and vorticity to the surrounding water, generating cyclonic circulations and vortex pairs that completely dominate the entire surface and deep circulation of the central and western gulf.

  8. 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.

  9. 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

  10. 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

  11. 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.

  12. 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

  13. 40 CFR 190.11 - Variances for unusual operations.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... PROTECTION PROGRAMS ENVIRONMENTAL RADIATION PROTECTION STANDARDS FOR NUCLEAR POWER OPERATIONS Environmental Standards for the Uranium Fuel Cycle § 190.11 Variances for unusual operations. The standards specified...

  14. 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

  15. 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.

  16. The phenotypic variance gradient – a novel concept

    PubMed Central

    Pertoldi, Cino; Bundgaard, Jørgen; Loeschcke, Volker; Barker, James Stuart Flinton

    2014-01-01

    Evolutionary ecologists commonly use reaction norms, which show the range of phenotypes produced by a set of genotypes exposed to different environments, to quantify the degree of phenotypic variance and the magnitude of plasticity of morphometric and life-history traits. Significant differences among the values of the slopes of the reaction norms are interpreted as significant differences in phenotypic plasticity, whereas significant differences among phenotypic variances (variance or coefficient of variation) are interpreted as differences in the degree of developmental instability or canalization. We highlight some potential problems with this approach to quantifying phenotypic variance and suggest a novel and more informative way to plot reaction norms: namely “a plot of log (variance) on the y-axis versus log (mean) on the x-axis, with a reference line added”. This approach gives an immediate impression of how the degree of phenotypic variance varies across an environmental gradient, taking into account the consequences of the scaling effect of the variance with the mean. The evolutionary implications of the variation in the degree of phenotypic variance, which we call a “phenotypic variance gradient”, are discussed together with its potential interactions with variation in the degree of phenotypic plasticity and canalization. PMID:25540685

  17. The Neuro/PsyGRID calibration experiment: identifying sources of variance and bias in multicenter MRI studies.

    PubMed

    Suckling, John; Barnes, Anna; Job, Dominic; Brennan, David; Lymer, Katherine; Dazzan, Paola; Marques, Tiago Reis; MacKay, Clare; McKie, Shane; Williams, Steve R; Williams, Steven C R; Deakin, Bill; Lawrie, Stephen

    2012-02-01

    Calibration experiments precede multicenter trials to identify potential sources of variance and bias. In support of future imaging studies of mental health disorders and their treatment, the Neuro/PsyGRID consortium commissioned a calibration experiment to acquire functional and structural MRI from twelve healthy volunteers attending five centers on two occasions. Measures were derived of task activation from a working memory paradigm, fractal scaling (Hurst exponent) from resting fMRI, and grey matter distributions from T(1) -weighted sequences. At each intracerebral voxel a fixed-effects analysis of variance estimated components of variance corresponding to factors of center, subject, occasion, and within-occasion order, and interactions of center-by-occasion, subject-by-occasion, and center-by-subject, the latter (since there is no intervention) a surrogate of the expected variance of the treatment effect standard error across centers. A rank order test of between-center differences was indicative of crossover or noncrossover subject-by-center interactions. In general, factors of center, subject and error variance constituted >90% of the total variance, whereas occasion, order, and all interactions were generally <5%. Subject was the primary source of variance (70%-80%) for grey-matter, with error variance the dominant component for fMRI-derived measures. Spatially, variance was broadly homogenous with the exception of fractal scaling measures which delineated white matter, related to the flip angle of the EPI sequence. Maps of P values for the associated F-tests were also derived. Rank tests were highly significant indicating the order of measures across centers was preserved. In summary, center effects should be modeled at the voxel-level using existing and long-standing statistical recommendations.

  18. Identification of additive, dominant, and epistatic variation conferred by key genes in cellulose biosynthesis pathway in Populus tomentosa†.

    PubMed

    Du, Qingzhang; Tian, Jiaxing; Yang, Xiaohui; Pan, Wei; Xu, Baohua; Li, Bailian; Ingvarsson, Pär K; Zhang, Deqiang

    2015-02-01

    Economically important traits in many species generally show polygenic, quantitative inheritance. The components of genetic variation (additive, dominant and epistatic effects) of these traits conferred by multiple genes in shared biological pathways remain to be defined. Here, we investigated 11 full-length genes in cellulose biosynthesis, on 10 growth and wood-property traits, within a population of 460 unrelated Populus tomentosa individuals, via multi-gene association. To validate positive associations, we conducted single-marker analysis in a linkage population of 1,200 individuals. We identified 118, 121, and 43 associations (P< 0.01) corresponding to additive, dominant, and epistatic effects, respectively, with low to moderate proportions of phenotypic variance (R(2)). Epistatic interaction models uncovered a combination of three non-synonymous sites from three unique genes, representing a significant epistasis for diameter at breast height and stem volume. Single-marker analysis validated 61 associations (false discovery rate, Q ≤ 0.10), representing 38 SNPs from nine genes, and its average effect (R(2) = 3.8%) nearly 2-fold higher than that identified with multi-gene association, suggesting that multi-gene association can capture smaller individual variants. Moreover, a structural gene-gene network based on tissue-specific transcript abundances provides a better understanding of the multi-gene pathway affecting tree growth and lignocellulose biosynthesis. Our study highlights the importance of pathway-based multiple gene associations to uncover the nature of genetic variance for quantitative traits and may drive novel progress in molecular breeding.

  19. Analysis of variance of designed chromatographic data sets: The analysis of variance-target projection approach.

    PubMed

    Marini, Federico; de Beer, Dalene; Joubert, Elizabeth; Walczak, Beata

    2015-07-31

    Direct application of popular approaches, e.g., Principal Component Analysis (PCA) or Partial Least Squares (PLS) to chromatographic data originating from a well-designed experimental study including more than one factor is not recommended. In the case of a well-designed experiment involving two or more factors (crossed or nested), data are usually decomposed into the contributions associated with the studied factors (and with their interactions), and the individual effect matrices are then analyzed using, e.g., PCA, as in the case of ASCA (analysis of variance combined with simultaneous component analysis). As an alternative to the ASCA method, we propose the application of PLS followed by target projection (TP), which allows a one-factor representation of the model for each column in the design dummy matrix. PLS application follows after proper deflation of the experimental matrix, i.e., to what are called the residuals under the reduced ANOVA model. The proposed approach (ANOVA-TP) is well suited for the study of designed chromatographic data of complex samples. It allows testing of statistical significance of the studied effects, 'biomarker' identification, and enables straightforward visualization and accurate estimation of between- and within-class variance. The proposed approach has been successfully applied to a case study aimed at evaluating the effect of pasteurization on the concentrations of various phenolic constituents of rooibos tea of different quality grades and its outcomes have been compared to those of ASCA.

  20. Camera Calibration with Radial Variance Component Estimation

    NASA Astrophysics Data System (ADS)

    Mélykuti, B.; Kruck, E. J.

    2014-11-01

    Camera calibration plays a more and more important role in recent times. Beside real digital aerial survey cameras the photogrammetric market is dominated by a big number of non-metric digital cameras mounted on UAVs or other low-weight flying platforms. The in-flight calibration of those systems has a significant role to enhance the geometric accuracy of survey photos considerably. It is expected to have a better precision of photo measurements in the center of images then along the edges or in the corners. With statistical methods the accuracy of photo measurements in dependency of the distance of points from image center has been analyzed. This test provides a curve for the measurement precision as function of the photo radius. A high number of camera types have been tested with well penetrated point measurements in image space. The result of the tests led to a general consequence to show a functional connection between accuracy and radial distance and to give a method how to check and enhance the geometrical capability of the cameras in respect to these results.

  1. 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

  2. 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...

  3. An Analysis of Variance Framework for Matrix Sampling.

    ERIC Educational Resources Information Center

    Sirotnik, Kenneth

    Significant cost savings can be achieved with the use of matrix sampling in estimating population parameters from psychometric data. The statistical design is intuitively simple, using the framework of the two-way classification analysis of variance technique. For example, the mean and variance are derived from the performance of a certain grade…

  4. 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…

  5. 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…

  6. Conceptual Complexity and the Bias/Variance Tradeoff

    ERIC Educational Resources Information Center

    Briscoe, Erica; Feldman, Jacob

    2011-01-01

    In this paper we propose that the conventional dichotomy between exemplar-based and prototype-based models of concept learning is helpfully viewed as an instance of what is known in the statistical learning literature as the "bias/variance tradeoff". The bias/variance tradeoff can be thought of as a sliding scale that modulates how closely any…

  7. 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 Regulations Relating to Labor (Continued) OCCUPATIONAL SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR RULES OF PRACTICE FOR VARIANCES, LIMITATIONS, VARIATIONS, TOLERANCES, AND EXEMPTIONS UNDER THE...

  8. 41 CFR 50-204.1a - Variances.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... same circumstances in which variances may be granted under sections 6(b)(6)(A) or 6(d) of the Williams... the Williams-Steiger Occupational Safety and Health Act of 1970, and any variance from a standard... the Williams-Steiger Occupational Safety and Health Act of 1970. In accordance with the...

  9. 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...

  10. 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...

  11. 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...

  12. 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. 27.4 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...

  13. 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...

  14. Evaluation of Mean and Variance Integrals without Integration

    ERIC Educational Resources Information Center

    Joarder, A. H.; Omar, M. H.

    2007-01-01

    The mean and variance of some continuous distributions, in particular the exponentially decreasing probability distribution and the normal distribution, are considered. Since they involve integration by parts, many students do not feel comfortable. In this note, a technique is demonstrated for deriving mean and variance through differential…

  15. 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…

  16. 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)

  17. 40 CFR 141.4 - Variances and exemptions.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 24 2012-07-01 2012-07-01 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....

  18. 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....

  19. 40 CFR 141.4 - Variances and exemptions.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 24 2013-07-01 2013-07-01 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....

  20. 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.

  1. A Variance Explanation Paradox: When a Little Is a Lot.

    ERIC Educational Resources Information Center

    Abelson, Robert P.

    1985-01-01

    Argues that percent variance explanation is a misleading index of the influence of systematic factors in cases where there are processes by which individually tiny influences cumulate to produce meaningful outcomes. An example is the computation of percentage of variance in batting performance among major league baseball players. (Author/CB)

  2. On the Endogeneity of the Mean-Variance Efficient Frontier.

    ERIC Educational Resources Information Center

    Somerville, R. A.; O'Connell, Paul G. J.

    2002-01-01

    Explains that the endogeneity of the efficient frontier in the mean-variance model of portfolio selection is commonly obscured in portfolio selection literature and in widely used textbooks. Demonstrates endogeneity and discusses the impact of parameter changes on the mean-variance efficient frontier and on the beta coefficients of individual…

  3. Multiple mating but not recombination causes quantitative increase in offspring genetic diversity for varying genetic architectures.

    PubMed

    Rueppell, Olav; Meier, Stephen; Deutsch, Roland

    2012-01-01

    Explaining the evolution of sex and recombination is particularly intriguing for some species of eusocial insects because they display exceptionally high mating frequencies and genomic recombination rates. Explanations for both phenomena are based on the notion that both increase colony genetic diversity, with demonstrated benefits for colony disease resistance and division of labor. However, the relative contributions of mating number and recombination rate to colony genetic diversity have never been simultaneously assessed. Our study simulates colonies, assuming different mating numbers, recombination rates, and genetic architectures, to assess their worker genotypic diversity. The number of loci has a strong negative effect on genotypic diversity when the allelic effects are inversely scaled to locus number. In contrast, dominance, epistasis, lethal effects, or limiting the allelic diversity at each locus does not significantly affect the model outcomes. Mating number increases colony genotypic variance and lowers variation among colonies with quickly diminishing returns. Genomic recombination rate does not affect intra- and inter-colonial genotypic variance, regardless of mating frequency and genetic architecture. Recombination slightly increases the genotypic range of colonies and more strongly the number of workers with unique allele combinations across all loci. Overall, our study contradicts the argument that the exceptionally high recombination rates cause a quantitative increase in offspring genotypic diversity across one generation. Alternative explanations for the evolution of high recombination rates in social insects are therefore needed. Short-term benefits are central to most explanations of the evolution of multiple mating and high recombination rates in social insects but our results also apply to other species.

  4. 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

  5. Genetic and Statistical Analyses of Strong Selection on Polygenic Traits: What, Me Normal?

    PubMed Central

    Turelli, M.; Barton, N. H.

    1994-01-01

    We develop a general population genetic framework for analyzing selection on many loci, and apply it to strong truncation and disruptive selection on an additive polygenic trait. We first present statistical methods for analyzing the infinitesimal model, in which offspring breeding values are normally distributed around the mean of the parents, with fixed variance. These show that the usual assumption of a Gaussian distribution of breeding values in the population gives remarkably accurate predictions for the mean and the variance, even when disruptive selection generates substantial deviations from normality. We then set out a general genetic analysis of selection and recombination. The population is represented by multilocus cumulants describing the distribution of haploid genotypes, and selection is described by the relation between mean fitness and these cumulants. We provide exact recursions in terms of generating functions for the effects of selection on non-central moments. The effects of recombination are simply calculated as a weighted sum over all the permutations produced by meiosis. Finally, the new cumulants that describe the next generation are computed from the non-central moments. Although this scheme is applied here in detail only to selection on an additive trait, it is quite general. For arbitrary epistasis and linkage, we describe a consistent infinitesimal limit in which the short-term selection response is dominated by infinitesimal allele frequency changes and linkage disequilibria. Numerical multilocus results show that the standard Gaussian approximation gives accurate predictions for the dynamics of the mean and genetic variance in this limit. Even with intense truncation selection, linkage disequilibria of order three and higher never cause much deviation from normality. Thus, the empirical deviations frequently found between predicted and observed responses to artificial selection are not caused by linkage

  6. Molecular diagnosis of autosomal dominant polycystic kidney disease.

    PubMed

    Torra Balcells, R; Ars Criach, E

    2011-01-01

    Autosomal dominant polycystic kidney disease (ADPKD) is the most common inherited renal disorder. Its estimated prevalence is 1 per 800 individuals. ADPKD patients constitute 8% of the population on dialysis or kidney transplantation. The disease can be diagnosed using radiological or genetic procedures. Direct genetic diagnosis of the disease can now be performed in Spain; however, it is not an easy or cheap test. This is why every case should be considered individually to determine whether genetic testing is appropriate, and to determine which genetic test is most adequate. Genetic testing in ADPKD is of special interest for living donors and neonatal and sporadic cases. Genetic testing offers the chance of performing prenatal or pre-implantation testing of embryos in families with severe cases of the disease. Also, this will enable the disease to be treated, when specific treatment becomes available, in cases that would not be candidates for treatment without genetic confirmation.

  7. Population dynamics of a natural red deer population over 200 years detected via substantial changes of genetic variation.

    PubMed

    Hoffmann, Gunther Sebastian; Johannesen, Jes; Griebeler, Eva Maria

    2016-05-01

    Most large mammals have constantly been exposed to anthropogenic influence over decades or even centuries. Because of their long generation times and lack of sampling material, inferences of past population genetic dynamics, including anthropogenic impacts, have only relied on the analysis of the structure of extant populations. Here, we investigate for the first time the change in the genetic constitution of a natural red deer population over two centuries, using up to 200-year-old antlers (30 generations) stored in trophy collections. To the best of our knowledge, this is the oldest DNA source ever used for microsatellite population genetic analyses. We demonstrate that government policy and hunting laws may have strong impacts on populations that can lead to unexpectedly rapid changes in the genetic constitution of a large mammal population. A high ancestral individual polymorphism seen in an outbreeding population (1813-1861) was strongly reduced in descendants (1923-1940) during the mid-19th and early 20th century by genetic bottlenecks. Today (2011), individual polymorphism and variance among individuals is increasing in a constant-sized (managed) population. Differentiation was high among periods (F ST > ***); consequently, assignment tests assigned individuals to their own period with >85% probability. In contrast to the high variance observed at nuclear microsatellite loci, mtDNA (D-loop) was monomorphic through time, suggesting that male immigration dominates the genetic evolution in this population. PMID:27096075

  8. 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. 260.33 Section 260.33 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) SOLID WASTES... from classification as a solid waste, for variances to be classified as a boiler, or for...

  9. 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. 260.33 Section 260.33 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) SOLID WASTES... from classification as a solid waste, for variances to be classified as a boiler, or for...

  10. 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...

  11. 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...

  12. 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...

  13. Wavelet variance analysis for random fields on a regular lattice.

    PubMed

    Mondal, Debashis; Percival, Donald B

    2012-02-01

    There has been considerable recent interest in using wavelets to analyze time series and images that can be regarded as realizations of certain 1-D and 2-D stochastic processes on a regular lattice. Wavelets give rise to the concept of the wavelet variance (or wavelet power spectrum), which decomposes the variance of a stochastic process on a scale-by-scale basis. The wavelet variance has been applied to a variety of time series, and a statistical theory for estimators of this variance has been developed. While there have been applications of the wavelet variance in the 2-D context (in particular, in works by Unser in 1995 on wavelet-based texture analysis for images and by Lark and Webster in 2004 on analysis of soil properties), a formal statistical theory for such analysis has been lacking. In this paper, we develop the statistical theory by generalizing and extending some of the approaches developed for time series, thus leading to a large-sample theory for estimators of 2-D wavelet variances. We apply our theory to simulated data from Gaussian random fields with exponential covariances and from fractional Brownian surfaces. We demonstrate that the wavelet variance is potentially useful for texture discrimination. We also use our methodology to analyze images of four types of clouds observed over the southeast Pacific Ocean.

  14. 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.

  15. Genetic Diversity of Mycobacterium tuberculosis Isolates from Assam, India: Dominance of Beijing Family and Discovery of Two New Clades Related to CAS1_Delhi and EAI Family Based on Spoligotyping and MIRU-VNTR Typing.

    PubMed

    Devi, Kangjam Rekha; Bhutia, Rinchenla; Bhowmick, Shovonlal; Mukherjee, Kaustab; Mahanta, Jagadish; Narain, Kanwar

    2015-01-01

    Tuberculosis (TB) is one of the major public health concerns in Assam, a remote state located in the northeastern (NE) region of India. The present study was undertaken to explore the circulating genotypes of Mycobacterium tuberculosis complex (MTBC) in this region. A total of 189 MTBC strains were collected from smear positive pulmonary tuberculosis cases from different designated microscopy centres (DMC) from various localities of Assam. All MTBC isolates were cultured on Lowenstein-Jensen (LJ) media and subsequently genotyped using spoligotyping and 24-loci mycobacterial interspersed repetitive units-variable number of tandem repeats (MIRU-VNTR) typing. Spoligotyping of MTBC isolates revealed 89 distinct spoligo patterns. The most dominant MTBC strain belonged to Beijing lineage and was represented by 35.45% (n = 67) of total isolates, followed by MTBC strains belonging to Central Asian-Delhi (CAS/Delhi) lineage and East African Indian (EAI5) lineage. In addition, in the present study 43 unknown spoligo patterns were detected. The discriminatory power of spoligotyping was found to be 0.8637 based on Hunter Gaston Discriminatory Index (HGDI). On the other hand, 24-loci MIRU-VNTR typing revealed that out of total 189 MTBC isolates from Assam 185 (97.9%) isolates had unique MIRU-VNTR profiles and 4 isolates grouped into 2 clusters. Phylogenetic analysis of 67 Beijing isolates based on 24-loci MIRU-VNTR typing revealed that Beijing isolates from Assam represent two major groups, each comprising of several subgroups. Neighbour-Joining (NJ) phylogenetic tree analysis based on combined spoligotyping and 24-loci MIRU-VNTR data of 78 Non-Beijing isolates was carried out for strain lineage identification as implemented by MIRU-VNTRplus database. The important lineages of MTBC identified were CAS/CAS1_Delhi (41.02%, n = 78) and East-African-Indian (EAI, 33.33%). Interestingly, phylogenetic analysis of orphan (23.28%) MTBC spoligotypes revealed that majority of these orphan

  16. Genetic Diversity of Mycobacterium tuberculosis Isolates from Assam, India: Dominance of Beijing Family and Discovery of Two New Clades Related to CAS1_Delhi and EAI Family Based on Spoligotyping and MIRU-VNTR Typing.

    PubMed

    Devi, Kangjam Rekha; Bhutia, Rinchenla; Bhowmick, Shovonlal; Mukherjee, Kaustab; Mahanta, Jagadish; Narain, Kanwar

    2015-01-01

    Tuberculosis (TB) is one of the major public health concerns in Assam, a remote state located in the northeastern (NE) region of India. The present study was undertaken to explore the circulating genotypes of Mycobacterium tuberculosis complex (MTBC) in this region. A total of 189 MTBC strains were collected from smear positive pulmonary tuberculosis cases from different designated microscopy centres (DMC) from various localities of Assam. All MTBC isolates were cultured on Lowenstein-Jensen (LJ) media and subsequently genotyped using spoligotyping and 24-loci mycobacterial interspersed repetitive units-variable number of tandem repeats (MIRU-VNTR) typing. Spoligotyping of MTBC isolates revealed 89 distinct spoligo patterns. The most dominant MTBC strain belonged to Beijing lineage and was represented by 35.45% (n = 67) of total isolates, followed by MTBC strains belonging to Central Asian-Delhi (CAS/Delhi) lineage and East African Indian (EAI5) lineage. In addition, in the present study 43 unknown spoligo patterns were detected. The discriminatory power of spoligotyping was found to be 0.8637 based on Hunter Gaston Discriminatory Index (HGDI). On the other hand, 24-loci MIRU-VNTR typing revealed that out of total 189 MTBC isolates from Assam 185 (97.9%) isolates had unique MIRU-VNTR profiles and 4 isolates grouped into 2 clusters. Phylogenetic analysis of 67 Beijing isolates based on 24-loci MIRU-VNTR typing revealed that Beijing isolates from Assam represent two major groups, each comprising of several subgroups. Neighbour-Joining (NJ) phylogenetic tree analysis based on combined spoligotyping and 24-loci MIRU-VNTR data of 78 Non-Beijing isolates was carried out for strain lineage identification as implemented by MIRU-VNTRplus database. The important lineages of MTBC identified were CAS/CAS1_Delhi (41.02%, n = 78) and East-African-Indian (EAI, 33.33%). Interestingly, phylogenetic analysis of orphan (23.28%) MTBC spoligotypes revealed that majority of these orphan

  17. Finger Enslaving in the Dominant and Non-Dominant Hand

    PubMed Central

    Wilhelm, Luke A.; Martin, Joel R.; Latash, Mark L.; Zatsiorsky, Vladimir M.

    2014-01-01

    During single-finger force production, the non-instructed fingers unintentionally produce force (finger enslaving). In this study, enslaving effects were compared between the dominant and non-dominant hands. The test consisted of a series of maximum voluntary contractions with different finger combinations. Enslaving matrices were calculated by means of training an artificial neural network. The dominant hand was found to be stronger, but there was found to be no difference between the overall enslaving effects in the dominant and non-dominant hands. There was no correlation between the magnitude of finger enslaving and the performance in such tests as the Edinburgh Handedness Inventory, the Grooved Pegboard test, and the Jebsen-Taylor Hand Function test. Each one of those three tests showed a significant difference between the dominant and non-dominant hand performances. Eleven subjects were retested after two months, and it was found that enslaving effects did not fluctuate significantly between the two testing sessions. While the dominant and non-dominant hands are involved differently in everyday tasks, e.g. in writing or eating, this practice does not cause significant differences in enslaving between the hands. PMID:24360253

  18. Finger enslaving in the dominant and non-dominant hand.

    PubMed

    Wilhelm, Luke A; Martin, Joel R; Latash, Mark L; Zatsiorsky, Vladimir M

    2014-02-01

    During single-finger force production, the non-instructed fingers unintentionally produce force (finger enslaving). In this study, enslaving effects were compared between the dominant and non-dominant hands. The test consisted of a series of maximum voluntary contractions with different finger combinations. Enslaving matrices were calculated by means of training an artificial neural network. The dominant hand was found to be stronger, but there was found to be no difference between the overall enslaving effects in the dominant and non-dominant hands. There was no correlation between the magnitude of finger enslaving and the performance in such tests as the Edinburgh Handedness Inventory, the Grooved Pegboard test, and the Jebsen-Taylor Hand Function test. Each one of those three tests showed a significant difference between the dominant and non-dominant hand performances. Eleven subjects were retested after two months, and it was found that enslaving effects did not fluctuate significantly between the two testing sessions. While the dominant and non-dominant hands are involved differently in everyday tasks, e.g. in writing or eating, this practice does not cause significant differences in enslaving between the hands. PMID:24360253

  19. Analytical formulae for computing dominance from species-abundance distributions.

    PubMed

    Fung, Tak; Villain, Laura; Chisholm, Ryan A

    2015-12-01

    The evenness of an ecological community affects ecosystem structure, functioning and stability, and has implications for biodiversity conservation. In uneven communities, most species are rare while a few dominant species drive ecosystem-level properties. In even communities, dominance is lower, with possibly many species playing key ecological roles. The dominance aspect of evenness can be measured as a decreasing function of the proportion of species required to make up a fixed fraction (e.g., half) of individuals in a community. Here we sought general rules about dominance in ecological communities by linking dominance mathematically to the parameters of common theoretical species-abundance distributions (SADs). We found that if a community's SAD was log-series or lognormal, then dominance was almost inevitably high, with fewer than 40% of species required to account for 90% of all individuals. Dominance for communities with an exponential SAD was lower but still typically high, with fewer than 40% of species required to account for 70% of all individuals. In contrast, communities with a gamma SAD only exhibited high dominance when the average species abundance was below a threshold of approximately 100. Furthermore, we showed that exact values of dominance were highly scale-dependent, exhibiting non-linear trends with changing average species abundance. We also applied our formulae to SADs derived from a mechanistic community model to demonstrate how dominance can increase with environmental variance. Overall, our study provides a rigorous basis for theoretical explorations of the dynamics of dominance in ecological communities, and how this affects ecosystem functioning and stability. PMID:26409166

  20. 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.

  1. Schizophrenia as Failure of Left Hemispheric Dominance for the Phonological Component of Language

    PubMed Central

    Angrilli, Alessandro; Spironelli, Chiara; Elbert, Thomas; Crow, Timothy J.; Marano, Gianfranco; Stegagno, Luciano

    2009-01-01

    Background T. J. Crow suggested that the genetic variance associated with the evolution in Homo sapiens of hemispheric dominance for language carries with it the hazard of the symptoms of schizophrenia. Individuals lacking the typical left hemisphere advantage for language, in particular for phonological components, would be at increased risk of the typical symptoms such as auditory hallucinations and delusions. Methodology/Principal Findings Twelve schizophrenic patients treated with low levels of neuroleptics and twelve matched healthy controls participated in an event-related potential experiment. Subjects matched word-pairs in three tasks: rhyming/phonological, semantic judgment and word recognition. Slow evoked potentials were recorded from 26 scalp electrodes, and a laterality index was computed for anterior and posterior regions during the inter stimulus interval. During phonological processing individuals with schizophrenia failed to achieve the left hemispheric dominance consistently observed in healthy controls. The effect involved anterior (fronto-temporal) brain regions and was specific for the Phonological task; group differences were small or absent when subjects processed the same stimulus material in a Semantic task or during Word Recognition, i.e. during tasks that typically activate more widespread areas in both hemispheres. Conclusions/Significance We show for the first time how the deficit of lateralization in the schizophrenic brain is specific for the phonological component of language. This loss of hemispheric dominance would explain typical symptoms, e.g. when an individual's own thoughts are perceived as an external intruding voice. The change can be interpreted as a consequence of “hemispheric indecision”, a failure to segregate phonological engrams in one hemisphere. PMID:19223971

  2. 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

  3. Variance Function Partially Linear Single-Index Models1

    PubMed Central

    LIAN, HENG; LIANG, HUA; CARROLL, RAYMOND J.

    2014-01-01

    We consider heteroscedastic regression models where the mean function is a partially linear single index model and the variance function depends upon a generalized partially linear single index model. We do not insist that the variance function depend only upon the mean function, as happens in the classical generalized partially linear single index model. We develop efficient and practical estimation methods for the variance function and for the mean function. Asymptotic theory for the parametric and nonparametric parts of the model is developed. Simulations illustrate the results. An empirical example involving ozone levels is used to further illustrate the results, and is shown to be a case where the variance function does not depend upon the mean function. PMID:25642139

  4. 40 CFR 190.11 - Variances for unusual operations.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... Standards for the Uranium Fuel Cycle § 190.11 Variances for unusual operations. The standards specified in... interest, and (b) Information is promptly made a matter of public record delineating the nature of...

  5. 40 CFR 59.509 - Can I get a variance?

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ...) NATIONAL VOLATILE ORGANIC COMPOUND EMISSION STANDARDS FOR CONSUMER AND COMMERCIAL PRODUCTS National Volatile Organic Compound Emission Standards for Aerosol Coatings § 59.509 Can I get a variance? (a)...

  6. 40 CFR 59.509 - Can I get a variance?

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ...) NATIONAL VOLATILE ORGANIC COMPOUND EMISSION STANDARDS FOR CONSUMER AND COMMERCIAL PRODUCTS National Volatile Organic Compound Emission Standards for Aerosol Coatings § 59.509 Can I get a variance? (a)...

  7. 40 CFR 59.509 - Can I get a variance?

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ...) NATIONAL VOLATILE ORGANIC COMPOUND EMISSION STANDARDS FOR CONSUMER AND COMMERCIAL PRODUCTS National Volatile Organic Compound Emission Standards for Aerosol Coatings § 59.509 Can I get a variance? (a)...

  8. 40 CFR 59.509 - Can I get a variance?

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ...) NATIONAL VOLATILE ORGANIC COMPOUND EMISSION STANDARDS FOR CONSUMER AND COMMERCIAL PRODUCTS National Volatile Organic Compound Emission Standards for Aerosol Coatings § 59.509 Can I get a variance? (a)...

  9. 40 CFR 59.509 - Can I get a variance?

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ...) NATIONAL VOLATILE ORGANIC COMPOUND EMISSION STANDARDS FOR CONSUMER AND COMMERCIAL PRODUCTS National Volatile Organic Compound Emission Standards for Aerosol Coatings § 59.509 Can I get a variance? (a)...

  10. 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.

  11. Sensitivity analyses of turbulence theory-based variance-covariance matrices of tropospheric slant delays

    NASA Astrophysics Data System (ADS)

    Vennebusch, M.; Schön, S.

    2009-04-01

    Atmospheric turbulence induces physical correlations on any space geodetic technique based on electromagnetic waves. Thus, also GNSS phase observations are both temporally and spatially correlated due to refractivity fluctuations along the signal's path from the transmitter to the receiver. Currently, these physical correlations are rarely considered in GNSS data analysis; yielding too optimistic parameter variances and covariances. Based on turbulence theory, Schön and Brunner (2008) developed a formulation of the variances and covariances induced by refractivity fluctuations in the troposphere. This model adequately describes the variance-covariance matrix (VCM) of tropospheric slant delays. The parametrisation is mainly based on the turbulence structure constant, the outer scale length, the integration height, the wind direction and the observation geometry. The VCM can adequately be used to determine synthetic slant delay time series. In this paper, this strategy will be described by using an exemplary GPS configuration. Furthermore, the latest results of simulation studies and sensitivity analyses of this VCM model w.r.t. the model parameters are presented. As a result, the most dominant parameters (that should be either determined with special care or precisely known) will be identified.

  12. On the correlation between variance in individual susceptibilities and infection prevalence in populations.

    PubMed

    Margheri, Alessandro; Rebelo, Carlota; Gomes, M Gabriela M

    2015-12-01

    The hypothesis that infection prevalence in a population correlates negatively with variance in the susceptibility of its individuals has support from experimental, field, and theoretical studies. However, its generality has never been formally demonstrated. Here we formulate an endemic SIS model with individual susceptibility distributed according to a discrete or continuous probability function to assess the generality of such hypothesis. We introduce an ordering among susceptibility distributions with the same mean, analogous to that considered in Katriel (J Math Biol 65:237-262, 2012) to order the attack rates in an epidemic SIR model with heterogeneity. It turns out that if one distribution dominates another in this order then it has greater variance and corresponds to a lower infection prevalence for R0 varying in a suitable maximal interval of the form ]1, R0*]. We show that in both the discrete and continuous frameworks R0* can be finite, so that the expected correlation among variance and prevalence does not always hold. For discrete distributions this fact is demonstrated analytically, and the proof introduces a constructive procedure to find ordered pairs for which R0* is arbitrarily close to 1. For continuous distributions our conclusion is based on numerical studies with the beta distribution. Finally, we present explicit partial orderings among discrete susceptibility distributions and among symmetric beta distributions which guarantee that R0* = +∞.

  13. Image embedded coding with edge preservation based on local variance analysis for mobile applications

    NASA Astrophysics Data System (ADS)

    Luo, Gaoyong; Osypiw, David

    2006-02-01

    Transmitting digital images via mobile device is often subject to bandwidth which are incompatible with high data rates. Embedded coding for progressive image transmission has recently gained popularity in image compression community. However, current progressive wavelet-based image coders tend to send information on the lowest-frequency wavelet coefficients first. At very low bit rates, images compressed are therefore dominated by low frequency information, where high frequency components belonging to edges are lost leading to blurring the signal features. This paper presents a new image coder employing edge preservation based on local variance analysis to improve the visual appearance and recognizability of compressed images. The analysis and compression is performed by dividing an image into blocks. Fast lifting wavelet transform is developed with the advantages of being computationally efficient and boundary effects minimized by changing wavelet shape for handling filtering near the boundaries. A modified SPIHT algorithm with more bits used to encode the wavelet coefficients and transmitting fewer bits in the sorting pass for performance improvement, is implemented to reduce the correlation of the coefficients at scalable bit rates. Local variance estimation and edge strength measurement can effectively determine the best bit allocation for each block to preserve the local features by assigning more bits for blocks containing more edges with higher variance and edge strength. Experimental results demonstrate that the method performs well both visually and in terms of MSE and PSNR. The proposed image coder provides a potential solution with parallel computation and less memory requirements for mobile applications.

  14. 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

  15. 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

  16. 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.

  17. 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.

  18. Efficiency control in large-scale genotyping using analysis of variance.

    PubMed

    Spijker, Geert T; Bruinenberg, Marcel; te Meerman, Gerard J

    2005-01-01

    The efficiency of the genotyping process is determined by many simultaneous factors. In actual genotyping, a production run is often preceded by small-scale experiments to find optimal conditions. We propose to use statistical analysis of production run data as well, to gain insight into factors important for the outcome of genotyping. As an example, we show that analysis of variance (ANOVA) applied to the first-pass results of a genetic study reveals important determinants of genotyping success. The largest factor limiting genotyping appeared to be interindividual variation among DNA samples, explaining 20% of the variance, and a smaller reaction volume, sizing failure, and differences among markers all explained approximately 10%. Other potentially important factors, such as sample position within the plate and reusing electrophoresis matrix, appeared to be of minor influence. About 55% of the total variance could be explained by systematic factors. These results show that ANOVA can provide valuable feedback to improve genotyping efficiency. We propose to adjust genotype production runs using principles of experimental design in order to maximize genotyping efficiency at little additional cost.

  19. Short communication: variance estimates among herds stratified by individual herd heritability.

    PubMed

    Dechow, C D; Norman, H D; Pelensky, C A

    2008-04-01

    The objectives of this study were to compare (co)variance parameter estimates among subsets of data that were pooled from herds with high, medium, or low individual herd heritability estimates and to compare individual herd heritability estimates to REML heritability estimates for pooled data sets. A regression model was applied to milk yield, fat yield, protein yield, and somatic cell score (SCS) records from 20,902 herds to generate individual-herd heritability estimates. Herds representing the 5th percentile or less (P5), 47th through the 53rd percentile (P50), and the 95th percentile or higher (P95) for herd heritability were randomly selected. Yield or SCS from the selected herds were pooled for each percentile group and treated as separate traits. Records from P5, P50, and P95 were then analyzed with a 3-trait animal model. Heritability estimates were 23, 31, 26, and 8% higher in P95 than in P5 for milk yield, fat yield, protein yield, and SCS, respectively. The regression techniques successfully stratified individual herds by heritability, and additive genetic variance increased progressively, whereas permanent environmental variance decreased progressively as herd heritability increased.

  20. 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.