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Single Trait (single + trait)
Selected AbstractsPhylogenetic analysis of the pearlfish tribe Carapini (Pisces: Carapidae)ACTA ZOOLOGICA, Issue 4 2000E. Parmentier Abstract Fishes of the tribe Carapini (Encheliophis and Carapus) share a noteworthy peculiarity: they shelter in holothurian echinoderms or bivalve hosts. Some species are considered parasitic, others commensal. This study focuses on the phylogeny of the tribe, using two other Carapidae species as an outgroup (Snyderidia canina and Onuxodon fowleri). Insofar as possible, the selected anatomical and behavioural characters where chosen in an ecomorphological perspective, as features that could be responses to various lifestyle-related constraints. Our character selection also took into account the fact that some features are (presumably) linked. Such features were grouped together as a single trait to avoid their overvaluation. This methodology enabled commensals to be separated from parasites, the former belonging to Carapus and the latter to Encheliophis. Carapus species reflect in their morphology the constraints imposed by a diet of hard, mobile, elusive prey, showing predator-type features: a strong dentition, a wide mouth opening, a robust food intake apparatus. On the other hand, the endoparasitic Encheliophis species show a generally weaker buccal apparatus and narrow mouth opening, in relation to the different constraints of their lifestyle where the diet constraints are less pronounced: they eat body parts of their host. Changes in both generic diagnoses are proposed and three species are transferred from Encheliophis to Carapus. [source] Pleiotropy and principal components of heritability combine to increase power for association analysisGENETIC EPIDEMIOLOGY, Issue 1 2008Lambertus Klei Abstract When many correlated traits are measured the potential exists to discover the coordinated control of these traits via genotyped polymorphisms. A common statistical approach to this problem involves assessing the relationship between each phenotype and each single nucleotide polymorphism (SNP) individually (PHN); and taking a Bonferroni correction for the effective number of independent tests conducted. Alternatively, one can apply a dimension reduction technique, such as estimation of principal components, and test for an association with the principal components of the phenotypes (PCP) rather than the individual phenotypes. Building on the work of Lange and colleagues we develop an alternative method based on the principal component of heritability (PCH). For each SNP the PCH approach reduces the phenotypes to a single trait that has a higher heritability than any other linear combination of the phenotypes. As a result, the association between a SNP and derived trait is often easier to detect than an association with any of the individual phenotypes or the PCP. When applied to unrelated subjects, PCH has a drawback. For each SNP it is necessary to estimate the vector of loadings that maximize the heritability over all phenotypes. We develop a method of iterated sample splitting that uses one portion of the data for training and the remainder for testing. This cross-validation approach maintains the type I error control and yet utilizes the data efficiently, resulting in a powerful test for association. Genet. Epidemiol. 2007. © 2007 Wiley-Liss, Inc. [source] New multivariate test for linkage, with application to pleiotropy: Fuzzy Haseman-ElstonGENETIC EPIDEMIOLOGY, Issue 4 2003Belhassen Kaabi Abstract We propose a new method of linkage analysis based on using the grade of membership scores resulting from fuzzy clustering procedures to define new dependent variables for the various Haseman-Elston approaches. For a single continuous trait with low heritability, the aim was to identify subgroups such that the grade of membership scores to these subgroups would provide more information for linkage than the original trait. For a multivariate trait, the goal was to provide a means of data reduction and data mining. Simulation studies using continuous traits with relatively low heritability (H=0.1, 0.2, and 0.3) showed that the new approach does not enhance power for a single trait. However, for a multivariate continuous trait (with three components), it is more powerful than the principal component method and more powerful than the joint linkage test proposed by Mangin et al. ([1998] Biometrics 54:88,99) when there is pleiotropy. Genet Epidemiol 24:253,264, 2003. © 2003 Wiley-Liss, Inc. [source] Predictive ability of models for calving difficulty in US HolsteinsJOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 3 2009E.L. De Maturana Summary The performance of alternative threshold models for analyzing calving difficulty (CD) in Holstein cows was evaluated in terms of predictive ability. Four models were considered, with CD classified into either three or four categories and analysed either as a single trait or jointly with gestation length (GL). The data contained GL and CD records from 90 393 primiparous cows, sired by 1122 bulls and distributed over 935 herd-calving year classes. Predictive ability of each model was evaluated using four criteria: mean squared error of the difference between observed and predicted CD scores; a Kullback-Leibler divergence measure between the observed and predicted distributions of CD scores; Pearson's correlation between observed and predicted CD scores and ability to correctly classify bulls as above or below average for incidence of CD. In general, the four models had similar predictive abilities. The joint analysis of CD with GL produced little, if any, improvement in predictive ability over univariate models. In light of the small difference in predictive ability between models treating CD with three or four categories and considering that a greater number of categories can provide more information, analysis of CD classified into four categories seems warranted. [source] Estimates of environmental effects and genetic parameters for body measurements and weight in Brahman cattle raised in MexicoJOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 4 2002C. D. U. Magnabosco Summary A Derivative Free Restricted Maximum Likelihood (DFREML) algorithm was used with single trait and two traits animal models to estimate the variance and covariance components and thus, heritabilities and phenotypic, genetic and environmental correlations among nine different body measurements and weights of Brahman cattle raised in Mexico. The following measurements were considered: hip width, pin width, hip-pin width, anterior height, posterior height, body length, thorax perimeter, scrotal circumference and weight. The analysis was based on a total of 1018 animals, born between 1992 and 1995, from 17 herds in the Mexican States of Chiapas, San Luis Potosi, Tabasco, Tamaulipas and Veracruz. The model included the following fixed effects: herd, year-season of birth, sex, age of the animal and feed management. The only random effect was the direct additive genetic contribution of each animal. All fixed effects in the model were significant for all traits (p < 0.05). Estimated heritabilities for the traits were: hip width 0.57, pin width 0.32, hip-pin width 0.41, anterior height 0.56, posterior height 0.54, body length 0.32, thorax perimeter 0.49, scrotal circumference 0.02 and weight 0.66. The magnitude of the heritabilities was medium to high, with the exception of scrotal circumference. The genetic correlations among all body measurements were consistently positive and high, ranging from 0.64 to 1.00. Although other measures showed higher genetic correlations with weight, thorax perimeter combines a high value (0.70) with ease and repeatability, making it a useful field measurement to estimate body weight when scales are not available. Resumen Estimados de efectos ambientales y parámetros genéticos para medidas corporales y peso vivo en ganado brahman criado en méjico Fue usado un algoritmo de Máxima Verosimilitud Restricta Libre de Derivadas (DFREML) con modelos animales para una y dos características para estimar componentes de (co)varianzas, heredabilidades y correlaciones fenotípicas, genéticas y ambientales entre nueve diferentes medidas corporales y peso vivo de ganado Brahman criado en México. Fueron considerados los siguientes rasgos: ancho anterior de la grupa, ancho posterior de la grupa, largo de la grupa, altura a la cruz, altura a la grupa, largo del cuerpo, perímetro toráxico, perímetro escrotal y peso vivo. Se usaron datos de 1018 animales, nacidos entre 1992 y 1995, procedentes de 17 rebaños de los Estados mejicanos de Chiapas, San Luis Potosí, Tabasco, Tamaulipas y Veracruz. El modelo matemático incluyó los siguientes efectos fijos: rebaño, año-época de nacimiento, sexo, clase de edad del animal y manejo alimentar. Se consideró el efecto aditivo directo de cada animal como el único efecto aleatorio. Todos los efectos fijos del modelo fueron significativos para todas las características (P < 0.05). Las heredabilidades estimadas fueron: ancho anterior de la grupa 0.57, ancho posterior de la grupa 0.32, largo de la grupa 0.41, altura a la cruz 0.56, altura a la grupa 0.54, largo del cuerpo 0.32, perímetro toráxico 0.49, perímetro escrotal 0.02 y peso vivo 0.66. Las magnitudes de las heredabilidades fueron de medias a altas, con excepción del perímetro escrotal. Las correlaciones genéticas entre todas las medidas corporales fueron consistentemente positivas y altas, variando de 0.64 a 1.00. Aunque otras medidas corporales mostraron altas correlaciones genéticas con el peso vivo, el perímetro toráxico combina un alto valor de esa correlación (0.70) con facilidad de medición y alta repetibilidad, haciendo de esta una medida útil, para estimar el peso vivo, en condiciones de campo donde no se dispone de balanza. [source] Carboxylate composition of root exudates does not relate consistently to a crop species' ability to use phosphorus from aluminium, iron or calcium phosphate sourcesNEW PHYTOLOGIST, Issue 1 2007Stuart J. Pearse Summary ,,The relationship between carboxylate release from roots and the ability of the species to utilize phosphorus from sparingly soluble forms was studied by comparing Triticum aestivum, Brassica napus, Cicer arietinum, Pisum sativum, Lupinus albus, Lupinus angustifolius and Lupinus cosentinii. ,,Plants were grown in sand and supplied with 40 mg P kg,1 in the sparingly soluble forms AlPO4, FePO4 or Ca5OH(PO4)3, or as soluble KH2PO4; control plants received no P. ,,The ability to utilize sparingly soluble forms of P differed between forms of P supplied and species. Pisum sativum and C. arietinum did not access AlPO4 or FePO4 despite releasing carboxylates into the rhizosphere. ,,Species accessed different forms of sparingly soluble P, but no species was superior in accessing all forms. We conclude that a single trait cannot explain access to different forms of sparingly soluble P, and hypothesize that in addition to carboxylates, rhizosphere pH and root morphology are key factors. [source] Discovery and transmission of functional QTL in the pedigree of an elite soybean cultivar Suinong14PLANT BREEDING, Issue 3 2010J. Qin With 3 figures and 5 tables Abstract In this study, we extended in silico mapping for single trait to analyse data from multiple environments by calculating intraclass correlations and to mapping pleiotropic QTL for multiple traits by defining new statistic to measure the correlation between multiple traits and the marker. Data sets include phenotypes of eight agronomic traits obtained from six different ecologic environments and years, and genotypic information from 477 polymorphic markers on 14 ancestral lines in the pedigree of ,Suinong14'. With in silico mapping, a total of 39 markers distributed on 14 linkage groups are detected as QTL responsible for eight agronomic traits and 10 QTL are identified as having pleiotropic effects. Tracing transmission of functional QTL in the pedigree indicated that certain QTL, such as Sat_036 on linkage group D1a, Satt182 on linkage group L, and Satt726 on linkage group B2 may be responsible for the contribution of exotic germplasm to the improved cultivars. [source] Gene function beyond the single trait: natural variation, gene effects, and evolutionary ecology in Arabidopsis thalianaPLANT CELL & ENVIRONMENT, Issue 1 2005S. J. TONSOR ABSTRACT The purpose of plant functional genomics is to describe the patterns of gene expression and internal plant function underlying the ecological functions that sustain plant growth and reproduction. Plants function as integrated systems in which metabolic and developmental pathways draw on common resource pools and respond to a relatively small number of signal/response systems. Plants are also integrated with their environment, exchanging energy and matter with their surroundings and are consequently sensitive to changes in energy and resource fluxes. These two levels of integration complicate the description of gene function. Internal integration results in single genes often affecting multiple characteristics (pleiotropy) and interacting with multiple other genes (epistasis). Integration with the external environment leads to gene expression and the genes' phenotypic effects varying across environmental backgrounds (gene,environment interaction). An accurate description of the function of all genes requires an augmentation, already underway, of the study of isolated developmental and metabolic pathways to a more integrated approach involving the study of genetic effects across scales of variation usually regarded as the purview of ecological and evolutionary research. Since the evolution of gene function also depends on this complex of gene effects, progress in evolutionary genetics will also require understanding the nature of gene interactions and pleiotropy and the constraints and patterns they impose on adaptive evolution. Studying gene function in the context of the integrated organism is a major challenge, best met by developing co-ordinated research efforts in model systems. This review highlights natural variation in A. thaliana as a system for understanding integrated gene function in an ecological and evolutionary context. The current state of this research integration in A. thaliana is described by summarizing relevant approaches, current knowledge, and some potentially fruitful future studies. By introducing some of the fundamental questions of ecological and evolutionary research, experimental approaches and systems that can reveal new facets of gene function and gene effect are also described. A glossary is included in the Appendix. [source] Height and body mass influence on human body outlines: A quantitative approach using an elliptic Fourier analysisAMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY, Issue 1 2010Alexandre Courtiol Abstract Many studies use representations of human body outlines to study how individual characteristics, such as height and body mass, affect perception of body shape. These typically involve reality-based stimuli (e.g., pictures) or manipulated stimuli (e.g., drawings). These two classes of stimuli have important drawbacks that limit result interpretations. Realistic stimuli vary in terms of traits that are correlated, which makes it impossible to assess the effect of a single trait independently. In addition, manipulated stimuli usually do not represent realistic morphologies. We describe and examine a method based on elliptic Fourier descriptors to automatically predict and represent body outlines for a given set of predicted variables (e.g., sex, height, and body mass). We first estimate whether these predictive variables are significantly related to human outlines. We find that height and body mass significantly influence body shape. Unlike height, the effect of body mass on shape differs between sexes. Then, we show that we can easily build a regression model that creates hypothetical outlines for an arbitrary set of covariates. These statistically computed outlines are quite realistic and may be used as stimuli in future studies. Am J Phys Anthropol, 2010. © 2009 Wiley-Liss, Inc. [source] Fine mapping of quantitative trait loci for mastitis resistance on bovine chromosome 11ANIMAL GENETICS, Issue 4 2009N. F. Schulman Summary Quantitative trait loci (QTL) affecting clinical mastitis (CM) and somatic cell score (SCS) were mapped on bovine chromosome 11. The mapping population consisted of 14 grandsire families belonging to three Nordic red cattle breeds: Finnish Ayrshire (FA), Swedish Red and White (SRB) and Danish Red. The families had previously been shown to segregate for udder health QTL. A total of 524 progeny tested bulls were included in the analysis. A linkage map including 33 microsatellite and five SNP markers was constructed. We performed combined linkage disequilibrium and linkage analysis (LDLA) using the whole data set. Further analyses were performed for FA and SRB separately to study the origin of the identified QTL/haplotype and to examine if it was common in both populations. Finally, different two-trait models were fitted. These postulated either a pleiotropic QTL affecting both traits; two linked QTL, each affecting one trait; or one QTL affecting a single trait. A QTL affecting CM was fine-mapped. In FA, a haplotype having a strong association with a high negative effect on mastitis resistance was identified. The mapping precision of an earlier detected SCS-QTL was not improved by the LDLA analysis because of lack of linkage disequilibrium between the markers used and the QTL in the region. [source] Estimating a Multivariate Familial Correlation Using Joint Models for Canonical Correlations: Application to Memory Score Analysis from Familial Hispanic Alzheimer's Disease StudyBIOMETRICS, Issue 2 2009Hye-Seung Lee Summary Analysis of multiple traits can provide additional information beyond analysis of a single trait, allowing better understanding of the underlying genetic mechanism of a common disease. To accommodate multiple traits in familial correlation analysis adjusting for confounders, we develop a regression model for canonical correlation parameters and propose joint modeling along with mean and scale parameters. The proposed method is more powerful than the regression method modeling pairwise correlations because it captures familial aggregation manifested in multiple traits through maximum canonical correlation. [source] | ||||||||||