Search results for "selection"

2014

Introduction: Many studies examine gene expression data that has been obtained under the influence of multiple factors, such as genetic background, environmental conditions, or exposure to diseases. The interplay of multiple factors may lead to effect modification and confounding. Higher order linear regression models can account for these effects. We present a new methodology for linear model selection and apply it to microarray data of bone marrow-derived macrophages. This experiment investigates the influence of three variable factors: the genetic background of the mice from which the macrophages were obtained, Yersinia enterocolitica infection (two strains, and a mock control),and treat…

An efficient method for fully automatic 3D digitization of unknown objects

2013

Our goal is to develop a complete and automatic scanning strategy with minimum prior information about the object shape. We aim to establish a methodology for the automation of the 3D digitization process. The paper presents a novel approach to determine the Next Best View (NBV) for an efficient reconstruction of highly accurate 3D models. Our method is based on the classification of the acquired surfaces into Well Visible and Barely Visible combined with a best view selection algorithm based on mean shift, which avoids unreachable positions. Our approach is applicable to all kinds of range sensors. To prove the efficiency and the robustness of our method, test objects are first scanned man…

Good-genes effects in sexual selection

1999

The magnitude of the effect of good genes as a viability benefit accruing to choosy females remains a controversial theoretical and empirical issue. We collected all available data from the literature to estimate the magnitude of good-genes viability effects, while adjusting for sample size. The average correlation coefficient between male traits and offspring survival in 22 studies was 0.122, which differed highly significantly from zero. This implies that male characters chosen by females reveal on average 1.5% of the variance in viability. The studies demonstrated considerable heterogeneity in effect size; some of this heterogeneity could be accounted for by differences among taxa (birds…

Mate choice for offspring performance: major benefits or minor costs?

1998

There is considerable disagreement over whether or not gaining viability benefits to offspring could be substantial enough to overcome the costs of female choosiness. A recent review suggested that the 'lek paradox' might be resolved by large indirect benefits as indicated by highly heritable ornamental traits. We selected males of a wolf spider Hygrolycosa rubrofasciata in relation to their sexual signalling rate (audible drumming). The estimated correlated response in offspring viability was rather small (0.12 s.d.). However, it may be large enough if the costs of being choosy are small. In fact, females mate with better-than-average males just by responding passively to a random drumming…

Using the dglars Package to Estimate a Sparse Generalized Linear Model

2015

dglars is a publicly available R package that implements the method proposed in Augugliaro et al. (J. R. Statist. Soc. B 75(3), 471-498, 2013) developed to study the sparse structure of a generalized linear model (GLM). This method, called dgLARS, is based on a differential geometrical extension of the least angle regression method. The core of the dglars package consists of two algorithms implemented in Fortran 90 to efficiently compute the solution curve. dglars is a publicly available R package that implements the method proposed in Augugliaro et al. (J. R. Statist. Soc. B 75(3), 471-498, 2013) developed to study the sparse structure of a generalized linear model (GLM). This method, call…

Genetic variability at neutral markers, quantitative trait loci and trait in a subdivided population under selection

2003

Abstract Genetic variability in a subdivided population under stabilizing and diversifying selection was investigated at three levels: neutral markers, QTL coding for a trait, and the trait itself. A quantitative model with additive effects was used to link genotypes to phenotypes. No physical linkage was introduced. Using an analytical approach, we compared the diversity within deme (HS) and the differentiation (FST) at the QTL with the genetic variance within deme (VW) and the differentiation (QST) for the trait. The difference between FST and QST was shown to depend on the relative amounts of covariance between QTL within and between demes. Simulations were used to study the effect of se…

Genetic diversity and trait genomic prediction in a pea diversity panel

2014

Background Pea (Pisum sativum L.), a major pulse crop grown for its protein-rich seeds, is an important component of agroecological cropping systems in diverse regions of the world. New breeding challenges imposed by global climate change and new regulations urge pea breeders to undertake more efficient methods of selection and better take advantage of the large genetic diversity present in the Pisum sativum genepool. Diversity studies conducted so far in pea used Simple Sequence Repeat (SSR) and Retrotransposon Based Insertion Polymorphism (RBIP) markers. Recently, SNP marker panels have been developed that will be useful for genetic diversity assessment and marker-assisted selection. Resu…

The Origins of Lactase Persistence in Europe

2009

Lactase persistence (LP) is common among people of European ancestry, but with the exception of some African, Middle Eastern and southern Asian groups, is rare or absent elsewhere in the world. Lactase gene haplotype conservation around a polymorphism strongly associated with LP in Europeans (−13,910 C/T) indicates that the derived allele is recent in origin and has been subject to strong positive selection. Furthermore, ancient DNA work has shown that the −13,910*T (derived) allele was very rare or absent in early Neolithic central Europeans. It is unlikely that LP would provide a selective advantage without a supply of fresh milk, and this has lead to a gene-culture coevolutionary model w…

Sex-Biased Inbreeding Effects on Reproductive Success and Home Range Size of the Critically Endangered Black Rhinoceros

2013

A central premise of conservation biology is that small populations suffer reduced viability through loss of genetic diversity and inbreeding. However, there is little evidence that variation in inbreeding impacts individual reproductive success within remnant populations of threatened taxa, largely due to problems associated with obtaining comprehensive pedigree information to estimate inbreeding. In the critically en- dangered black rhinoceros, a species that experienced severe demographic reductions, we used model selection to identify factors associated with variation in reproductive success (number of offspring). Factors examined as predictors of reproductive success were age, home ran…

Genomic basis of drought resistance inFagus sylvatica

2020

In the course of global climate change, central Europe is experiencing more frequent and prolonged periods of drought. These drought events have severe and detrimental impacts on the forest ecosystem. The drought years 2018 and 2019 affected European beeches (Fagus sylvatica L.) in noticeably different ways: even in the same local stand, badly drought damaged trees immediately neighboured apparently healthy trees. This led to the hypothesis that the genotype rather than the environment was responsible for this conspicuous pattern. We used this natural experiment to study the genomic basis of drought resistance in a Pool-GWAS approach. Contrasting the extreme phenotypes, we identified 106 si…