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The recent settlement of cattle in West Africa after several waves of migration from remote centres of domestication has imposed dramatic changes in their environmental conditions, in particular through exposure to new pathogens. West African cattle populations thus represent an appealing model to unravel the genome response to adaptation to tropical(More)
A set of eleven pig breeds originating from six European countries, and including a small sample of wild pigs, was chosen for this study of genetic diversity. Diversity was evaluated on the basis of 18 microsatellite markers typed over a total of 483 DNA samples collected. Average breed heterozygosity varied from 0.35 to 0.60. Genotypic frequencies(More)
The diversity of a set of breeds or species is defined in the Weitzman approach by a recursion formula using the pairwise genetic distances between the elements of the set. The algorithm for computing the diversity function of Weitzman is described. It also provides a taxonomy of the set which is interpreted as the maximum likelihood phylogeny. The theory(More)
Gene regulatory networks refer to the interactions that occur among genes and other cellular products. The topology of these networks can be inferred from measurements of changes in gene expression over time. However, because the measurement device (i.e., microarrays) typically yields information on thousands of genes over few biological replicates, these(More)
BACKGROUND The recent advent of high-throughput SNP genotyping technologies has opened new avenues of research for population genetics. In particular, a growing interest in the identification of footprints of selection, based on genome scans for adaptive differentiation, has emerged. METHODOLOGY/PRINCIPAL FINDINGS The purpose of this study is to develop(More)
This article gives a formal proof of a formula for the precision of estimated genetic distances proposed by Barker et al. which can be used in designing experimental sampling programmes. The derivation is given in the general multi-allelic case using the Sanghvi distance. Two sources of sampling are considered, i.e. i) among individuals (or gametes) within(More)
This paper presents procedures for implementing the PX-EM algorithm of Liu, Rubin and Wu to compute REML estimates of variance covariance components in Henderson's linear mixed models. The class of models considered encompasses several correlated random factors having the same vector length e.g., as in random regression models for longitudinal data analysis(More)
Generalized linear mixed models (GLMM) form a very general class of random effects models for discrete and continuous responses in the exponential family. They are useful in a variety of applications. The traditional likelihood approach for GLMM usually involves high dimensional integrations which are computationally intensive. In this work, we investigate(More)
Dairy cattle breeds have been subjected over the last fifty years to intense artificial selection towards improvement of milk production traits. In this study, we performed a whole genome scan for differentiation using 42,486 SNPs in the three major French dairy cattle breeds (Holstein, Normande and Montbéliarde) to identify the main physiological pathways(More)
MOTIVATION With the proliferation of microarray experiments and their availability in the public domain, the use of meta-analysis methods to combine results from different studies increases. In microarray experiments, where the sample size is often limited, meta-analysis offers the possibility to considerably increase the statistical power and give more(More)