Thierry De Meeûs

Bio: Thierry De Meeûs is an academic researcher from Centre national de la recherche scientifique. The author has contributed to research in topics: Population & Population genetics. The author has an hindex of 36, co-authored 89 publications receiving 5236 citations. Previous affiliations of Thierry De Meeûs include Centre de coopération internationale en recherche agronomique pour le développement & University of Montpellier.

Testing differentiation in diploid populations

Abstract: We examine the power of different exact tests of differentiation for diploid populations. Since there is not necessarily random mating within populations, the appropriate hypothesis to construct exact tests is that of independent sampling of genotypes. There are two categories of tests, Fsrestimator tests and goodness of fit tests. In this latter category, we distinguish “allelic statistics”, which account for the nature of alleles within genotypes, from “genotypic statistics” that do not. We show that the power of Fs+stimator tests and of allelic goodness of fit tests are similar when sampling is balanced, and higher than the power of genotypic goodness of fit tests. When sampling is unbalanced, the most powerful tests are shown to belong to the allelic goodness of fit group.

The Population Genetics of Clonal and Partially Clonal Diploids

Abstract: The consequences of variable rates of clonal reproduction on the population genetics of neutral markers are explored in diploid organisms within a subdivided population (island model). We use both analytical and stochastic simulation approaches. High rates of clonal reproduction will positively affect heterozygosity. As a consequence, nearly twice as many alleles per locus can be maintained and population differentiation estimated as F(ST) value is strongly decreased in purely clonal populations as compared to purely sexual ones. With increasing clonal reproduction, effective population size first slowly increases and then points toward extreme values when the reproductive system tends toward strict clonality. This reflects the fact that polymorphism is protected within individuals due to fixed heterozygosity. Contrarily, genotypic diversity smoothly decreases with increasing rates of clonal reproduction. Asexual populations thus maintain higher genetic diversity at each single locus but a lower number of different genotypes. Mixed clonal/sexual reproduction is nearly indistinguishable from strict sexual reproduction as long as the proportion of clonal reproduction is not strongly predominant for all quantities investigated, except for genotypic diversities (both at individual loci and over multiple loci).

International variability of ages at menarche and menopause: patterns and main determinants.

Abstract: 1 Abstract The purpose of this study was to review published studies on the variability of age at menarche and age at menopause throughout the world, and to identify the main causes for age variation in the timing of these events. We first present a summary table including mean (or median) values of the age at menarche in 67 countries, and of the age at menopause in 26 countries. General linear models showed that mean age at menarche was strongly linked to the mean female life expectancy, suggesting that one or several variables responsible for inequalities in longevity similarly influ- enced the onset of menarche. A closer examination of the data revealed that among several variables reflecting living conditions, the factors best explain- ing the variation in age at menarche were adult illiteracy rate and vegetable calorie consumption. Because adult illiteracy rate has some correlation with the age at which children are involved in physical activities that can be detri- mental in terms of energy expenditure, our results suggest that age at menar- che reflects more a trend in energy balance than merely nutritional status. In addition, we found the main determinant of age at menopause to be the mean fertility. This study thus suggests that, on a large scale, age at menarche is mainly determined by extrinsic factors such as living conditions, while age at menopause seems to be mainly influenced by intrinsic factors such as the re- productive history of individuals. Finally, these findings suggest that human patterns cannot be addressed solely by traditional, small-scale investigations on single populations. Rather, complementary research on a larger scale, such as this study, may be more appropriate in defining some interesting ap- plications to the practical problems of human ecology.

Extreme inbreeding in Leishmania braziliensis

Abstract: Leishmania species of the subgenus Viannia and especially Leishmania braziliensis are responsible for a large proportion of New World leishmaniasis cases. The reproductive mode of Leishmania species has often been assumed to be predominantly clonal, but remains unsettled. We have investigated the genetic polymorphism at 12 microsatellite loci on 124 human strains of Leishmania braziliensis from 2 countries, Peru and Bolivia. There is substantial genetic diversity, with an average of 12.4 ± 4.4 alleles per locus. There is linkage disequilibrium at a genome-wide scale, as well as a substantial heterozygote deficit (more than 50% the expected value from Hardy−Weinberg equilibrium), which indicates high levels of inbreeding. These observations are inconsistent with a strictly clonal model of reproduction, which implies excess heterozygosity. Moreover, there is large genetic heterogeneity between populations within countries (Wahlund effect), which evinces a strong population structure at a microgeographic scale. Our findings are compatible with the existence of population foci at a microgeographic scale, where clonality alternates with sexuality of an endogamic nature, with possible occasional recombination events between individuals of different genotypes. These findings provide key clues on the ecology and transmission patterns of Leishmania parasites.

Arlequin (version 3.0): An integrated software package for population genetics data analysis

Abstract: Arlequin ver 3.0 is a software package integrating several basic and advanced methods for population genetics data analysis, like the computation of standard genetic diversity indices, the estimation of allele and haplotype frequencies, tests of departure from linkage equilibrium, departure from selective neutrality and demographic equilibrium, estimation or parameters from past population expansions, and thorough analyses of population subdivision under the AMOVA framework. Arlequin 3 introduces a completely new graphical interface written in C++, a more robust semantic analysis of input files, and two new methods: a Bayesian estimation of gametic phase from multi-locus genotypes, and an estimation of the parameters of an instantaneous spatial expansion from DNA sequence polymorphism. Arlequin can handle several data types like DNA sequences, microsatellite data, or standard multi-locus genotypes. A Windows version of the software is freely available on http://cmpg.unibe.ch/software/arlequin3.

adegenet: a R package for the multivariate analysis of genetic markers

Abstract: Summary: The package adegenet for the R software is dedicated to the multivariate analysis of genetic markers. It extends the ade4 package of multivariate methods by implementing formal classes and functions to manipulate and analyse genetic markers. Data can be imported from common population genetics software and exported to other software and R packages. adegenet also implements standard population genetics tools along with more original approaches for spatial genetics and hybridization. Availability: Stable version is available from CRAN: http://cran. r-project.org/mirrors.html. Development version is available from adegenet website: http://adegenet.r-forge.r-project.org/. Both versions can be installed directly from R. adegenet is distributed under the GNU General Public Licence (v.2). Contact: jombart@biomserv.univ-lyon1.fr Supplementary information: Supplementary data are available at Bioinformatics online.

HIERFSTAT , a package for R to compute and test hierarchical F -statistics

Abstract: The package hierfstat for the statistical software r , created by the R Development Core Team, allows the estimate of hierarchical F -statistics from a hierarchy with any numbers of levels. In addition, it allows testing the statistical significance of population differentiation for these different levels, using a generalized likelihood-ratio test. The package hierfstat is available at http://www.unil.ch/popgen/softwares/hierfstat.htm.

Genetic Data Analysis

Abstract: LEARNING The objectives of BIOS 781 are to present: OBJECTIVES: 1. basic population and quantitative genetic principles, including classical genetics, chromosomal theory of inheritance, and meiotic recombination 2. an exposure to QTL mapping methods of complex quantitative traits and linkage methods to detect co-segregation with disease 3. methods for assessing marker-disease linkage disequilibrium, including case-control approaches 4. methods for genome-wide association and stratification control.