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A note on the accuracy of PAC-likelihood inference with microsatellite data Inra
Cornuet, J.M.; Beaumont, M.A..
Stephens and Donnelly have introduced a simple yet powerful importance sampling scheme for computing the likelihood in population genetic models. Fundamental to the method is an approximation to the conditional probability of the allelic type of an additional gene, given those currently in the sample. As noted by Li and Stephens.. the product of these conditional probabilities for a sequence of draws that gives the frequency of allelic types in a sample is an approximation to the likelihood, and can be used directly in inference. The aim of this note is to demonstrate the high level of accuracy of "product of approximate conditionals" (PAC) likelihood when used with microsatellite data. Results obtained on simulated microsatellite data show that this...
Tipo: Journal Article Palavras-chave: MICROSATELLITE; MUTATION MODEL; IMPORTANCE SAMPLING; PAC-LIKELIHOOD.
Ano: 2007 URL: http://www.prodinra.inra.fr/prodinra/pinra/doc.xsp?id=PROD200847d20143&uri=/notices/prodinra1/2008/08/
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A third-generation microsatellite-based linkage map of the honey bee, Apis mellifera, and its comparison with the sequence-based physical map Inra
Solignac, M.; Mougel, F.; Vautrin, D.; Monnerot, M.; Cornuet, J.M..
Background: The honey bee is a key model for social behavior and this feature led to the selection of the species for genome sequencing. A genetic map is a necessary companion to the sequence. In addition, because there was originally no physical map for the honey bee genome project, a meiotic map was the only resource for organizing the sequence assembly on the chromosomes.Results: We present the genetic (meiotic) map here and describe the main features that emerged from comparison with the sequence-based physical map. The genetic map of the honey bee is saturated and the chromosomes are oriented from the centromeric to the telomeric regions. The map is based on 2,008 markers and is about 40 Morgans (M) long, resulting in a marker density of one every...
Tipo: Journal Article Palavras-chave: ABEILLE DOMESTIQUE GENETIC MAP; SOCIAL BEHAVIOR; RECOMBINATION; HONEY BEE.
Ano: 2007 URL: http://www.prodinra.inra.fr/prodinra/pinra/doc.xsp?id=PROD2008d6cd86d1&uri=/notices/prodinra1/2008/08/
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Adaptive approximate Bayesian computation Inra
Beaumont, M.A.; Cornuet, J.M.; Marin, J.M.; Robert, C.P..
Sequential techniques can enhance the efficiency of the approximate Bayesian computation algorithm, as in Sisson et al.'s (2007) partial rejection control version. While this method is based upon the theoretical works of Del Moral et al. (2006), the application to approximate Bayesian computation results in a bias in the approximation to the posterior. An alternative version based on genuine importance sampling arguments bypasses this difficulty, in connection with the population Monte Carlo method of Cappe et al. (2004), and it includes an automatic scaling of the forward kernel. When applied to a population genetics example, it compares favourably with two other versions of the approximate algorithm
Tipo: Journal Article Palavras-chave: IMPORTANCE SAMPLING; MARKOV CHAIN MONTE CARLO; PARTIAL REJECTION CONTROL; SEQUENTIAL MONTE CARLO.
Ano: 2009 URL: http://www.prodinra.inra.fr/prodinra/pinra/doc.xsp?id=PROD2010b719e4fa&uri=/notices/prodinra1/2010/12/
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Bread, beer and wine: Saccharomyces cerevisiae diversity reflects human history Inra
Legras, J.L.; Merdinoglu, D.; Cornuet, J.M.; Karst, F..
Fermented beverages and foods have played a significant role in most societies worldwide for millennia. To better understand how the yeast species Saccharomyces cerevisiae , the main fermenting agent, evolved along this historical and expansion process, we analysed the genetic diversity among 651 strains from 56 different geographical origins, worldwide. Their genotyping at 12 microsatellite loci revealed 575 distinct genotypes organized in subgroups of yeast types, i.e. bread, beer, wine, sake. Some of these groups presented unexpected relatedness: Bread strains displayed a combination of alleles intermediate between beer and wine strains, and strains used for rice wine and sake were most closely related to beer and bread strains. However, up to 28% of...
Tipo: Journal Article Palavras-chave: BIERE; INFERENCE BAYESIENNE DOMESTICATION; MICROSATELLITE; POPULATION GENETICS; SACCHAROMYCES CEREVISIAE; BAYESIAN INFERENCE.
Ano: 2007 URL: http://www.prodinra.inra.fr/prodinra/pinra/doc.xsp?id=PROD20083bedc889&uri=/notices/prodinra1/2008/08/
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Bridgehead effect in the worldwide invasion of the biocontrol Harlequin Ladybird Inra
Lombaert, E.; Guillemaud, T.; Cornuet, J.M.; Malausa, T.; Facon, B.; Estoup, A..
Recent studies of the routes of worldwide introductions of alien organisms suggest that many widespread invasions could have stemmed not from the native range, but from a particularly successful invasive population, which serves as the source of colonists for remote new territories. We call here this phenomenon the invasive bridgehead effect. Evaluating the likelihood of such a scenario is heuristically challenging. We solved this problem by using approximate Bayesian computation methods to quantitatively compare complex invasion scenarios based on the analysis of population genetics (microsatellite variation) and historical (first observation dates) data. We applied this approach to the Harlequin ladybird Harmonia axyridis (HA), a coccinellid native to...
Tipo: Journal Article Palavras-chave: ESPECE INVASIVE; COCCINELLE; COLONISATION; PREVENTION DES RISQUES COCCINELLIDAE; HARMONIA AXYRIDIS.
Ano: 2010 URL: http://www.prodinra.inra.fr/prodinra/pinra/doc.xsp?id=PROD2010951f6b93&uri=/notices/prodinra1/2010/11/
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Combining genetic, historical and geographical data to reconstruct the dynamics of bioinvasions: application to the cane toad Bufo marinus Inra
Estoup, A.; Baird, S.; Ray, N.; Currat, M.; Cornuet, J.M.; Santos, F.; Beaumont, M.A.; Excoffier, L..
We developed a spatially explicit model of a bioinvasion and used an approximate Bayesian computation (ABC) framework to make various inferences from a combination of genetic (microsatellite genotypes), historical (first observation dates) and geographical (spatial coordinates of introduction and sampled sites) information. Our method aims to discriminate between alternative introduction scenarios and to estimate posterior densities of demographically relevant parameters of the invasive process. The performance of our landscape-ABC method is assessed using simulated data sets differing in their information content (genetic and/or historical data). We apply our methodology to the recent introduction and spatial expansion of the cane toad, Bufo marinus, in...
Tipo: Journal Article Palavras-chave: BIOINVASION; INFERERENCE BAYESIENNE; EXPANSION SPATIALE; INFERENCE DEMOGRAPHIQUE; DONNES HISTORIQUES BAYESIAN INFERENCE; BIOINVASION; DEMOGRAPHIC INFERENCES; GENETIC DATA; HISTORICAL DATA; SPATIAL EXPANSION.
Ano: 2010 URL: http://www.prodinra.inra.fr/prodinra/pinra/doc.xsp?id=PROD2011c7948a67&uri=/notices/prodinra1/2011/06/
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Estimating effective population size from linkage disequilibrium: severe bias in small samples Inra
England, P.R.; Cornuet, J.M.; Berthier, P.; Tallmon, D.A.; Luikart, G..
Effective population size (Ne) is a central concept in evolutionary biology and conservation genetics. It predicts rates of loss of neutral genetic variation, .xation of deleterious and favourable alleles, and the increase of inbreeding experienced by a population. A method exists for the estimation of Ne from the observed linkage disequilibrium between unlinked loci in a population sample. While an increasing number of studies have applied this method in natural and managed populations, its reliability has not yet been evaluated. We developed a computer program to calculate this estimator of Ne using the most widely used linkage disequilibrium algorithm and used simulations to show that this estimator is strongly biased when the sample size is small...
Tipo: Journal Article Palavras-chave: TAILLE EFFECTIVE POPULATION; CONSANGUINITE; BIAIS METHODOLOGIQUE EFFECTIVE POPULATION SIZE; LINKAGE DISEQUILIBRIUM; SAMPLING BIAS.
Ano: 2006 URL: http://www.prodinra.inra.fr/prodinra/pinra/doc.xsp?id=PROD200831431e8d&uri=/notices/prodinra1/2008/08/
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Etude biometrique de colonies d'abeilles d'Espagne et du Portugal Inra
Cornuet, J.M.; Fresnaye, J..
Tipo: Journal Article Palavras-chave: APIS MELLIFICA.
Ano: 1989 URL: http://www.prodinra.inra.fr/prodinra/pinra/doc.xsp?id=PUB8900004010797&uri=/notices/prodinra1/2009/12/
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Etude biometrique de populations d'abeilles marocaines Inra
Cornuet, J.M.; Daoudi, A.; Mohssine, H.; Fresnaye, J..
Tipo: Journal Article Palavras-chave: DISTRIBUTION GEOGRAPHIQUE; PHYLOGENESE; APIS MELLIFICA.
Ano: 1988 URL: http://www.prodinra.inra.fr/prodinra/pinra/doc.xsp?id=PUB8900005010798&uri=/notices/prodinra1/2009/12/
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Etude biometrique de populations d'abeilles tunisiennes Inra
Grissa, K.; Cornuet, J.M.; Msadda, K.; Fresnaye, J..
Tipo: Journal Article Palavras-chave: HYMENOPTERA; APOIDEA; APIS MELLIFERA.
Ano: 1990 URL: http://www.prodinra.inra.fr/prodinra/pinra/doc.xsp?id=PUB9000024056016906&uri=/notices/prodinra1/2009/12/
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Etude biometrique d'une population d'abeilles landaises Inra
Cornuet, J.M.; Albisetti, J.; Mallet, N.; Fresnaye, J..
Tipo: Journal Article Palavras-chave: INSECTE UTILE; APIS MELLIFICA; APIDAE; HYMENOPTERA; POPULATION ANIMALE.
Ano: 1982 URL: http://www.prodinra.inra.fr/prodinra/pinra/doc.xsp?id=PUB8700001004347&uri=/notices/prodinra1/2009/12/
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Etude theorique sur la selection du caractere "production de miel" chez l'abeille. I Modele genetique et statistique Inra
Chevalet, C.; Cornuet, J.M..
Tipo: Journal Article Palavras-chave: PRODUCTION DE MIEL; MODELE GENETIQUE; MODELE STATISTIQUE; APIDAE; HYMENOPTERA; APIS.
Ano: 1982 URL: http://www.prodinra.inra.fr/prodinra/pinra/doc.xsp?id=PUB8707607003969&uri=/notices/prodinra1/2009/12/
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Etude theorique sur la selection du caractere "production de miel" chez l'abeille. II. Plan de selection combinee de reines en fecondation naturelle Inra
Cornuet, J.M.; Chevalet, C..
Tipo: Journal Article Palavras-chave: HYMENOPTERA; APIS MELLIFICA; APIDAE; SELECTION; REINE; PRODUCTION DE MIEL; CONSANGUINITE; INSECTE SOCIAL.
Ano: 1987 URL: http://www.prodinra.inra.fr/prodinra/pinra/doc.xsp?id=PUB8700001005423&uri=/notices/prodinra1/2009/12/
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Evolution de la consanguinite dans une population d'abeilles Inra
Chevalet, C.; Cornuet, J.M..
Tipo: Journal Article Palavras-chave: CONSANGUINITE; APIDAE; HYMENOPTERA; APIS.
Ano: 1982 URL: http://www.prodinra.inra.fr/prodinra/pinra/doc.xsp?id=PUB8707608003970&uri=/notices/prodinra1/2009/12/
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Genetic diversity of the west European honey bee (Apis mellifera mellifera and A. m. iberia). I. Mitochondrial DNA Inra
Garnery, L.; Franck, P.; Baudry, E.; Vautrin, D.; Cornuet, J.M.; Solignac, M..
La variabilité de l’ADN mitochondrial a été étudiée chez l’abeille ouest européenne (lignée évolutive M) à partir de 973 colonies représentant 23 populations, grâce à l’analyse des profils de restriction des produits de PCR de la région intergénique COI-COII. Cette étude confirme que l’haplotype M est caractéristique de cette lignée, même si certaines populations sont lourdement introgressées par des haplotypes des deux autres lignées évolutives (A et C). Les populations de la péninsule ibérique (Apis mellifera iberica) sont caractérisées par un cline de fréquence des haplotypes A et M, le premier étant virtuellement fixé en Espagne du sud et au Portugal, le second à peu près pur dans le nord de la péninsule. Cette introgression est attribuée à...
Tipo: Journal Article Palavras-chave: ABEILLE HONEY BEE; MITOCHONDRIAL DNA; PCR; INTROGRESSION.
Ano: 1998 URL: http://www.prodinra.inra.fr/prodinra/pinra/doc.xsp?id=PROD20073fcb3d42&uri=/notices/prodinra1/2011/02/
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Genetic diversity of the west European honey bee (Apis mellifera mellifera and A. m. iberia). II.Microsatellite loci Inra
Garnery, L.; Franck, P.; Baudry, E.; Vautrin, D.; Cornuet, J.M.; Solignac, M..
La variabilité génétique et la différenciation entre populations a été étudiée pour 11 locus microsatellites dans 15 populations de l’abeille ouest européenne. Les deux sous-espèces qui constituent ce rameau (Apis mellifera mellifera et A. m. iberica) ont une variabilité génétique plus réduite que la plupart des autres populations étudiées avec les mêmes outils moléculaires et plusieurs tests statistiques sont révélateurs d’une réduction récente de leur effectif. De plus, les profils génétiques des populations sont très comparables, du sud de l’Espagne à la Scandinavie, Les populations françaises sont plus ou moins introgressées (de quelques pourcentages jusqu’à 57 %) par des gènes de la lignée nordméditerranéenne, les races ligustica et carnica...
Tipo: Journal Article Palavras-chave: ABEILLE HONEY BEE; MICROSATELLITES; POPULATION GENETICS; INTROGRESSION; CONSERVATION.
Ano: 1998 URL: http://www.prodinra.inra.fr/prodinra/pinra/doc.xsp?id=PROD2007f04ca494&uri=/notices/prodinra1/2011/02/
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Heritability of the queen brood post-capping stage duration in Apis mellifera mellifera L. Inra
Le Conte, Y.; Bruchou, C.; Benhamouda, K.; Gauthier, C.; Cornuet, J.M..
Tipo: Journal Article Palavras-chave: RELATION HOTE PARASITE; DUREE D'OPERCULATION; APIS MELLIFERA MELLIFERA; VARROA JACOBSONI; HERITABILITE; DEVELOPPEMENT POSTEMBRYONNAIRE; SELECTION; REINE.
Ano: 1994 URL: http://www.prodinra.inra.fr/prodinra/pinra/doc.xsp?id=PUB9500025146043438&uri=/notices/prodinra1/2009/12/
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In defence of model-based inference in phylogeography (Reply) Inra
Beaumont, M.A.; Nielsen, R.; Robert, C.; Hey, J.; Gaggiotti, O; Knowles, L.; Estoup, A.; Panchal, M.; Corander, J.; Hickerson, M.; Sisson, S.A.; Fagundes, N.; Chikhi, L.; Beerli, P.; Vitalis, R.; Cornuet, J.M.; Huelsenbeck, J.; Foll, M.; Yang, Z.; Rousset, F.; Balding, D.; Excoffier, L..
Recent papers have promoted the view that model-based methods in general, and those based on Approximate Bayesian Computation (ABC) in particular, are flawed in a number of ways, and are therefore inappropriate for the analysis of phylogeographic data. These papers further argue that Nested Clade Phylogeographic Analysis (NCPA) offers the best approach in statistical phylogeography. In order to remove the confusion and misconceptions introduced by these papers, we justify and explain the reasoning behind model-based inference. We argue that ABC is a statistically valid approach, alongside other computational statistical techniques that have been successfully used to infer parameters and compare models in population genetics. We also examine the NCPA method...
Tipo: Journal Article Palavras-chave: PHYLOGEOGRAPHIE MOLECULAR EVOLUTION; PHYLOGEOGRAPHY; POPULATION GENETICS-EMPIRICAL; POPULATION GENETICS-THEORETICAL.
Ano: 2010 URL: http://www.prodinra.inra.fr/prodinra/pinra/doc.xsp?id=PROD2010a6a04229&uri=/notices/prodinra1/2010/12/
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Inférence bayésienne dans des scénarios évolutifs complexes avec populations mélangées: application à l’abeille domestique Inra
Cornuet, J.M.; Excoffier, L.; Franck, P.; Estoup, A..
Nous présentons une méthode d'inférence statistique sur des paramètres démographiques et historiques de scénarios évolutifs. Cette méthode, fondée sur l'approche Approximate Bayesian Computation (ABC), aborde des scénarios complexes incluant des divergences et des remises en contact de populations. Nous l'avons appliquée à un jeu de données d'abeilles domestiques caractérisées à huit locus microsatellites. Le scénario concerne quatre populations reliées par deux divergences et deux remises en contact. Quatre groupes de populations ont subi chacun une double analyse afin d'évaluer la stabilité des estimations. De plus, les erreurs et biais relatifs moyens, calculés sur 500 jeux de données simulés avec des valeurs de paramètres voisines des estimations...
Tipo: Conference Paper Palavras-chave: ABEILLE DOMESTIQUE; INFERENCE BAYESIENNE; DIVERGENCE INFERENCE; DEMOGRAPHY; ADMIXTURE; MICROSATELLITE.
Ano: 2006 URL: http://www.prodinra.inra.fr/prodinra/pinra/doc.xsp?id=PROD2008c3c32ea6&uri=/notices/prodinra1/2008/08/
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Inference on microsatellite mutation processes in the invasive mite, Varroa destructor, using reversible jump Markov Chain Monte Carlo Inra
Cornuet, J.M.; Beaumont, M.A.; Estoup, A.; Solignac, M..
Varroa destructor is a parasitic mite of the Eastern honeybee Apis cerana. Fifty years ago, two distinct evolutionary lineages (Korean and Japanese) invaded the Western honeybee Apis mellifera. This haplo–diploid parasite species reproduces mainly through brother–sister matings, a system which largely favors the .xation of new mutations. In a worldwide sample of 225 individuals from 21 locations collected on Western honeybees and analyzed at 19 microsatellite loci, a series of de novo mutations was observed. Using historical data concerning the invasion, this original biological system has been exploited to compare three mutation models with allele size constraints for microsatellite markers: stepwise (SMM) and generalized (GSM) mutation models, and a...
Tipo: Journal Article Palavras-chave: ABEILLE DOMESTIQUE MICROSATELLITE; MUTATION MODEL; MCMC; MARKOV CHAIN MONTE CARLO.
Ano: 2006 URL: http://www.prodinra.inra.fr/prodinra/pinra/doc.xsp?id=PROD20083c3ba28&uri=/notices/prodinra1/2008/08/
Registros recuperados: 32
Primeira ... 12 ... Última
 

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