- Principal component analysis under population genetic models of range expansion and admixtureOlivier Francois
Laboratoire Techniques de l Ingénierie Médicale et de la Complexité, Faculty of Medicine, University Joseph Fourier, Grenoble Institute of Technology, Centre National de la Recherche Scientifique UMR5525, La Tronche, France
Mol Biol Evol 27:1257-68. 2010..We propose that this surprising pattern is an outcome of the "allele surfing" phenomenon, which creates sectors of high allele-frequency differentiation that align perpendicular to the direction of the expansion...
- Correcting principal component maps for effects of spatial autocorrelation in population genetic dataEric Frichot
Universite Joseph Fourier Grenoble, Centre National de la Recherche Grenoble, France
Front Genet 3:254. 2012..We demonstrate our approach by analyzing single nucleotide polymorphism data from the Human Genome Diversity Panel, and provide comparisons with other recently introduced methods...
- Bayesian clustering using hidden Markov random fields in spatial population geneticsOlivier Francois
TIMC, TIMB Department of Mathematical Biology, La Tronche, France
Genetics 174:805-16. 2006..We illustrate and discuss the implementation issues with the Scandinavian brown bear and the human CEPH diversity panel data set...
- Gaussian approximations for phylogenetic branch length statistics under stochastic models of biodiversityOlivier Francois
TIMC TIMB Dept Math Biology, INP Grenoble, UJF CNRS, Faculte de Medecine, F38706 La Tronche, France
Math Biosci 209:108-23. 2007..Under an appropriate normalization the model is shown to behave similarly as the coalescent, and the approximations given here are also valid in this context...
- Demographic history of european populations of Arabidopsis thalianaOlivier Francois
Institut National Polytechnique de Grenoble, Grenoble, France
PLoS Genet 4:e1000075. 2008..However, the speed and time frame of the model also suggest that the migration of A. thaliana into Europe may have accompanied the spread of agriculture during the Neolithic transition...
- apTreeshape: statistical analysis of phylogenetic tree shapeNicolas Bortolussi
Team of Mathematical Biology TIMB, TIMC, Faculty of Medicine, F38706 La Tronche, France
Bioinformatics 22:363-4. 2006..One strength of the package is to include appropriate corrections of classical shape statistics as well as new tests based on the statistical theory of likelihood ratios...
- Spatial inference of admixture proportions and secondary contact zonesEric Durand
Faculty of Medicine, Laboratoire des Techniques de 1 Ingénierie Médicale et de la Complexité, University Joseph Fourier, Grenoble IT, Group of Mathematical Biology, La Tronche, France
Mol Biol Evol 26:1963-73. 2009..We also apply our approach to understand the population structure of the killifish, Fundulus heteroclitus, for which the algorithm uncovers a presumed contact zone in the Atlantic coast of North America...
- Genome scan methods against more complex models: when and how much should we trust them?Pierre de Villemereuil
Centre National de la Recherche Scientifique, Université Jospeh Fourier, LECA, UMR 5553, 2233 Rue de la Piscine, 38400, Saint Martin d Heres, France
Mol Ecol 23:2006-19. 2014..We found that it is possible to greatly reduce error rates by considering the results of all three methods when identifying outlier loci. ..
- On statistical tests of phylogenetic tree imbalance: the Sackin and other indices revisitedMichael G B Blum
TIMC TIMB, Faculte de Medecine, F38706 La Tronche Cedex, France
Math Biosci 195:141-53. 2005..As an illustration, the tests are applied to the HIV-1 reconstructed phylogeny...
- Approximate Bayesian Computation (ABC) in practiceKatalin Csilléry
Laboratoire Techniques de l Ingénierie Médicale et de la Complexité, Centre National de la Recherche Scientifique UMR5525, Universite Joseph Fourier, 38706 La Tronche, France
Trends Ecol Evol 25:410-8. 2010..ABC can be a powerful tool to make inferences with complex models if these principles are carefully applied...
- Brownian models and coalescent structuresMichael G B Blum
Laboratoire Ecologie, Systematique et Evolution, Universite Paris Sud, Batiment 360, F91405 Orsay, France
Theor Popul Biol 65:249-61. 2004..The last approach consists of computing the likelihood by a Markov chain Monte Carlo sampling method. In the one-dimensional Brownian motion, this method seems less reliable than pseudomaximum-likelihood...
- Probabilistic analysis of a genealogical model of animal group patternsEric Durand
TIMB Group of Mathematical Biology, TIMC UMR 5525, Fac Med, Grenoble Universités, La Tronche Cedex, France
J Math Biol 60:451-68. 2010..Computer simulations are also utilized to measure the extent to which the asymptotic approximation can be applied with confidence...
- Predictions of native American population structure using linguistic covariates in a hidden regression frameworkFlora Jay
Laboratoire des Techniques de l Ingénierie Médicale et de la Complexité, Equipe Biologie Computationnelle et Mathématique, Faculte de Medecine, Universite Joseph Fourier, Grenoble, Centre National de la Recherche Scientifique, La Tronche, France
PLoS ONE 6:e16227. 2011..Here we investigate to which extent geography and languages can predict the genetic structure of Native American populations...
- Testing for associations between loci and environmental gradients using latent factor mixed modelsEric Frichot
TIMC IMAG UMR 5525, Universite Joseph Fourier Grenoble, Centre National de la Recherche Scientifique, Grenoble, France
Mol Biol Evol 30:1687-99. 2013..We then apply these models to plant and human genetic data, identifying several genes with functions related to development that exhibit strong correlations with climatic gradients...
- Matrilineal fertility inheritance detected in hunter-gatherer populations using the imbalance of gene genealogiesMichael G B Blum
Laboratoire TIMC TIMB, Faculte de Medecine, Grenoble, France
PLoS Genet 2:e122. 2006..One possible explanation for this result is that in hunter-gatherer populations, individuals belonging to large kin networks may benefit from stronger social support and may be more likely to have a large number of offspring...
- Prediction of group patterns in social mammals based on a coalescent modelEric Durand
TIMC, University Joseph Fourier, INP Grenoble, CNRS, Grenoble, France
J Theor Biol 249:262-70. 2007..The test is then applied to ecological data from social herbivores and carnivores. Our findings support the hypothesis that genetic relatedness is likely to predict group patterns when large mammals have few or no predators...
- Fast and efficient estimation of individual ancestry coefficientsEric Frichot
Universite Joseph Fourier Grenoble 1, Centre National de la Recherche Scientifique, Techniques de l Ingénierie Médicale et de la Complexité Informatique, Mathématiques et Applications, Grenoble Unité Mixte de Recherche 5525, 38042 Grenoble, France
Genetics 196:973-83. 2014..Without loss of accuracy, sNMF computed estimates of ancestry coefficients with runtimes ∼10-30 times shorter than those of ADMIXTURE. ..
- Forecasting changes in population genetic structure of alpine plants in response to global warmingFlora Jay
Universite Joseph Fourier Grenoble 1, Centre National de la Recherche Scientifique, TIMC IMAG UMR 5525, 38041 Grenoble, France
Mol Ecol 21:2354-68. 2012....
- A statistical approach to estimating the strength of cell-cell interactions under the differential adhesion hypothesisMathieu Emily
TIMC TIMB, Universite Joseph Fourier, INP Grenoble, Faculty of Medicine, 38706 La Tronche Cedex, France
Theor Biol Med Model 4:37. 2007..The Differential Adhesion Hypothesis (DAH) is a theory of the organization of cells within a tissue which has been validated by several biological experiments and tested against several alternative computational models...
- Spatially explicit Bayesian clustering models in population geneticsOlivier Francois
Grenoble IT, Joseph Fourier University, CNRS UMR 5525, TIMC, Group of Computational and Mathematical Biology, 38706 La Tronche, France
Mol Ecol Resour 10:773-84. 2010..In contrast, admixture models are robust to an absence of admixture in the sample. We also give statistical and conceptual reasons why data should be explored using spatially explicit models that include admixture...