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Papers by Olivier Marvens Francois

Annual Review of Ecology, Evolution, and Systematics, 2012

There is a growing interest in identifying ecological factors that influence adaptive genetic div... more There is a growing interest in identifying ecological factors that influence adaptive genetic diversity patterns in both model and nonmodel species. The emergence of large genomic and environmental data sets, as well as the increasing sophistication of population genetics methods, provides an opportunity to characterize these patterns in relation to the environment. Landscape genetics has emerged as a flexible analytical framework that connects patterns of adaptive genetic variation to environmental heterogeneity in a spatially explicit context. Recent growth in this field has led to the development of numerous spatial statistical methods, prompting a discussion of the current benefits and limitations of these approaches. Here we provide a review of the design of landscape genetics studies, the different statistical tools, some important case studies, and perspectives on how future advances in this field are likely to shed light on important processes in evolution and ecology.

Frontiers in Genetics, 2012

Statistics and Computing, 2009

Molecular Ecology Resources, 2010

This article reviews recent developments in Bayesian algorithms that explicitly include geographi... more This article reviews recent developments in Bayesian algorithms that explicitly include geographical information in the inference of population structure. Current models substantially differ in their prior distributions and background assumptions, falling into two broad categories: models with or without admixture. To aid users of this new generation of spatially explicit programs, we clarify the assumptions underlying the models, and we test these models in situations where their assumptions are not met. We show that models without admixture are not robust to the inclusion of admixed individuals in the sample, thus providing an incorrect assessment of population genetic structure in many cases. 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.

Molecular Ecology, 2012

Species range shifts in response to climate and land use change are commonly forecasted with spec... more Species range shifts in response to climate and land use change are commonly forecasted with species distribution models based on species occurrence or abundance data. Although appealing, these models ignore the genetic structure of species, and the fact that different populations might respond in different ways because of adaptation to their environment. Here, we introduced ancestry distribution models, that is, statistical models of the spatial distribution of ancestry proportions, for forecasting intra‐specific changes based on genetic admixture instead of species occurrence data. Using multi‐locus genotypes and extensive geographic coverage of distribution data across the European Alps, we applied this approach to 20 alpine plant species considering a global increase in temperature from 0.25 to 4 °C. We forecasted the magnitudes of displacement of contact zones between plant populations potentially adapted to warmer environments and other populations. While a global trend of mov...

Methods in Ecology and Evolution, 2012

Summary1. Many recent statistical applications involve inference under complex models, where it i... more Summary1. Many recent statistical applications involve inference under complex models, where it is computationally prohibitive to calculate likelihoods but possible to simulate data. Approximate Bayesian computation (ABC) is devoted to these complex models because it bypasses the evaluation of the likelihood function by comparing observed and simulated data.2. We introduce the R package ‘abc’ that implements several ABC algorithms for performing parameter estimation and model selection. In particular, the recently developed nonlinear heteroscedastic regression methods for ABC are implemented. The ‘abc’ package also includes a cross‐validation tool for measuring the accuracy of ABC estimates and to calculate the misclassification probabilities when performing model selection. The main functions are accompanied by appropriate summary and plotting tools.3. R is already widely used in bioinformatics and several fields of biology. The R package ‘abc’ will make the ABC algorithms availabl...

Journal of Mathematical Biology, 2009

PloS one, Jan 31, 2011

The mainland of the Americas is home to a remarkable diversity of languages, and the relationship... more The mainland of the Americas is home to a remarkable diversity of languages, and the relationships between genes and languages have attracted considerable attention in the past. Here we investigate to which extent geography and languages can predict the genetic structure of Native American populations.

The Annals of Applied Probability, 2006

In interphase, microtubules form a more or less dynamic network of fibers, usually originating at... more In interphase, microtubules form a more or less dynamic network of fibers, usually originating at the centrosome.They play a role in intracellular movement and positioning of organelles (mitochondria, Golgi apparatus, cytoplasmic vesi- cles). When the cell enters mitosis, the interphase network disappears and microtubules start to assemble the mitotic spindle, the function of which is to segregate the chromo- somes

Annual Review of Ecology, Evolution, and Systematics, 2012

There is a growing interest in identifying ecological factors that influence adaptive genetic div... more There is a growing interest in identifying ecological factors that influence adaptive genetic diversity patterns in both model and nonmodel species. The emergence of large genomic and environmental data sets, as well as the increasing sophistication of population genetics methods, provides an opportunity to characterize these patterns in relation to the environment. Landscape genetics has emerged as a flexible analytical framework that connects patterns of adaptive genetic variation to environmental heterogeneity in a spatially explicit context. Recent growth in this field has led to the development of numerous spatial statistical methods, prompting a discussion of the current benefits and limitations of these approaches. Here we provide a review of the design of landscape genetics studies, the different statistical tools, some important case studies, and perspectives on how future advances in this field are likely to shed light on important processes in evolution and ecology.

Frontiers in Genetics, 2012

Statistics and Computing, 2009

Molecular Ecology Resources, 2010

This article reviews recent developments in Bayesian algorithms that explicitly include geographi... more This article reviews recent developments in Bayesian algorithms that explicitly include geographical information in the inference of population structure. Current models substantially differ in their prior distributions and background assumptions, falling into two broad categories: models with or without admixture. To aid users of this new generation of spatially explicit programs, we clarify the assumptions underlying the models, and we test these models in situations where their assumptions are not met. We show that models without admixture are not robust to the inclusion of admixed individuals in the sample, thus providing an incorrect assessment of population genetic structure in many cases. 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.

Molecular Ecology, 2012

Species range shifts in response to climate and land use change are commonly forecasted with spec... more Species range shifts in response to climate and land use change are commonly forecasted with species distribution models based on species occurrence or abundance data. Although appealing, these models ignore the genetic structure of species, and the fact that different populations might respond in different ways because of adaptation to their environment. Here, we introduced ancestry distribution models, that is, statistical models of the spatial distribution of ancestry proportions, for forecasting intra‐specific changes based on genetic admixture instead of species occurrence data. Using multi‐locus genotypes and extensive geographic coverage of distribution data across the European Alps, we applied this approach to 20 alpine plant species considering a global increase in temperature from 0.25 to 4 °C. We forecasted the magnitudes of displacement of contact zones between plant populations potentially adapted to warmer environments and other populations. While a global trend of mov...

Methods in Ecology and Evolution, 2012

Summary1. Many recent statistical applications involve inference under complex models, where it i... more Summary1. Many recent statistical applications involve inference under complex models, where it is computationally prohibitive to calculate likelihoods but possible to simulate data. Approximate Bayesian computation (ABC) is devoted to these complex models because it bypasses the evaluation of the likelihood function by comparing observed and simulated data.2. We introduce the R package ‘abc’ that implements several ABC algorithms for performing parameter estimation and model selection. In particular, the recently developed nonlinear heteroscedastic regression methods for ABC are implemented. The ‘abc’ package also includes a cross‐validation tool for measuring the accuracy of ABC estimates and to calculate the misclassification probabilities when performing model selection. The main functions are accompanied by appropriate summary and plotting tools.3. R is already widely used in bioinformatics and several fields of biology. The R package ‘abc’ will make the ABC algorithms availabl...

Journal of Mathematical Biology, 2009

PloS one, Jan 31, 2011

The mainland of the Americas is home to a remarkable diversity of languages, and the relationship... more The mainland of the Americas is home to a remarkable diversity of languages, and the relationships between genes and languages have attracted considerable attention in the past. Here we investigate to which extent geography and languages can predict the genetic structure of Native American populations.

The Annals of Applied Probability, 2006

In interphase, microtubules form a more or less dynamic network of fibers, usually originating at... more In interphase, microtubules form a more or less dynamic network of fibers, usually originating at the centrosome.They play a role in intracellular movement and positioning of organelles (mitochondria, Golgi apparatus, cytoplasmic vesi- cles). When the cell enters mitosis, the interphase network disappears and microtubules start to assemble the mitotic spindle, the function of which is to segregate the chromo- somes