Francois Rousset

• Senior Researcher at Université de Montpellier

Understanding the selection of breeding sites in cities is key for the effective management of urban bird populations. We analysed 16 years of data collected within a relocation program for female mallards in Berlin (Germany), with the goal of (i) characterizing the breeding output and breeding sites in urban environments, (ii) identifying factors...

We describe and evaluate a method of statistical inference of model parameters, which revisits the idea of inferring a likelihood surface using simulation when the likelihood function cannot be evaluated. The method aims in particular to provide confidence intervals with controlled coverage, and its performance is assessed accordingly. It is based...

Introgression, the incorporation of foreign variants through hybridization and repeated backcross, is increasingly being studied for its potential evolutionary consequences, one of which is adaptive introgression (AI). In recent years, several statistical methods have been proposed for the detection of loci that have undergone adaptive introgressio...

Maternal investment influences the survival and reproduction of both mothers and their progeny and plays a crucial role in understanding individuals’ life-history and population ecology. To reveal the complex mechanisms associated with reproduction and investment, it is necessary to examine variations in maternal investment across species. Comparis...

Behavioral discrimination of kin is a key process structuring social relationships in animals. In this study, we provide evidence for discrimination towards non-kin by third-parties through a mechanism of phenotype matching. In mandrills, we recently demonstrated increased facial resemblance among paternally related juvenile and adult females indic...

The 2020 global spatial targets for protected areas set by the Convention on Biological Diversity have almost been achieved, but management effectiveness remains deficient. Personnel shortages are widely cited as major contributing factors but have not previously been quantified. Using data from 176 countries and territories, we estimate a current...

The black truffle Tuber melanosporum was disseminated all over the world, propelled by the development of a wide variety of empirical practices. A widespread practice, called ‘truffle trap’, consists of placing pieces of truffles into excavations dug under host trees, and of collecting truffle in these traps in the next years. This research aims at...

Historically, mothers producing twins gave birth, on average, more often than non-twinners. This observation has been interpreted as twinners having higher intrinsic fertility – a tendency to conceive easily irrespective of age and other factors – which has shaped both hypotheses about why twinning persists and varies across populations, and the de...

Behavioral discrimination of kin is a key process structuring social relationships in animals. In this study, we provide a first example of discrimination towards non-kin by third-parties through a mechanism of phenotype matching. In mandrills, we recently demonstrated increased facial resemblance among paternally-related juvenile and adult females...

Kin discrimination is a key process structuring social relationships in animals. We show how it may be generalized to entail discrimination towards non-kin, and provide a first example of this process in a primate. In mandrills, we recently demonstrated increased facial resemblance among paternally-related females indicating adaptive opportunities...

Motivation Simulation-based inference can bypass the limitations of statistical methods based on analytical approximations, but software allowing simulation of structured population genetic data without the classical n-coalescent approximations (such as those following from assuming large population size) are scarce or slow. Results We present GSp...

Sexual dimorphism in plants may emerge as a result of sex‐specific selection on traits enhancing access to nutritive resources and/or to sexual partners. Here we investigated sex‐specific differences in selection of sexually dimorphic traits and in the spatial distribution of effective fecundity (our fitness proxy) in a highly dimorphic dioecious w...

It is commonly asserted that when extrinsic mortality is high, individuals should invest early in reproduction. This intuition thrives in the literature on life-history theory and human behavior, yet it has been criticized repeatedly on the basis of mathematical models. The intuition is indeed wrong; but a recent theoretical criticism has confused...

Selection of the fittest can promote individual competitiveness but often results in the erosion of group performance. Recently, several authors revisited this idea in crop production and proposed new practices based on selection for cooperative phenotypes, i.e. phenotypes that increase crop yield through decreased competitiveness. These recommenda...

Adaptation is often described in behavioral ecology as individuals maximizing their inclusive fitness. Under what conditions does this hold and how does this relate to the gene-centered perspective of adaptation? We unify and extend the literature on these questions to class-structured populations. From a gene-centered perspective, we demonstrate t...

Adaptation is often described in behavioral ecology as individuals maximizing their inclusive fitness. Under what conditions does this hold, and how does this relate to the gene-centered perspective of adaptation? We unify and extend the literature on these questions to class-structured populations. We demonstrate that the maximization (in the best...

It is commonly asserted that when extrinsic mortality is high, individuals should invest early in reproduction. This intuition thrives in the literature on life-history theory and human behavior, yet it has been criticized repeatedly on the basis of mathematical models. The intuition is indeed wrong; but a recent theoretical criticism has confused...

Biological responses to climate change have been widely documented across taxa and regions, but it remains unclear whether species are maintaining a good match between phenotype and environment, i.e. whether observed trait changes are adaptive. Here we reviewed 10,090 abstracts and extracted data from 71 studies reported in 58 relevant publications...

Identifying how dominance within and between the sexes is established is pivotal to understanding sexual selection and sexual conflict. In many species, members of one sex dominate those of the other in one-on-one interactions. Whether this results from a disparity in intrinsic attributes, such as strength and aggressiveness, or in extrinsic factor...

Likelihood methods are being developed for inference of migration rates and past demographic changes from population genetic data. We survey an approach for such inference using sequential importance sampling techniques derived from coalescent and diffusion theory. The consistent application and assessment of this approach has required the re-imple...

Likelihood methods are being developed for inference of migration rates and past demographic changes from population genetic data. We survey an approach for such inference using sequential importance sampling techniques derived from coalescent and diffusion theory. The consistent application and assessment of this approach has required the re-imple...

Isoscapes are maps depicting the continuous spatial (and sometimes temporal) variation in isotope composition. They have various applications ranging from the study of isotope circulation in the main earth systems to the determination of the provenance of migratory animals. Isoscapes can be produced from the fit of statistical models to observation...

IsoriX can be used for building isoscapes using mixed models and inferring the geographic origin of organisms based on their isotopic signature. This package is essentially a simplified interface combining several other packages. It uses the package spaMM for fitting and predicting isoscapes, and for performing the assignment. IsoriX also heavily r...

Hybridization is increasingly recognized as a significant evolutionary process, in particular because it can lead to introgression of genes from one species to another. A striking pattern of discordance in the amount of introgression between mitochondrial and nuclear markers exists such that substantial mitochondrial introgression is often found in...

The life cycle of the black truffle (Tuber melanosporum) includes a mating before sporulation: although the species is hermaphroditic, mating turns out to involve parents with very different features, that mostly behave as male or female only, suggesting that this species undergoes forced dioecism.

Truffe en quête de pères : un champignon à l’orientation sexuelle forcée, et pas encore domestiqué !

La truffe révèle les secrets de sa sexualité

In recent years, simulation methods such as approximate Bayesian computation have extensively been used to infer parameters of population genetic models where the likelihood is intractable. We describe an alternative approach, summary likelihood, that provides a likelihood-based analysis of the information retained in the summary statistics whose d...

The life cycles and dispersal of edible fungi are still poorly known, thus limiting our understanding of their evolution and domestication. The prized Tuber melanosporum produces fruitbodies (fleshy organs where meiospores mature) gathered in natural, spontaneously inoculated forests or harvested in plantations of nursery-inoculated trees. Yet, how...

In nature, the intensity of mate choice (i.e., choosiness) is highly variable within and between sexes. Despite growing empirical evidence of male and/or mutual mate choice, theoretical investigations of the joint evolution of female and male choosiness are few. In addition, previous approaches have often assumed an absence of trade-off between the...

Significance Will plants species survive climate warming? By which mechanisms? Ignoring pollen dispersal, previous models have predicted that species may escape extinction by tracking in space the climatic conditions to which they were previously adapted. Using quantitative genetics models, we demonstrate that plants dispersing their pollen could s...

Sequential importance sampling algorithms have been defined to estimate likelihoods in models of ancestral population processes. However, these algorithms are based on features of the models with constant population size, and become inefficient when the population size varies in time, making likelihood-based inferences difficult in many demographic...

Sequential importance sampling algorithms have been defined to estimate likelihoods in models of ancestral population processes. However, these algorithms are based on features of the models with constant population size, and become inefficient when the population size varies in time, making likelihood-based inferences difficult in many demographic...

A general version of inclusive fitness based on regression is re-derived with minimal mathematics and directly from the verbal interpretation of its terms that motivated the original formulation of the inclusive fitness concept. This verbal interpretation is here extended to provide the two relationships required to determine the two coefficients -...

Previous studies have addressed why and how mono-stratified epithelia adopt a polygonal topology. One major additional, and yet unanswered question is how the frequency of different cell shapes is achieved and whether the same distribution applies between non-proliferative and proliferative epithelia. We compared different proliferative and non-pro...

Plasmodium falciparum infections in malaria endemic areas often harbor multiple clones of parasites. However, the transmission success of the different genotypes within the mosquito vector has remained elusive so far. The genetic diversity of malaria parasites was measured by using microsatellite markers in gametocyte isolates from 125 asymptomatic...

In Arthropods, the intracellular bacteria Wolbachia often induce cytoplasmic incompatibility (CI) between sperm and egg, which causes conditional embryonic death and promotes the spatial spread of Wolbachia infections into host populations. The ability of Wolbachia to spread in natural populations through CI has attracted attention for using these...

Chromosomal inversions allow genetic divergence of locally adapted populations by reducing recombination between chromosomes with different arrangements. While patterns of genetic variation within inverted regions are increasingly documented, inferential methods are largely missing to analyze such data. Previous work has provided expectations for c...

Reproductive success and survival are influenced by wealth in human populations. Wealth is transmitted to offsprings and strategies of transmission vary over time and among populations, the main variation being how equally wealth is transmitted to children. Here we propose a model where we simulate both the dynamics of wealth in a population and th...

Understanding the demographic history of populations and species is a central issue in evolutionary biology and molecular ecology. In this work, we develop a maximum-likelihood method for the inference of past changes in population size from microsatellite allelic data. Our method is based on importance sampling of gene genealogies, extended for ne...

Most theoretical research in sexual selection has focused on indirect selection. However, empirical studies have not strongly supported indirect selection. A well-established finding is that direct benefits and costs exert a strong influence on the evolution of mate choice. We present an analytical model in which unilateral mate choice evolves sole...

We survey the population genetic basis of social evolution, using a logically consistent set of arguments to cover a wide range of biological scenarios. We start by reconsidering Hamilton's (Hamilton 1964 J. Theoret. Biol. 7, 1-16 (doi:10.1016/0022-5193(64)90038-4)) results for selection on a social trait under the assumptions of additive gene acti...

Individual-as-maximizing agent analogies result in a simple understanding of the functioning of the biological world. Identifying the conditions under which individuals can be regarded as fitness maximizing agents is thus of considerable interest to biologists. Here, we compare different concepts of fitness maximization, and discuss within a single...

Spatial autocorrelation is a well-recognized concern for observational data in general, and more specifically for spatial data in ecology. Generalized linear mixed models (GLMMs) with spatially autocorrelated random effects are a potential general framework for handling these spatial correlations. However, as the result of statistical and practical...

A canon of population genetics concerns the properties of FST, a descriptor of spatial genetic structure. Interest for FST arose from Wright's early insights linking FST to dispersal parameters as well as to his concept of effective population size (e.g., Wright 1938, 1951). Although there is continued interest in this topic, FST also serves in oth...

Dispersal and dormancy are two strategies that allow recolonization of empty patches and escape from kin competition. Because they presumably respond to similar evolutionary forces, it is tempting to consider that these strategies may substitute for each other. Yet in order to predict the outcome of the evolution of dispersal and dormancy, and to c...

In heterogeneous landscapes, the genetic and demographic consequences of dispersal influence the evolution of niche width. Unless pollen is limiting, pollen dispersal does not contribute directly to population growth. However, by disrupting local adaptation, it indirectly affects population dynamics. We compare the effect of pollen versus seed disp...

Since the mid 1970s, cancer has been described as a process of Darwinian evolution, with somatic cellular selection and evolution being the fundamental processes leading to malignancy and its many manifestations (neoangiogenesis, evasion of the immune system, metastasis, and resistance to therapies). Historically, little attention has been placed o...

Alternative splicing provides a critical and flexible layer of regulation intervening in many biological processes to regulate the diversity of proteins and impact cell phenotype. To identify alternative splicing differences that distinguish epithelial from mesenchymal tissues, we have investigated hundreds of cassette exons using a high-throughput...

Likelihood-based methods of inference of population parameters from genetic data in structured populations have been implemented but still little tested in large networks of populations. In this work, a previous software implementation of inference in linear habitats is extended to two-dimensional habitats, and the coverage properties of confidence...

Chromosomal inversions allow genetic divergence of locally adapted populations by reducing recombination between chromosomes with different arrangements. Divergence between populations (or hybridization between species) is expected to leave signatures in the neutral genetic diversity of the inverted region. Quantitative expectations for these patte...

The simple and partial Mantel tests are routinely used in many areas of evolutionary biology to assess the significance of the association between two or more matrices of distances relative to the same pairs of individuals or demes. Partial Mantel tests rather than simple Mantel tests are widely used to assess the relationship between two variables...

The expression of a social behaviour may affect the fitness of actors and recipients living in the present and in the future of the population. When there is a risk that a future reward will not be experienced in such a context, the value of that reward should be discounted; but by how much? Here, we evaluate social discount rates for delayed fitne...

Calls for an extended evolutionary synthesis are flourishing in the scientific literature (as highlighted by a recent Review article in this journal (Beyond DNA: integrating exclusive inheritance into an extended theory of evolution. Nature Reviews Genetics 12, 475–486 (2011)¹) and Refs 2, 3), so the identification of the necessary 'extensions' has...

Plant-fungal symbiosis is stabilized by the extent of reciprocal nutrient supply.

In a recent article, Nowak et al. claim that the mathematical basis of inclusive fitness theory does not stand to scrunity and to have found an alternative explanation for eusociality. We show that these claims are based on false premises, many of which have been exposed more than 25 years ago, such as misrepresentations of the basic components of...

Landscape genetics, which combines population genetics, landscape ecology and spatial statistics, has emerged recently as a new discipline that can be used to assess how landscape features or environmental variables can influence gene flow and spatial genetic variation. We applied this approach to the invasive plant pathogenic fungus Mycosphaerella...

Arising from M. A. Nowak, C. E. Tarnita & E. O. Wilson 466, 1057-1062 (2010); Nowak et al. reply. Nowak et al. argue that inclusive fitness theory has been of little value in explaining the natural world, and that it has led to negligible progress in explaining the evolution of eusociality. However, we believe that their arguments are based upon a...

Deviations from HWE for 10 neutral microsatellite markers. (0.02 MB XLS)

Deviations from HWE for the final 6 SNPs for Isolates 1–3. * P<0.05. (0.02 MB XLS)

Kruskal-Wallis test for association and deviations from HWE. Data given for 21 SNPs (previously significant based on mosquitoes with extreme phenotype only) for all mosquitoes fed on Isolate 1. * P<0.05. (0.02 MB XLS)

Immune related gene, primer and SNP details. + indicates primers from [37], # indicates primers from [63] and ∧ indicates primers from [64] (Nested Primers). (0.05 MB XLS)

Many genes involved in the immune response of Anopheles gambiae, the main malaria vector in Africa, have been identified, but whether naturally occurring polymorphisms in these genes underlie variation in resistance to the human malaria parasite, Plasmodium falciparum, is currently unknown. Here we carried out a candidate gene association study to...

In the malaria vector Anopheles gambiae, understanding diversity in natural populations and genetic components of important phenotypes such as resistance to malaria infection is crucial for developing new malaria transmission blocking strategies. The design and interpretation of many studies here depends critically on Linkage disequilibrium (LD). F...

Staphylococcus aureus nasal carriage is influenced by multifactorial interactions which are difficult to study in open populations. Therefore, we concomitantly assessed the epidemiological, microbiological, and human-genetic carriage-related factors in a nearly closed population. In 2006 and 2008, we collected nasal S. aureus strains, human DNA, an...

In natural populations, dispersal tends to be limited so that individuals are in local competition with their neighbours. As a consequence, most behaviours tend to have a social component, e.g. they can be selfish, spiteful, cooperative or altruistic as usually considered in social evolutionary theory. How social behaviours translate into fitness c...

Intestinal carriage is a key factor in extended-spectrum beta-lactamase (ESBL) infection epidemiology but is difficult to study in open communities. To overcome this problem, we studied a highly stable group of Amerindians for whom we reported an ESBL carriage prevalence of 3.2% in 2001. In 2006, ESBL carriage was assessed among 163 healthy volunte...

Hunter-gatherer Pygmies from Central Africa are described as being extremely mobile. Using neutral genetic markers and population genetics theory, we explored the dispersal behaviour of the Baka Pygmies from Cameroon, one of the largest Pygmy populations in Central Africa. We found a strong correlation between genetic and geographical distances: a...

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 appr...

The local density of individuals is seldom uniform in space and time within natural populations. Yet, formal approaches to the process of isolation by distance in continuous populations have encountered analytical difficulties in describing genetic structuring with demographic heterogeneities, usually disregarding local correlations in the movement...

Using the coalescence theory, we derived a simple expression for the asymptotic inbreeding effective population size of Plasmodium falciparum, the most malignant agent of malaria, in relationship to F-statistics at different hierarchical levels. We consider the effective size of malaria parasites, both for the intrinsic interest of the result for t...

Disruption of gene flow among demes after landscape fragmentation can facilitate local adaptation but increase the effect of genetic drift and inbreeding. The joint effects of these conflicting forces on the mean fitness of individuals in a population are unknown. Through simulations, we explored the effect of increased isolation on the evolution o...

Natural populations are of finite size and organisms carry multilocus genotypes. There are, nevertheless, few results on multilocus models when both random genetic drift and natural selection affect the evolutionary dynamics. In this paper we describe a formalism to calculate systematic perturbation expansions of moments of allelic states around ne...

Natural selection may favor two very different types of social behaviors that have costs in vital rates (fecundity and/or survival) to the actor: helping behaviors, which increase the vital rates of recipients, and harming behaviors, which reduce the vital rates of recipients. Although social evolutionary theory has mainly dealt with helping behavi...

When dispersal is limited, crosses between different regions may generate progeny of higher fitness than crosses within regions, due to the fact that individuals from the same region are more likely to share the same recessive deleterious alleles. This phenomenon (termed heterosis) generates a selective force favouring dispersal; however, the impor...

When dispersal is limited, crosses between different regions may generate progeny of higher fitness than crosses within regions, due to the fact that individuals from the same region are more likely to share the same recessive deleterious alleles. This phenomenon (termed heterosis) generates a selective force favouring dispersal; however, the impor...

Despite abundant empirical evidence that inbreeding depression varies with both the environment and the genotypic context, theoretical predictions about such effects are still rare. Using a quantitative genetics model, we predict amounts of inbreeding depression for fitness emerging from Gaussian stabilizing selection on some phenotypic trait, on w...

Programmed cell death is one of the most fascinating demonstrations of the plasticity of biological systems. It is classically described to act upstream of and govern major developmental patterning processes (e.g. inter-digitations in vertebrates, ommatidia in Drosophila). We show here the first evidence that massive apoptosis can also be controlle...

The debate over the role of stochasticity is central in evolutionary biology, often summarised by whether or not evolution is predictable or repeatable. Here we distinguish three types of stochasticity: stochasticity of mutation and variation, of individual life histories and of environmental change. We then explain when stochasticity matters in ev...