Arnaud Estoup

French National Institute for Agricultural Research and Environment (INRAE)

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...

In an era marked by rapid global changes, the reinforcement and modernization of plant health surveillance systems have become imperative. Sixty-five scientists present here a research agenda for an enhanced and modernized plant health surveillance to anticipate and mitigate disease and pest emergence. Our approach integrates a wide range of scient...

Both local adaptation and adaptive phenotypic plasticity can influence the match between phenotypic traits and local environmental conditions. Theory predicts that environments stable for multiple generations promote local adaptation, whereas highly heterogeneous environments favor adaptive phenotypic plasticity. However, when environments have per...

The invasive pest Drosophila suzukii is a fruit fly native to Asia that infests a wide variety of fruits. Wild plant species are major reservoirs for D . suzukii populations but their infestation rates vary greatly among geographical areas. We aimed at disentangling the relative roles of macroclimatic, landscape and local factors in the rate of D ....

Both adaptive phenotypic plasticity and local adaptation can influence the match between phenotypic traits and local environmental conditions. Theory predicts that coarse-grained environments, which are stable for multiple generations, promote local adaptation, while fine-grained environments, in which individuals encounter more than one environmen...

Experiments comparing native to introduced populations or distinct introduced populations to each other show that phenotypic evolution is common and often involves a suit of interacting phenotypic traits. We define such sets of traits that evolve in concert and contribute to the success of invasive populations as an invasion syndrome. The invasive...

By capturing various patterns of the structuring of genetic variation across populations, f ‐statistics have proved highly effective for the inference of demographic history. Such statistics are defined as covariance of SNP allele frequency differences among sets of populations without requiring haplotype information and are hence particularly rele...

The process of local adaptation involves differential changes in fitness over time across different environments. While experimental evolution studies have extensively tested for patterns of local adaptation at a single time point, there is relatively little research that examines fitness more than once during the time course of adaptation. We allo...

By capturing various patterns of the structuring of genetic variation across populations, f -statistics have proved highly effective for the inference of demographic history. Such statistics are defined as covariance of SNP allele frequency differences among sets of populations without requiring haplotype information and are hence particularly rele...

Transposable Elements (TEs) are ubiquitous and mobile repeated sequences. They are major determinants of host fitness. Here, we characterized the TE content of the spotted wing fly Drosophila suzukii. Using a recently improved genome assembly, we reconstructed TE sequences de novo, and found that TEs occupy 47% of the genome and are mostly located...

Simulation‐based methods such as Approximate Bayesian Computation (ABC) are well‐adapted to the analysis of complex scenarios of populations and species genetic history. In this context, supervised machine learning (SML) methods provide attractive statistical solutions to conduct efficient inferences about scenario choice and parameter estimation....

Transposable Elements (TEs) are ubiquitous and mobile repeated sequences. They are major determinants of host fitness. Here, we portrayed the TE content of the spotted wing fly Drosophila suzukii . Using a recently improved genome assembly, we reconstructed TE sequences de novo , and found that TEs occupy 47% of the genome and are mostly located in...

Dating population divergence within species from molecular data and relating such dating to climatic and biogeographic changes is not trivial. Yet it can help formulating evolutionary hypotheses regarding local adaptation and future responses to changing environments. Key issues include statistical selection of a demographic and historical scenario...

Over the past decade, the spotted wing Drosophila, Drosophila suzukii, has invaded Europe and America and has become a major agricultural pest in these areas, thereby prompting intense research activities to better understand its biology. Two draft genome assemblies already exist for this species but contain pervasive assembly errors and are highly...

Evidence is accumulating that evolutionary changes are not only common during biological invasions but may also contribute directly to invasion success. The genomic basis of such changes is still largely unexplored. Yet, understanding the genomic response to invasion may help to predict the conditions under which invasiveness can be enhanced or sup...

Dating population divergence within species from molecular data and relating such dating to climatic and biogeographic changes is not trivial. Yet it can help formulating evolutionary hypotheses regarding local adaptation and future responses to changing environments. Key issues include statistical selection of a demographic and historical scenario...

Experiments comparing native to introduced populations or distinct introduced populations to each other show that phenotypic evolution is common and often involves a suit of interacting phenotypic traits. We define such sets of traits that evolve in concert and contribute to the success of invasive populations as an "invasion syndrome". The invasiv...

Evidence is accumulating that evolutionary changes are not only common during biological invasions but may also contribute directly to invasion success. The genomic basis of such changes is still largely unexplored. Yet, understanding the genomic response to invasion may help to predict the conditions under which invasiveness can be enhanced or sup...

CRISPR gene drive has recently been proposed as a promising technology for population management, including in conservation genetics. The technique would consist in releasing genetically engineered individuals that are designed to rapidly propagate a desired mutation or transgene into wild populations. Potential applications in conservation biology...

A better understanding of the factors affecting host plant use by spotted-wing drosophila (Drosophila suzukii) could aid in the development of efficient management tools and practices to control this pest. Here, proxies of both preference (maternal oviposition behavior) and performance (adult emergence) were evaluated for 12 different fruits in the...

Motivation: Approximate Bayesian computation (ABC) has grown into a standard methodology that manages Bayesian inference for models associated with intractable likelihood functions. Most ABC implementations require the preliminary selection of a vector of informative statistics summarizing raw data. Furthermore, in almost all existing implementatio...

Males of polyandrous species have to overcome sperm competition. They should select their mate based on the reproductive status of the female to increase their own fitness. Because the sexual behavior of lady beetles relies on semiochemicals, with cuticular hydrocarbons (CHCs) being used for mate recognition, we developed and tested two hypotheses....

In evolutionary biology, simulation-based methods such as Approximate Bayesian Computation (ABC) are well adapted to make statistical inferences about complex models of natural population histories. Pudlo et al. (2016) recently developed a novel approach based on the Random Forests method (RF): the ABC-RF algorithm. Here we present the results of a...

Excel table containing 5 tabs describing (a) statistics characterizing reads for the four different MinION sequencing flow-cells (HaxR assembly); (b) statistics characterizing the read mapping for each of the six individuals used for the sexing of HaxR contigs; (c) preparation kit, sequencer type and read mapping statistics for the 14 different DNA...

Data S2. Information on the Ratio of Female-to-Male Read Coverage for Each Contig of the Assembly HaxR, Related to STAR Methods For X-linked contigs, the coverage is halved in males.

French version: La coccinelle arlequin, Harmonia axyridis, présente un polymorphisme remarquable des motifs colorés qui ornent ses élytres. Cette grande variété de formes n'est pourtant due qu'à un seul gène, pannier, dont la séquence codante est identique chez tous les individus mais dont les séquences régulatrices varient. En fonction des allèl...

In evolutionary biology, approximate Bayesian computation (ABC) methods are well adapted to the complex models of species and population history in which serial or independent divergence events, change of population sizes, and genetic admixture, or migration events are often suspected. Here, we present the results of using a set of recent ABC-based...

Many animal species comprise discrete phenotypic forms. A common example in natural populations of insects is the occurrence of different color patterns, which has motivated a rich body of ecological and genetic research [1-6]. The occurrence of dark, i.e., melanic, forms displaying discrete color patterns is found across multiple taxa, but the und...

A. Background The Oxford NanoPore long fragment sequencing technology (ONT) is based on the sequencing of nucleic acids via the passage of single molecules through protein nanopores and allows sequences of several tens of kilobases to be obtained. It has recently experienced an exponential phase of development and its scope has expanded to many are...

Many animal species are comprised of discrete phenotypic forms. Understanding the genetic mechanisms generating and maintaining such phenotypic variation within species is essential to comprehending morphological diversity. A common and conspicuous example of discrete phenotypic variation in natural populations of insects is the occurrence of diffe...

La technologie de séquençage long fragments d'Oxford NanoPore (ONT) est basée sur le séquençage des acides nucléiques via le passage de molécules uniques au travers de nano pores protéiques et permet l’obtention de séquences de plusieurs dizaines de kilobases. Elle a très récemment connu une phase exponentielle de développement et son champ d'appli...

Among arthropods, ability to survive cold conditions may be instrumental for species invading temperate or colder climatic zones. Cold tolerance can be influenced by multiple environmental and physiological factors. We experimentally investigated the effects of mating status (unmated, mated, or mated, and reproductive) on cold tolerance and subsequ...

Knowledge of the genetic make-up and demographic history of invasive populations is critical to understand invasion mechanisms. Commensal rodents are ideal models to study whether complex invasion histories are typical of introductions involving human activities. The house mouse Mus musculus domesticus is a major invasive synanthropic rodent origin...

Deciphering invasion routes from molecular data is crucial to understanding biological invasions, including identifying bottlenecks in population size and admixture among distinct populations. Here, we unravel the invasion routes of the invasive pest Drosophila suzukii using a multi-locus microsatellite dataset (25 loci on 23 worldwide sampling loc...

Understanding biological invasion is currently one of the main scientific challenges for ecologists. The introduction process is crucial for the success of an invasion, especially when it involves a demographic bottleneck. A small introduced population is expected to face a higher risk of extinction before the first stage of invasion is complete if...

Bottlenecks in population size can reduce fitness and evolutionary potential, yet introduced species often become invasive. This poses a dilemma referred to as the genetic paradox of invasion. Three characteristics must hold true for an introduced population to be considered paradoxical in this sense. First, it must pass through a bottleneck that r...

Bottlenecks in population size can reduce fitness and evolutionary potential, yet introduced species often become invasive. This poses a dilemma referred to as the genetic paradox of invasion. Three characteristics must hold true for an introduced population to be considered paradoxical in this sense. First, it must pass through a bottleneck that r...

The harlequin ladybird, Harmonia axyridis (Pallas) (Coleoptera: Coccinellidae), is native to Asia but has been intentionally introduced to many countries as a biological control agent of pest insects. In numerous countries, however, it has been introduced unintentionally. The dramatic spread of H. axyridis within many countries has been met with co...

Bottlenecks in population size can reduce fitness and evolutionary potential, yet introduced species often become invasive. This poses a dilemma referred to as the genetic paradox of invasion. Three characteristics must hold true for an introduced population to be considered paradoxical in this sense. First, it must pass through a bottleneck that r...

Motivation: Approximate Bayesian computation (ABC) methods provide an elaborate approach to Bayesian inference on complex models, including model choice. Both theoretical arguments and simulation experiments indicate, however, that model posterior probabilities may be poorly evaluated by standard ABC techniques. Results: We propose a novel approach...

We have recently made available (July 2015) a new version of the computer program DIYABC (DIYABC v2.1.0) which represents a user-friendly approach to approximate Bayesian computation for inference on population history using molecular markers. This new version includes several major and minor improvements.The document proposed here include six sect...

Species distribution models (SDM) have often been used to predict the potential ranges of introduced species and prioritize management strategies. However, this approach assumes equilibrium between occurrences and environmental gradients, an assumption which is violated during the invasion process, where many suitable sites are empty because the sp...

Historical and observational data for invasive species are often sparse and incomplete, so molecular genetic markers are increasingly used and have proved to be efficient tools to make inferences about invasion histories. Here, we report the development of 28 polymorphic microsatellite markers in the invasive spotted-wing drosophila, Drosophila suz...

Biological invaders have long been hypothesized to exhibit the fast end of the life-history spectrum, with early reproduction and a short lifespan. Here, we examine the rapid evolution of life history within the harlequin ladybird Harmonia axyridis. The species, once used as a biological control agent, is now a worldwide invader. We show that bioco...

Inferences about introduction histories of invasive species remain challenging because of the stochastic demographic processes involved. Approximate Bayesian computation (ABC) can help to overcome these problems, but such method requires a prior understanding of population structure over the study area, necessitating the use of alternative methods...

Invasive species are characterized by the rapid growth and spread of their populations after establishing a foothold in new habitats, and there are now many examples of such species negatively affecting biodiversity and the economy. It is unclear why some species can become successful invaders, whereas most (even if closely related) remain non-inva...

Studies focusing on geographical genetic patterns of commensal species and on human history complement each other, and provide proxies to trace common colonisation events. On Madagascar, the unintentional introduction and spread of the commensal species Rattus rattus by people may have left a living clue of human colonization patterns and history....

Cannibalism is widespread in both vertebrates and invertebrates but its extent is variable between and within species. Cannibalism depends on population density and nutritional conditions, and could be beneficial during colonisation of new environments. Empirical studies are needed to determine whether this trait might facilitate invasion of a new...

The evolutionary trajectories associated with demographic, genetic and spatial disequilibrium have become an issue of growing interest in population biology. Invasive species provide unique opportunities to explore the impact of recent range expansion on life-history traits, making it possible to test for a spatial arrangement of dispersal abilitie...

DIYABC is a software package for a comprehensive analysis of population history using approximate Bayesian computation (ABC) on DNA polymorphism data. Version 2.0 implements a number of new features and analytical methods. It allows: (i) the analysis of single nucleotide polymorphism (SNP) data at large number of loci, apart from microsatellite and...

Reproductive strategy affects population dynamics and genetic parameters that can, in turn, affect evolutionary processes during the course of biological invasion. Life-history traits associated with reproductive strategy are therefore potentially good candidates for rapid evolutionary shifts during invasions. In a series of mating trials, we exami...

Androgenesis is the production of an offspring containing exclusively the nuclear genome of the fathering male via the maternal eggs. This unusual mating system is generally considered a male trait, giving to androgenetic males a substantial fitness advantage over their sexually reproducing relatives. We here provide the first empirical study of th...

Inexpensive short-read sequencing technologies applied to reduced representation genomes is revolutionizing genetic research, especially population genetics analysis, by allowing the genotyping of massive numbers of single-nucleotide polymorphisms (SNP) for large numbers of individuals and populations. Restriction site-associated DNA (RAD) sequenci...

Molecular markers produced by next-generation sequencing (NGS) technologies are revolutionizing genetic research. However, the costs of analysing large numbers of individual genomes remain prohibitive for most population genetics studies. Here, we present results based on mathematical derivations showing that, under many realistic experimental desi...