Arnaud Estoup - Academia.edu (original) (raw)

Papers by Arnaud Estoup

Peer Community Journal, Nov 26, 2021

Experiments comparing native to introduced populations or distinct introduced populations to each... more 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 Harlequin ladybird Harmonia axyridis displays such an invasion syndrome with, for instance, females from invasive populations being larger and heavier than individuals from native populations, allocating more resources to reproduction, and spreading reproduction over a longer lifespan. Invasion syndromes could emerge due to selection acting jointly and directly on a multitude of traits, or due to selection on one or a few key traits that drive correlated indirect responses in other traits. Here, we investigated the degree to which the H. axyridis invasion syndrome would emerge in response to artificial selection on either female body mass or on age at first reproduction, two traits involved in their invasion syndrome. To further explore the interaction between environmental context and evolutionary change in molding the phenotypic response, we phenotyped the individuals from the selection experiments in two environments, one with abundant food resources and one with limited resources. The two artificial selection experiments show that the number of traits showing a correlated response depends upon the trait undergoing direct selection. Artificial selection on female body mass resulted in few correlated responses and hence poorly reproduced the invasion syndrome. In contrast, artificial selection on age at first reproduction resulted in more widespread phenotypic changes, which nevertheless corresponded only partly to the invasion syndrome. The artificial selection experiments also revealed a large impact of diet on the traits, with effects dependent on the trait considered and the selection regime. Overall, our results indicate that direct selection on multiple traits was likely necessary in the evolution of the H. axyridis invasion syndrome. Furthermore, they show the strength of using artificial selection to identify the traits that are correlated in different selective contexts, which represents a crucial first step in understanding the evolution of complex phenotypic patterns, including invasion syndromes.

Is There a Genetic Paradox of Biological Invasion?

Annual Review of Ecology, Evolution, and Systematics, Nov 1, 2016

Bottlenecks in population size can reduce fitness and evolutionary potential, yet introduced spec... more 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 reduces genetic variation. Second, despite the bottleneck, the introduced population must not succumb to the many problems associated with low genetic variation. Third, it must adapt to the novel environment. Some introduced populations are not paradoxical as they do not combine these conditions. In some cases, an apparent paradox is spurious, as seen in introduced populations with low diversity in neutral markers that maintain high genetic variation in ecologically relevant traits. Even when the genetic paradox is genuine, unique aspects of a species' biology can allow a population to thrive. We propose research directions into remaining paradoxical aspects of invasion genetics.

HAL (Le Centre pour la Communication Scientifique Directe), Feb 24, 2020

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Molecular Ecology Resources, Dec 17, 2021

HAL is a multi-disciplinary open access archive for the deposit and dissemination of scientific r... more HAL is a multi-disciplinary open access archive for the deposit and dissemination of scientific research documents, whether they are published or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers. L'archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d'enseignement et de recherche français ou étrangers, des laboratoires publics ou privés.

Du génotype au phénotype : les motifs des coccinelles arlequins

HAL (Le Centre pour la Communication Scientifique Directe), Oct 12, 2018

Planet Vie - Ressources en science de la vie pour les EnseignantsLa coccinelle arlequin, Harmonia... more Planet Vie - Ressources en science de la vie pour les EnseignantsLa 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 allèles qu'elles possèdent, les coccinelles vont donc produire la protéine Pannier, impliquée dans la coloration noire, à des endroits différents de leurs élytres

Molecular Biology and Evolution, Jul 1, 1999

Two populations which have diverged from an ancestral population may come back into contact due t... more Two populations which have diverged from an ancestral population may come back into contact due to human action via stocking or introduction programs. We report here a method to measure genetic admixture in such situations based on juxtaposed microsatellite systems (JMSs). A JMS is composed of two microsatellite repeat arrays separated by a sequence of less than 200 bp. The advantage of a JMS stems from the superior genealogical information carried by the two microsatellite sites to that carried by just one. If five assumptions are fulfilled, JMSs provide reliable diagnostic markers which eliminate the need to know the genetic structure of the native population in the absence of admixture. Simulations show that optimal features at both microsatellite sites of the JMS are the occurrence of multistep mutations, moderately high mutation rates, and limited allele size constraints. Optimal demographic features include a relatively large number of generations since the separation of the alien and native populations and small population sizes, especially for the alien population. Substantial sampling of the alien population is also necessary.

HAL (Le Centre pour la Communication Scientifique Directe), 1994

Nous avons examiné le polymorphisme électrophorétique de 47 locus enzymatiques dans 24 population... more Nous avons examiné le polymorphisme électrophorétique de 47 locus enzymatiques dans 24 populations naturelles et domestiques de truite commune de France ainsi que la variabilité à 5 locus microsatellites dans 4 de ces populations. La proportion de locus enzymatiques polymorphes sur l'ensemble des échantillons est de 57% et varie de 0 à 37% entre populations. Ce polymorphisme permet de distinguer 2 sous-espèces distinctes occu- pant respectivement les bassins atlantique et méditerranéen et dont la distance génétique standard (Nei) s'établit, en moyenne, à 0,10. La variabilité des populations atlantiques s'avère nettement plus élevée que celle des populations méditerranéennes et présente un certain degré de structuration géographique. Toutes les souches domestiques étudiées ont une origine atlantique. Les 5 locus microsatellites examinés se sont avérés polymorphes avec un nombre d'allèles variant de 2 à 8 et des taux d'hétérozygotie intrapopulation de 0 à 74%. Ils permettent aussi de distinguer la population méditerranéenne étudiée des 3 populations d'origine atlantique. L'intérêt de ces résultats pour la gestion de la diversité génétique des populations naturelles de truite commune est brièvement présenté. protéine / microsatellite / polymorphisme moléculaire / gestion génétique / Salmo trutta Summary -Genetic diversity and management of brown trout: the value of studying variation at protein and microsatellite loci. The electrophoretic polymorphism at 47 protein loci was studied in 24 domesticated and natural French brown trout populations. The variation at 5 microsatellite loci in 4 of these populations was also investigated. The total proportion of polymorphic loci was 57% for all the populations analysed and mnged from 0 to 37% between populations. This polymorphism allowed us to distinguish 2 subspecies which occupy the Atlantic and Mediterranean areas, respectively. The average standard genetic distance between these 2 groups was estimated to be 0.10. The genetic diversity of the Atlantic populations was substantially higher than that of the Mediterranean populations and showed some geographic structuration. All the domesticated stocks originated from the Atlantic area. The 5 microsatellite loci were polymorphic with a total number of alleles per locus ranging from 2 to 8 and heteroxygosity was between 0 and 74 %. These microsatellite loci also allowed us to distinguish the Mediterranean population from the 3 populations originating from the Atlantic area. The value of these results for the genetic management of brown trout is briefly discussed. protein / microsatellite / molecular polymorphism / genetic management / Salmo trutta

Scientific Reports, Jul 8, 2020

Over the past decade, the spotted wing Drosophila, Drosophila suzukii, has invaded Europe and Ame... more 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 fragmented, which limits their values. Our purpose here was to improve the assembly of the D. suzukii genome and to annotate it in a way that facilitates comparisons with D. melanogaster. For this, we generated PacBio longread sequencing data and assembled a novel, high-quality D. suzukii genome assembly. it is one of the largest Drosophila genomes, notably because of the expansion of its repeatome. We found that despite 16 rounds of full-sib crossings the D. suzukii strain that we sequenced has maintained high levels of polymorphism in some regions of its genome. As a consequence, the quality of the assembly of these regions was reduced. We explored possible origins of this high residual diversity, including the presence of structural variants and a possible heterogeneous admixture pattern of North American and Asian ancestry. Overall, our assembly and annotation constitute a high-quality genomic resource that can be used for both high-throughput sequencing approaches, as well as manipulative genetic technologies to study D. suzukii. Drosophila suzukii (Matsumura, 1931), the spotted wing Drosophila (Diptera: Drosophilidae), is an invasive fruit fly species originating from eastern Asia that has spread since 2008 in major parts of America and Europe. This species is still expanding its distribution 1,2 and is classified as a major pest on a variety of berries and stone fruit crops 3 . Its behavior and phenotypic traits are now the subject of intense scrutiny both in the lab and in the field (reviewed in 4 ). Understanding the biology and the population dynamics of D. suzukii benefits from the production and mining of genomic and transcriptomic data, as well as manipulative genetic technologies including functional transgenesis and genome editing . Yet, the efficacy of these approaches relies critically on high-quality genomic resources. Currently, two D. suzukii genome assemblies, obtained from two different strains, have been generated based on short-read sequencing technologies 8,9 .

Conservation Genetics, Apr 1, 2019

CRISPR gene drive has recently been proposed as a promising technology for population management,... more 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 include the control of invasive pest populations that threaten biodiversity (eradication and suppression drives), or the introduction of beneficial mutations in endangered populations (rescue drives). The propagation of a gene drive is affected by different factors that depend on the drive construct (e.g. its fitness effect and timing of expression) or on the target species (e.g. its mating system and population structure). We review potential applications of the different types of gene drives for conservation. We examine the challenges posed by the evolution of resistance to gene drives and review the various molecular and environmental risks associated with gene drives (e.g. propagation to non target populations or species and unintended detrimental ecosystem impacts). We provide some guidelines for future gene drive research and discuss ethical, biosafety and regulation issues.

Agritrop (Cirad), Aug 29, 2019

This is an open access article under the terms of the Creat ive Commo ns Attri butio n-NonCo mmer... more This is an open access article under the terms of the Creat ive Commo ns Attri butio n-NonCo mmerc ial-NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made.

HAL (Le Centre pour la Communication Scientifique Directe), Jun 30, 2020

The AbcRanger library provides methodologies for model choice and parameter estimation based on f... more The AbcRanger library provides methodologies for model choice and parameter estimation based on fast and scalable Random Forests, tuned to handle large and/or high dimensional datasets. The library, initially intended for the population genetics ABC framework DIYABC, has been generalized to any ABC reference table generator. At first, computational issues were encountered with the reference ABC-Random Forest. Those issues have been diagnosed by us as friction between "strict" Machine Learning setup and ABC context, and this incited us to modify the C++ implementation of stateof-the-art random forests, ranger, to tailor it for ABC needs: potentially "deep" decision trees are not stored in memory anymore, but are processed by batches in parallel. We focused on memory and thread scalability, ease of use (minimal hyperparameter set). R and python interfaces are provided. A toy example and a population genetics example are presented.

HAL (Le Centre pour la Communication Scientifique Directe), Aug 19, 2018

HAL (Le Centre pour la Communication Scientifique Directe), Mar 30, 2021

HAL (Le Centre pour la Communication Scientifique Directe), Oct 22, 2018

and lastly by the P:C ratio. These results highlight the importance of considering a resource as ... more and lastly by the P:C ratio. These results highlight the importance of considering a resource as a whole. Considering only the ratio of protein to carbohydrates is not sufficient for understanding variation in key life-history traits.

bioRxiv (Cold Spring Harbor Laboratory), Nov 7, 2020

Transposable Elements (TEs) are ubiquitous and mobile repeated sequences. They are major determin... more 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 gene poor regions. The majority of TE insertions segregate at low frequencies, indicating a recent and probably ongoing TE activity. To explore TE dynamics in the context of biological invasions, we studied variation of TE abundance in genomic data from 16 invasive and six native populations (of D. suzukii). We found a large increase of the TE load in invasive populations correlated with a reduced Watterson estimate of genetic diversity θw a proxy of effective population size. We did not find any correlation between TE contents and bio-climatic variables, indicating a minor effect of environmentally induced TE activity. A genome-wide association study revealed that ca. 5,000 genomic regions are associated with TE abundance. We did not find, however, any evidence in such regions of an enrichment for genes known to interact with TE activity (e.g. transcription factor encoding genes or genes of the piRNA pathway). Finally, the study of TE insertion frequencies revealed 15 putatively adaptive TE insertions, six of them being likely associated with the recent invasion history of the species.

Agricultural and Forest Entomology

The invasive pest Drosophila suzukii is a fruit fly native to Asia that infests a wide variety of... more 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. suzukii infestation of elderberry fruits (Sambucus nigra), a major wild host plant in Europe. We collected elderberry fruits across 215 sites distributed in 13 regions from North to South of France. We counted the number of emerging D. suzukii adults and tested for the effect of macroclimatic, landscape, local biotic and abiotic variables, as well as plant traits using linear mixed models. Site latitude and mean daily maximum temperature since the beginning of the year had respectively the strongest positive and negative effects on mean infestation rates across regions. Infestation rates also increased with forest cover in a 100 m radius ar...

Many animal species are comprised of discrete phenotypic forms. Understanding the genetic mechani... more 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 different colour patterns, which has motivated a rich body of ecological and genetic research1–6. The occurrence of dark, i.e. melanic, forms, displaying discrete colour patterns, is found across multiple taxa, but the underlying genomic basis remains poorly characterized. In numerous ladybird species (Coccinellidae), the spatial arrangement of black and orange patches on adult elytra varies wildly within species, forming strikingly different complex colour patterns7,8. In the harlequin ladybirdHarmonia axyridis, more than 200 distinct colour forms have been described, which classic genetic studies suggest result from allelic variation at a sin...

Heredity, 2017

Knowledge of the genetic make-up and demographic history of invasive populations is critical to u... more 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 originating from South-West Asia. It has been largely studied in Europe and on several remote islands, but the genetic structure and invasion history of this taxon have been little investigated in several continental areas, including West Africa. In this study, we focussed on invasive populations of M. m. domesticus in Senegal. In this focal area for European settlers, the distribution area and invasion spread of the house mouse is documented by decades of data on commensal rodent communities. Genetic variation at one mitochondrial locus and 16 nuclear microsatellite markers was analysed from individuals sampled in 36 sites distributed across the country. A combination of phylogeographic and population genetics methods showed that there was a single introduction event on the northern coast of Senegal, from an exogenous (probably West European) source, followed by a secondary introduction from northern Senegal into a coastal site further south. The geographic locations of these introduction sites were consistent with the colonial history of Senegal. Overall, the marked microsatellite genetic structure observed in Senegal, even between sites located close together, revealed a complex interplay of different demographic processes occurring during house mouse spatial expansion, including sequential founder effects and stratified dispersal due to human transport along major roads.

Molecular Ecology, 1999

No. 2T0059) and is a part of a collaborative study (R. Gadagkar and C. Peeters) on indian Diacamm... more No. 2T0059) and is a part of a collaborative study (R. Gadagkar and C. Peeters) on indian Diacamma ants financed by CEFIPRA/ IFCPAR (grant No. 1709 -1). Formica lugubris B and their variability in other ant species.