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181 results on '"Arnaud Estoup"'

1. Rapid and transient evolution of local adaptation to seasonal host fruits in an invasive pest fly

Author: Laure Olazcuaga, Julien Foucaud, Candice Deschamps, Anne Loiseau, Jean‐Loup Claret, Romain Vedovato, Robin Guilhot, Cyril Sévely, Mathieu Gautier, Ruth A. Hufbauer, Nicolas O. Rode, and Arnaud Estoup
Subjects: Adaptive phenotypic plasticity, Drosophila suzukii, genetic effects, host fruits, local adaptation, reciprocal common garden experiment, Evolution, QH359-425
Abstract: Abstract 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 periods of stability mixed with heterogeneity, the relative importance of local adaptation and adaptive phenotypic plasticity is unclear. Here, we used Drosophila suzukii as a model system to evaluate the relative influence of genetic and plastic effects on the match of populations to environments with periods of stability from three to four generations. This invasive pest insect can develop within different fruits, and persists throughout the year in a given location on a succession of distinct host fruits, each one being available for only a few generations. Using reciprocal common environment experiments of natural D. suzukii populations collected from cherry, strawberry, and blackberry, we found that both oviposition preference and offspring performance were higher on medium made with the fruit from which the population originated than on media made with alternative fruits. This pattern, which remained after two generations in the laboratory, was analyzed using a statistical method we developed to quantify the contributions of local adaptation and adaptive plasticity in determining fitness. Altogether, we found that genetic effects (local adaptation) dominate over plastic effects (adaptive phenotypic plasticity). Our study demonstrates that spatially and temporally variable selection does not prevent the rapid evolution of local adaptation in natural populations. The speed and strength of adaptation may be facilitated by several mechanisms including a large effective population size and strong selective pressures imposed by host plants.
Published: 2022
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2. New set of microsatellite markers for the spotted-wing Drosophila suzukii (Diptera: Drosophilidae): A promising molecular tool for inferring the invasion history of this major insect pest

Author: Antoine FRAIMOUT, Anne LOISEAU, Donald K. PRICE, Anne XUÉREB, MARTIN Jean-François, Renaud VITALIS, Simon FELLOUS, Vincent DEBAT, and Arnaud ESTOUP
Subjects: diptera, drosophilidae, drosophila suzukii, population genetics, microsatellite, invasion routes, invasive species, genetic structure, Zoology, QL1-991
Abstract: 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 suzukii (Matsumura, 1931) (Diptera: Drosophilidae) designed from recent genomics resources, and their cross-amplification in closely related Drosophila species of the suzukii subgroup. The markers, located on autosomal chromosomes, were characterized in two distinct invasive populations from France and Hawaii (USA), and in four sister species of the suzukii subgroup. They all showed substantial polymorphism as well as revealing strong genetic differentiation between the two genotyped populations. These markers represent a promising molecular tool for population genetic studies on D. suzukii, more especially in order to reconstruct the pathways and demographic processes of the world-wide invasion in this major insect pest.
Published: 2015
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3. Mating Status Influences Cold Tolerance and Subsequent Reproduction in the Invasive Ladybird Harmonia axyridis

Author: Benoit Facon, Arnaud Estoup, Ruth A. Hufbauer, Julien Foucaud, and Ashraf Tayeh
Subjects: cold tolerance, mating status, invasive species, overwintering, Harmonia axyridis, Evolution, QH359-425, Ecology, QH540-549.5
Abstract: 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 subsequent reproduction of the invasive harlequin ladybird Harmonia axyridis. We found that unmated adults survived cold better than mated ones. Among mated individuals, those that had not reproduced survived better than those that had reproduced. After cold stress, formerly unmated females were mated, and we evaluated their ability to reproduce. Females that reproduced prior to cold stress were less likely to reproduce after cold stress than females from the other treatments. We discuss what these results mean for the proportion of unmated females in H. axyridis aggregates at overwintering sites. This study highlights the importance of physiological status on cold tolerance of invasive arthropods.
Published: 2017
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4. Characterization of polymorphic microsatellite loci in the neotropical plant-ant Allomerus decemarticulatus (Formicidae: Myrmicinae) and multiplexing with other microsatellites from the ant subfamily Myrmicinae

Author: Pierre-Jean G. MALÉ, Anne LOISEAU, Arnaud ESTOUP, Angélique QUILICHINI, and Jérôme ORIVEL
Subjects: hymenoptera, formicidae, myrmicinae, allomerus, ant-plant mutualism, microsatellites, plant-ant, Zoology, QL1-991
Abstract: Five polymorphic microsatellite loci of the arboreal ant Allomerus decemarticulatus (Myrmicinae) were isolated and characterized. The amplification and polymorphism of seven additional microsatellite loci, previously developed for the ant species A. octoarticulatus and Wasmannia auropunctata, were also tested and the amplification conditions necessary for genotyping the complete set of 12 multiplexed markers in A. decemarticulatus determined. The number of alleles per locus ranged from three to 15 and observed heterozygosity varied from 0.09 to 0.95. Cross-species amplification of these loci was also successfully achieved in additional species of the same ant subfamily, Myrmicinae. This set of microsatellite markers will be used in studies on the mating system and population genetic structure of Myrmicinae in general and A. decemarticulatus in particular.
Published: 2010
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5. Distribution of endosymbiotic reproductive manipulators reflects invasion process and not reproductive system polymorphism in the little fire ant Wasmannia auropunctata.

Author: Olivier Rey, Arnaud Estoup, Benoit Facon, Anne Loiseau, Alexandre Aebi, Olivier Duron, Fabrice Vavre, and Julien Foucaud
Subjects: Medicine, Science
Abstract: Endosymbiotic reproductive manipulators may have drastic effects on the ecological and evolutionary dynamics of their hosts. The prevalence of these endosymbionts reflects both their ability to manipulate their hosts and the history of the host populations. The little fire ant Wasmannia auropunctata displays a polymorphism in both its reproductive system (sexual versus clonal populations) and the invasive status of its populations (associated to a habitat shift). We first screened for the presence of a diverse array of reproductive parasites in sexual and clonal populations of W. auropunctata, as a means to investigate the role of endosymbionts in reproductive phenotypes. Wolbachia was the only symbiont found and we then focused on its worldwide distribution and diversity in natural populations of W. auropunctata. Using a multilocus scheme, we further characterized the Wolbachia strains present in these populations. We found that almost all the native sexual populations and only a few clonal populations are infected by Wolbachia. The presence of similar Wolbachia strains in both sexual and clonal populations indicates that they are probably not the cause of the reproductive system polymorphism. The observed pattern seems rather associated to the invasion process of W. auropunctata. In particular, the observed loss of Wolbachia in clonal populations, that recurrently emerged from sexual populations, likely resulted from natural heat treatment and/or relaxed selection during the shift in habitat associated to the invasion process.
Published: 2013
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6. Increase in male reproductive success and female reproductive investment in invasive populations of the harlequin ladybird Harmonia axyridis.

Author: Guillaume J M Laugier, Gilles Le Moguédec, Ashraf Tayeh, Anne Loiseau, Naoya Osawa, Arnaud Estoup, and Benoît Facon
Subjects: Medicine, Science
Abstract: 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 examined mixed groups of four males from invasive and native populations of the harlequin ladybird Harmonia axyridis mating freely during 48 hours with one female of either type. We recorded the identity of the first male to copulate and after the 48 h-period, we examined female fecundity and share of paternity, using molecular markers. We found that invasive populations have a different profile of male and female reproductive output. Males from invasive populations are more likely to mate first and gain a higher proportion of offspring with both invasive and native females. Females from invasive populations reproduce sooner, lay more eggs, and have offspring sired by a larger number of fathers than females from native populations. We found no evidence of direct inbreeding avoidance behaviour in both invasive and native females. This study highlights the importance of investigating evolutionary changes in reproductive strategy and associated traits during biological invasions.
Published: 2013
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7. Bridgehead effect in the worldwide invasion of the biocontrol harlequin ladybird.

Author: Eric Lombaert, Thomas Guillemaud, Jean-Marie Cornuet, Thibaut Malausa, Benoît Facon, and Arnaud Estoup
Subjects: Medicine, Science
Abstract: Recent studies of the routes of worldwide introductions of alien organisms suggest that many widespread invasions could have stemmed not from the native range, but from a particularly successful invasive population, which serves as the source of colonists for remote new territories. We call here this phenomenon the invasive bridgehead effect. Evaluating the likelihood of such a scenario is heuristically challenging. We solved this problem by using approximate Bayesian computation methods to quantitatively compare complex invasion scenarios based on the analysis of population genetics (microsatellite variation) and historical (first observation dates) data. We applied this approach to the Harlequin ladybird Harmonia axyridis (HA), a coccinellid native to Asia that was repeatedly introduced as a biocontrol agent without becoming established for decades. We show that the recent burst of worldwide invasions of HA followed a bridgehead scenario, in which an invasive population in eastern North America acted as the source of the colonists that invaded the European, South American and African continents, with some admixture with a biocontrol strain in Europe. This demonstration of a mechanism of invasion via a bridgehead has important implications both for invasion theory (i.e., a single evolutionary shift in the bridgehead population versus multiple changes in case of introduced populations becoming invasive independently) and for ongoing efforts to manage invasions by alien organisms (i.e., heightened vigilance against invasive bridgeheads).
Published: 2010
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8. ƒ‐statistics estimation and admixture graph construction with Pool‐Seq or allele count data using the R package poolfstat

Author: Laurence Flori, Arnaud Estoup, Renaud Vitalis, Mathieu Gautier, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Systèmes d'élevage méditerranéens et tropicaux (UMR SELMET), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, This work was supported by the French National Research Agency (ANR) for the projects SWING (ANR-16-CE02-0015) and GANDHI (ANR-20-CE02-0018)., ANR-16-CE02-0015,SWING,Invasion mondiale de la drosophile à aile tachetée: Génétique, plasticité et potentiel évolutif(2016), ANR-20-CE02-0018,GANDHI,Génomique de l'invasion de la coccinelle Harmonia axyridis(2020), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)
Subjects: 0106 biological sciences, Genotype, Population, Inference, Biology, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Gene Frequency, Genetic variation, Statistics, Drosophila suzukii, Genetics, Admixture Graph, Demographic Inference, Allele, education, Allele frequency, Alleles, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Mathematics, ƒ-statistics, 0303 health sciences, education.field_of_study, Pool-Seq, High-Throughput Nucleotide Sequencing, Estimator, Covariance, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Genetics, Population, F-statistics, Introduced Species, Biotechnology, Count data
Abstract: 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 relevant for the analysis of pooled sequencing (Pool-Seq) data. We here propose a reinterpretation of the F (and D) parameters in terms of probability of gene identity and derive from this unified definition unbiased estimators for both Pool-Seq and standard allele count data obtained from individual genotypes. We implemented these estimators in a new version of the R package poolfstat, which now includes a wide range of inference methods: (i) three-population test of admixture; (ii) four-population test of treeness; (iii) F4-ratio estimation of admixture rates; and (iv) fitting, visualization and (semi-automatic) construction of admixture graphs. A comprehensive evaluation of the methods implemented in poolfstat on both simulated Pool-Seq (with various sequencing coverages and error rates) and allele count data confirmed the accuracy of these approaches, even for the most cost-effective Pool-Seq design involving low sequencing coverages. We further analyzed a real Pool-Seq data made of 14 populations of the invasive species Drosophila suzukii which allowed refining both the demographic history of native populations and the invasion routes followed by this emblematic pest. Our new package poolfstat provides the community with a user-friendly and efficient all-in-one tool to unravel complex population genetic histories from large-size Pool-Seq or allele count SNP data.
Published: 2022

9. Macroecological patterns of fruit infestation rates by the invasive fly Drosophila suzukii in the wild reservoir host plant Sambucus nigra

Author: Romain Ulmer, Aude Couty, Patrice Eslin, Manuella Catterou, Lucas Baliteau, Anne Bonis, Nicolas Borowiec, Hervé Colinet, Lionel Delbac, Françoise Dubois, Arnaud Estoup, Joris Froissard, Emilie Gallet‐Moron, Benjamin Gard, Romain Georges, Patricia Gibert, Isabelle Le Goff, Servane Lemauviel‐Lavenant, Gregory Loucougaray, Alice Michelot‐Antalik, Jean‐Francois Odoux, Sylvain Pincebourde, Nicolas O. Rode, Marcel Thaon, Irène Till‐Bottraud, Olivier Chabrerie, Ecologie et Dynamique des Systèmes Anthropisés - UMR CNRS 7058 (EDYSAN), Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS), Centre Permanent d'Initiatives pour l'Environnement (CPIE) des Pays de l’Oise (CPIE), Laboratoire de Géographie Physique et Environnementale (GEOLAB), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut Sciences de l'Homme et de la Société (IR SHS UNILIM), Université de Limoges (UNILIM)-Université de Limoges (UNILIM)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne (UCA), Institut Sophia Agrobiotech (ISA), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Côte d'Azur (UCA), Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Santé et agroécologie du vignoble (UMR SAVE), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB)-Institut des Sciences de la Vigne et du Vin (ISVV)-Ecole Nationale Supérieure des Sciences Agronomiques de Bordeaux-Aquitaine (Bordeaux Sciences Agro), Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Centre Technique Interprofessionnel des Fruits et Légumes (CTIFL), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Ecophysiologie Végétale, Agronomie et Nutritions NCS (EVA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire des EcoSystèmes et des Sociétés en Montagne (UR LESSEM), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire Agronomie et Environnement (LAE), Université de Lorraine (UL)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de recherche sur la biologie de l'insecte UMR7261 (IRBI), Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS), Ministere de l'Agriculture et de l'Alimentation, INRAE-SPE, and ANR-20-CE02-0011,DroThermal,Qu'est-ce qui fait de Drosophila suzukii un envahisseur si efficace? Une analyse intégrative de son écologie thermique.(2020)
Subjects: insect invasion, spotted-wing drosophila, non-crop host plant, plant traits, Insect Science, landscape composition, polyphagous insect, food and beverages, temperature, Forestry, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, climatic cline, Agronomy and Crop Science
Abstract: International audience; 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 around sampling sites. This study shows the importance of taking into account multiple scales and factors, from the fruit characteristics (i.e. maturity) to landscape composition and macroclimatic variables, when studying the interaction between D. suzukii and its host plants.
Published: 2022

10. The Worldwide Invasion of Drosophila suzukii Is Accompanied by a Large Increase of Transposable Element Load and a Small Number of Putatively Adaptive Insertions

Author: Cristina Vieira, Arnaud Estoup, Mathieu Gautier, V. Merel, V. Rodriguez Rada, Marie Fablet, Matthieu Boulesteix, I. Buch, Patricia Gibert, Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Equipe de recherche européenne en algorithmique et biologie formelle et expérimentale (ERABLE), Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), This work was supported by the French National Research Agency (ANR-16-CE02-0015, SWING) and performed using the computing facilities of the CC LBBE/PRABI., ANR-16-CE02-0015,SWING,Invasion mondiale de la drosophile à aile tachetée: Génétique, plasticité et potentiel évolutif(2016), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génétique et évolution des interactions hôtes-parasites, Département génétique, interactions et évolution des génomes [LBBE] (GINSENG), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Eléments transposables, évolution, populations, This work was supported by the French National Research Agency (ANR-16-CE02-0015 SWING) and performed using the computing facilities of the CC LBBE/PRABI., and This work was supported by the French National Research Agency (ANR-16-CE02-0015-01 SWING).
Subjects: 0106 biological sciences, Transposable element, [SDV]Life Sciences [q-bio], [SDE.MCG]Environmental Sciences/Global Changes, Piwi-interacting RNA, Sequence assembly, Context (language use), biological invasion, adaptation, Biology, AcademicSubjects/SCI01180, 010603 evolutionary biology, 01 natural sciences, Genome, Evolution, Molecular, 03 medical and health sciences, Effective population size, Drosophila suzukii, Genetics, Animals, RNA, Small Interfering, Molecular Biology, Gene, Discoveries, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 0303 health sciences, Genetic diversity, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], AcademicSubjects/SCI01130, PoolSeq, biology.organism_classification, populations, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, Evolutionary biology, DNA Transposable Elements, Drosophila, Adaptation, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, transposable elements, Genome-Wide Association Study, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: The reference assembly used in this article is available on NCBI website (https://www.ncbi.nlm.nih.gov/genome/18317?genome_assembly_id=910956) (Paris et al. 2020). Population sequencing data are available online (SRA repository under the BioProject accession number PRJNA576997) (Olazcuaga et al. 2020). The generated TE database and scripts are available in a github (https://github.com/vmerel/Dsu-TE).; International audience; 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 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 the 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 bioclimatic variables, indicating a minor effect of environmentally induced TE activity. A genome-wide association study revealed that ca. 2,000 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.
Published: 2021

11. Oviposition Preference and Larval Performance of Drosophila suzukii (Diptera: Drosophilidae), Spotted-Wing Drosophila: Effects of Fruit Identity and Composition

Author: Anne Loiseau, Ruth A. Hufbauer, Nicolas O. Rode, Arnaud Estoup, Julien Foucaud, Virginie Ravigné, Aurélien Ausset, Mathieu Gautier, Nicolas Leménager, Laure Olazcuaga, Benoit Facon, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université de La Réunion (UR), Colorado State University [Fort Collins] (CSU), Region Occitanie, INRA Scientific Department SPE (AAP-SPE), French National Research Agency (ANR) : ANR-16-CE02-0015-01, National Science Foundation (NSF) : DEB-0949619, USDA Agriculture and Food Research Initiative award : 2014-67013-21594, United States Department of Agriculture (USDA) : 1012868, French Agropolis Fondation (LabEx Agro-Montpellier) : CfP 2015-02, French National Research Agency (ANR), LabEx CEMEB, CeMEB LabEx/University of Montpellier : ANR-10-LABX-04-01, European Union (EU), and Conseil Regional de la Reunion
Subjects: 0106 biological sciences, Integrated pest management, compound, Oviposition, Biology, Fragaria, 01 natural sciences, 03 medical and health sciences, Drosophilidae, Animals, chemical composition, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Drosophila suzukii, Drosophila, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, Larva, Ecology, [SDV.BA]Life Sciences [q-bio]/Animal biology, fungi, food and beverages, biology.organism_classification, Preference, Blowing a raspberry, 010602 entomology, Horticulture, mother knows best hypothesis, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Fruit, Insect Science, host use, Female, PEST analysis
Abstract: 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 form of purees. The effect of the chemical composition of the fruits on preference and performance traits was then estimated. We synthesized the literature to interpret our findings in the light of previous studies that measured oviposition preference and larval performance of D. suzukii. We show that fruit identity influences different parts of the life cycle, including oviposition preference under both choice and no-choice conditions, emergence rate, development time, and number of emerging adults. Blackcurrant was always among the most preferred fruit we used, while grape and tomato were the least preferred fruits. Larvae performed better in cranberry, raspberry, strawberry, and cherry than in the other fruits tested. We found that fruit chemical compounds can explain part of the effect of fruit on D. suzukii traits. In particular, oviposition preference under choice conditions was strongly influenced by fruit phosphorus content. In general, the consensus across studies is that raspberry, blackberry, and strawberry are among the best hosts while blackcurrant, grape and rose hips are poor hosts. Our results generally confirm this view but also suggest that oviposition preferences do not necessarily match larval performances. We discuss opportunities to use our results to develop new approaches for pest management.
Published: 2019

12. Author response for 'Adaptation and correlated fitness responses over two time scales in Drosophila suzukii populations evolving in different environments'

Author: Nicolas Leménager, Nicolas O. Rode, Virginie Ravigné, Laure Olazcuaga, Ruth A. Hufbauer, Julien Foucaud, Anne Loiseau, Mathieu Gautier, Candice Deschamps, Arnaud Estoup, and Benoit Facon
Subjects: Evolutionary biology, Biology, Adaptation, Drosophila suzukii, biology.organism_classification
Published: 2021

13. Extending approximate Bayesian computation with supervised machine learning to infer demographic history from genetic polymorphisms using DIYABC Random Forest

Author: Renaud Vitalis, Eric Lombaert, Arnaud Estoup, Louis Raynal, Mathieu Gautier, Jean-Michel Marin, François-David Collin, Ghislain Durif, Institut Montpelliérain Alexander Grothendieck (IMAG), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut Sophia Agrobiotech (ISA), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Côte d'Azur (UCA), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), This work was supported by funds from the French Agence Nationale pour la Recherche (projects SWING ANR-16-CE02-0015, GANDHI ANR-20-CE02-0018), ABSint ANR-18-CE40-0034, the INRAE scientific division SPE (AAP-SPE 2016), and the LabEx NUMEV ANR-10-LABX-0020., ANR-16-CE02-0015,SWING,Invasion mondiale de la drosophile à aile tachetée: Génétique, plasticité et potentiel évolutif(2016), ANR-20-CE02-0018,GANDHI,Génomique de l'invasion de la coccinelle Harmonia axyridis(2020), ANR-18-CE40-0034,ABSint,Solutions bayésiennes approchées pour l'inférence dans de grands jeux de données et dans des modèles complexes(2018), ANR-10-LABX-0020,NUMEV,Digital and Hardware Solutions and Modeling for the Environement and Life Sciences(2010), Université Nice Sophia Antipolis (... - 2019) (UNS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0106 biological sciences, 0301 basic medicine, [SDV]Life Sciences [q-bio], Feature vector, Population, SNP, Context (language use), Biology, Machine learning, computer.software_genre, 010603 evolutionary biology, 01 natural sciences, Polymorphism, Single Nucleotide, Set (abstract data type), 03 medical and health sciences, approximate Bayesian computation, Genetics, Computer Simulation, supervised machine learning, education, Ecology, Evolution, Behavior and Systematics, Selection (genetic algorithm), Demography, education.field_of_study, Estimation theory, business.industry, Special Issue, RESOURCE ARTICLES, pool‐sequencing, 0402 animal and dairy science, population genetics, Bayes Theorem, 04 agricultural and veterinary sciences, demographic history, 040201 dairy & animal science, Molecular and Statistical Advances, Random forest, 030104 developmental biology, Genetics, Population, model or scenario selection, Artificial intelligence, Approximate Bayesian computation, business, parameter estimation, computer, Algorithms, random forest, Biotechnology
Abstract: International audience; 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. The Random Forest methodology (RF) is a powerful ensemble of SML algorithms used for classification or regression problems. RF allows conducting inferences at a low computational cost, without preliminary selection of the relevant components of the ABC summary statistics, and bypassing the derivation of ABC tolerance levels. We have implemented a set of RF algorithms to process inferences using simulated datasets generated from an extended version of the population genetic simulator implemented in DIYABC v2.1.0. The resulting computer package, named DIYABC Random Forest v1.0, integrates two functionalities into a user-friendly interface: the simulation under custom evolutionary scenarios of different types of molecular data (microsatellites, DNA sequences or SNPs) and RF treatments including statistical tools to evaluate the power and accuracy of inferences. We illustrate the functionalities of DIYABC Random Forest v1.0 for both scenario choice and parameter estimation through the analysis of pseudo-observed and real datasets corresponding to pool-sequencing and individual-sequencing SNP datasets. Because of the properties inherent to the implemented RF methods and the large feature vector (including various summary statistics and their linear combinations) available for SNP data, DIYABC Random Forest v1.0 can efficiently contribute to the analysis of large SNP datasets to make inferences about complex population genetic histories.
Published: 2021

14. Macroecological Patterns of Fruit Infestation Rates by the Invasive Fly Drosophila suzukii in the Reservoir Host Plant Sambucus nigra †

Author: Arnaud Estoup, Isabelle Le Goff, Irène Till-Bottraud, Olivier Chabrerie, Nicolas O. Rode, Emilie Gallet-Moron, Nicolas Borowiec, Sylvain Pincebourde, Patrice Eslin, Romain Georges, Servanne Lemauviel-Lavenant, Marcel Thaon, Aude Couty, Anne Bonis, Joris Froissard, Lionel Delbac, Alice Michelot-Antalik, Jean-François Odoux, Hervé Colinet, Romain Ulmer, Grégory Loucougaray, Lucas Baliteau, Patricia Gibert, and Benjamin Gard
Subjects: 2. Zero hunger, Abiotic component, education.field_of_study, Ecology, Population, food and beverages, Context (language use), Introduced species, 15. Life on land, Biology, Sambucus nigra, biology.organism_classification, medicine.disease_cause, Infestation, medicine, PEST analysis, education, Drosophila suzukii
Abstract: The invasive pest Drosophila suzukii (Matsumura, 1931) is a fruit fly native to Asia that infests a wide variety of cultivated and wild fruits, causing important damages on agricultural production. Wild plant species are major reservoirs for D. suzukii populations but their infestation rates varies greatly among geographical areas. This heterogeneity could partly be caused by a heterogeneity of environmental conditions acting across different spatial scales. This study aimed to disentangle the relative roles of macroclimatic, landscape and local factors that could affect the success of D. suzukii infestation of elderberry fruits (Sambucus nigra), a major and widespread host plant along climatic gradients. We collected elderberry fruits and measured vegetative and reproductive life traits of the plants in 215 sites distributed in 13 regions from North to South France during summer 2020. We counted the number of D. suzukii emerging from sampled fruits and tested for an effect of macroclimatic, landscape and local abiotic and biotic variables, as well as plant traits using linear mixed models with region as random factor. Latitude and mean maximum temperature had respectively the strongest positive and negative effects on mean infestation rates across regions (R = 0.761, p = 0.003 and R = −0.758, p = 0.004). Mixed models also showed that fruit infestation rate increased with the number of mature fruits within corymb and with forest cover in a 100 m radius around sampling sites and decreased with mean maximum temperature. The latitudinal and climatic clines in infestation rates suggests that D. suzukii population size might vary greatly among geographic regions. Our results also suggest that population sizes are larger in the presence of semi-natural habitats such as forest patches in the surrounding landscape. Our work contributes to enhancing our understanding of D. suzukii ecology, which is important to predict how infestation rates might change in the context of global climatic changes.
Published: 2021

15. How do invasion syndromes evolve? An experimental evolution approach using the ladybird Harmonia axyridis

Author: Arnaud Estoup, Aurélien Ausset, Nicolas Leménager, Bastien Poutout, Anne Loiseau, Pauline Gneux, Arthur Weyna, Laure Olazcuaga, Lian-Sheng Zang, Virginie Ravigné, Julien Foucaud, Benoit Facon, Elise Bonnet, Ruth A. Hufbauer, Vincent Dreuilhe, Su Wang, Ashraf Tayeh, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Colorado State University [Fort Collins] (CSU), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de La Réunion (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Beijing Academy of Agriculture and Forestry Sciences, Jilin Agricultural University (JAU), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0106 biological sciences, 0303 health sciences, Experimental evolution, biology, [SDV]Life Sciences [q-bio], media_common.quotation_subject, Context (language use), Phenotypic trait, biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, Phenotype, Harmonia axyridis, 03 medical and health sciences, Evolutionary biology, Trait, Reproduction, Selection (genetic algorithm), 030304 developmental biology, media_common, Espèce envahissante
Abstract: Ce rapport est disponible dans : BioRxiv. This article has been peer-reviewed and recommended by Peer Community in Evolutionary Biology; 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.
Published: 2021

16. Rapid evolution of local adaptation to different host fruits in wild D. suzukii populations

Author: Laure Olazcuaga, Julien Foucaud, Candice Deschamps, Anne Loiseau, Mathieu Gautier, Hufbauer, Ruth A., Arnaud Estoup, Nicolas Rode, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Colorado State University [Fort Collins] (CSU), Instituto Gulbenkian de Ciência, Oeiras, Portugal, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and Rode, Nicolas
Subjects: [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], [SDV.BID.EVO] Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], [SDV.GEN.GA] Life Sciences [q-bio]/Genetics/Animal genetics, ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2020

17. Near-chromosome level genome assembly of the fruit pest Drosophila suzukii using long-read sequencing

Author: Mathieu Gautier, Nicolas Gompel, Roxane Boyer, Jack E. Green, Arnaud Estoup, Hugues Parinello, Rita Jaenichen, Jochen B. W. Wolf, Marianthi Karageorgi, Mathilde Cagnon, Mathilde Paris, Benjamin Prud'homme, Institut de Biologie du Développement de Marseille (IBDM), Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Centre National de la Recherche Scientifique (CNRS), Inflammasome NLRP3 – NLRP3 Inflammasome, Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Génome et Transcriptome - Plateforme Génomique ( GeT-PlaGe), Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Ludwig-Maximilians-Universität München (LMU), Uppsala University, University of California [Berkeley] (UC Berkeley), University of California (UC), Institut de Génomique Fonctionnelle - Montpellier GenomiX (IGF MGX), Institut de Génomique Fonctionnelle (IGF), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-BioCampus (BCM), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), ANR-16-CE02-0015,SWING,Invasion mondiale de la drosophile à aile tachetée: Génétique, plasticité et potentiel évolutif(2016), European Project: 615789,EC:FP7:ERC,ERC-2013-CoG,SPOT.COM(2014), Centre International de Recherche en Infectiologie - UMR (CIRI), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of California [Berkeley], University of California, Centre National de la Recherche Scientifique (CNRS)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 1 (UM1)-Centre National de la Recherche Scientifique (CNRS)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 1 (UM1), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: Male, 0106 biological sciences, [SDV]Life Sciences [q-bio], Genome, Insect, Sequence assembly, lcsh:Medicine, Biology, 010603 evolutionary biology, 01 natural sciences, Genome, Article, Evolutionsbiologi, Contig Mapping, 03 medical and health sciences, Genetics, Animals, Genetik, Drosophila suzukii, lcsh:Science, Drosophila, 030304 developmental biology, 0303 health sciences, Evolutionary Biology, Polymorphism, Genetic, Invasive species, Whole Genome Sequencing, Contig, Comparative genomics, Strain (biology), lcsh:R, Ecological genetics, High-Throughput Nucleotide Sequencing, Chromosome, Genomics, Gene Annotation, Genetic hybridization, biology.organism_classification, Chromosomes, Insect, DNA transposable elements, Evolutionary biology, Fruit, Female, lcsh:Q, Structural variation
Abstract: 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 based on short-read sequencing were released in 2013 for this species. Although valuable, these resources contain pervasive assembly errors and are highly fragmented, two features limiting their values. Our purpose here was to improve the assembly of the D. suzukii genome. For this, we generated PacBio long-read sequencing data at 160X sequence coverage and assembled a novel, contiguous D. suzukii genome. We obtained a high-quality assembly of 270 Mb (with 546 contigs, a N50 of 2.6Mb, a L50 of 15, and a BUSCO score of 95%) that we called WT3-2.0. 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 (ca. 19Mb). 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 WT3-2.0 assembly provides a higher quality genomic resource compared to the previous one in terms of general assembly statistics, sequence quality and gene annotation. This new D. suzukii genome assembly is therefore an improved resource for high-throughput sequencing approaches, as well as manipulative genetic technologies to study D. suzukii.
Published: 2020

18. A whole-genome scan for association with invasion success in the fruit fly Drosophila suzukii using contrasts of allele frequencies corrected for population structure

Author: Mathieu Gautier, Marc Kenis, Mathilde Paris, Arnaud Estoup, Nicolas Borowiec, Heiko Vogel, Heidrun Vogt, Lauren M Diepenbrock, Anne Loiseau, Benoit Facon, Benjamin Prud'homme, Donald K. Price, Christelle Guédot, Jinping Zhang, Xiao Chen, Antoine Fraimout, Hugues Parrinello, Laure Olazcuaga, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut de Génomique Fonctionnelle - Montpellier GenomiX (IGF MGX), Institut de Génomique Fonctionnelle (IGF), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-BioCampus (BCM), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie du Développement de Marseille (IBDM), Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Centre National de la Recherche Scientifique (CNRS), University of Wisconsin-Madison, North Carolina State University [Raleigh] (NC State), University of North Carolina System (UNC), Centre for Agricultural and Biosciences International Europe - Switzerland (CABI Europe - Switzerland), Chinese Academy of Agricultural Sciences (CAAS), Yunnan Agricultural University, Institut Sophia Agrobiotech (ISA), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Côte d'Azur (UCA), Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de La Réunion (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Julius Kühn-Institut (JKI), University of Nevada [Las Vegas] (WGU Nevada), Max Planck Institute for Chemical Ecology, Max-Planck-Gesellschaft, ANR-16-CE02-0015,SWING,Invasion mondiale de la drosophile à aile tachetée: Génétique, plasticité et potentiel évolutif(2016), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), and Université Nice Sophia Antipolis (... - 2019) (UNS)
Subjects: 0106 biological sciences, BayPass, [SDV]Life Sciences [q-bio], Genome, Insect, Population, Adaptation, Biological, Genome Scan, Genome-wide association study, Single-nucleotide polymorphism, Biology, AcademicSubjects/SCI01180, 010603 evolutionary biology, 01 natural sciences, Genome, 03 medical and health sciences, Gene Frequency, Drosophila suzukii, Genetics, Animals, GWAS, Biological invasions, education, Molecular Biology, Allele frequency, Drosophila, Discoveries, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 0303 health sciences, education.field_of_study, Pool-Seq 1, Models, Genetic, Pool-Seq, AcademicSubjects/SCI01130, 15. Life on land, biology.organism_classification, Evolutionary biology, Drosophila melanogaster, Introduced Species
Abstract: 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 suppressed. Here we characterized the genome response of the spotted wing drosophilaDrosophila suzukiiduring the worldwide invasion of this pest insect species, by conducting a genome-wide association study to identify genes involved in adaptive processes during invasion. Genomic data from 22 population samples were analyzed to detect genetic variants associated with the status (invasive versus native) of the sampled populations based on a newly developed statistic, we calledC2, that contrasts allele frequencies corrected for population structure. This new statistical framework has been implemented in an upgraded version of the program BayPass. We identified a relatively small set of single nucleotide polymorphisms (SNPs) that show a highly significant association with the invasive status of populations. In particular, two genesRhoGEF64Candcpo, the latter contributing to natural variation in several life-history traits (including diapause) inDrosophila melanogaster, contained SNPs significantly associated with the invasive status in the two separate main invasion routes ofD. suzukii. Our methodological approaches can be applied to any other invasive species, and more generally to any evolutionary model for species characterized by non-equilibrium demographic conditions for which binary covariables of interest can be defined at the population level.
Published: 2019
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19. Adaptation and correlated fitness responses over two time scales in Drosophila suzukii populations evolving in different environments

Author: Mathieu Gautier, Benoit Facon, Arnaud Estoup, Nicolas O. Rode, Laure Olazcuaga, Anne Loiseau, Ruth A. Hufbauer, Virginie Ravigné, Julien Foucaud, Nicolas Leménager, and Candice Deschamps
Subjects: 0106 biological sciences, 0303 health sciences, education.field_of_study, Experimental evolution, Fitness landscape, Population, Replicate, Biology, biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Evolutionary biology, Adaptation, education, Drosophila suzukii, 030304 developmental biology, Maladaptation, Local adaptation
Abstract: 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 allowed replicate populations of the fruit pest Drosophila suzukii to evolve in one of eight different fruit media. After five generations, populations with the highest initial levels of maladaptation had mostly gone extinct, whereas experimental populations evolving on cherry, strawberry and cranberry media had survived. We measured the fitness of each surviving population in each of the three fruit media after five and after 26 generations of evolution. After five generations, adaptation to each medium was associated with increased fitness in the two other media. This was also true after 26 generations, except when populations that evolved on cranberry medium developed on cherry medium. These results suggest that, in the theoretical framework of a fitness landscape, the fitness optima of cherry and cranberry media are the furthest apart. Our results show that studying how fitness changes across several environments and across multiple generations provides insights into the dynamics of local adaptation that would not be evident if fitness were analyzed at a single point in time. By allowing a qualitative mapping of an experimental fitness landscape, our approach will improve our understanding of the ecological factors that drive the evolution of local adaptation in D. suzukii.
Published: 2019

20. A young age of subspecific divergence in the desert locust Schistocerca gregaria, inferred by ABC Random Forest

Author: Louis Raynal, Christophe Plantamp, Christine N. Meynard, Marie Pierre Chapuis, Jean-Michel Marin, Arnaud Estoup, Laurence Blondin, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institut Montpelliérain Alexander Grothendieck (IMAG), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Lyon [ANSES], Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Biologie et Génétique des Interactions Plante-Parasite (UMR BGPI), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), This work was supported by research funds from the French Agricultural Research Centre for International Development (CIRAD), the project ANR-16-CE02-0015 (SWING), the INRA scientific department SPE (AAP-SPE 2016), and the Labex NUMEV (NUMEV, ANR10-LABX-0020). The data used in this work were partly produced through the technical facilities of the Centre Méditerranéen Environnement Biodiversité (CeMEB, ANR-10-LABX-0004), Montpellier, France., ANR-16-CE02-0015,SWING,Invasion mondiale de la drosophile à aile tachetée: Génétique, plasticité et potentiel évolutif(2016), ANR-10-LABX-0020,NUMEV,Digital and Hardware Solutions and Modeling for the Environement and Life Sciences(2010), ANR-10-LABX-0004,CeMEB,Mediterranean Center for Environment and Biodiversity(2010), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), CAractérisation et Suivi des Phénomènes d'Evolution de Résistance aux pesticides (CASPER), Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Université de Lyon-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro
Subjects: 0106 biological sciences, [SDV]Life Sciences [q-bio], Population, divergence time, 010603 evolutionary biology, 01 natural sciences, paleo-vegetation, 03 medical and health sciences, Glacial period, Desert locust, education, 030304 developmental biology, Local adaptation, 0303 health sciences, education.field_of_study, Random Forest, biology, Holocene, Ecology, 15. Life on land, biology.organism_classification, colonization, Geography, Habitat, Orthoptera, Schistocerca, Approximate Bayesian computation, Locust
Abstract: This article has been peer-reviewed and recommended by Peer Community in Evolutionary Biology.; International audience; 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 among a set of possible scenarios, and estimation of the parameter(s) of interest under the chosen scenario. Such inferences greatly benefit from new statistical approaches including approximate Bayesian computation - Random Forest (ABC-RF), the latter providing reliable inference at a low computational cost, with the possibility to take into account prior knowledge on both biogeographical history and genetic markers. Here, we used ABC-RF, including independent information on evolutionary rate and pattern at microsatellite markers, to decipher the evolutionary history of the African arid-adapted pest locust, Schistocerca gregaria . We found that the evolutionary processes that have shaped the present geographical distribution of the species in two disjoint northern and southern regions of Africa were recent, dating back 2.6 Ky (90% CI: 0.9 – 6.6 Ky). ABC-RF inferences also supported a southern colonization of Africa from a low number of founders of northern origin. The inferred divergence history is better explained by the peculiar biology of S. gregaria , which involves a density-dependent swarming phase with some exceptional spectacular migrations, rather than a continuous colonization resulting from the continental expansion of open vegetation habitats during more ancient Quaternary glacial climatic episodes.
Published: 2019
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21. Population management using gene drive: molecular design, spread dynamics modelling and assessment of ecological risks

Author: Nicolas O. Rode, Arnaud Estoup, Denis Bourguet, Virginie Courtier-Orgogozo, and Florence Débarre
Subjects: genetic rescue, conservation genetics, assisted gene flow, genetic population management, endangered species, invasive species
Abstract: 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., Funding for this project was provided by the CeMEB LabEx/University of Montpellier to NOR, ANR-14-ACHN-0003 to FD, INRA to AE and DB, INRA-SPE (SUZUCTICID project) to NOR and AE and European Research Council (FP7/2007-2013 Grant Agreement no. 337579) to VCO.
Published: 2019
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22. Cuticular hydrocarbon composition does not allow Harmonia axyridis males to identify the mating status of sexual partners

Author: Julien Foucaud, Philippe Maesen, Andreas Vilcinskas, Heiko Vogel, Frédéric Francis, Benoit Facon, Arnaud Estoup, Maryse Vanderplanck, Georges Lognay, François Verheggen, Stéphanie Lorge, Pauline Legrand, Université de Liège, Justus-Liebig-Universität Gießen (JLU), Department of Entomology, Michigan State University [East Lansing], Michigan State University System-Michigan State University System, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université de La Réunion (UR), and BiodivERsA (Horizon 2020 ERA-NET COFUND scheme) grant
Subjects: 0106 biological sciences, animal structures, biology, [SDV.BA]Life Sciences [q-bio]/Animal biology, Zoology, biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, Mating preferences, Harmonia axyridis, 010602 entomology, Mate choice, Chemical signal, Insect Science, behavior and behavior mechanisms, Natural enemies, Mating, reproductive and urinary physiology
Abstract: International audience; 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. First, we hypothesized that the cuticular hydrocarbon profile qualitatively and quantitatively differs between virgin and mated Harmonia axyridis females, regardless of the color morph. Second, we hypothesized that males discriminate virgin and mated females, preferring copulating with virgin females, rather than previously mated ones, to avoid sperm competition and subsequently
Published: 2019

23. ABC random forests for Bayesian parameter inference

Author: Mathieu Ribatet, Arnaud Estoup, Jean-Michel Marin, Pierre Pudlo, Louis Raynal, Christian P. Robert, Institut Montpelliérain Alexander Grothendieck (IMAG), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Model selection in statistical learning (SELECT), Laboratoire de Mathématiques d'Orsay (LMO), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS)-Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Institut de Mathématiques de Marseille (I2M), Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Centre National de la Recherche Scientifique (CNRS), University of Warwick [Coventry], CEntre de REcherches en MAthématiques de la DEcision (CEREMADE), Centre National de la Recherche Scientifique (CNRS)-Université Paris Dauphine-PSL, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Centre de Recherche en Economie et en Statistique (CREST-INSEE), Institut national de la statistique et des études économiques (INSEE), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), National Research Fund ANR (France) through the European Union program ERA-Net BiodivERsA (project EXOTIC), National Research Fund ANR (France) through the INRA scientific department SPE (AAP-SPE 2016), ANR-16-CE02-0015,SWING,Invasion mondiale de la drosophile à aile tachetée: Génétique, plasticité et potentiel évolutif(2016), ANR-10-LABX-0020,NUMEV,Digital and Hardware Solutions and Modeling for the Environement and Life Sciences(2010), European Project: 266546,EC:FP7:ENV,FP7-ERANET-2010-RTD,BIODIVERSA2(2010), Inria Saclay - Ile de France, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire de Mathématiques d'Orsay (LMO), Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay, Université Paris Dauphine-PSL-Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Université Paris Dauphine-PSL, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), and Centre National de la Recherche Scientifique (CNRS)-École Centrale de Marseille (ECM)-Aix Marseille Université (AMU)
Subjects: FOS: Computer and information sciences, Statistics and Probability, Biometry, Computer science, Calibration (statistics), Bayesian probability, Posterior probability, Inference, Machine Learning (stat.ML), Bayesian inference, Biochemistry, Statistics - Computation, Methodology (stat.ME), 03 medical and health sciences, Bayes' theorem, Statistics - Machine Learning, Humans, Computer Simulation, QA, Molecular Biology, Computation (stat.CO), Statistic, Statistics - Methodology, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, Likelihood Functions, QH, 030302 biochemistry & molecular biology, Bayes Theorem, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, Computer Science Applications, Random forest, Statistics::Computation, Computational Mathematics, Genetics, Population, Computational Theory and Mathematics, Approximate Bayesian computation, Algorithm
Abstract: This preprint has been reviewed and recommended by Peer Community In Evolutionary Biology (http://dx.doi.org/10.24072/pci.evolbiol.100036). 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 implementations, the tolerance level that separates acceptance from rejection of simulated parameter values needs to be calibrated. We propose to conduct likelihood-free Bayesian inferences about parameters with no prior selection of the relevant components of the summary statistics and bypassing the derivation of the associated tolerance level. The approach relies on the random forest methodology of Breiman (2001) applied in a (non parametric) regression setting. We advocate the derivation of a new random forest for each component of the parameter vector of interest. When compared with earlier ABC solutions, this method offers significant gains in terms of robustness to the choice of the summary statistics, does not depend on any type of tolerance level, and is a good trade-off in term of quality of point estimator precision and credible interval estimations for a given computing time. We illustrate the performance of our methodological proposal and compare it with earlier ABC methods on a Normal toy example and a population genetics example dealing with human population evolution. All methods designed here have been incorporated in the R package abcrf (version 1.7) available on CRAN., Main text: 24 pages, 6 figures Supplementary Information: 14 pages, 5 figures
Published: 2019

24. Application of ABC to Infer the Genetic History of Pygmy Hunter-Gatherer Populations from Western Central Africa

Author: Alex Dehne-Garcia, Arnaud Estoup, Jean-Marie Cornuet, Christian P. Robert, Paul Verdu, Pierre Pudlo, Jean-Michel Marin, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Eco-Anthropologie et Ethnobiologie (EAE), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7), Université de Montpellier (UM), Institut Montpelliérain Alexander Grothendieck (IMAG), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), University of Warwick [Coventry], CEntre de REcherches en MAthématiques de la DEcision (CEREMADE), Université Paris Dauphine-PSL, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Scott A. Sisson, Yanan Fan, Mark A. Beaumont, S. Sisson, Y. Fan, M. Beaumont, Muséum national d'Histoire naturelle (MNHN)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Paris Dauphine-PSL, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), and Mark Beaumont
Subjects: 0303 health sciences, Genetic diversity, education.field_of_study, [STAT.AP]Statistics [stat]/Applications [stat.AP], Demographic history, [SDV]Life Sciences [q-bio], [SDV.BA]Life Sciences [q-bio]/Animal biology, Population, Genetic admixture, Population genetics, 01 natural sciences, 010104 statistics & probability, 03 medical and health sciences, Geography, Homo sapiens, Evolutionary biology, 0101 mathematics, Approximate Bayesian computation, education, Hunter-gatherer, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology
Abstract: International audience; 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 methods to analyse a microsatellite genetic dataset composed of Pygmy populations from Western Central Africa and non-Pygmy human populations, partly stemming from the dataset originally investigated in Verdu et al. (2009). Although archaeological remains attest to Homo sapiens’ presence in the Congo Basin for at least 40,000 years, the demographic history of these groups, including divergence and admixture, remains little known. In this chapter, we will successively describe (1) the observed microsatellite dataset for which one wants to conduct a Bayesian analysis, the set(s) of models we compared, with their parameters and associated priors, and the way datasets were simulated for ABC analyses; (2) the model choice analyses we carried out using a recently developed method, ABC random forest (Pudlo et al., 2015); (3) the estimates we obtained for Pygmy historical and demographic parameters under the most likely model; and (4) model-posterior checking to evaluate the goodness of fit between the final inferred genetic history and the observed dataset. We found a probable recent (about 4,900 YBP) common origin of all Western Central African Pygmy populations, despite the vast cultural, morphological, and genetic diversity observed today among these populations. We also confirmed recent asymmetrical and heterogeneous genetic introgressions from non-Pygmies into each Pygmy population. These results are consistent with previous population genetics studies on Pygmies from Western Central Africa by Verdu et al. (2009), Batini et al. (2011), and Patin et al. (2009).
Published: 2019

25. Is There a Genetic Paradox of Biological Invasion?

Author: Benoit Facon, Virginie Ravigné, Ruth A. Hufbauer, Arnaud Estoup, Mathieu Gautier, and Renaud Vitalis
Subjects: 0106 biological sciences, 0301 basic medicine, F40 - Écologie végétale, Population, Évolution, Introduced species, Biology, 010603 evolutionary biology, 01 natural sciences, Bottleneck, Interactions biologiques, 03 medical and health sciences, Variation génétique, Génétique des populations, Genetic variation, Dynamique des populations, Adaptation, education, Ecology, Evolution, Behavior and Systematics, Selection (genetic algorithm), Adaptabilité, education.field_of_study, Genetic diversity, Ecology, Animal, Population size, 030104 developmental biology, Evolutionary biology, Plante, L20 - Écologie animale, Espèce envahissante
Abstract: 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.
Published: 2016

26. What are the benefits and risks of gene drives for population management and conservation biology?

Author: Nicolas O. Rode, Arnaud Estoup, Denis Bourguet, Virginie Courtier-Orgogozo, and Florence Débarre
Subjects: genetic rescue, conservation genetics, assisted gene flow, genetic population management, endangered species, invasive species
Abstract: Gene drive has recently been proposed as a promising technology for population management, including in conservation genetics; it is based on the release of genetically engineered individuals designed to rapidly propagate a desired mutation or transgene to high frequencies in 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). We examine the challenges posed by the evolution of resistance to gene drives and review the various environmental risks associated with gene drives. Contrary to suppression and eradication drives, the evolution of resistance should not prevent the fixation of rescue drives, while countermeasures to stop their spread are likely to fail. For eradication and suppression drives, minimizing the chances of resistance evolution requires targeting genes whose sequences have low polymorphism in natural populations (e.g. that are functionally constrained), which might however increase the odds of gene drive propagation to non-target populations/species. Conversely, targeting sequences that are present in the target population/species, but absent in non-target populations/species, might increase the odds of resistance evolution due to the introgression of resistant alleles from non-target populations/species. Once a gene drive has fixed in a target population, the time it persists before being inactivated by mutations influences its risk of spread to non-target populations/species. Finally, ethical values along with a clear regulatory framework for risk assessment should guide gene drive research.
Published: 2018
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27. The genomic basis of colour pattern polymorphism in the harlequin ladybird

Author: Benjamin Prud'homme, Aurelien Ausset, Arnaud Estoup, Hélène Bergès, Cécile Donnadieu, Julien Foucaud, Junichi Yamaguchi, Heiko Vogel, Danny Severac, Jacques Lagnel, Céline Lopez-Roques, Lian-Sheng Zang, B Gschloessl, Etienne Loire, Anne Loiseau, Benoit Facon, Lori Lawson-Handley, Maxime Manno, Karim Gharbi, Mathieu Gautier, Hugues Parrinello, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut de Biologie du Développement de Marseille (IBDM), Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Centre National de la Recherche Scientifique (CNRS), Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de La Réunion (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génétique et Amélioration des Fruits et Légumes (GAFL), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Animal, Santé, Territoires, Risques et Ecosystèmes (UMR ASTRE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Génomique Fonctionnelle (IGF), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut de Génomique Fonctionnelle - Montpellier GenomiX (IGF MGX), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-BioCampus (BCM), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Génome et Transcriptome - Plateforme Génomique (GeT-PlaGe), Institut National de la Recherche Agronomique (INRA)-Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre National de Ressources Génomiques Végétales (CNRGV), Edinburgh Genomics, University of Edinburgh, Norwich Research Park, Evolutionary and Environmental Genomics Group, School of Environmental Sciences, University of Hull, Jilin Agricultural University (JAU), Department of Entomology, Michigan State University [East Lansing], Michigan State University System-Michigan State University System, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ProdInra, Migration, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro - Montpellier SupAgro, and Centre National de la Recherche Scientifique (CNRS)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 1 (UM1)-Centre National de la Recherche Scientifique (CNRS)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 1 (UM1)
Subjects: 0106 biological sciences, 0303 health sciences, biology, Locus (genetics), biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, Phenotype, Harmonia axyridis, Population genomics, 03 medical and health sciences, Taxon, Evolutionary biology, Coccinellidae, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BV] Life Sciences [q-bio]/Vegetal Biology, Allele, Gene, 030304 developmental biology
Abstract: 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 single, unknown, locus9,10. Here, we combined whole-genome sequencing, population genomics, gene expression and functional analyses, to establish that the genepanniercontrols melanic pattern polymorphism inH. axyridis. We show thatpannier, which encodes an evolutionary conserved transcription factor, is necessary for the formation of melanic elements on the elytra. Allelic variation inpannierleads to protein expression in distinct domains on the elytra, and thus determines the distinct colour patterns inH. axyridis. Recombination betweenpannieralleles may be reduced by a highly divergent sequence of ca. 170 kb in thecis-regulatory regions ofpannierwith a 50 kb inversion between colour forms. This likely helps maintaining the distinct alleles found in natural populations. Thus we propose that highly variable discrete colour forms can arise in natural populations throughcis-regulatory allelic variation of a single gene.
Published: 2018
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28. Likelihood-free model choice

Author: Christian P. Robert, Pierre Pudlo, Arnaud Estoup, Jean-Michel Marin, Institut Montpelliérain Alexander Grothendieck (IMAG), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut de Mathématiques de Marseille (I2M), Aix Marseille Université (AMU)-École Centrale de Marseille (ECM)-Centre National de la Recherche Scientifique (CNRS), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), University of Warwick [Coventry], CEntre de REcherches en MAthématiques de la DEcision (CEREMADE), Université Paris Dauphine-PSL-Centre National de la Recherche Scientifique (CNRS), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Université de Montpellier (UM), Computational Biology Institute (IBC), University of Warwick, Centre National de la Recherche Scientifique (CNRS)-Université Paris Dauphine-PSL, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Sisson, S., Fan, Y., Beaumont, M., and Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)
Subjects: 0301 basic medicine, Computer science, [SDV]Life Sciences [q-bio], Posterior probability, 01 natural sciences, Summary statistics, Random forest, [STAT]Statistics [stat], 010104 statistics & probability, 03 medical and health sciences, 030104 developmental biology, Free model, Statistics, [SDE]Environmental Sciences, 0101 mathematics, [STAT.ME]Statistics [stat]/Methodology [stat.ME], ComputingMilieux_MISCELLANEOUS
Abstract: Fan, and Beaumont (2017). Beyond exposing the potential pitfalls of ABC approximations to posterior probabilities, the review emphasizes mostly the solution proposed by [25] on the use of random forests for aggregating summary statistics and for estimating the posterior probability of the most likely model via a secondary random forest.
Published: 2018

29. Model choice using Approximate Bayesian Computation and Random Forests: analyses based on model grouping to make inferences about the genetic history of Pygmy human populations

Author: Arnaud Estoup, Louis Raynal, Paul Verdu, Jean-Michel Marin, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Université de Montpellier (UM), Eco-Anthropologie et Ethnobiologie (EAE), Muséum national d'Histoire naturelle (MNHN)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Institut Montpelliérain Alexander Grothendieck (IMAG), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), and Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Muséum national d'Histoire naturelle (MNHN)
Subjects: [STAT]Statistics [stat], Random Forests, [STAT.AP]Statistics [stat]/Applications [stat.AP], model selection, [SDV.BA]Life Sciences [q-bio]/Animal biology, Approximate Bayesian Computation, evolutionary biology, genetic variation, population genetics, ComputingMilieux_MISCELLANEOUS, microsatellites
Abstract: International audience; 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 analyses based on ABC-RF to make inferences about the history of Pygmy human populations from Western Central Africa from a microsatellite genetic dataset. A noticeable novelty of the statistical analyses presented here is the application of ABC-RF methodology to make model choice on predefined groups of models. We formalized eight complex evolutionary scenarios which incorporate (or not) three major events: (i) whether there exists an ancestral common Pygmy population, (ii) the possibility of introgression/migration events between Pygmy and non-Pygmy populations, and (iii) the possibility of a change in size in the past in the non-Pygmy African population. We show that our grouping approach allows disentangling with strong confidence the main evolutionary events characterizing the population history of interest. The selected final scenario corresponds to a common origin of all Western Central African Pygmy groups, with the ancestral Pygmy population having diverged, with asymmetrical genetic introgression, from a demographically expanding non-Pygmy population.
Published: 2018

30. Genetic structure and invasion history of the house mouse (Mus musculus domesticus) in Senegal, West Africa: a legacy of colonial and contemporary times

Author: Mamadou Kane, Sylvain Piry, Raphaël Leblois, Anne Loiseau, Youssoupha Niang, Cédric Lippens, Karine Berthier, Mamoudou Diallo, Jean-Marc Duplantier, Arnaud Estoup, M.K. Hima, Carine Brouat, Caroline Tatard, Aliou Sow, Khalilou Bâ, Ambroise Dalecky, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut de Biologie Computationnelle (IBC), Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Station de Pathologie Végétale (AVI-PATHO), Institut National de la Recherche Agronomique (INRA), Funding provided by the Institut de Recherche pour le Developpement (IRD)., ANR-11-JSV7-0006,ENEMI,Conséquences évolutives des ennemis naturels dans des invasions biologiques majeures : le rôle des parasites dans le succès de l'invasion de deux rongeurs commensaux(2011), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS), Institut de recherche pour le développement (IRD [Sénégal]), and Unité de Pathologie Végétale (PV)
Subjects: 0106 biological sciences, 0301 basic medicine, Demographic history, MESH: Bayes Theorem, Population genetics, MESH: Genetics, Population, 010603 evolutionary biology, 01 natural sciences, DNA, Mitochondrial, House mouse, 03 medical and health sciences, Mice, MESH: Senegal, Genetic variation, Genetics, Animals, MESH: Animals, MESH: Genetic Variation, MESH: Models, Genetic, MESH: Mice, Genetics (clinical), [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], biology, Models, Genetic, Ecology, MESH: Animal Distribution, MESH: DNA, Mitochondrial, Genetic Variation, Bayes Theorem, biology.organism_classification, Senegal, Phylogeography, 030104 developmental biology, Genetics, Population, MESH: Phylogeography, Genetic structure, Biological dispersal, Original Article, MESH: Microsatellite Repeats, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Animal Distribution, Founder effect, Microsatellite Repeats, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: 12 pages; International audience; 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.
Published: 2017

31. The evolutionary ecology of invasive pests

Author: Ruth Hufbauer, Arnaud Estoup, Laure Olazcuaga, Julien Foucaud, Colorado State University [Fort Collins] (CSU), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)
Subjects: [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, ComputingMilieux_MISCELLANEOUS
Abstract: National audience
Published: 2017

32. A valuable work lying at the crossroad of neuro-ethology, evolution and ecology in the fruit pest Drosophila suzukii

Author: Arnaud Estoup, Ruth A. Hufbauer, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Colorado State University [Fort Collins] (CSU), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and ANR-16-CE02-0015,SWING,Invasion mondiale de la drosophile à aile tachetée: Génétique, plasticité et potentiel évolutif(2016)
Subjects: 0303 health sciences, Ecology, Ecology (disciplines), [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], adaptation, Biology, Agricultural pest, Ethology, biology.organism_classification, 03 medical and health sciences, 0302 clinical medicine, evolution, PEST analysis, ecological niche, agricultural pest, Drosophila suzukii, 030217 neurology & neurosurgery, 030304 developmental biology
Abstract: Il s'agit d'une recommandation de l'article : Evolution of multiple sensory systems drives novel egg-laying behavior in the fruit pest Drosophila suzukii Marianthi Karageorgi, Lasse B. Bräcker, Sébastien Lebreton, Caroline Minervino, Matthieu Cavey, K.P. Siju, Ilona C. Grunwald Kadow, Nicolas Gompel, Benjamin Prud’homme https://doi.org/10.1016/j.cub.2017.01.055; International audience; A recommendation of: Karageorgi M, Bräcker LB, Lebreton S, Minervino C, Cavey M, Siju KP, Grunwald Kadow IC, Gompel N, Prud’homme B. 2017. Evolution of multiple sensory systems drives novel egglaying behavior in the fruit pest Drosophila suzukii. Current Biology 27: 1-7. doi: 10.1016/j.cub.2017.01.055
Published: 2017

33. Modeling spatial expansion of invasive alien species: relative contributions of environmental and anthropogenic factors to the spreading of the harlequin ladybird in France

Author: Sylvain Piry, Sophie Veran, Benoit Facon, Christine N. Meynard, Arnaud Estoup, Vincent Ternois, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), CPIE Pays Soulaines, Virginia Institute of Marine Science (VIMS), This work was funded by a grant from the French Agropolis Fondation (RTRA, Montpellier, BIOFIS project #1001-001)., Coll William & Mary, and grant from the French Agropolis Fondation (RTRA, Montpellier, BIOFIS project #1001-001)
Subjects: 0106 biological sciences, Occupancy, Spatial expansion, [SDV]Life Sciences [q-bio], Species distribution, Distribution (economics), Introduced species, 010603 evolutionary biology, 01 natural sciences, modelling, expansion, Urbanization, Colonization, logical, espèce invasive, Ecology, Evolution, Behavior and Systematics, modélisation, harmonia axyridis, biology, business.industry, Ecology, 15. Life on land, biology.organism_classification, Harmonia axyridis, 010602 entomology, Environmental science, business
Abstract: 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 species has not yet reached them. Here we considered the invasive ladybird Harmonia axyridis as a case study to show the benefits of using a dynamic colonization-extinction model that does not assume equilibrium. We used a multi-year occupancy model incorporating environmental, anthropogenic and neighborhood effects, to identify factors that explained spreading variation of this species in France from 2004, when only a few occupied sites were detected, to 2011. We found that anthropogenic factors (urbanization, agriculture, vineyards, and presence/absence of highways) explained more variation in the diffusion process than environmental factors (winter and summer temperatures, wind-speed, and rainfall). The surface of urbanization was the major anthropogenic factor increasing the probability of colonization. The average summer temperature was the main environmental factor affecting colonization, with a negative effect when high or low. The neighborhood effect revealed that colonization was mostly influenced by contributions coming from a radius of 24 km around the focal cell. The contribution of neighborhood decreases over time, suggesting that H. axyridis is reaching its equilibrium in France. This is confirmed by the small discrepancy observed between the performance of our approach and a SDM approach when predicting a single year occupancy pattern at the end of the study period. Our approach has the advantage of explicitly modelling the state of the biological system during the spatial expansion and identifying colonization constraints. This allows managers to explore the effect of different actions on the system at key moments of the invasion process, hence providing a powerful approach to prioritize management strategies.
Published: 2016

34. The harlequin ladybird, Harmonia axyridis: global perspectives on invasion history and ecology

Author: Alexandra Magro, Artur Gil, A.J.M. Loomans, Cang Hui, Katie M. Murray, Sandra Viglášová, Paul S. van Wielink, Axel Vandereycken, Arnaud Estoup, Susana Clusella-Trullas, Benoit Facon, Annette Herz, May-Guri Saethre, Zdenka Martinkova, Richard Comont, Isabel Borges, Dirk Maes, Sergey K. Ryndevich, Thomas Guillemaud, Helen E. Roy, António O. Soares, Marina J. Orlova-Bienkowskaja, Mary M. Gardiner, Alexander Ok Lukashuk, Tim Adriaens, William D. Hutchison, Ingrid A. Minnaar, Patrick De Clercq, John J. Sloggett, Peter M. J. Brown, Alois Honek, Marc Kenis, Audrey A. Grez, Hans Peter Ravn, Tania Zaviezo, Nick Berkvens, Wolfgang Rabitsch, Danny Haelewaters, Riaan Stals, Zihua Zhao, Ján Kulfan, John E. Losey, Peter Zach, Andy G. Howe, Eric Lombaert, I. A. Zakharov, Lori Lawson Handley, Oldrich Nedved, Robert L. Koch, Steph L. Rorke, Matthew C. Tinsley, Gabriele Rondoni, René Eschen, Naoya Osawa, Edward W. Evans, Gilles San Martin, Centre for Ecology and Hydrology [Wallingford] (CEH), Natural Environment Research Council (NERC), Anglia Ruskin University (ARU), Research Institute for Nature and Forest (INBO), Research Institute for Agricultural, Fisheries and Food (ILVO), University of the Azores, Centre for Ecology, Evolution and Environmental Changes (cE3c) / Azorean Biodiversity Group and Universidade dos Açores, Departamento de Ciências e Engenharia do Ambiente, Açores, Stellenbosch University, Centre for Invasion Biology, Department of Botany and Zoology, Bumblebee Conservation Trust, Universiteit Gent = Ghent University [Belgium] (UGENT), Department of Crop Protection, Centre for Agricultural and Biosciences International Europe - Switzerland (CABI Europe - Switzerland), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Utah State University (USU), Ohio State University [Columbus] (OSU), Ohio Agricultural Research and Development Center, Universidad de Chile = University of Chile [Santiago] (UCHILE), Institut Sophia Agrobiotech (ISA), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Recherche Agronomique (INRA), Department of Organismic and Evolutionary Biology [Cambridge] (OEB), Harvard University [Cambridge], Julius Kühn-Institut - Federal Research Centre for Cultivated Plants (JKI), Crop Res Inst, Div Crop Genet & Breeding, Prague, Czech Republic, Partenaires INRAE, Department of Geosciences and Natural Resource Management [Copenhagen] (IGN), Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Centre for Invasion Biology, Department of Mathematical Sciences, Stellenbosch University, University of Minnesota System, Institute of Forest Ecology - SAS, University of Hull [United Kingdom], National Plant Protection Organization (NPPO), Cornell University [New York], Berezinskiy Biosphere Reserve, Belarus, Evolution et Diversité Biologique (EDB), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, University of Stirling, Department of Biological and Environmental Sciences, University of Stirling, Walloon Agricultural Research Centre, Department of Botany and Zoology, Centre of Excellence for Invasion Biology, University of South Bohemia, Institute of Entomology [České Budějovice] (BIOLOGY CENTRE CAS), Biology Centre of the Czech Academy of Sciences (BIOLOGY CENTRE CAS), Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS), A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences [Moscow] (RAS), Kyoto University [Kyoto], Laboratory of Insect Ecology, Graduate School of Agriculture, Kyoto University, Environment Agency Austria, Department of Agricultural, Food and Environmental Sciences, University of Perugia (DSA3), Università degli Studi di Perugia (UNIPG), The paper had its origin at a workshop on 'Drivers, impacts, mechanisms and adaptation in insect invasions' hosted by the DST-NRF Centre of Excellence for Invasion Biology in Stellenbosch, South Africa, in November 2014. Additional financial support was provided by HortGro, the National Research Foundation of South Africa, Stellenbosch University, and SubTrop. We thank all our collaborators, and particularly the volunteer community, who have contributed to research around the world on H. axyridis. The number of references included reflects the range of inspiring studies on H. axyridis from so many people-we look forward to new and continued collaborations in the future. We are grateful to the editors of this special issue for inviting this review and providing an opportunity to explore ideas through the 'Invasive Insects Workshop funding (NRF South Africa, CIB)'. We also thank the anonymous reviewers for all their useful comments and reflections. The UK Ladybird Survey and associated coauthors are supported by the Biological Records Centre (part of the Centre for Ecology & Hydrology), which receives support from both the Natural Environment Research Council and the Joint Nature Conservation Committee. The IOBC WPRS and Global Working Groups 'Benefits and Risks of Exotic Biological Control Agents' and the COST Action TD1209 'Alien Challenge' have facilitated discussions and collaborations on H. axyridis. This study was supported by the French Agropolis Fondation (Labex Agro-Montpellier, BIOFIS Project Number 1001-001) and by a grant from the ERA-Net BiodivERsA, with the national funders ANR (France), DFG (Germany) and BELSPO (Belgium), as part of the 2012-2013 BiodivERsA call for research proposals. Support has been also received from FONDECYT 1140662 (Chile). The study of M.J. Orlova-Bienkowskaja and I. A. Zakharov was supported by Russian Science Foundation, Project No. 16-16-00079. Gabriele Rondoni acknowledges financial support from Fondazione Cassa di Risparmio di Perugia. Riaan Stals acknowledges funding from the Department of Science and Technology, South Africa. The research of Peter Zach and colleagues was funded by the project VEGA 2/0035/13 and VEGA 2/0052/15. A. Honek and Z. Martinkova were supported by grants GACR 14-26561S and COST CZ LD14084. Research in Switzerland is funded by the Swiss Federal Office for the Environment. Hans Peter Ravn was supported by the Villum Foundation. Danny Haelewaters acknowledges funding from the David Rockefeller Center for Latin American Studies at Harvard University and from the Mycological Society of America., Sobell Department of Motor Neuroscience and Movement Disorders, Institute of Neurology, Research Institute for Nature and Forest, Institut Sophia Agrobiotech [Sophia Antipolis] (ISA), Institut National de la Recherche Agronomique (INRA)-Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA)-Centre National de la Recherche Scientifique (CNRS), Julius Kühn Institute (JKI), CABI Europe Switzerland, Universität der Bundeswehr München [Neubiberg], Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Grad Sch Agr, Lab Forest Ecol, Department of Biodiversity and Nature Conservation, NEMOD Biotherapeutics GmbH & Co. KG, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile (UC), RS: FSE MSP, and Maastricht Science Programme
Subjects: 0106 biological sciences, Range (biology), Ecology (disciplines), ADALIA-BIPUNCTATA, Population, Biodiversity, INTRAGUILD PREDATION, Generalist and specialist species, NATURAL ENEMIES, 010603 evolutionary biology, 01 natural sciences, Ecology and Environment, 1ST RECORD, Competitive interactions, MYZUS-PERSICAE HOMOPTERA, education, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, Apex predator, education.field_of_study, APHIS-GLYCINES, Ecology, biology, PALLAS COLEOPTERA-COCCINELLIDAE, Biocontrol, 15. Life on land, biology.organism_classification, Harmonia axyridis, 010602 entomology, MULTICOLORED ASIAN LADYBIRD, Coccinellidae, Invasion history, Species traits, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, BEETLE COLEOPTERA, BIOLOGICAL-CONTROL, Intraguild predation
Abstract: International audience; 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 considerable trepidation. It is a generalist top predator, able to thrive in many habitats and across wide climatic conditions. It poses a threat to biodiversity, particularly aphidophagous insects, through competition and predation, and in many countries adverse effects have been reported on other species, particularly coccinellids. However, the patterns are not consistent around the world and seem to be affected by many factors including landscape and climate. Research on H. axyridis has provided detailed insights into invasion biology from broad patterns and processes to approaches in surveillance and monitoring. An impressive number of studies on this alien species have provided mechanistic evidence alongside models explaining large-scale patterns and processes. The involvement of citizens in monitoring this species in a number of countries around the world is inspiring and has provided data on scales that would be otherwise unachievable. Harmonia axyridis has successfully been used as a model invasive alien species and has been the inspiration for global collaborations at various scales. There is considerable scope to expand the research and associated collaborations, particularly to increase the breadth of parallel studies conducted in the native and invaded regions. Indeed a qualitative comparison of biological traits across the native and invaded range suggests that there are differences which ultimately could influence the population dynamics of this invader. Here we provide an overview of the invasion history and ecology of H. axyridis globally with consideration of future research perspectives. We reflect broadly on the contributions of such research to our understanding of invasion biology while also informing policy and people.
Published: 2016

35. Reliable ABC model choice via random forests

Author: Mathieu Gautier, Christian P. Robert, Arnaud Estoup, Pierre Pudlo, Jean-Michel Marin, Jean-Marie Cornuet, Institut Montpelliérain Alexander Grothendieck (IMAG), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), CEntre de REcherches en MAthématiques de la DEcision (CEREMADE), Centre National de la Recherche Scientifique (CNRS)-Université Paris Dauphine-PSL, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), University of Warwick [Coventry], and Université Paris Dauphine-PSL-Centre National de la Recherche Scientifique (CNRS)
Subjects: FOS: Computer and information sciences, 0301 basic medicine, Statistics and Probability, random forests, Computer science, Posterior probability, Word error rate, Machine Learning (stat.ML), Bayesian inference, computer.software_genre, Biochemistry, Statistics - Computation, Methodology (stat.ME), Bayesian model choice, 03 medical and health sciences, Discriminative model, [STAT.ML]Statistics [stat]/Machine Learning [stat.ML], Statistics - Machine Learning, Computer Simulation, Quantitative Biology - Populations and Evolution, [STAT.CO]Statistics [stat]/Computation [stat.CO], Molecular Biology, Computation (stat.CO), Statistics - Methodology, Models, Genetic, Model selection, Populations and Evolution (q-bio.PE), Bayes Theorem, Computer Science Applications, Random forest, Computational Mathematics, 030104 developmental biology, Genetics, Population, Computational Theory and Mathematics, FOS: Biological sciences, Data mining, Approximate Bayesian computation, computer, ABC, [STAT.ME]Statistics [stat]/Methodology [stat.ME], Algorithms
Abstract: 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. We propose a novel approach based on a machine learning tool named random forests to conduct selection among the highly complex models covered by ABC algorithms. We thus modify the way Bayesian model selection is both understood and operated, in that we rephrase the inferential goal as a classification problem, first predicting the model that best fits the data with random forests and postponing the approximation of the posterior probability of the predicted MAP for a second stage also relying on random forests. Compared with earlier implementations of ABC model choice, the ABC random forest approach offers several potential improvements: (i) it often has a larger discriminative power among the competing models, (ii) it is more robust against the number and choice of statistics summarizing the data, (iii) the computing effort is drastically reduced (with a gain in computation efficiency of at least fifty), and (iv) it includes an approximation of the posterior probability of the selected model. The call to random forests will undoubtedly extend the range of size of datasets and complexity of models that ABC can handle. We illustrate the power of this novel methodology by analyzing controlled experiments as well as genuine population genetics datasets. The proposed methodologies are implemented in the R package abcrf available on the CRAN., 39 pages, 15 figures, 6 tables
Published: 2016

36. Reduced population size can induce quick evolution of inbreeding depression in the invasive ladybird Harmonia axyridis

Author: Ashraf Tayeh, Arnaud Estoup, Gilles Le Moguédec, Bruno Serrate, Wang Su, Benoit Facon, Guillaume J. M. Laugier, Laurent Soldati, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Beijing Academy of Agriculture and Forestry Sciences, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])
Subjects: 0106 biological sciences, 0301 basic medicine, Population fragmentation, Harmonia axyridis, [SDV]Life Sciences [q-bio], Population, Genetic purging, 010603 evolutionary biology, 01 natural sciences, Bottleneck, 03 medical and health sciences, Effective population size, Inbreeding depression, education, Ecology, Evolution, Behavior and Systematics, Genetics, education.field_of_study, Ecology, biology, Population size, 15. Life on land, biology.organism_classification, Fixation, Fixation (population genetics), 030104 developmental biology, Evolutionary biology, Purging
Abstract: 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 inbreeding depression, caused by the expression of deleterious alleles, is important. Changes in mating regimes or in population size can induce the evolution of deleterious allele frequencies, either by selection or by drift, possibly resulting in the purging or the fixation of such alleles within the population. The harlequin ladybird Harmonia axyridis became invasive on several continents following a scenario including at least one event of demographic bottleneck. Although native populations suffered from severe inbreeding depression, it was greatly reduced in invasive ones suggesting that deleterious alleles were purged during the invasion process. In this study, we performed an experiment designed to manipulate the effective population size of H. axyridis across successive generations to mimic contrasting introduction events. We used the measurement of two fitness-related phenotypic traits in order to test (1) if inbreeding depression can evolve at the time-scale of an invasion; and (2) if the changes in inbreeding depression following a bottleneck in laboratory conditions are compatible with the purging of deleterious alleles observed in this species. We found that two generations of very low population size are enough to induce a substantial change in inbreeding depression. Although the genetic changes mostly consisted in fixation of deleterious alleles, purging did also occur, sometimes simultaneously with fixation.
Published: 2016

37. Anthropogenically induced adaptation to invade (AIAI): contemporary adaptation to human-altered habitats within the native range can promote invasions

Author: Virginie Ravigné, Benoit Facon, Olivier Rey, Arnaud Estoup, Julie Turgeon, Ruth A. Hufbauer, Julien Foucaud, and Carol Eunmi Lee
Subjects: 0106 biological sciences, 0303 health sciences, Ecology, 15. Life on land, Biology, 010603 evolutionary biology, 01 natural sciences, Invasive species, 03 medical and health sciences, Habitat destruction, Habitat, Propagule, 13. Climate action, Genetics, Local environment, General Agricultural and Biological Sciences, Ecology, Evolution, Behavior and Systematics, Evolutionary theory, 030304 developmental biology, Adaptive evolution
Abstract: Adaptive evolution is currently accepted as playing a significant role in biological invasions. Adaptations relevant to invasions are typically thought to occur either recently within the introduced range, as an evolutionary response to novel selection regimes, or within the native range, because of long-term adaptation to the local environment. We propose that recent adaptation within the native range, in particular adaptations to human-altered habitat, could also contribute to the evolution of invasive populations. Populations adapted to human-altered habitats in the native range are likely to increase in abundance within areas frequented by humans and associated with human transport mechanisms, thus enhancing the likelihood of transport to a novel range. Given that habitats are altered by humans in similar ways worldwide, as evidenced by global environmental homogenization, propagules from populations adapted to human-altered habitats in the native range should perform well within similarly human-altered habitats in the novel range. We label this scenario ‘Anthropogenically Induced Adaptation to Invade’. We illustrate how it differs from other evolutionary processes that may occur during invasions, and how it can help explain accelerating rates of invasions.
Published: 2011

38. Inferring the origin of populations introduced from a genetically structured native range by approximate Bayesian computation: case study of the invasive ladybird Harmonia axyridis

Author: P. De Clercq, Cathleen E. Thomas, I. Goryacheva, Walker A. Jones, Su Wang, Jianlong Li, Eric Lombaert, Arnaud Estoup, Thomas Guillemaud, Hong Pang, Emmanuelle Jousselin, J.C. van Lenteren, Alain Migeon, Nick Berkvens, Lori Lawson Handley, Remy Poland, and I. A. Zakharov
Subjects: 0106 biological sciences, 0303 health sciences, education.field_of_study, Genetic diversity, biology, Ecology, Population, Introduced species, biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, Harmonia axyridis, Gene flow, 03 medical and health sciences, F-statistics, Genetic structure, Genetics, Approximate Bayesian computation, education, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology
Abstract: Correct identification of the source population of an invasive species is a prerequisite for testing hypotheses concerning the factors responsible for biological invasions. The native area of invasive species may be large, poorly known and/or genetically structured. Because the actual source population may not have been sampled, studies based on molecular markers may generate incorrect conclusions about the origin of introduced populations. In this study, we characterized the genetic structure of the invasive ladybird Harmonia axyridis in its native area using various population genetic statistics and methods. We found that native area of H. axyridis most probably consisted of two geographically distinct genetic clusters located in eastern and western Asia. We then performed approximate Bayesian computation (ABC) analyses on controlled simulated microsatellite data sets to evaluate (i) the risk of selecting incorrect introduction scenarios, including admixture between sources, when the populations of the native area are genetically structured and sampling is incomplete and (ii) the ability of ABC analysis to minimize such risks by explicitly including unsampled populations in the scenarios compared. Finally, we performed additional ABC analyses on real microsatellite data sets to retrace the origin of biocontrol and invasive populations of H. axyridis, taking into account the possibility that the structured native area may have been incompletely sampled. We found that the invasive population in eastern North America, which has served as the bridgehead for worldwide invasion by H. axyridis, was probably formed by an admixture between the eastern and western native clusters. This admixture may have facilitated adaptation of the bridgehead population.
Published: 2011

39. The global spread of Harmonia axyridis (Coleoptera: Coccinellidae): distribution, dispersal and routes of invasion

Author: Arnaud Estoup, Cathleen E. Thomas, Lori-Jayne Lawson Handley, Daniel L. Jeffries, Eric Lombaert, Peter M. J. Brown, Anglia Ruskin University (ARU), University of Hull, Institut Sophia Agrobiotech (ISA), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Recherche Agronomique (INRA), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)
Subjects: 0106 biological sciences, Entomology, espèces invasives, Multicolored Asian lady beetle, Range (biology), [SDV]Life Sciences [q-bio], Alien species, propagation mondiale, Introduced species, Biology, 010603 evolutionary biology, 01 natural sciences, Invasive species, Range expansion, Dispersal mechanism, Harlequin ladybird, Ecology, biology.organism_classification, Harmonia axyridis, Coleoptera, 010602 entomology, Coccinellidae, Animal ecology, Biological control, Insect Science, espèces exotiques, Biological dispersal, GENETIQUE DES POPULATIONS, Agronomy and Crop Science
Abstract: Contact : peter.brown@anglia.ac.uk UMR IBSV : Equipe ‘Biologie des Populations en Interaction’; International audience; Released as a biological control agent of aphids and coccids, Harmonia axyridis (Coleoptera: Coccinellidae) has spread from Asia to four additional continents. Since 1988 H. axyridis has established in at least 38 countries in its introduced range: three countries in North America, six in South America, 26 in Europe and three in Africa. In different continents the species has spread at rates estimated between 100 and 500 km year-1. Here, the global spread of H. axyridis is thoroughly reviewed. Mechanisms of short- and long-distance dispersal in coccinellids are discussed, as are the reasons for them, with particular emphasis on H. axyridis. Dispersal via anthropogenic means has been particularly important in the case of H. axyridis. Preliminary studies investigating the invasion routes of H. axyridis using genetic analyses (involving both microsatellite and mitochondrial DNA) are outlined.
Published: 2011

40. Experimental evidence for the phenotypic impact of admixture between wild and biocontrol Asian ladybird (Harmonia axyridis) involved in the European invasion

Author: P. De Clercq, Eric Lombaert, Ashraf Tayeh, Julie Turgeon, Jonathan G. Lundgren, Nick Berkvens, Benoit Facon, and Arnaud Estoup
Subjects: 0106 biological sciences, 0303 health sciences, Ecology, Biological pest control, Introduced species, 15. Life on land, Biology, biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, Harmonia axyridis, Invasive species, Life history theory, 03 medical and health sciences, Genetic variation, Coccinellidae, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Hybrid
Abstract: Hybridization can fuel evolutionary processes during biological invasions. The harlequin ladybird Harmonia axyridis has long been used as a biocontrol agent before the species became invasive worldwide. Previous analysis based on microsatellite data has shown that European invasive populations bear traces of admixture between an eastern North American source, which is at the origin of the worldwide invasion, and biocontrol strains used in Europe. In this study, we tested the hypothesis that this early admixture event may have fostered the European invasion by impacting on the phenotypes of wild European populations. Mean life history traits of experimental F(1) hybrids are compared with pure parental sources and wild European crosses. Our results reveal a biased impact whereby North American beetles benefitted from being admixed with European biocontrol strains. Resemblance between experimental hybrids and wild European invasive crosses further suggests a long-lasting effect of admixture that may still be at work and fostering invasiveness.
Published: 2011

41. Stratified dispersal and increasing genetic variation during the invasion of Central Europe by the western corn rootworm,Diabrotica virgifera virgifera

Author: Stefan Toepfer, Thomas Guillemaud, Nicholas J. Miller, Arnaud Estoup, and Marc Ciosi
Subjects: 0106 biological sciences, 0303 health sciences, education.field_of_study, Ecology, Population, 15. Life on land, Biology, biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, Population density, Gene flow, 03 medical and health sciences, Western corn rootworm, Effective population size, Genetic variation, Genetics, Biological dispersal, Colonization, General Agricultural and Biological Sciences, education, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology
Abstract: Invasive species provide opportunities for investigating evolutionary aspects of colonization processes, including initial foundations of populations and geographic expansion. Using microsatellite markers and historical information, we characterized the genetic patterns of the invasion of the western corn rootworm (WCR), a pest of corn crops, in its largest area of expansion in Europe: Central and South-Eastern (CSE) Europe. We found that the invaded area probably corresponds to a single expanding population resulting from a single introduction of WCR and that gene flow is geographically limited within the population. In contrast to what is expected in classical colonization processes, an increase in genetic variation was observed from the center to the edge of the outbreak. Control measures against WCR at the center of the outbreak may have decreased effective population size in this area which could explain this observed pattern of genetic variation. We also found that small remote outbreaks in southern Germany and north-eastern Italy most likely originated from long-distance dispersal events from CSE Europe. We conclude that the large European outbreak is expanding by stratified dispersal, involving both continuous diffusion and discontinuous long-distance dispersal. This latter mode of dispersal may accelerate the expansion of WCR in Europe in the future.
Published: 2010

42. Can things get worse when an invasive species hybridizes? The harlequin ladybirdHarmonia axyridisin France as a case study

Author: Laurent Crespin, Arnaud Estoup, Anne Loiseau, Eric Lombaert, Alexandra Magro, and Benoit Facon
Subjects: 0106 biological sciences, 0303 health sciences, education.field_of_study, biology, Population, Zoology, Population genetics, Reproductive isolation, Quantitative genetics, biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, Invasive species, Harmonia axyridis, Life history theory, 03 medical and health sciences, Genetic variation, Genetics, General Agricultural and Biological Sciences, education, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology
Abstract: So far, only a few studies have explicitly investigated the consequences of admixture for the adaptative potential of invasive populations. We addressed this question in the invasive ladybird Harmonia axyridis. After decades of use as a biological control agent against aphids in Europe and North America, H. axyridis recently became invasive in four continents and has now spread widely in Europe. Despite this invasion, a flightless strain is still sold as a biological control agent in Europe. However, crosses between flightless and invasive individuals yield individuals able to fly, as the flightless phenotype is caused by a single recessive mutation. We investigated the potential consequences of admixture between invasive and flightless biological control individuals on the invasion in France. We used three complementary approaches: (i) population genetics, (ii) a mate-choice experiment, and (iii) a quantitative genetics experiment. The invasive French population and the biological control strain showed substantial genetic differentiation, but there are no reproductive barriers between the two. Hybrids displayed a shorter development time, a larger size and a higher genetic variance for survival in starvation conditions than invasive individuals. We discuss the potential consequences of our results with respect to the invasion of H. axyridis in Europe.
Published: 2010

43. Combining genetic, historical and geographical data to reconstruct the dynamics of bioinvasions: application to the cane toad Bufo marinus

Author: Jean-Marie Cornuet, Mathias Currat, Stuart J. E. Baird, Nicolas Ray, Laurent Excoffier, Arnaud Estoup, Filipe Santos, and Mark A. Beaumont
Subjects: 0106 biological sciences, 0303 health sciences, biology, Ecology, Bayesian probability, Context (language use), 15. Life on land, Bayesian inference, biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, Field (geography), Cane toad, 03 medical and health sciences, Genetics, Statistical inference, Biological dispersal, Approximate Bayesian computation, Cartography, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Biotechnology
Abstract: We developed a spatially explicit model of a bioinvasion and used an approximate Bayesian computation (ABC) framework to make various inferences from a combination of genetic (microsatellite genotypes), historical (first observation dates) and geographical (spatial coordinates of introduction and sampled sites) information. Our method aims to discriminate between alternative introduction scenarios and to estimate posterior densities of demographically relevant parameters of the invasive process. The performance of our landscape-ABC method is assessed using simulated data sets differing in their information content (genetic and/or historical data). We apply our methodology to the recent introduction and spatial expansion of the cane toad, Bufo marinus, in northern Australia. We find that, at least in the context of cane toad invasion, historical data are more informative than genetic data for discriminating between introduction scenarios. However, the combination of historical and genetic data provides the most accurate estimates of demographic parameters. For the cane toad, we find some evidence for a strong bottleneck prior to introduction, a small initial number of founder individuals (about 15), a large population growth rate (about 400% per generation), a standard deviation of dispersal distance of 19 km per generation and a high invasion speed at equilibrium (50 km per year). Our approach strengthens the application of the ABC method to the field of bioinvasion by allowing statistical inferences to be made on the introduction and the spatial expansion dynamics of invasive species using a combination of various relevant sources of information.
Published: 2010

44. Reconstructing routes of invasion using genetic data: why, how and so what?

Author: Thomas Guillemaud and Arnaud Estoup
Subjects: 0106 biological sciences, 0303 health sciences, Ecology, Ecology (disciplines), Counterintuitive, Genetic data, Context (language use), Biology, 010603 evolutionary biology, 01 natural sciences, Data science, 03 medical and health sciences, Bayes' theorem, Invasion process, Genetics, Statistical inference, Approximate Bayesian computation, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology
Abstract: Detailed knowledge about the geographical pathways followed by propagules from their source to the invading populations—referred to here as routes of invasion—provides information about the history of the invasion process and the origin and genetic composition of the invading populations. The reconstruction of invasion routes is required for defining and testing different hypotheses concerning the environmental and evolutionary factors responsible for biological invasions. In practical terms, it facilitates the design of strategies for controlling or preventing invasions. Most of our knowledge about the introduction routes of invasive species is derived from historical and observational data, which are often sparse, incomplete and, sometimes, misleading. In this context, population genetics has proved a useful approach for reconstructing routes of introduction, highlighting the complexity and the often counterintuitive nature of the true story. This approach has proved particularly useful since the recent development of new model-based methods, such as approximate Bayesian computation, making it possible to make quantitative inferences in the complex evolutionary scenarios typically encountered in invasive species. In this review, we summarize some of the fundamental aspects of routes of invasion, explain why the reconstruction of these routes is useful for addressing both practical and theoretical questions, and comment on the various reconstruction methods available. Finally, we consider the main insights obtained to date from studies of invasion routes.
Published: 2010

45. Worldwide invasion by the little fire ant: routes of introduction and eco-evolutionary pathways

Author: Merav Vonshak, Jan Oettler, Anne Loiseau, Jean Luc Mercier, Arnaud Estoup, Hervé Jourdan, Alexander S. Mikheyev, Jean-Bruno Mikissa, Djoël Konghouleux, Maurice Tindo, Jérôme Orivel, Terry McGlynn, Dominique Fresneau, Jacques H. C. Delabie, and Julien Foucaud
Subjects: 0106 biological sciences, 0303 health sciences, Fire ant, biology, Eco evolutionary, Ecology, Range (biology), Human evolutionary genetics, 15. Life on land, Wasmannia, biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, Invasive species, 03 medical and health sciences, Habitat, Genetics, General Agricultural and Biological Sciences, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology
Abstract: Biological invasions are generally thought to occur after human aided migration to a new range. However, human activities prior to migration may also play a role. We studied here the evolutionary genetics of introduced populations of the invasive ant Wasmannia auropunctata at a worldwide scale. Using microsatellite markers, we reconstructed the main routes of introduction of the species. We found three main routes of introduction, each of them strongly associated to human history and trading routes. We also demonstrate the overwhelming occurrence of male and female clonality in introduced populations of W. auropunctata, and suggest that this particular reproduction system is under selection in human-modified habitats. Together with previous researches focused on native populations, our results suggest that invasive clonal populations may have evolved within human modified habitats in the native range, and spread further from there. The evolutionarily most parsimonious scenario for the emergence of invasive populations of the little fire ant might thus be a two-step process. The W. auropunctata case illustrates the central role of humans in biological change, not only due to changes in migration patterns, but also in selective pressures over species.
Published: 2010

46. Reproductive system, social organization, human disturbance and ecological dominance in native populations of the little fire ant, Wasmannia auropunctata

Author: Arnaud Estoup, Julien Le Breton, Jérôme Orivel, Julien Foucaud, Philippe Cerdan, Jacques H. C. Delabie, Denis Fournier, and Anne Loiseau
Subjects: 0106 biological sciences, 0303 health sciences, education.field_of_study, Ecology, Population, Niche, Interspecific competition, 15. Life on land, Biology, Wasmannia, biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, Intraspecific competition, Invasive species, 03 medical and health sciences, Habitat, Genetics, Dominance (ecology), education, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology
Abstract: The invasive ant species Wasmannia auropunctata displays both ecologically dominant and non-dominant populations within its native range. Three factors could theoretically explain the ecological dominance of some native populations of W. auropunctata: (i) its clonal reproductive system, through demographic and/or adaptive advantages; (ii) its unicolonial social organization, through lower intraspecific and efficient interspecific competition; (iii) the human disturbance of its native range, through the modification of biotic and abiotic environmental conditions. We used microsatellite markers and behavioural tests to uncover the reproductive modes and social organization of dominant and non-dominant native populations in natural and human-modified habitats. Microsatellite and mtDNA data indicated that dominant and non-dominant native populations (supercolonies as determined by aggression tests) of W. auropunctata did not belong to different evolutionary units. We found that the reproductive system and the social organization are neither necessary nor sufficient to explain W. auropunctata ecological dominance. Dominance rather seems to be set off by unknown ecological factors altered by human activities, as all dominant populations were recorded in human-modified habitats. The clonal reproductive system found in some populations of W. auropunctata may however indirectly contribute to its ecological dominance by allowing the species to expand its environmental niche, through the fixation over time of specific combinations of divergent male and female genotypes. Unicoloniality may rather promote the range expansion of already dominant populations than actually trigger ecological dominance. The W. auropunctata model illustrates the strong impact of human disturbance on species' ecological features and the adaptive potential of clonal reproductive systems.
Published: 2009

47. Introduction history ofDrosophila subobscurain the New World: a microsatellite-based survey using ABC methods

Author: L. Serra, George W. Gilchrist, Raymond B. Huey, Marta Pascual, Arnaud Estoup, Francesc Mestres, Joan Balanyà, and Marie Pierre Chapuis
Subjects: 0106 biological sciences, Mediterranean climate, 0303 health sciences, Ecology, Biology, 010603 evolutionary biology, 01 natural sciences, Drosophila subobscura, Invasive species, 03 medical and health sciences, Effective population size, Propagule, South american, Genetics, Microsatellite, Approximate Bayesian computation, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology
Abstract: Drosophila subobscura is a Palearctic species that was first observed in South and North America in the early 1980s, and that rapidly invaded broad latitudinal ranges on both continents. To trace the source and history of this invasion, we obtained genotypic data on nine microsatellite loci from two South American, two North American and five European populations of D. subobscura. We analysed these data with traditional statistics as well as with an approximate Bayesian computation (ABC) framework. ABC methods yielded the strongest support for the scenario involving a serial introduction with founder events from Europe into South America, and then from South America into North America. Stable effective population size of the source population was very large (around one million individuals), and the propagule size was notably smaller for the introduction into South America (i.e. high bottleneck severity index with only a few effective founders) but considerably larger for the subsequent introduction into North America (i.e. low bottleneck severity index with around 100–150 effective founders). Finally, the Mediterranean region of Europe (and most likely Barcelona from the localities so far analysed) is proposed as the source of the New World flies, based on mean individual assignment statistics.
Published: 2007

48. Evolutionary ecology of microsporidia associated with the invasive ladybird Harmonia axyridis

Author: Benoit Facon, Andreas Vilcinskas, Heiko Vogel, Arnaud Estoup, Henrike Schmidtberg, Ashraf Tayeh, Institute of Phytopathology and Applied Zoology (IPAZ), Justus-Liebig-Universität Gießen (JLU), Fraunhofer (Fraunhofer-Gesellschaft), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Max Planck Institute for Chemical Ecology, Max-Planck-Gesellschaft, ERA-Net BiodivERsA, with the national funders ANR (France), DFG (Germany) and BELSPO (Belgium), as part of the 2012–2013 BiodivERsA call for research propos- als. AV acknowledges financial support from the Hessen State Ministry of Higher Education, Research and the Arts (HMWK) via the LOEWE research center 'In- sect Biotechnology.', and Publica
Subjects: 0106 biological sciences, Harmonia axyridis, [SDV]Life Sciences [q-bio], Biodiversity, Introduced species, 010603 evolutionary biology, 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, Invasive species, Predation, 03 medical and health sciences, Animals, invasion biology, innate immunity, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Ovum, 0303 health sciences, biology, Ecology, fungi, 15. Life on land, biology.organism_classification, Biological Evolution, Coleoptera, Coccinellidae, Insect Science, Larva, Predatory Behavior, evolutionary ecology, microsporidia, Evolutionary ecology, Introduced Species, Agronomy and Crop Science, Intraguild predation, intraguild predation
Abstract: International audience; 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 noninvasive. We previously proposed a hypothesis that parasites associated with invading species can promote their invasive success if they are harmless toward the invaders but harmful to their competitors and/or predators in the newly colonized habitat. Here we discuss whether microsporidia that have recently been discovered in the invasive ladybird Harmonia axyridis contribute to its invasive success. We show that all H. axyridis beetles sourced from diverse collection sites all over the world carry abundant microsporidia. This suggests that both native and invasive H. axyridis populations are associated with these tolerated parasites, which were likely to have existed in native populations before expansion rather than being acquired in newly colonized areas. We describe the pathogenesis of the microsporidia during different developmental stages of H. axyridis and we address the possibility that the predation of its infected eggs and larvae by competing native ladybird species may lead to their infection and ultimately to their decline. Finally, we discuss our initial hypothesis: microsporidia that are tolerated by an invasive vector insect can be active against susceptible native competitors and/or predator species.
Published: 2015

49. Biological invasion and biological control select for different life histories

Author: Léa Frachon, Ruth A. Hufbauer, Benoit Facon, Ashraf Tayeh, Virginie Ravigné, Arnaud Estoup, Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Department of Bioagricultural Science and Pest Management, Graduate Degree Program in Ecology, Colorado State University [Fort Collins] (CSU), Biologie et Génétique des Interactions Plante-Parasite (UMR BGPI), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), This study was supported by the French Agropolis Fondation (Labex Agro-Montpellier, BIOFIS Project Number 1001-001) and by a grant from the ERA-Net BiodivERsA, with the national funders ANR (France), DFG (Germany) and BELSPO (Belgium), as part of the 2012–2013 BiodivERsA call for research proposals. R.A.H. acknowledges support from US NSF grants DEB-0949619 and 0541673 as well as the US Department of Agriculture via the Colorado Agricultural Experiment Station, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Facon, Benoit
Subjects: 0106 biological sciences, Reproduction (economics), [SDV]Life Sciences [q-bio], Biological pest control, General Physics and Astronomy, Introduced species, lutte biologique, coccinelle, 010603 evolutionary biology, 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, Invasive species, Article, Predation, 03 medical and health sciences, Life Expectancy, Animals, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Life history, Selection, Genetic, 030304 developmental biology, H20 - Maladies des plantes, harmonia axyridis, 0303 health sciences, Multidisciplinary, biology, Ecology, Reproduction, food and beverages, General Chemistry, 15. Life on land, biology.organism_classification, H10 - Ravageurs des plantes, cycle de développement, Biological Evolution, Harmonia axyridis, Coleoptera, Life expectancy, invasion biologique, L20 - Écologie animale, Introduced Species
Abstract: 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 biocontrol populations have evolved a classic fast life history during their maintenance in laboratories. Invasive populations also reproduce earlier than native populations, but later than biocontrol ones. Invaders allocate more resources to reproduction than native and biocontrol individuals, and their reproduction is spread over a longer lifespan. This life history is best described as a bet-hedging strategy. We assert that invasiveness cannot be explained only by invoking faster life histories. Instead, the evolution of life history within invasive populations can progress rapidly and converge to a fine-tuned evolutionary match between the invaded environment and the invader., Understanding how biological invaders displace native species is challenging. Here, the authors compare the evolution of life-history strategies in the harlequin ladybird under laboratory conditions and show that invaders reproduce earlier and allocate more resources to reproduction than natives.
Published: 2015

50. Genetics of recent habitat contraction and reduction in population size: does isolation by distance matter?

Author: Arnaud Estoup, Réjane Streiff, and Raphaël Leblois
Subjects: 0106 biological sciences, Conservation genetics, 0303 health sciences, education.field_of_study, Demographic history, Ecology, Population size, Population, Small population size, 15. Life on land, Biology, 010603 evolutionary biology, 01 natural sciences, Population density, 03 medical and health sciences, Genetics, Biological dispersal, education, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Isolation by distance
Abstract: Fragmentation and loss of natural habitats are recognized as major threats to contemporary flora and fauna. Detecting past or current reductions in population size is therefore a major aim in conservation genetics. Statistical methods developed to this purpose have tended to ignore the effects of spatial population structure. However in many species, individual dispersal is restricted in space and fine-scale spatial structure such as isolation by distance (IBD) is commonly observed in continuous populations. Using a simulation-based approach, we investigated how comparative and single-point methods, traditionally used in a Wright–Fisher (WF) population context for detecting population size reduction, behave for IBD populations. We found that a complex ‘quartet’ of factors was acting that includes restricted dispersal, population size (i.e. habitat size), demographic history, and sampling scale. After habitat reduction, IBD populations were characterized by a stronger inertia in the loss of genetic diversity than WF populations. This inertia increases with the strength of IBD, and decreases when the sampling scale increases. Depending on the method used to detect a population size reduction, a local sampling can be more informative than a sample scaled to habitat size or vice versa. However, IBD structure led in numerous cases to incorrect inferences on population demographic history. The reanalysis of a real microsatellite data set of skink populations from fragmented and intact rainforest habitats confirmed most of our simulation results.
Published: 2006

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