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72 results on '"Raphaël Leblois"'

1. Genetic diversity and structure related to expansion history and habitat isolation: stone marten populating rural–urban habitats

Author: Anna Wereszczuk, Raphaël Leblois, and Andrzej Zalewski
Subjects: Genetic structure, Genetic diversity, Isolation, Environmental barrier, Expansion, Martes foina, Ecology, QH540-549.5
Abstract: Abstract Background Population genetic diversity and structure are determined by past and current evolutionary processes, among which spatially limited dispersal, genetic drift, and shifts in species distribution boundaries have major effects. In most wildlife species, environmental modifications by humans often lead to contraction of species’ ranges and/or limit their dispersal by acting as environmental barriers. However, in species well adapted to anthropogenic habitat or open landscapes, human induced environmental changes may facilitate dispersal and range expansions. In this study, we analysed whether isolation by distance and deforestation, among other environmental features, promotes or restricts dispersal and expansion in stone marten (Martes foina) populations. Results We genotyped 298 martens from eight sites at twenty-two microsatellite loci to characterize the genetic variability, population structure and demographic history of stone martens in Poland. At the landscape scale, limited genetic differentiation between sites in a mosaic of urban, rural and forest habitats was mostly influenced by isolation by distance. Statistical clustering and multivariate analyses showed weak genetic structuring with two to four clusters and a high rate of gene flow between them. Stronger genetic differentiation was detected for one stone marten population (NE1) located inside a large forest complex. Genetic differentiation between this site and all others was 20% higher than between other sites separated by similar distances. The genetic uniqueness index of NE1 was also twofold higher than in other sites. Past demographic history analyses showed recent expansion of this species in north-eastern Poland. A decrease in genetic diversity from south to north, and MIGRAINE analyses indicated the direction of expansion of stone marten. Conclusions Our results showed that two processes, changes in species distribution boundaries and limited dispersal associated with landscape barriers, affect genetic diversity and structure in stone marten. Analysis of local barriers that reduced dispersal and large scale analyses of genetic structure and demographic history highlight the importance of isolation by distance and forest cover for the past colonization of central Europe by stone marten. This confirmed the hypothesis that human-landscape changes (deforestation) accelerated stone marten expansion, to which climate warming probably has also been contributing over the last few decades.
Published: 2017
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2. Demographic inference through approximate-Bayesian-computation skyline plots

Author: Miguel Navascués, Raphaël Leblois, and Concetta Burgarella
Subjects: Microsatellites, Population genetics, Population size change, Generalized stepwise mutation model, Approximate Bayesian computation, Medicine, Biology (General), QH301-705.5
Abstract: The skyline plot is a graphical representation of historical effective population sizes as a function of time. Past population sizes for these plots are estimated from genetic data, without a priori assumptions on the mathematical function defining the shape of the demographic trajectory. Because of this flexibility in shape, skyline plots can, in principle, provide realistic descriptions of the complex demographic scenarios that occur in natural populations. Currently, demographic estimates needed for skyline plots are estimated using coalescent samplers or a composite likelihood approach. Here, we provide a way to estimate historical effective population sizes using an Approximate Bayesian Computation (ABC) framework. We assess its performance using simulated and actual microsatellite datasets. Our method correctly retrieves the signal of contracting, constant and expanding populations, although the graphical shape of the plot is not always an accurate representation of the true demographic trajectory, particularly for recent changes in size and contracting populations. Because of the flexibility of ABC, similar approaches can be extended to other types of data, to multiple populations, or to other parameters that can change through time, such as the migration rate.
Published: 2017
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3. The impact of human conflict on the genetics of Mastomys natalensis and Lassa virus in West Africa.

Author: Aude Lalis, Raphaël Leblois, Emilie Lecompte, Christiane Denys, Jan Ter Meulen, and Thierry Wirth
Subjects: Medicine, Science
Abstract: Environmental changes have been shown to play an important role in the emergence of new human diseases of zoonotic origin. The contribution of social factors to their spread, especially conflicts followed by mass movement of populations, has not been extensively investigated. Here we reveal the effects of civil war on the phylogeography of a zoonotic emerging infectious disease by concomitantly studying the population structure, evolution and demography of Lassa virus and its natural reservoir, the rodent Mastomys natalensis, in Guinea, West Africa. Analysis of nucleoprotein gene sequences enabled us to reconstruct the evolutionary history of Lassa virus, which appeared 750 to 900 years ago in Nigeria and only recently spread across western Africa (170 years ago). Bayesian demographic inferences revealed that both the host and the virus populations have gone recently through severe genetic bottlenecks. The timing of these events matches civil war-related mass movements of refugees and accompanying environmental degradation. Forest and habitat destruction and human predation of the natural reservoir are likely explanations for the sharp decline observed in the rodent populations, the consequent virus population decline, and the coincident increased incidence of Lassa fever in these regions. Interestingly, we were also able to detect a similar pattern in Nigeria coinciding with the Biafra war. Our findings show that anthropogenic factors may profoundly impact the population genetics of a virus and its reservoir within the context of an emerging infectious disease.
Published: 2012
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4. A timescale for evolution, population expansion, and spatial spread of an emerging clone of methicillin-resistant Staphylococcus aureus.

Author: Ulrich Nübel, Janina Dordel, Kevin Kurt, Birgit Strommenger, Henrik Westh, Sanjay K Shukla, Helena Zemlicková, Raphaël Leblois, Thierry Wirth, Thibaut Jombart, François Balloux, and Wolfgang Witte
Subjects: Immunologic diseases. Allergy, RC581-607, Biology (General), QH301-705.5
Abstract: Due to the lack of fossil evidence, the timescales of bacterial evolution are largely unknown. The speed with which genetic change accumulates in populations of pathogenic bacteria, however, is a key parameter that is crucial for understanding the emergence of traits such as increased virulence or antibiotic resistance, together with the forces driving pathogen spread. Methicillin-resistant Staphylococcus aureus (MRSA) is a common cause of hospital-acquired infections. We have investigated an MRSA strain (ST225) that is highly prevalent in hospitals in Central Europe. By using mutation discovery at 269 genetic loci (118,804 basepairs) within an international isolate collection, we ascertained extremely low diversity among European ST225 isolates, indicating that a recent population bottleneck had preceded the expansion of this clone. In contrast, US isolates were more divergent, suggesting they represent the ancestral population. While diversity was low, however, our results demonstrate that the short-term evolutionary rate in this natural population of MRSA resulted in the accumulation of measurable DNA sequence variation within two decades, which we could exploit to reconstruct its recent demographic history and the spatiotemporal dynamics of spread. By applying Bayesian coalescent methods on DNA sequences serially sampled through time, we estimated that ST225 had diverged since approximately 1990 (1987 to 1994), and that expansion of the European clade began in 1995 (1991 to 1999), several years before the new clone was recognized. Demographic analysis based on DNA sequence variation indicated a sharp increase of bacterial population size from 2001 to 2004, which is concordant with the reported prevalence of this strain in several European countries. A detailed ancestry-based reconstruction of the spatiotemporal dispersal dynamics suggested a pattern of frequent transmission of the ST225 clone among hospitals within Central Europe. In addition, comparative genomics indicated complex bacteriophage dynamics.
Published: 2010
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5. GSpace: an exact coalescence simulator of recombining genomes under isolation by distance.

Author: Thimothée Virgoulay, François Rousset, Camille Noûs, and Raphaël Leblois
Published: 2021
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6. Correction to: GSpace: an exact coalescence simulator of recombining genomes under isolation by distance.

Author: Thimothée Virgoulay, François Rousset, and Raphaël Leblois
Published: 2022
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7. Phylogeographic breaks and how to find them: An empirical attempt at separating vicariance from isolation by distance in a lizard with restricted dispersal

Author: Loïs Rancilhac, Aurélien Miralles, Philippe Geniez, Daniel Mendez-Aranda, Menad Beddek, José Carlos Brito, Raphaël Leblois, and Pierre-André Crochet
Abstract: AimDiscontinuity in the distribution of genetic diversity (often based on mtDNA) is usually interpreted as evidence for phylogeographic breaks, underlying vicariant units. However, a misleading signal of phylogeographic break can arise in the absence of barrier to gene flow, under mechanisms of isolation by distance (IBD). How and under which conditions phylogeographic breaks can be reliably differentiated from populations evolving under IBD remain unclear. Here, we use multi-locus sequence data from a widely distributed lizard species to address these questions in an empirical setting.LocationMoroccoTaxonSpiny-footed lizard (Acanthodactylus erythrurus), Squamata: LacertidaeMethodsUsing 325 samples from 40 localities, we identified genetic discontinuities withinA. erythrurusbased on a mitochondrial fragment and nine nuclear markers independently. Using the nuclear markers, we then applied linear regression models to investigate whether genetic divergence could be explained by geographical distances alone, or barriers to gene flow (real phylogeographic breaks).ResultA. erythrurusis characterized by an important mitochondrial diversity, with 11 strongly supported phylogeographic lineages with a crown age of 6 Mya. Nuclear markers, however, yielded weak phylogenetic support for these lineages. Using clustering methods based on genotypes at nine nuclear loci, we identified phylogeographic clusters that were partly discordant with the mtDNA lineages. Tests of IBD delimited at least four groups of populations separated by barriers to gene flow, but unambiguous separation of vicariance from IBD remained challenging in several cases.Main conclusionsThe genetic diversity ofA. erythrurusoriginates from a mix of IBD and vicariance, which were difficult to distinguish, and resulted in similar levels of mitochondrial differentiation. These results highlight that phylogeographic breaks inferred from mitochondrial data should be further investigated using multi-locus data and explicit testing to rule out alternative processes generating discontinuities in mitochondrial diversity, including IBD. We identified four groups of populations withinA. erythrurus, separated by barriers to gene flow, but even using nine independent nuclear makers the power of our approach was limited, and further investigation using genome-wide data will be required to resolve the phylogeographic history of this species.
Published: 2022
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8. Combining RADseq and contact zone analysis to decipher cryptic diversification in reptiles: insights from Acanthodactylus erythrurus (Reptilia: Lacertidae)

Author: Paul Doniol-Valcroze, Loïs Rancilhac, José Carlos Brito, Aurélien Miralles, Philippe Geniez, Laure Benoit, Anne Loiseau, Raphaël Leblois, Christophe Dufresnes, and Pierre-André Crochet
Abstract: Linnaean and Wallacean shortfalls (Uncertainties on species taxonomy and distribution, respectively) are major factors hampering efficient conservation planning in the current context of biodiversity erosion. These shortfalls concern even widespread and abundant species in relatively well-studied regions such as the Mediterranean biodiversity hotspot which still hosts a large fraction of unrecognised biodiversity, notably in small vertebrates. Species delimitations have long been based on phylogenetic analyses of a small number of standard markers, but accurate lineage identification in this context can be obscured by incomplete lineage sorting, introgression or isolation by distance. Recently, integrative approaches coupling various sets of characters or analyses of contact zones aiming at estimating reproductive isolation (RI) have been advocated instead. Analyses of introgression patterns in contact zone with genomic data represent a powerful way to confirm the existence of independent lineages and estimate the strength of their RI at the same time. The Spiny-footed Lizard Acanthodactylus erythrurus (Schinz, 1833) is widespread in the Iberian Peninsula and the Maghreb and exhibits a large amount of genetic diversity, although the precise number and distribution of its genetic lineages remain poorly understood. We applied a RADseq approach to obtain a genome wide SNPs dataset on a contact zone in central Morocco between the previously described Rif and Middle-Atlas lineages. We show that these two lineages exhibit strong RI across this contact zone, as shown by the limited amount and restricted spatial extant of gene flow. We interpret these results as evidence for species-level divergence of these two lineages. Our study confirms the usefulness of RADseq approaches applied on contact zones for cryptic diversity studies and therefore to resolve Linnaean and Wallacean shortfalls.
Published: 2022
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9. Translocations maintain genetic diversity and increase connectivity in sea otters, <scp> Enhydra lutris </scp>

Author: Lizabeth Bowen, Roderick B. Gagne, Michael J. Murray, James L. Bodkin, Shawn Larson, Holly B. Ernest, Katherine Ralls, Maria Cecilia T. Penedo, Sylvain Piry, M. Tim Tinker, and Raphaël Leblois
Subjects: Genetic diversity, Enhydra lutris, biology, Evolutionary biology, biology.animal, Population structure, Microsatellite, Chromosomal translocation, Aquatic Science, Ecology, Evolution, Behavior and Systematics
Published: 2021
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10. Coalescent-Based DNA Barcoding: Multilocus Analysis and Robustness.

Author: Olivier David, Catherine Larédo, Raphaël Leblois, Brigitte Schaeffer, and Nicolas Vergne
Published: 2012
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11. DIYABC v2.0: a software to make approximate Bayesian computation inferences about population history using single nucleotide polymorphism, DNA sequence and microsatellite data.

Author: Jean-Marie Cornuet, Pierre Pudlo, Julien Veyssier, Alexandre Dehne-Garcia, Mathieu Gautier, Raphaël Leblois, Jean-Michel Marin, and Arnaud Estoup
Published: 2014
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12. Gradients of genetic diversity and differentiation across the distribution range of a Mediterranean coral: Patterns, processes and conservation implications

Author: Annie Machordom, Cristina Linares, Jamila Ben Souissi, Oscar H. Ocaña, Valèria Romero-Soriano, Nathaniel Bensoussan, Raouia Ghanem, Mathilde Horaud, Jean-Baptiste Ledoux, Paula López-Sendino, Raphaël Leblois, José Templado, Agostinho Antunes, Daniel Gómez-Gras, Joaquim Garrabou, Fundação para a Ciência e a Tecnologia (Portugal), Fondation Prince Albert II de Monaco, Agencia Estatal de Investigación (España), European Commission, Interdisciplinary Centre of Marine and Environmental Research [Matosinhos, Portugal] (CIIMAR), Universidade do Porto = University of Porto, Interdisciplinary Center of Marine and Environmental Research (CIMAR), Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Institut National Agronomique de Tunisie, Université de Tunis El Manar (UTM), University of Liverpool, Institut de Recerca de la Biodiversitat - Biodiversity Research Institute [Barcelona, Spain] (IRBio UB), Universitat de Barcelona (UB), Museo Nacional de Ciencias Naturales [Madrid] (MNCN), Fundacion Museo del Mar Ceuta, 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 Computationnelle (IBC), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), JBL was funded by a Postdoctoral Grant (SFRH/BPD/74400/2010) from the Portuguese Foundation for Science and Technology (FCT). This research was supported by national funds through FCT within the scope of UIDB/04423/2020 and UIDP/04423/2020 and by the MIMOSA project funded by the Foundation Prince Albert II Monaco. JG, DGG and PL acknowledge the funding of the Spanish government through the 'Severo Ochoa Centre of Excellence' accreditation (CEX2019-000928-S). This work was partially supported by the European Union's Horizon 2020 research and innovation program under grant agreement SEP-210597628 (FutureMARES, https://www.futuremares.eu)., ANR-16-CE02-0008,GenoSpace,Nouveaux outils statistiques pour l'analyse spatiale des données génétiques(2016), European Project: 869300,FutureMARES, Universidade do Porto, 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 National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Montpellier (UM)
Subjects: 0106 biological sciences, Mediterranean climate, Postglacial range expansion hypothesis, Range (biology), Coral, marine protected area, [SDV]Life Sciences [q-bio], Distribution (economics), Biology, 010603 evolutionary biology, 01 natural sciences, genetic gradient, 03 medical and health sciences, Mediterranean sea, postglacial range expansion hypothesis, Central-peripheral hypothesis, Marine protected areas, Mediterranean Sea, 14. Life underwater, coral, Ecology, Evolution, Behavior and Systematics, Coralls, 030304 developmental biology, Marine Protected Area, 0303 health sciences, Genetic diversity, Mediterrània (Mar), business.industry, Ecology, 15. Life on land, Genetic gradient, central-peripheral hypothesis, Corals, Marine protected area, business, human activities, Àrees marines protegides
Abstract: 20 pages, 5 figures, 4 tables, supporting information https://doi.org/10.1111/ddi.13382.-- Data availability statement: Microsatellite genotypes are available on Dryad (DOI https://doi.org/10.5061/dryad.xgxd254gw), Aim: How historical and contemporary eco-evolutionary processes shape the patterns of genetic diversity and differentiation across species’ distribution range remains an open question with strong conservation implications. Focusing on the orange stony coral, Astroides calycularis, we (a) characterized the pattern of neutral genetic diversity across the distribution range; (b) gave insights into the underlying processes; and (c) discussed conservation implications with emphasis on a national park located on a hotspot of genetic diversity. Location: South Mediterranean Sea and Zembra National Park. Methods: We combined new data from 12 microsatellites in 13 populations located in the Centre and in the Western Periphery of the distribution range with a published dataset including 16 populations from the Western and Eastern Peripheries. We analysed the relationship among parameters of genetic diversity (He, Ar(g)) and structure (population-specific FST) and two measures of geographic peripherality. We compared two estimators of pairwise genetic structure (GST, DEST) across the distribution range. The evolutionary and demographic history of the populations following the Last Glacial Maximum was reconstructed using approximate Bayesian computations and maximum-likelihood analyses. We inferred the contemporary connectivity among populations from Zembra National Park and with the neighbouring area of Cap Bon. Results: We demonstrate a decrease in genetic diversity and an increase in genetic differentiation from the Centre to the Eastern and Western Peripheries of the distribution range. Populations from Zembra show the highest genetic diversity reported in the species. We identified a spillover effect towards Cap Bon. Main conclusions: The patterns of genetic diversity and differentiation are most likely explained by “the postglacial range expansion hypothesis” rather than the “central–peripheral hypothesis.” Enforcement of conservation measures should be considered to protect this genetic diversity pattern, in particular when considering the low effective population size inferred at many sites, JBL was funded by a Postdoctoral Grant (SFRH/BPD/74400/2010) from the Portuguese Foundation for Science and Technology (FCT). This research was supported by national funds through FCT within the scope of UIDB/04423/2020 and UIDP/04423/2020 and by the MIMOSA project funded by the Foundation Prince Albert II Monaco. JG, DGG and PL acknowledge the funding of the Spanish government through the “Severo Ochoa Centre of Excellence” accreditation (CEX2019-000928-S). This work was partially supported by the European Union's Horizon 2020 research and innovation program under grant agreement SEP-210597628 (FutureMARES)
Published: 2021
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13. Agricultural intensification alters marbled newt genetic diversity and gene flow through density and dispersal reduction

Author: Raphaël Leblois, Pierre Grillet, Olivier Lourdais, Alexandre Boissinot, Bertrand Gauffre, Vincent Quiquempois, Sophie Morin, Damien Picard, Cécile Ribout, School of Biological Sciences [Clayton], Monash University [Clayton], Unité de recherche Plantes et Systèmes de Culture Horticoles (PSH), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre d'Études Biologiques de Chizé - UMR 7372 (CEBC), Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Réserve Naturelle Régionale du Bocage des Antonins [France], Office français de la biodiversité (OFB), Département de Biologie UFR Sciences - Université d'Angers [France], Université d'Angers (UA), and Centre d’Etudes Biologiques de Chizé (CEBC), UMR 7372 CNRS - La Rochelle Université, France, 79360, Villiers-en-Bois, France
Subjects: 0106 biological sciences, Gene Flow, Triturus marmoratus, [SDV]Life Sciences [q-bio], Population, Biology, 010603 evolutionary biology, 01 natural sciences, microsatellites, 03 medical and health sciences, demographic inferences, Effective population size, Genetics, Animals, education, dispersal, ComputingMilieux_MISCELLANEOUS, Ecology, Evolution, Behavior and Systematics, Ecosystem, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, education.field_of_study, Genetic diversity, Ecology, Genetic Variation, landscape genetics, genetic diversity, 15. Life on land, Salamandridae, Habitat destruction, Genetics, Population, Genetic distance, Genetic structure, [SDE]Environmental Sciences, Biological dispersal, Arable land, Microsatellite Repeats
Abstract: International audience; Recent agricultural intensification threatens global biodiversity with amphibians being one of the most impacted groups. Because of their biphasic life cycle, amphibians are particularly vulnerable to habitat loss and fragmentation that often result in small, isolated populations and loss of genetic diversity. Here, we studied how landscape heterogeneity affects genetic diversity, gene flow and demographic parameters in the marbled newt, Triturus marmoratus, over a hedgerow network landscape in Western France. While the northern part of the study area consists of preserved hedged farm-land, the southern part was more profoundly converted for intensive arable crops production after WWII. Based on 67 sampled ponds and 10 microsatellite loci, we characterized regional population genetic structure and evaluated the correlation between landscape variables and (i) local genetic diversity using mixed models and (ii) genetic distance using multiple regression methods and commonality analysis. We identified a single genetic population characterized by a spatially heterogeneous isolation- by- distance pattern. Pond density in the surrounding landscape positively affected local genetic diversity while arable crop land cover negatively affected gene flow and connectivity. We used demographic inferences to quantitatively assess dif-ferences in effective population density and dispersal between the contrasted land-scapes characterizing the northern and southern parts of the study area. Altogether, results suggest recent land conversion affected T. marmoratus through reduction in both effective population density and dispersal due to habitat loss and reduced connectivity.
Published: 2021
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14. Integrating population genetics to define conservation units from the core to the edge of Rhinolophus ferrumequinum western range

Author: Raphaël Leblois, Jean-Baptiste Pons, Ondine Filippi-Codaccioni, Anne Loiseau, Dominique Pontier, Jeanne Duhayer, Fiona Mathews, Maxime Leuchtmann, Sylvain Piry, Sébastien J. Puechmaille, Nathalie Charbonnel, Inazio Garin, Orianne Tournayre, 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), Université de Lyon, Nature environment, Partenaires INRAE, Department of Zoology and Animal Cell Biology, Faculty of Science and Technology, University of Sussex, GCMP, CREN, Toulouse, France, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), LABEX CEMEB : ANR-11-IDEX-0007, LABEX ECOFECT : ANR-11-LABX-0048 European Union (EU), DREAL Nouvelle-Aquitaine, Region Auvergne-Rhone-Alpes, Region Bourgogne-Franche-Comte, Region Hauts-de-France, Region Nouvelle-Aquitaine, ANR-16-CE02-0008,GenoSpace,Nouveaux outils statistiques pour l'analyse spatiale des données génétiques(2016), 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), École pratique des hautes études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226
Subjects: 0106 biological sciences, Demographic history, Population, 010603 evolutionary biology, 01 natural sciences, microsatellites, 03 medical and health sciences, Chiroptera, lcsh:QH540-549.5, Biologie animale, IUCN Red List, 14. Life underwater, education, Ecology, Evolution, Behavior and Systematics, connectivity, conservation, demographic inference, population genetics, 030304 developmental biology, Nature and Landscape Conservation, Isolation by distance, Animal biology, 0303 health sciences, education.field_of_study, Near-threatened species, Habitat fragmentation, Ecology, biology, [SDV.BA]Life Sciences [q-bio]/Animal biology, Rhinolophus ferrumequinum, 15. Life on land, biology.organism_classification, Geography, Threatened species, Biological dispersal, lcsh:Ecology
Abstract: The greater horseshoe bat(Rhinolophus ferrumequinum)is among the most widespread bat species in Europe but it has experienced severe declines, especially in Northern Europe. This species is listed Near Threatened in the EuropeanIUCN Red List of Threatened Animalsand it is considered to be highly sensitive to human activities and particularly to habitat fragmentation. Therefore, understanding the population boundaries and demographic history of populations of this species is of primary importance to assess relevant conservation strategies. In this study, we used 17 microsatellite markers to assess the genetic diversity, the genetic structure and the demographic history ofR. ferrumequinumcolonies in the Western European part of its distribution. We found high levels of genetic diversity and large population size on the European mainland and lower estimates in England and Northern France. Analyses of clustering and isolation by distance showed a barrier effect of the Channel and potentially of the Mediterranean Sea onR. ferrumequinumbat dispersal. Conversely, we could not reveal any gene flow disruption from both sides of the Western Pyrenees. These results provide important information to improve the delineation ofR. ferrumequinummanagement units in its western range. We suggest that a large management unit corresponding to the European mainland population must be considered. Particular attention should be given to mating territories as they seem to play a key role in maintaining the high levels of genetic mixing between colonies. Smaller management units corresponding to English and Northern France colonies must also be implemented. These insular or peripheral colonies could be at higher risk of extinction in a near future.
Published: 2019
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15. GSpace: an exact coalescence simulator of recombining genomes under isolation by distance

Author: Raphaël Leblois, Camille Noûs, François Rousset, Thimothée Virgoulay, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, 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), Laboratoire Cogitamus, This work used the following HPC platforms: INRA MIGALE (http://migale.jouy.inra.fr) and GENOTOUL (Toulouse Midi-Pyre ' ne ' es), Montpellier Bioinformatics Biodiversity supported by the LabEx CeMEB (ANR-10LABX-04-01), and CBGP host platform. All authors were supported by the Agence Nationale de la Recherche (RL & TV: projects GENOSPACE ANR16-CE02-0008 and Labex CeMEB ProLag, FR & RL: project INTROSPEC ANR-19-CE02-0011)., ANR-16-CE02-0008,GenoSpace,Nouveaux outils statistiques pour l'analyse spatiale des données génétiques(2016), ANR-10-LABX-0004,CeMEB,Mediterranean Center for Environment and Biodiversity(2010), ANR-19-CE02-0011,IntroSpec,Impact génomique et causes évolutives de l'introgression aux stades avancés de la spéciation(2019), Cogitamus Laboratory, All authors were supported by the Agence Nationale de la Recherche (RL & TV: projects GENOSPACE ANR-16-CE02-0008 and Labex CeMEB ANR-10-LABX-0004, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), 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, 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: Statistics and Probability, Computer science, Genomic data, [SDV]Life Sciences [q-bio], Population, Inference, Biochemistry, Genome, 03 medical and health sciences, 0302 clinical medicine, Software, Coalescence (chemistry), education, Molecular Biology, Simulation, 030304 developmental biology, Isolation by distance, 0303 health sciences, education.field_of_study, business.industry, Small population size, Computer Science Applications, Computational Mathematics, Computational Theory and Mathematics, business, 030217 neurology & neurosurgery
Abstract: Motivation Simulation-based inference can bypass the limitations of statistical methods based on analytical approximations, but software allowing simulation of structured population genetic data without the classical n-coalescent approximations (such as those following from assuming large population size) are scarce or slow. Results We present GSpace, a simulator for genomic data, based on a generation-by-generation coalescence algorithm taking into account small population size, recombination and isolation by distance. Availability and implementation Freely available at site web INRAe (http://www1.montpellier.inra.fr/CBGP/software/gspace/download.html).
Published: 2020
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16. Limited genetic structure and demographic expansion of theBrassicogethes aeneuspopulations in France and in Europe

Author: Amandine Suzanne Juhel, Raphaël Leblois, Jérôme Olivares, Corentin M. Barbu, Bertrand Gauffre, Pierre Franck, and Muriel Valantin-Morison
Subjects: 0106 biological sciences, Genetic diversity, education.field_of_study, Demographic history, Ecology, Population size, Population, General Medicine, Biology, 01 natural sciences, 010602 entomology, Insect Science, Genetic structure, Biological dispersal, Genetic variability, education, Agronomy and Crop Science, 010606 plant biology & botany, Isolation by distance
Abstract: Background The pollen beetle, Brassicogethes aeneus (Fabricius, 1775), is one of the most significant pests of oilseed rape. To shed light on past and current pollen beetle demography (dispersal, population size), 12 microsatellite markers were developed, and population genetic diversity and structure were analysed at different spatial scales in France and in Europe from 433 individuals collected in 18 winter oilseed rape fields. Results Genetic differentiation among the population samples was low but was significant between the Estonian sample and the rest of Europe. Isolation by distance was significant only at the European scale. Genetic variability was similar among the 18 population samples. Demographic inferences suggested a recent expansion of B. aeneus population size over Europe, possibly corresponding to an increase in oilseed rape crop area during past decades. Conclusion Current population size and dispersal are not straightforward to estimate from the distribution of genetic variability in B. aeneus over Europe because of the complexity of the demographic history of this pest. Nevertheless, because gene flow was important enough to prevent strong genetic differentiation at large geographical scales, the management of pollen beetle populations should likely be thought of at a continental Europe level. © 2018 Society of Chemical Industry.
Published: 2018
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17. A reassessment of explanations for discordant introgressions of mitochondrial and nuclear genomes

Author: Raphaël Leblois, François Rousset, Timothée Bonnet, and Pierre-André Crochet
Subjects: 0106 biological sciences, 0301 basic medicine, Genetics, Mitochondrial DNA, Nuclear gene, Introgression, Biology, 010603 evolutionary biology, 01 natural sciences, Genome, Gene flow, 03 medical and health sciences, Negative selection, 030104 developmental biology, General Agricultural and Biological Sciences, Ecology, Evolution, Behavior and Systematics, Selection (genetic algorithm), Isolation by distance
Abstract: Hybridization is increasingly recognized as a significant evolutionary process, in particular because it can lead to introgression of genes from one species to another. A striking pattern of discordance in the amount of introgression between mitochondrial and nuclear markers exists such that substantial mitochondrial introgression is often found in combination with no or little nuclear introgression. Multiple mechanisms have been proposed to explain this discordance, including positive selection for introgressing mitochondrial variants, several types of sex-biases, drift, negative selection against introgression in the nuclear genome, and spatial expansion. Most of these hypotheses are verbal, and have not been quantitatively evaluated so far. We use individual-based, multilocus, computer simulations of secondary contact under a wide range of demographic and genetic scenarios to evaluate the ability of the different mechanisms to produce discordant introgression. Sex-biases and spatial expansions fail to produce substantial mito-nuclear discordance. Drift and nuclear selection can produce strong discordance, but only under a limited range of conditions. In contrast, selection on the mitochondrial genome produces strong discordance, particularly when dispersal rates are low. However, commonly used statistical tests have little power to detect this selection. Altogether, these results dismiss several popular hypotheses, and provide support for adaptive mitochondrial introgression.
Published: 2017
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18. From sympatry to parapatry: a rapid change in the spatial context of incipient allochronic speciation

Author: Carole Kerdelhué, Raphaël Leblois, S. Rocha, Christian Burban, Jean-Pierre Rossi, Manuela Branco, Laure Sauné, Biodiversité, Gènes & Communautés (BioGeCo), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Universidade de Lisboa = University of Lisbon (ULISBOA), Instituto Superior de Agronomia [Lisboa] (ISA), 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 Computationnelle (IBC), Institut National de Recherche en Informatique et en Automatique (Inria)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Data used in this work were partly produced through the GenSeq molecular genetic analysis technical facilities of the Labex CeMEB, and ANR 'Investissements d'Avenir' program (ANR-10-LABX-0004). This study was partly financed by Fundacao para a Ciencia e Tecnologia, FCT-MCES, Portugal, (Project Pest-OE/AGR/UI0239/2011) and the Agence Nationale de la Recherche, France (Project GENO-SPACE ANR-16-CE02-0008). It was also supported by Susana Rocha Ph.D. scholarship with the reference SFRH/BD/90188/2012(FCT-MCES)., ANR-16-CE02-0008,GenoSpace,Nouveaux outils statistiques pour l'analyse spatiale des données génétiques(2016), ANR-10-LABX-0004,CeMEB,Mediterranean Center for Environment and Biodiversity(2010), Universidade de Lisboa (ULISBOA), Instituto Superior de Agronomia - Universidade de Lisboa, 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, Sympatry, Population, Parapatric speciation, Biology, 010603 evolutionary biology, 01 natural sciences, Parapatry, 03 medical and health sciences, education, Hybridization, Ecology, Evolution, Behavior and Systematics, Isolation by distance, Allochronic speciation, education.field_of_study, Ecology, Thaumetopoea pityocampa, [SDV.BA]Life Sciences [q-bio]/Animal biology, Reproductive isolation, Incipient speciation, 030104 developmental biology, Phenology, Sympatric speciation, Animal ecology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: International audience; Speciation is nowadays recognized as a dynamic process in which the respective roles of forces driving ecological differentiation and reproductive isolation can change through time and space. Incipient speciation events are particularly useful to follow such processes that are not tractable when considering well-differentiated taxa. A promising case study was discovered in the pine processionary moth, Thaumetopoea pityocampa, a Mediterranean defoliator of Pinus species, for which allochrony acting as an automatic magic trait was recognized as the major driver of an incipient speciation process. In Portugal, a unique population with a shifted phenology, known as the summer population (SP), co-occurs with a population following the typical life cycle, known as the winter population (WP). We monitored male activity of both populations in the Leiria region, i.e. over the whole SP distribution range using a systematic sampling along two transects, and studied Portuguese WPs at a larger geographical scale to explore their genetic diversity and spatial pattern of differentiation. Results showed that the WPs were genetically more diverse than the SP, with a strong pattern of isolation by distance both at large and small spatial scales, while the SP was very homogeneous over its whole range, without signature of its recent spatial expansion. Contrary to our expectations, no F1 hybrids were identified, even though we found an extended flight period of the SP, overlapping with the beginning of the WP reproductive period. Interestingly, the SP was found to be mostly limited to the sea shore where the WP is now scarce or absent, which could suggest competitive exclusion. Once clearly occurring in a sympatric context, the allochronic differentiation tends to develop nowadays in parapatry.
Published: 2020
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19. Sampling schemes and drift can bias admixture proportions inferred by structure

Author: Pierre-André Crochet, Raphaël Leblois, Ken S. Toyama, Department of Ecology and Evolutionary Biology [University of Toronto] (EEB), University of Toronto, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-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), 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), ANR-16-CE02-0008,GenoSpace,Nouveaux outils statistiques pour l'analyse spatiale des données génétiques(2016), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-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 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
Subjects: 0106 biological sciences, 0301 basic medicine, Population, Biology, 010603 evolutionary biology, 01 natural sciences, unbalanced sampling, 03 medical and health sciences, Bias, Sampling design, Statistics, Prior probability, Genetics, Computer Simulation, structure, education, Ecology, Evolution, Behavior and Systematics, education.field_of_study, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], drift, Small number, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Sampling (statistics), Uncorrelated, 030104 developmental biology, Genetics, Population, admixture, Evolutionary ecology, simulations, Software, Biotechnology
Abstract: International audience; The interbreeding of individuals coming from genetically differentiated but incompletely isolated populations can lead to the formation of admixed populations, having important implications in ecology and evolution. In this simulation study, we evaluate how individual admixture proportions estimated by the software structure are quantitatively affected by different factors. Using various scenarios of admixture between two diverging populations, we found that unbalanced sampling from parental populations may seriously bias the inferred admixture proportions; moreover, proportionally large samples from the admixed population can also decrease the accuracy and precision of the inferences. As expected, weak differentiation between parental populations and drift after the admixture event strongly increase the biases caused by uneven sampling. We also show that admixture proportions are generally more biased when parental populations unequally contributed to the admixed population. Finally, with few exceptions, using a large number of markers reduces those biases, but using alternative priors for individual ancestry or the uncorrelated allele model only marginally affect the inference of admixture in most situations. We conclude that unbalanced sampling may cause important biases in the admixture proportions estimated by structure, especially when a small number of markers are used, and those biases can be worsened by the effect of drift and unequal genetic contribution of parental populations. Empirical studies should thus be careful with their sampling design and consider historical characteristics when using this software to estimate the ancestry of individuals from admixed populations.
Published: 2020
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20. Quaternary terrestrial microvertebrates from mediterranean northwestern Africa: State-of-the-art focused on recent multidisciplinary studies

Author: Roland Nespoulet, Touria Benazzou, Christiane Denys, Violaine Nicolas, François-Joseph Lapointe, Annemarie Ohler, Emmanuelle Stoetzel, Yannicke Dauphin, Eva-Maria Geigl, Mohammed Fekhaoui, Soumia Fahd, Ahmed El Hassani, Mohammed Abdeljalil El Hajraoui, Raphaël Leblois, Stéphane Aulagnier, Aude Lalis, Mission archéologique El Harhoura-Témara. Muséum national d'histoire naturelle, Département de Préhistoire, UMR 5198, Origine, structure et évolution de la biodiversité, Centre National de la Recherche Scientifique (CNRS), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Université des Antilles (UA)-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE)-Sorbonne Université (SU)-Muséum national d'Histoire naturelle (MNHN), Unité de recherche Comportement et Ecologie de la Faune Sauvage (CEFS), Institut National de la Recherche Agronomique (INRA), Laboratoire de Zoologie, Département de Biologie, Université Internationale de Rabat (UIR), Interactions et dynamique des environnements de surface (IDES), Université Paris-Sud - Paris 11 (UP11)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), Institut National des Sciences de l'Archéologie et du Patrimoine (INSAP), Ministère de la Culture et de la Communication (MCC), Université MohammedV-Agdal, Rabat, Université Abdelmalek Essaâdi (UAE), Institut Jacques Monod (IJM (UMR_7592)), Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7), Université de Montréal [Montréal], Biologie Intégrative des Populations, École pratique des hautes études (EPHE)-Centre National de la Recherche Scientifique (CNRS), Histoire naturelle de l'Homme préhistorique (HNHP), Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)-Université de Perpignan Via Domitia (UPVD), Département Systématique et Évolution, Muséum national d'Histoire naturelle (MNHN), Muséum national d'Histoire naturelle (MNHN)-Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut Scientifique Rabat, Université de Paris (UP)-Centre National de la Recherche Scientifique (CNRS), Université de Montréal (UdeM), Projet PHC TASSILI - CMEP 09mdu755, ANR-09-PEXT-0004,Mohmie,Influence de l'installation des hommes modernes au Maroc sur l'évolution de la biodiversité des petits vertébrés terrestres(2009), Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), and Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)
Subjects: Mediterranean climate, 010506 paleontology, Archeology, Taphonomy, 010504 meteorology & atmospheric sciences, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, Maghreb, [SDV]Life Sciences [q-bio], Biodiversity, Climate change, Micromammals, 01 natural sciences, Prehistory, Herpetofauna, Ecosystem diversity, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, 0105 earth and related environmental sciences, Global and Planetary Change, Ecology, Geology, 15. Life on land, Geography, 13. Climate action, Paleoecology, Quaternary, integrative approach
Abstract: International audience; Northwestern Africa is today characterized by high geographical, climatic and ecological diversity; it is recognized as a hotspot of biodiversity and a major area for both human and faunal evolution. Studies of North African fossil microvertebrates have increased considerably in recent years, but they no longer just provide palaeontological descriptions of the species found in the assemblages. They also aim at better understanding the evolution of faunal communities in relation to Quaternary climate changes and at reconstructing the palaeoenvironmental background of prehistoric human occupations, in well-established taphonomic and chronological contexts. These studies are also increasingly adopting an integrative approach by combining archaeology, palaeontology, (palaeo)genetics, taphonomy, palaeoecology and systematics, and using new methods such as geometric morphometrics and isotopic analyses on both fossil and modern specimens. This paper aims to present a history of the studies on Quaternary terrestrial microvertebrates from northwestern Africa, and show how recent multidisciplinary studies have provided new perspectives and evidence on the respective influences of climate change and increasing human pressure on their evolution.
Published: 2019
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21. DNA barcode analysis: a comparison of phylogenetic and statistical classification methods.

Author: Frederic Austerlitz, Olivier David, Brigitte Schaeffer, Kevin Bleakley, Madalina Olteanu, Raphaël Leblois, Michel Veuille, and Catherine Larédo
Published: 2009
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22. Limited genetic structure and demographic expansion of the Brassicogethes aeneus populations in France and in Europe

Author: Amandine S, Juhel, Corentin M, Barbu, Muriel, Valantin-Morison, Bertrand, Gauffre, Raphaël, Leblois, Jérôme, Olivares, Pierre, Franck, Agronomie, Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Unité de recherche Plantes et Systèmes de Culture Horticoles (PSH), 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), 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), LabEx BASC, ANR-11-LABX-0034, project GENOSPACE, ANR-16-CE02-0008, project PEERLESS, ANR-12-AGRO-0006, and ANR-16-CE02-0008,GenoSpace,Nouveaux outils statistiques pour l'analyse spatiale des données génétiques(2016)
Subjects: microsatellite, coleoptera, oilseed rape, microsatellites, genetic structure, Animals, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Brassicogethes aeneus, genetic diversity, pollen beetles, structure génétique des populations, Vegetal Biology, insecte ravageur, oléagineux, Genetic Variation, meligethes aeneus, Sequence Analysis, DNA, dendroctonus, Genetics, Population, colza graine, diversité génétique, France, europe, Animal Distribution, Biologie végétale, Microsatellite Repeats
Abstract: International audience; The pollen beetles, Brassicogethes aeneus (Fabricius, 1775), is one of the most significant pests of oilseed rape. To shed light on past and present pollen beetle demography (dispersal, population size), twelve microsatellite markers were developed and population genetic diversity and structure were analyzed at different spatial scales in France and in Europe from 433 individuals collected in 18 winter oilseed rape fields. RESULTS: The genetic differentiation among the population samples was low but significant between the Estonian sample and the rest of Europe. Isolation by distance was only significant at the European scale. The genetic variability was similar among the 18 population samples. Demographic inferences suggested a recent expansion of B. aeneus population size over Europe, possibly corresponding to an increase of oilseed rape crop’s area during the last decades. CONCLUSION: Current population size and dispersal are not straightforward to estimate from the distribution of genetic variability in B. aeneus over Europe because of the complexity of the demographic history of the pests. Nevertheless, as gene flow was important enough to prevent strong genetic differentiation at large geographical scales, the management of pollen beetle populations should likely be thought at the European continental level.
Published: 2019
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23. Artificial barriers prevent genetic recovery of small isolated populations of a low-mobility freshwater fish

Author: Bertrand Gauffre, Jarod Lyon, Luciano B. Beheregaray, Alexandra Pavlova, Rhys A. Coleman, Raphaël Leblois, Carla M. Sgrò, Paul Sunnucks, Minami Sasaki, Joanne Kearns, Melbourne Water Corporation, Partenaires INRAE, Monash University [Clayton], Centre d'Études Biologiques de Chizé - UMR 7372 (CEBC), Institut National de la Recherche Agronomique (INRA)-La Rochelle Université (ULR)-Centre National de la Recherche Scientifique (CNRS), Flinders University [Adelaide, Australia], Arthur Rylah Institute for Environmental Research (ARI), 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), This work was supported by an Australian Research Council Linkage Grant (LP110200017) to Monash University, Flinders University of South Australia, the University of Canberra, and University of Montana. Funding and other support was also contributed by industry partner organizations namely, Melbourne Water Corporation, ACTEW Corporation, Victorian Department of Sustainability and Environment (now Department of Environment, Land, Water and Planning) and Fisheries Victoria (now Department of Economic Development, Jobs, Transport and Resources). L.B.B. was supported by an ARC FT130101068 grant. Justin O'Mahony, Renae Ayres, Scott Raymond and Mike Nicol from the Arthur Rylah Institute assisted with the collection of tissue samples. This publication has been written with the support of the AgreenSkills+fellowship programme, which has received funding from the EU's Seventh Framework Programme under grant agreement No FP7-609398 (AgreenSkills+ contract). RL was supported by the Agence Nationale de la Recherche (GENOSPACE project, ANR-16-CE02-0008)., ANR-16-CE02-0008,GenoSpace,Nouveaux outils statistiques pour l'analyse spatiale des données génétiques(2016), European Project: 609398,EC:FP7:PEOPLE,FP7-PEOPLE-2013-COFUND,AGREENSKILLSPLUS(2014), Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université de La Rochelle (ULR), School of Biological Sciences [Norwich], University of East Anglia [Norwich] (UEA), School of Biological Sciences, Flinders University, Arthur Rylah Institute, Australian Research Council : LP110200017, University of Canberra, Flinders University of South Australia, University of Montana, ACTEW Corporation, Department of Environment, Land, Water and Planning, Department of Economic Development, Jobs, Transport and Resources, ARC : FT130101068, Agence Nationale de la Recherche : GENOSPACE ANR-16-CE02-0008, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre d'Etudes Biologiques de Chizé, and Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, 0301 basic medicine, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Reproductive Isolation, Population, Population Dynamics, Fresh Water, Biology, 010603 evolutionary biology, 01 natural sciences, Article, 03 medical and health sciences, Effective population size, Genetic variation, Genetics, Inbreeding depression, Animals, Inbreeding, 14. Life underwater, education, ComputingMilieux_MISCELLANEOUS, Genetics (clinical), Ecosystem, Population Density, education.field_of_study, Genetic diversity, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Geography, Models, Genetic, Ecology, Fishes, Genetic Variation, Small population size, Agricultural sciences, 030104 developmental biology, Genetics, Population, Genetic structure, [SDE]Environmental Sciences, Genetic Background, Sciences agricoles
Abstract: This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons. org/licenses/by/4.0/., Habitat loss and fragmentation often result in small, isolated populations vulnerable to environmental disturbance and loss of genetic diversity. Low genetic diversity can increase extinction risk of small populations by elevating inbreeding and inbreeding depression, and reducing adaptive potential. Due to their linear nature and extensive use by humans, freshwater ecosystems are especially vulnerable to habitat loss and fragmentation. Although the effects of fragmentation on genetic structure have been extensively studied in migratory fishes, they are less understood in low-mobility species. We estimated impacts of instream barriers on genetic structure and diversity of the low-mobility river blackfish (Gadopsis marmoratus) within five streams separated by weirs or dams constructed 45–120 years ago. We found evidence of small-scale (, This work was supported by an Australian Research Council Linkage Grant (LP110200017) to Monash University, Flinders University of South Australia, the University of Canberra, and University of Montana. Funding and other support was also contributed by industry partner organizations namely, Melbourne Water Corporation, ACTEW Corporation, Victorian Department of Sustainability and Environment (now Department of Environment, Land, Water and Planning) and Fisheries Victoria (now Department of Economic Development, Jobs, Transport and Resources). L.B.B. was supported by an ARC FT130101068 grant. This publication has been written with the support of the AgreenSkills+fellowship programme, which has received funding from the EU’s Seventh Framework Programme under grant agreement N° FP7-609398 (AgreenSkills+contract). Part of this work was carried out by using the resources of the INRA MIGALE (http://migale.jouy.inra.fr) and GENOTOUL (Toulouse Midi-Pyrénées) bioinformatics platforms and the Montpellier Bioinformatics Biodiversity platform services. RL was supported by the Agence Nationale de la Recherche (project GENOSPACE ANR-16-CE02-0008).
Published: 2018
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24. Measuring Genetic Differentiation from Pool-seq Data

Author: Raphaël Leblois, Mathieu Gautier, Valentin Hivert, Eric J. Petit, Renaud Vitalis, 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), 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), Écologie et santé des écosystèmes (ESE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, 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), Institut National de la Recherche Agronomique's Plant Health and Environment (SPE) Division, Biodi-vERsA project EXOTIC : ANR-13-EBID-0001, project SWING of the French National Research Agency : ANR-16-CE02-0015, CORBAM project of the French region Hauts-de-France, ANR-16-CE02-0015,SWING,Invasion mondiale de la drosophile à aile tachetée: Génétique, plasticité et potentiel évolutif(2016), 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, 0301 basic medicine, population genomics, Genotype, F-ST, genetic differentiation, pool sequencing, Computational biology, Biology, Investigations, 010603 evolutionary biology, 01 natural sciences, Polymorphism, Single Nucleotide, DNA sequencing, Population genomics, 03 medical and health sciences, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Gene Frequency, [SDV.BA.ZV]Life Sciences [q-bio]/Animal biology/Vertebrate Zoology, Databases, Genetic, Genetics, Computer Simulation, Genotyping, ComputingMilieux_MISCELLANEOUS, Alleles, 030304 developmental biology, 0303 health sciences, [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], Estimator, Robustness (evolution), Genetic Variation, High-Throughput Nucleotide Sequencing, DNA, Genomics, Sequence Analysis, DNA, biology.organism_classification, Genetic differentiation, [SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, 030104 developmental biology, Genetic structure, Cottus asper, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: The recent advent of high throughput sequencing and genotyping technologies enables the comparison of patterns of polymorphisms at a very large number of markers. While the characterization of genetic structure from individual sequencing data remains expensive for many non-model species, it has been shown that sequencing pools of individual DNAs (Pool-seq) represents an attractive and cost-effective alternative. However, analyzing sequence read counts from a DNA pool instead of individual genotypes raises statistical challenges in deriving correct estimates of genetic differentiation. In this article, we provide a method-of-moments estimator ofFSTfor Pool-seq data, based on an analysis-of-variance framework. We show, by means of simulations, that this new estimator is unbiased, and outperforms previously proposed estimators. We evaluate the robustness of our estimator to model misspecification, such as sequencing errors and uneven contributions of individual DNAs to the pools. Last, by reanalyzing published Pool-seq data of different ecotypes of the prickly sculpinCottus asper, we show how the use of an unbiasedFSTestimator may question the interpretation of population structure inferred from previous analyses.
Published: 2018
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25. Crossing the Mid-Aegean Trench: vicariant evolution of the Eastern pine processionary moth, Thaumetopoea wilkinsoni (Lepidoptera: Notodontidae), in Crete

Author: Raphaël Leblois, Dimitrios Petsopoulos, Carole Kerdelhué, Kahraman İpekdal, Filippos A. Aravanopoulos, Laure Sauné, Dimitrios N. Avtzis, Kırşehir Ahi Evran Üniversitesi, Fen-Edebiyat Fakültesi, Biyoloji Bölümü, Aristotle University of Thessaloniki, 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), Kırşehir Ahi Evran University, and Hellenic Agricultural Organization Demeter (HAO Demeter)
Subjects: 0106 biological sciences, 0301 basic medicine, [SDV]Life Sciences [q-bio], Zoology, Aegean region, Notodontidae, 15. Life on land, Biology, Thaumetopoea wilkinsoni, biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, Lepidoptera genitalia, 03 medical and health sciences, 030104 developmental biology, [SDE]Environmental Sciences, Trench, Vicariance, genetic structure, Pine processionary moth, phylogeographical patterns, Ecology, Evolution, Behavior and Systematics, biogeography
Abstract: International audience; Thaumetopoea wilkinsoni Tams, 1924 occurs in the southeast Mediterranean basin and infests pine and cedar stands. Our objective was to decipher the biogeography of the species and, in particular, to explore its evolutionary history on the island of Crete. We collected 135 individuals from 14 sites on Crete, Turkey, Samos and Rhodes. We sequenced one mitochondrial fragment (cytochrome c subunit I) and used 12 microsatellite loci for population genetic analyses. All results supported the deep divergence of Cretan populations from the neighbouring areas, with the differentiation between Crete and neighbouring regions being similar to the interspecific divergence between T. wilkinsoni and its sibling species, Thaumetopoea pityocampa (Denis and Schiffermuller, 1775). Both mitochondrial and microsatellite markers showed a clear longitudinal (east-west) differentiation of populations within Crete. Our results thus suggest that T. wilkinsoni crossed the Mid-Aegean Trench, became isolated on Crete and differentiated through vicariance after the end of the Messinian Salinity Crisis, favouring the emergence of an endemic lineage. There, Quaternary climatic oscillations coupled with geographical barriers to gene flow have given rise to the currently observed east-west differentiation of Cretan populations.
Published: 2018
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26. Deciphering the demographic history of allochronic differentiation in the pine processionary moth Thaumetopoea pityocampa

Author: Audrey Rohfritsch, Anne Loiseau, Mathieu Gautier, Carole Kerdelhué, Christian Burban, Maxime Galan, Karim Gharbi, Julien Foucaud, Renaud Vitalis, Raphaël Leblois, Manuela Branco, Laure Sauné, 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), 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), Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), Universidade de Lisboa (ULISBOA), Centro de Estudos Florestais, Technical University of Lisbon-Instituto Superior de Agronomia, University of Edinburgh, Edinburgh Genomics, This work was supported by a grant from the French National Research Agency (ANR-10-JCJC-1705—GENOPHENO) and by the Institut National de la Recherche Agronomique (GAPP project, INRA AIP BioRessources 2012). Part of this work was carried out with the resources of the INRA MIGALE (http://migale.jouy.inra.fr) and GENOTOUL bioinformatics platforms. We also relied on the HPC of the CBGP and of the Montpellier Bioinformatics Biodiversity (MBB) platform of the LabEx CeMEB (Laboratoire d'Excellence Centre Méditerranéen de l'Environnement et de la Biodiversité), and we benefitted from the technical assistance of A. Dehne-Garcia. Edinburgh Genomics is funded in part by grants from the UK Natural Environment Research Council (R8/H10/56) and Medical Research Council (G0900740). The work in Portugal was partially funded by the FCT national project UID/AGR/00239/2013., ANR-10-JCJC-1705,GenoPheno,Génomique de la phénologie chez la processionnaire du pin, Thaumetopoea pityocampa(2010), ANR-10-LABX-0004,CeMEB,Mediterranean Center for Environment and Biodiversity(2010), Universidade de Lisboa = University of Lisbon (ULISBOA), Technical University of Lisbon-Instituto Superior de Agronomia [Lisboa] (ISA), and Universidade de Lisboa = University of Lisbon (ULISBOA)-Universidade de Lisboa = University of Lisbon (ULISBOA)
Subjects: Gene Flow, 0106 biological sciences, 0301 basic medicine, Time Factors, population genomics, Demographic history, Lineage (evolution), [SDV]Life Sciences [q-bio], Genome, Insect, Population, detection of selection, Moths, Biology, Polymorphism, Single Nucleotide, 010603 evolutionary biology, 01 natural sciences, phenology, Gene flow, Population genomics, 03 medical and health sciences, Gene Frequency, Genetic drift, Genetics, Animals, education, Phylogeny, Ecology, Evolution, Behavior and Systematics, Demography, Principal Component Analysis, education.field_of_study, Ecology, Population size, Genetic Variation, RAD-sequencing, demographic inference, pine processionary moth, Adaptation, Physiological, Genetics, Population, 030104 developmental biology, Evolutionary biology, Sympatric speciation, [SDE]Environmental Sciences, Seasons
Abstract: Understanding the processes of adaptive divergence, which may ultimately lead to speciation, is a major question in evolutionary biology. Allochronic differentiation refers to a particular situation where gene flow is primarily impeded by temporal isolation between early and late reproducers. This process has been suggested to occur in a large array of organisms, even though it is still overlooked in the literature. We here focused on a well-documented case of incipient allochronic speciation in the winter pine processionary moth Thaumetopoea pityocampa. This species typically reproduces in summer and larval development occurs throughout autumn and winter. A unique, phenologically shifted population (SP) was discovered in 1997 in Portugal. It was proved to be strongly differentiated from the sympatric "winter population" (WP), but its evolutionary history could only now be explored. We took advantage of the recent assembly of a draft genome and of the development of pan-genomic RAD-seq markers to decipher the demographic history of the differentiating populations and develop genome scans of adaptive differentiation. We showed that the SP diverged relatively recently, i.e. few hundred years ago, and went through two successive bottlenecks followed by population size expansions, while the sympatric WP is currently experiencing a population decline. We identified outlier SNPs that were mapped onto the genome, but none were associated with the phenological shift or with subsequent adaptations. The strong genetic drift that occurred along the SP lineage certainly challenged our capacity to reveal functionally important loci. This article is protected by copyright. All rights reserved.
Published: 2018
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27. Likelihood analysis of population genetic data under coalescent models: computational and inferential aspects

Author: François Rousset, Champak Reddy Beeravolu, and Raphaël Leblois
Subjects: education.field_of_study, Computer science, business.industry, Population, Sampling (statistics), Inference, Context (language use), Parameter space, Machine learning, computer.software_genre, Coalescent theory, Kriging, Artificial intelligence, business, education, computer, Importance sampling, Smoothing
Abstract: Likelihood methods are being developed for inference of migration rates and past demographic changes from population genetic data. We survey an approach for such inference using sequential importance sampling techniques derived from coalescent and diffusion theory. The consistent application and assessment of this approach has required the re-implementation of methods often considered in the context of computer experiments methods, in particular of Kriging which is used as a smoothing technique to infer a likelihood surface from likelihoods estimated in various parameter points, as well as reconsideration of methods for sampling the parameter space appropriately for such inference. We illustrate the performance and application of the whole tool chain on simulated and actual data, and highlight desirable developments in terms of data types and biological scenarios.RésuméDiverses approches ont été développées pour l’inférence des taux de migration et des changements démo-graphiques passés à partir de la variation génétique des populations. Nous décrivons une de ces approches utilisant des techniques d’échantillonnage pondéré séquentiel, fondées sur la modélisation par approches de coalescence et de diffusion de l’évolution de ces polymorphismes. L’application et l’évaluation systématique de cette approche ont requis la ré-implémentation de méthodes souvent considérées pour l’analyse de fonctions simulées, en particulier le krigeage, ici utilisé pour inférer une surface de vraisemblance à partir de vraisemblances estimées en différents points de l’espace des paramètres, ainsi que des techniques d’échantillonage de ces points. Nous illustrons la performance et l’application de cette série de méthodes sur données simulées et réelles, et indiquons les améliorations souhaitables en termes de types de données et de scénarios biologiques.Mots-cléshistoire démographique, processus de coalescence, importance sampling, genetic polymorphismAMS 2000 subject classifications92D10, 62M05, 65C05
Published: 2017
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28. 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
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29. Genetic structure of a vulnerable species, the freshwater blenny (Salaria fluviatilis)

Author: Pierre Magnan, François Bonhomme, Patrick Berrebi, Raphaël Leblois, Aurélie Coulon, Martin Laporte, Université de Montpellier (UM), 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), Muséum national d'Histoire naturelle (MNHN), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Université du Québec à Trois-Rivières (UQTR), and This research received financial support from DREAL–Corsica and grants from the Natural Sciences and Engineering Research Council of Canada, the Canada Research Chair program, and the Basler Stiftung fur biologische Forschung to P. Magnan
Subjects: Mediterranean climate, education.field_of_study, Salaria, biology, Glacial refuge, Ecology, [SDV]Life Sciences [q-bio], Freshwater blenny, Population, Endangered species, Freshwater fish conservation, biology.organism_classification, Evolutionarily significant unit, Blenniidae, Fishery, Mediterranean sea, Genetic structure, Genetics, Vulnerable species, Allele size permutation test, Endemic species, 14. Life underwater, education, Ecology, Evolution, Behavior and Systematics
Abstract: International audience; The freshwater blenny (Salaria fluviatilis), an endemic fish to the tributaries of the Mediterranean and Black seas, is considered endangered in five of the nine Mediterranean-European countries. Substantial effort has recently been made to improve our understanding of its biology (i.e., habitat modelling, morphology, behaviour), but developing a conservation program for a species is less effective without a thorough knowledge of its genetic heterogeneity. The goal of this study was to assess the existence and boundaries of freshwater blenny genetic clusters in the occidental basin of the Mediterranean Sea. Our results suggest a genetic structure at two levels. The first is a range-wide product of two different glacial refuges, potentially the Iberian Peninsula (South of Spain; the origin of the "western" group) and Corsica (the "eastern" group). Subsequent northward migration likely took place along the Mediterranean coasts from these two glacial refuges to the southern part of mainland France, where a second contact zone potentially occurred. The second level is a fine-scale genetic structure corresponding to eight genetic groups-four to the west from the "western" refuge and four to the east from the "eastern" refuge. Furthermore, we demonstrate that population differentiation between the western and eastern groups had occurred far enough in the past that new mutations and not solely drift effects were detectable. These results provide a foundation on which to design future conservation efforts of the freshwater blenny in the occidental basin of the Mediterranean Sea.
Published: 2014
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30. Genetic diversity and structure related to expansion history and habitat isolation: stone marten populating rural-urban habitats

Author: Andrzej Zalewski, Raphaël Leblois, Anna Wereszczuk, Polish Academy of Sciences (PAN), 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), ANR-16-CE02-0008,GenoSpace,Nouveaux outils statistiques pour l'analyse spatiale des données génétiques(2016), 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 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)
Subjects: 0106 biological sciences, 0301 basic medicine, Expansion, [SDV]Life Sciences [q-bio], Species distribution, 01 natural sciences, Genetic diversity, Martes foina, MARKERS, Phylogeny, QH540-549.5, General Environmental Science, 2. Zero hunger, education.field_of_study, ALLELE FREQUENCY DATA, CLIMATE-CHANGE, Ecology, POLYMORPHIC MICROSATELLITE LOCI, MINK MUSTELA-VISON, Genetic structure, Isolation, Environmental barrier, AMERICAN MINK, COALESCENT HISTORIES, COMPUTER-PROGRAM, FOUNDING EVENTS, PATTERNS, Geography, [SDE]Environmental Sciences, Research Article, Gene Flow, Genotype, Population, 010603 evolutionary biology, 03 medical and health sciences, Genetic drift, Mustelidae, Animals, Genetic variability, education, Ecology, Evolution, Behavior and Systematics, Ecosystem, Isolation by distance, Genetic Variation, 15. Life on land, 030104 developmental biology, Genetics, Population, Biological dispersal, Poland, Microsatellite Repeats
Abstract: Background Population genetic diversity and structure are determined by past and current evolutionary processes, among which spatially limited dispersal, genetic drift, and shifts in species distribution boundaries have major effects. In most wildlife species, environmental modifications by humans often lead to contraction of species’ ranges and/or limit their dispersal by acting as environmental barriers. However, in species well adapted to anthropogenic habitat or open landscapes, human induced environmental changes may facilitate dispersal and range expansions. In this study, we analysed whether isolation by distance and deforestation, among other environmental features, promotes or restricts dispersal and expansion in stone marten (Martes foina) populations. Results We genotyped 298 martens from eight sites at twenty-two microsatellite loci to characterize the genetic variability, population structure and demographic history of stone martens in Poland. At the landscape scale, limited genetic differentiation between sites in a mosaic of urban, rural and forest habitats was mostly influenced by isolation by distance. Statistical clustering and multivariate analyses showed weak genetic structuring with two to four clusters and a high rate of gene flow between them. Stronger genetic differentiation was detected for one stone marten population (NE1) located inside a large forest complex. Genetic differentiation between this site and all others was 20% higher than between other sites separated by similar distances. The genetic uniqueness index of NE1 was also twofold higher than in other sites. Past demographic history analyses showed recent expansion of this species in north-eastern Poland. A decrease in genetic diversity from south to north, and MIGRAINE analyses indicated the direction of expansion of stone marten. Conclusions Our results showed that two processes, changes in species distribution boundaries and limited dispersal associated with landscape barriers, affect genetic diversity and structure in stone marten. Analysis of local barriers that reduced dispersal and large scale analyses of genetic structure and demographic history highlight the importance of isolation by distance and forest cover for the past colonization of central Europe by stone marten. This confirmed the hypothesis that human-landscape changes (deforestation) accelerated stone marten expansion, to which climate warming probably has also been contributing over the last few decades. Electronic supplementary material The online version of this article (10.1186/s12898-017-0156-6) contains supplementary material, which is available to authorized users.
Published: 2017
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31. Resampling: an improvement of Importance Sampling in varying population size models

Author: Raphaël Leblois, François Rousset, Pierre Pudlo, Coralie Merle, 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 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), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-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), gence Nationale de la Recherche (project IM-Model CORAL.FISH 2010-BLAN-1726-01) and by the Institut National de Recherche en Agronomie (Project INRAStartingGroup‘‘IGGiPop’’, 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), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS)
Subjects: FOS: Computer and information sciences, 0106 biological sciences, 0301 basic medicine, Computer science, Inference, Importance Sampling, 01 natural sciences, [MATH.MATH-ST]Mathematics [math]/Statistics [math.ST], Resampling, Statistics, Range (statistics), [STAT.CO]Statistics [stat]/Computation [stat.CO], Computation (stat.CO), education.field_of_study, Likelihood Functions, [STAT.AP]Statistics [stat]/Applications [stat.AP], Population size, Probability distribution, [STAT.ME]Statistics [stat]/Methodology [stat.ME], Mathematics - Probability, Algorithms, Population, Mathematics - Statistics Theory, Statistics Theory (math.ST), Statistics - Applications, Statistics - Computation, 010603 evolutionary biology, Methodology (stat.ME), 03 medical and health sciences, resampling, FOS: Mathematics, Humans, Applications (stat.AP), coalescent, education, Statistics - Methodology, Ecology, Evolution, Behavior and Systematics, Demography, Population Density, jump Markov process, [SDV.GEN]Life Sciences [q-bio]/Genetics, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Models, Genetic, Probability (math.PR), population genetics, demographic inference, Statistics::Computation, [MATH.MATH-PR]Mathematics [math]/Probability [math.PR], 030104 developmental biology, Genetics, Population, Pairwise comparison, Importance sampling
Abstract: International audience; Sequential importance sampling algorithms have been defined to estimate likelihoods in models of ancestral population processes. However, these algorithms are based on features of the models with constant population size, and become inefficient when the population size varies in time, making likelihood-based inferences difficult in many demographic situations. In this work, we modify a previous sequential importance sampling algorithm to improve the efficiency of the likelihood estimation. Our procedure is still based on features of the model with constant size, but uses a resampling technique with a new resampling probability distribution depending on the pairwise composite likelihood. We tested our algorithm, called sequential importance sampling with resampling (SISR) on simulated data sets under different demographic cases. In most cases, we divided the computational cost by two for the same accuracy of inference, in some cases even by one hundred. This study provides the first assessment of the impact of such resampling techniques on parameter inference using sequential importance sampling, and extends the range of situations where likelihood inferences can be easily performed.
Published: 2017
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32. Phylogeography and demographic history of Shaw's Jird ( Meriones shawii complex) in North Africa

Author: Karim Souttou, Raphaël Leblois, Violaine Nicolas, Aude Lalis, Christiane Denys, Touria Benazzou, Emmanuelle Stoetzel, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Université des Antilles (UA)-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE)-Sorbonne Université (SU)-Muséum national d'Histoire naturelle (MNHN), 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), Histoire naturelle de l'Homme préhistorique (HNHP), Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)-Université de Perpignan Via Domitia (UPVD), Faculté des sciences [Rabat], Université Mohammed V de Rabat [Agdal], Institut National d'Agronomie d'Alger (INAA), Ministère de l'Education nationale, de l’Enseignement supérieur et de la Recherche (M.E.N.E.S.R.), Lalis, Aude, Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Muséum national d'Histoire naturelle (MNHN)-Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Université Mohammed V de Rabat [Agdal] (UM5), Projet CMEP TASSILI MDU 09MDU755, Projet INRA Starting Group ‘IGGiPop’, Allocation post-doctorale LabEx BCDiv, ATM MNHN 'Taxonomie moléculaire, DNA Barcode & Gestion Durable des Collections', Service de Systématique Moléculaire du MNHN (UMS 2700, Paris, France), network Bibliothèque du Vivant (CNRS, MNHN, INRA, CEA), ANR-09-PEXT-0004,Mohmie,Influence de l'installation des hommes modernes au Maroc sur l'évolution de la biodiversité des petits vertébrés terrestres(2009), ANR-09-BLAN-0145,EMILE,Etude de Méthodes Inférentielles et Logiciels pour l'Evolution(2009), ANR-10-BLAN-1726,IM-MODEL@CORALFISH,Modèle isolement-migration de l'histoire des communautés de poissons des récifs coralliens : théorie et données(2010), ANR-10-LABX-0003,BCDiv,Biological and Cultural Diversities : Origins, Evolution, Interactions, Future(2010), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), 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), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Université de Perpignan Via Domitia (UPVD), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, 0301 basic medicine, Mediterranean climate, Pleistocene, Demographic history, Climate change, Biology, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Ecoregion, fossil calibration, Ecology, Evolution, Behavior and Systematics, Holocene, ComputingMilieux_MISCELLANEOUS, afrique du nord, Ecology, rodent, population genetics, 15. Life on land, Phylogeography, 030104 developmental biology, biogeographical patterns, 13. Climate action, Interglacial, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, meriones shawi
Abstract: International audience; Palaeoenvironmental data and climatic reconstructions show that the Mediterranean ecoregion of North Africa underwent drastic ecological changes during the Pleistocene. Given its rich palaeontological record, North Africa is a pertinent region for documenting the role of climate change and human mediated-habitat changes on the demography and genetic structure of faunal species. In the present study, we collected data from this species in Morocco, Algeria, and Tunisia, and we combined molecular (mitochondrial and nuclear DNA sequences, microsatellites), fossil, palaeoenvironmental, and human context data to propose an explanation for the fluctuations of populations belonging to the Meriones shawii complex in the past. Genetic and fossil data both indicate a strong bottleneck in Moroccan populations at the Middle Holocene (last interglacial optimum) compared to the Late Pleistocene. Our mitochondrial DNA data suggest a diversification event within Morocco corresponding to the 130-125 kya interglacial optimum. Given that (1) major demographic changes in the M.shawii complex coincide with the interglacial optimums, and (2) the impact of human activities on the landscape and faunal communities was moderate during the Middle Holocene (beginnings of the Neolithic culture), our results demonstrate that climate, rather than anthropogenic influences, likely explains the M.shawii complex population decline in the Holocene.
Published: 2016
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33. Conservation of the endangered Mediterranean tortoise Testudo hermanni hermanni: The contribution of population genetics and historical demography

Author: Giorgio Bertorelle, Raphaël Leblois, Giuseppe Sotgiu, Véronique Arnal, Albert Bertolero, Saliha Zenboudji, Marc Cheylan, Claudine Montgelard, Guillelme Astruc, Joan Lluís Pretus, Mario Lo Valvo, Zenboudji, S., Cheylan, M., Arnal, V., Bertolero, A., Leblois, R., Astruc, G., Bertorelle, G., Pretus, J., LO VALVO, M., Sotgiu, G., Montgelard, C., Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-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 de Recherche pour le Développement (IRD [France-Sud]), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL), Picampall, the Terres de l'Ebre Ornithological Association, Partenaires INRAE, 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), Università degli Studi di Ferrara (UniFE), Dept Ecol, University of São Paulo (USP), Università degli Studi di Palermo, Association Zirichiltaggi Sardinia Wildlife Conservation, University of Johannesburg (UJ), and Foundation for Research on Biodiversity (FRB: Fondation pour la Recherche sur la Biodiversite) , CORSEPYR project , French National Action Plan (PNA: Plan National d'Action) , French ministery of ecology grants (DREAL-PACA): CNRS contract, Ebro Delta Natural Park , Generalitat de Catalunya, Institut Menorqui d'Estudis (IME) , Spanish Ministry of Science and Technology
Subjects: 0106 biological sciences, 0301 basic medicine, Conservation genetics, Demographic history, Tortoise, [SDV]Life Sciences [q-bio], Population, Endangered species, Settore BIO/05 - Zoologia, Zoology, Biology, 010603 evolutionary biology, 01 natural sciences, Testudo hermanni, 03 medical and health sciences, 14. Life underwater, education, Microsatellites, Conservation genetic, Ecology, Evolution, Behavior and Systematics, Nature and Landscape Conservation, Testudo hermanni Genetic structure, Conservation issues, education.field_of_study, Ecology, Ambientale, Microsatellite, 15. Life on land, biology.organism_classification, Conservation genetics, Demographic history, Microsatellites, Testudo hermanni, Genetic structure, Conservation issues, 030104 developmental biology, Threatened species, Genetic structure
Abstract: International audience; Estimating the genetic variation and demographic trends of species in decline is of major concern in conservation genetics. This study contributes to understanding how historical and anthropogenic factors shape the distribution of current genetic diversity in one of the most endangered reptiles in Western Europe, the Hermann's tortoise Testudo hermanni hermanni. We used 17 microsatellite loci, chosen from a pyrosequencing library specifically developed for the subspecies to genotype eight populations distributed over about 30 sample localities covering almost the entire geographic distribution of the sub-species. The population genetic results reflect a very strong genetic structure and identify three major clusters among the Hermann's tortoise in the occidental Mediterranean basin: a continental cluster (Albera in Spain, Var in France and continental Italy), an insular cluster (Corsica, Sardinia and Sicily) and a cluster of mixed lineage (Minorca). Each of the eight studied populations is characterized by only one lineage except for Minorca, in which two lineages were identified. In contrast to what most empirical studies predict, the genetic diversity of the Hermann's tortoise is greater on islands than on the continent. Islands can therefore be considered as genetic sanctuaries with high conservation potential for this species, particularly in Corsica. Historical demographic patterns inferred with a generalized stepwise-mutation model (GSM) using maximum likelihood showed significant past demographic changes in only two of the eight sampled populations: a demographic bottleneck was detected in the Albera population (Spain) and a demographic expansion in Corsica (France). In contrast to what was argued in previous studies, these results indicate that the Hermann's tortoise lineage found in Corsica is autochthonous. The origin of both lineages found in Minorca remains speculative. Lastly, our study identifies the six most relevant management units (sensu Moritz, 1994) for conservation purposes on the basis that they represent a significant part of the evolutionary legacy of the species. Some conservation recommendations were proposed, in particular for the most threatened population in Albera.
Published: 2016
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34. Effects of landscape features and demographic history on the genetic structure of Testudo marginata populations in the southern Peloponnese and Sardinia

Author: Raphaël Leblois, Melanie Perez, Marie-Catherine Boisselier, Roger Bour, Josie Lambourdière, Barbara Livoreil, and Sarah Samadi
Subjects: 0106 biological sciences, 0303 health sciences, education.field_of_study, Ecology, Demographic history, Population, Population genetics, Introduced species, 15. Life on land, Biology, Testudo marginata, biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Habitat destruction, Genetic structure, education, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Isolation by distance
Abstract: Testudo marginata, the largest European land tortoise, is suffering habitat degradation and destruction. Some populations, in markedly degraded habitats, are characterized by divergent morphotypes. However, the evolutionary significance of these morphotypes is of debate. Using 11 polymorphic microsatellites, we studied: (1) marginated tortoises from Sardinia that display a divergent morphotype – this population was potentially introduced from Greece; and (2) an area in the southern Peloponnese that includes a small and degraded zone in which marginated tortoises are dwarf. Genetic analyses run without any a priori assignment clearly acknowledge the specimens sampled in the territory of the dwarf form as a single group whilst Sardinian specimens are clustered with other specimens from the northern part of the area sampled in Greece. Demographic analyses suggest that Sardinian tortoises originated recently from some of the populations sampled in the northern part of the area sampled in Greece. Over locations sampled in Greece, a landscape-genetic analysis allowed us to detect potential landscape features that may reduce gene flow between the dwarf form territory and surrounding areas. Our results suggest that the territory of the dwarf form is particularly propitious for marginated tortoises and that conservation regulations in Greece should be reinforced to protect this area from increasing impact of human activities changing from traditional agriculture to mechanization and extensive use of chemicals. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105, 591–606.
Published: 2011
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35. Limited dispersal in mobile hunter–gatherer Baka Pygmies

Author: Alain Froment, Serge Bahuchet, Evelyne Heyer, Renaud Vitalis, Paul Verdu, Raphaël Leblois, François Rousset, Sylvain Théry, Eco-Anthropologie et Ethnobiologie (EAE), Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Muséum national d'Histoire naturelle (MNHN), Biologie Intégrative des Populations, École pratique des hautes études (EPHE)-Centre National de la Recherche Scientifique (CNRS), Patrimoines Locaux et Gouvernance (PALOC), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-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), Muséum national d'Histoire naturelle (MNHN)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-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), Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE)
Subjects: Adult, Male, education, Population Dynamics, isolation by distance, Black People, Population genetics, Biology, microsatellites, 03 medical and health sciences, Ethnicity, Humans, 0601 history and archaeology, Cameroon, dispersal, ComputingMilieux_MISCELLANEOUS, Hunter-gatherer, 030304 developmental biology, Isolation by distance, 0303 health sciences, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], 060101 anthropology, Ecology, population genetics, Central africa, 06 humanities and the arts, African Pygmies, Emigration and Immigration, Agricultural and Biological Sciences (miscellaneous), Biological dispersal, Female, General Agricultural and Biological Sciences, Population Genetics, Microsatellite Repeats
Abstract: International audience; Hunter-gatherer Pygmies from Central Africa are described as being extremely mobile. Using neutral genetic markers and population genetics theory, we explored the dispersal behaviour of the Baka Pygmies from Cameroon, one of the largest Pygmy populations in Central Africa. We found a strong correlation between genetic and geographical distances: a pattern of isolation by distance arising from limited parent-offspring dispersal. Our study suggests that mobile hunter-gatherers do not necessarily disperse over wide geographical areas.
Published: 2010
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36. Four years of DNA barcoding: Current advances and prospects

Author: Lise Frézal, Raphaël Leblois, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biologie Intégrative des Populations, École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Origine, structure et évolution de la biodiversité (OSEB), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), and École Pratique des Hautes Études (EPHE)
Subjects: 0106 biological sciences, MESH: Sequence Analysis, DNA, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Barcode, 01 natural sciences, DNA barcoding, law.invention, law, MESH: DNA Fingerprinting, Species identification, MESH: Animals, DNA taxonomy, 0303 health sciences, Animal life, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Classification, DNA Barcoding, MESH: Classification, Infectious Diseases, Cytochrome c oxidase, Microbiology (medical), Cytochrome C Oxidase Subunit 1, Zoology, Biology, DNA, Mitochondrial, International species databank, 010603 evolutionary biology, Microbiology, COI, 03 medical and health sciences, Species Specificity, DNA barcode, Genetics, Animals, MESH: Species Specificity, Dna taxonomy, Animal species, Molecular Biology, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Electronic Data Processing, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], MESH: DNA, Mitochondrial, Sequence Analysis, DNA, DNA Fingerprinting, Evolutionary biology, Classification methods, MESH: Automatic Data Processing, BOLD
Abstract: International audience; Research using cytochrome c oxidase barcoding techniques on zoological specimens was initiated by Hebert et al. [Hebert, P.D.N., Ratnasingham, S., deWaard, J.R., 2003. Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proc. R. Soc. Lond. B 270, S96-S99]. By March 2004, the Consortium for the Barcode of Life started to promote the use of a standardized DNA barcoding approach, consisting of identifying a specimen as belonging to a certain animal species based on a single universal marker: the DNA barcode sequence. Over the last 4 years, this approach has become increasingly popular and advances as well as limitations have clearly emerged as increasing amounts of organisms have been studied. Our purpose is to briefly expose DNA Barcode of Life principles, pros and cons, relevance and universality. The initially proposed Barcode of life framework has greatly evolved, giving rise to a flexible description of DNA barcoding and a larger range of applications.
Published: 2008
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37. New molecular data favour an anthropogenic introduction of the wood mouse (Apodemus sylvaticus) in North Africa

Author: Adel Hamani, Raphaël Leblois, Aude Lalis, Johan Michaux, Ali Ouarour, Sohaib Liefried, Champak Reddy Beeravolu, Violaine Nicolas, Christiane Denys, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-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), Université Abdelmalek Essaâdi (UAE), Université de Liège, Unité de génétique de la conservation, Institut de Botanique, ENSA El Harrach, Partenaires INRAE, This study was supported by the ANR call '6eme extinction' project 'ANR-09-PEXT-004' and the project CMEP TASSILI MDU 09MDU755. RL and CRB have been partially funded by ANR projects: EMILE 'ANR-09-BLAN-0145' and IM-MODEL@CORAL.FISH 'ANR-10-BLAN-1726', and by the Project INRA Starting Group 'IGGiPop'. Molecular analyses were supported by the ATM 'Taxonomie moleculaire, DNA Barcode et Gestion Durable des Collections', the Service de Systematique Moleculaire of the MNHN (UMS 2700, Paris, France) and the network 'Bibliotheque du Vivant' funded by CNRS, MNHN, INRA and CEA (Genoscope)., ANR-09-PEXT-0004,Mohmie,Influence de l'installation des hommes modernes au Maroc sur l'évolution de la biodiversité des petits vertébrés terrestres(2009), ANR-09-BLAN-0145,EMILE,Etude de Méthodes Inférentielles et Logiciels pour l'Evolution(2009), ANR-10-BLAN-1726,IM-MODEL@CORALFISH,Modèle isolement-migration de l'histoire des communautés de poissons des récifs coralliens : théorie et données(2010), Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-École Pratique des Hautes Études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, 0301 basic medicine, Early Pleistocene, Demographic history, [SDV]Life Sciences [q-bio], population expansion, Biology, 010603 evolutionary biology, 01 natural sciences, Mediterranean Basin, 03 medical and health sciences, Peninsula, Genetics, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Mesolithic, geography, geography.geographical_feature_category, Ecology, Population size, Mediterranean basin, rodent, biology.organism_classification, demographic history, Wood mouse, Anthropogenic introduction, 030104 developmental biology, Apodemus, Animal Science and Zoology
Abstract: International audience; According to fossil data, the wood mouse arrived in North Africa 7500 ya, while it was present in Europe since Early Pleistocene. Previous molecular studies suggested that its introduction in North Africa probably occurred via the Strait of Gibraltar more than 0.4 Mya ago. In this study, we widely sampled wood mice to get a better understanding of the geographic and demographic history of this species in North Africa and possibly to help resolving the discrepancy between genetic and palaeontological data. Specifically, we wanted to answer the following questions: (1) When and how did the wood mouse arrive in North Africa? and (2) What is its demographic and geographic history in North Africa since its colonization? We collected in the field 438 new individuals and used both mtDNA and six microsatellite markers to answer these questions. Our results confirm that North African wood mice have a south-western European origin and colonized the Maghreb through the Strait of Gibraltar probably during the Mesolithic or slightly after. They first colonized the Tingitana Peninsula and then expanded throughout North Africa. Our genetic data suggest that the ancestral population size comprised numerous individuals reinforcing the idea that wood mice did not colonize Morocco accidentally through rafting of a few individuals, but via recurrent/multiple anthropogenic translocations. No spatial structuring of the genetic variability was recorded in North Africa, from Morocco to Tunisia.
Published: 2016
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38. Evidence for low-level hybridization between two allochronic populations of the pine processionary moth, Thaumetopoea pityocampa (Lepidoptera: Notodontidae)

Author: Julie Landes, Raphaël Leblois, Christian Burban, Maria Rosa Paiva, Carole Kerdelhué, Mathieu Gautier, Manuela Branco, Helena Santos, Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), 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), Sorbonne Universités (COMUE), Eco-Anthropologie et Ethnobiologie (EAE), Muséum national d'Histoire naturelle (MNHN)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Universidade de Lisboa (ULISBOA), and Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)
Subjects: 0106 biological sciences, 0301 basic medicine, Sympatry, [SDV]Life Sciences [q-bio], Population, Allopatric speciation, Zoology, incipient speciation, Biology, 010603 evolutionary biology, 01 natural sciences, sympatry, Gene flow, 03 medical and health sciences, education, Ecology, Evolution, Behavior and Systematics, hybrid identification, education.field_of_study, Ecology, Reproductive isolation, Notodontidae, Incipient speciation, biology.organism_classification, 030104 developmental biology, Sympatric speciation, allochrony, gene flow
Abstract: International audience; Divergence between populations sharing the same habitat can be initiated by different reproductive times, leading to allochronic differentiation. A spatially localized allochronic summer population (SP) of the pine processionary moth Thaumetopoea pityocampa, recently discovered in Portugal, occurs in sympatry with the local winter population (WP). We examined the level of genetic differentiation between the two populations and estimated the current gene flow within the spatial framework of their co-occurrence. Mitochondrial data indicated that the two sympatric populations were genetically closer than other WP populations. Conversely, microsatellite genotyping uncovered greater differentiation between the two sympatric populations than between allopatric ones. While male trapping confirmed that reproduction of SP and WP occurred at distinct times, clustering approaches demonstrated the presence of a few LateSP individuals emerging within the WP flight period, although genetically identified as SP. We also identified rare recent hybridization events apparently occurring mainly in the margins of the current SP range. The ongoing gene flow detected between the ancestral and the emerging allochronic populations revealed an incomplete reproductive isolation, which must therefore be taken into account and integrated with studies focussed on ecological drivers, so that a complete understanding of the ongoing speciation process might be achieved.
Published: 2016
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39. Black rat invasion of inland Sahel: insights from interviews and population genetics in south-western Niger

Author: Raphaël Leblois, Sama Gagaré, Ambroise Dalecky, Anne Loiseau, Sylvain Piry, Philippe Gauthier, Gauthier Dobigny, Karine Berthier, Madougou Garba, Carine Brouat, Miguel Navascués, Caroline Tatard, Unité de Pathologie Végétale (PV), Institut National de la Recherche Agronomique (INRA), Université Abdou Moumouni [Niamey], Direction Générale de la Protection des Végétaux, Ministère de l'Agriculture du Niger, 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), 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), Centre Régional AGRHYMET (CRA), Laboratoire Population-Environnement-Développement (LPED), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU), partnership agreement (number 301027/00) between IRD and the Republic of Niger, SRC-IRD research bursary for international mobility (2011–2012), 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 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 Station de Pathologie Végétale (AVI-PATHO)
Subjects: 0106 biological sciences, 0301 basic medicine, Current distribution, [SDE.MCG]Environmental Sciences/Global Changes, Population, Population genetics, 010603 evolutionary biology, 01 natural sciences, Rattus rattus, Interview data, 03 medical and health sciences, trade-mediated invasion, education, Ecology, Evolution, Behavior and Systematics, education.field_of_study, biology, Ecology, Propagule pressure, Genetic data, biology.organism_classification, [SDE.ES]Environmental Sciences/Environmental and Society, 030104 developmental biology, Black rat, Africa, Biological dispersal, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, urban habitat
Abstract: International audience; Human population migrations, as well as long-distance trade activities, have been responsible for the spread of many invasive organisms. The black rat, Rattus rattus, has colonized most of the world following ship-mediated trade. Owing to its tight association with human infrastructures, this species has been able to survive in unfavourable environments, such as Sahelian Africa. In this work, we combined interview-based and population genetic surveys to investigate the processes underlying the ongoing invasion of southwestern Niger by black rats, with special emphasis on the capital city, Niamey. Our trapping and interview data are quite congruent, and all together point towards a patchy, but rather widespread, current distribution of R. rattus. Genetic data strongly suggest that road network development for truck-based commercial flow from/to international harbours located in neighbouring countries (Benin, Togo, and Nigeria) facilitates the passive dispersal of black rats over a long distance through unfavourable landscapes. Another potentially, more ancient, invasion route may be associated with boat transport along the Niger River. Human-mediated dispersal thus probably allows the foundation of persisting populations within highly anthropized areas while population dynamics may be more unstable in remote areas and mostly depends on propagule pressure.
Published: 2016
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40. Likelihood and Approximate Likelihood Analyses of Genetic Structure in a Linear Habitat: Performance and Robustness to Model Mis-Specification

Author: François Rousset, Raphaël Leblois, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-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), Origine, structure et évolution de la biodiversité (OSEB), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE)
Subjects: 0106 biological sciences, coalescence, Mutation rate, Insecta, Population Dynamics, Population, isolation by distance, Biology, Models, Biological, 010603 evolutionary biology, 01 natural sciences, microsatellites, 03 medical and health sciences, Statistics, Genetics, Animals, Quantitative Biology::Populations and Evolution, maximum likelihood, dispersal, education, Molecular Biology, Scaling, Ecosystem, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Isolation by distance, Likelihood Functions, 0303 health sciences, education.field_of_study, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Ecology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Statistical model, [SDE]Environmental Sciences, Mutation, Biological dispersal, Scale parameter, Importance sampling
Abstract: International audience; We evaluate the performance of maximum likelihood (ML) analysis of allele frequency data in a linear array of populations. The parameters are a mutation rate and either the dispersal rate in a stepping stone model or a dispersal rate and a scale parameter in a geometric dispersal model. An approximate procedure known as maximum product of approximate conditional (PAC) likelihood is found to perform as well as ML. Mis-specification biases may occur because the importance sampling algorithm is formally defined in term of mutation and migration rates scaled by the total size of the population, and this size may differ widely in the statistical model and in reality. As could be expected, ML generally performs well when the statistical model is correctly specified. Otherwise, mutation rate estimates are much closer to mutation probability scaled by number of demes in the statistical model than scaled by number of demes in reality when mutation probability is high and dispersal is most limited. This mis-specification bias actually has practical benefits. However, opposite results are found in opposite conditions. Migration rate estimates show roughly similar trends, but they may not always be easily interpreted as low-bias estimates of dispersal rate under any scaling. Estimation of the dispersal scale parameter is also affected by mis-specification of the number of demes, and the different biases compensate each other in such a way that good estimation of the so-called neighborhood size (or more precisely the product of population density and mean-squared parent–offspring dispersal distance) is achieved. Results congruent with these findings are found in an application to a damselfly data set.
Published: 2007
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41. Compatible genetic and ecological estimates of dispersal rates in insect (Coenagrion mercuriale: Odonata: Zygoptera) populations: analysis of ‘neighbourhood size’ using a more precise estimator

Author: David J. Thompson, Ilik J. Saccheri, Fran{ c c}ois Rousset, Phillip C. Watts, Stephen J. Kemp, and Raphaël Leblois
Subjects: 0106 biological sciences, 0303 health sciences, education.field_of_study, Ecology, Population, Biology, biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, Population density, Spatial heterogeneity, 03 medical and health sciences, Damselfly, Genetic structure, Genetics, Biological dispersal, Coenagrion mercuriale, education, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Isolation by distance
Abstract: Genetic and demographic estimates of dispersal are often thought to be inconsistent. In this study, we use the damselfly Coenagrion mercuriale (Odonata: Zygoptera) as a model to evaluate directly the relationship between estimates of dispersal rate measured during capture-mark-recapture fieldwork with those made from the spatial pattern of genetic markers in linear and two-dimensional habitats. We estimate the 'neighbourhood size' (Nb) - the product of the mean axial dispersal rate between parent and offspring and the population density - by a previously described technique, here called the regression method. Because C. mercuriale is less philopatric than species investigated previously by the regression method we evaluate a refined estimator that may be more applicable for relatively mobile species. Results from simulations and empirical data sets reveal that the new estimator performs better under most situations, except when dispersal is very localized relative to population density. Analysis of the C. mercuriale data extends previous results which demonstrated that demographic and genetic estimates of Nb by the regression method are equivalent to within a factor of two at local scales where genetic estimates are less affected by habitat heterogeneity, stochastic processes and/or differential selective regimes. The corollary is that with a little insight into a species' ecology the pattern of spatial genetic structure provides quantitative information on dispersal rates and/or population densities that has real value for conservation management.
Published: 2006
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42. 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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43. Spatial heterogeneity in landscape structure influences dispersal and genetic structure: empirical evidence from a grasshopper in an agricultural landscape

Author: Sabrina Delaunay, Raphaël Leblois, Isabelle Litrico, Bertrand Gauffre, Sophie Mallez, Isabelle Badenhausser, Marie Pierre Chapuis, Centre d'Études Biologiques de Chizé - UMR 7372 (CEBC), Institut National de la Recherche Agronomique (INRA)-Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS), 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), 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), Unité de Recherche Pluridisciplinaire Prairies et Plantes Fourragères (P3F), Institut National de la Recherche Agronomique (INRA), Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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), 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 d'Etudes Biologiques de Chizé [France] (USC 1339 INRA), and Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université de La Rochelle (ULR)
Subjects: 0106 biological sciences, Population, Geostatistics, Grasshoppers, Biology, 010603 evolutionary biology, 01 natural sciences, Grassland, microsatellites, 03 medical and health sciences, Gene Frequency, clustering methods, Genetics, Animals, Cluster Analysis, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, computer simulations, education, dispersal, Ecology, Evolution, Behavior and Systematics, Ecosystem, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, geography, education.field_of_study, Spatial Analysis, geography.geographical_feature_category, pezotettix giornae, Ecology, Agriculture, Bayes Theorem, landscape genetics, 15. Life on land, H10 - Ravageurs des plantes, Spatial heterogeneity, Genetics, Population, Habitat, Genetic structure, Biological dispersal, Common spatial pattern, France, L20 - Écologie animale, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Animal Distribution
Abstract: Dispersal may be strongly influenced by landscape and habitat characteristics that could either enhance or restrict movements of organisms. Therefore, spatial heterogeneity in landscape structure could influence gene flow and the spatial structure of populations. In the past decades, agricultural intensification has led to the reduction in grassland surfaces, their fragmentation and intensification. As these changes are not homogeneously distributed in landscapes, they have resulted in spatial heterogeneity with generally less intensified hedged farmland areas remaining alongside streams and rivers. In this study, we assessed spatial pattern of abundance and population genetic structure of a flightless grasshopper species, Pezotettix giornae, based on the surveys of 363 grasslands in a 430-km(2) agricultural landscape of western France. Data were analysed using geostatistics and landscape genetics based on microsatellites markers and computer simulations. Results suggested that small-scale intense dispersal allows this species to survive in intensive agricultural landscapes. A complex spatial genetic structure related to landscape and habitat characteristics was also detected. Two P.giornae genetic clusters bisected by a linear hedged farmland were inferred from clustering analyses. This linear hedged farmland was characterized by high hedgerow and grassland density as well as higher grassland temporal stability that were suspected to slow down dispersal. Computer simulations demonstrated that a linear-shaped landscape feature limiting dispersal could be detected as a barrier to gene flow and generate the observed genetic pattern. This study illustrates the relevance of using computer simulations to test hypotheses in landscape genetics studies.
Published: 2015
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44. Congruent signals of population history but radically different patterns of genetic diversity between mitochondrial and nuclear markers in a mountain lizard

Author: Rémy Eudeline, Raphaël Leblois, Anne-Laure Ferchaud, Véronique Arnal, Pierre-André Crochet, Marc Cheylan, Gilles Pottier, Department of Bioscience [Roskilde], Aarhus University [Aarhus], Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-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 de Recherche pour le Développement (IRD [France-Sud]), Nature Midi Pyrénées, Partenaires INRAE, 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), Computational Biology Institute (IBC), Parc National des Pyrenees as part of a project on the conservation of the Pyrenean rock lizards, PPF ('Populations fractionnees et insulaires') of the Ecole Pratique des Hautes Etudes, Agence Nationale de la Recherche [EMILE 09-blan-0145-01], and Institut National de Recherche en Agronomie (Project INRA Starting Group 'IGGiPop')
Subjects: 0106 biological sciences, Gene Flow, conservation biology, Mitochondrial DNA, life history evolution, Genotype, [SDV]Life Sciences [q-bio], Population, phylogeography, Biology, 010603 evolutionary biology, 01 natural sciences, DNA, Mitochondrial, 03 medical and health sciences, Gene Frequency, Genetics, Animals, education, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Cell Nucleus, 0303 health sciences, education.field_of_study, Genetic diversity, Ecology, Population size, Genetic Variation, Bayes Theorem, Lizards, habitat degradation, Sequence Analysis, DNA, 15. Life on land, reptiles, Nuclear DNA, Phylogeography, Genetics, Population, Evolutionary biology, Biological dispersal, Conservation biology, France, Microsatellite Repeats
Abstract: International audience; Historical factors, current population size, population connectivity and selective processes at linked loci contribute to shaping contemporary patterns of neutral genetic diversity. It is now widely acknowledged that nuclear and mitochondrial markers react differently to current demography as well as to past history, so the use of both types of markers is often advocated to gain insight on both historical and contemporary processes. We used 12 microsatellite loci genotyped in 13 populations of a mountain lizard (Iberolacerta bonnali) to test whether the historical scenario favoured by a previous mitochondrial study was also supported by nuclear markers and thereby evaluated the consequences of postglacial range movements on nuclear diversity. Congruent signals of recent history were revealed by nuclear and mitochondrial markers using an Approximate Bayesian computation approach, but contemporary patterns of mtDNA and nuclear DNA diversity were radically different. Although dispersal in this species is probably highly restricted at all spatial scales, colonization abilities have been historically good, suggesting capability for reestablishment of locally extinct populations except in fully disconnected habitats.
Published: 2015
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45. Maximum-likelihood inference of population size contractions from microsatellite data

Author: Renaud Vitalis, Pierre Pudlo, Raphaël Leblois, Joseph Néron, Champak Reddy Beeravolu, François Rousset, François Bertaux, 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), Origine, structure et évolution de la biodiversité (OSEB), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Institut de Mathématiques et de Modélisation de Montpellier (I3M), Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Computational systems biology and optimization (Lifeware), Inria Paris-Rocquencourt, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), This study was supported by the Agence Nationale de la Recherche (EMILE ANR-09-BLAN-0145 and IM-MODEL@CORALFISH ANR-10-BLAN-1726 projects) and by the Institut National de Recherche en Agronomie (Project INRA Starting Group 'IGGiPop')., ANR-09-BLAN-0145,EMILE,Etude de Méthodes Inférentielles et Logiciels pour l'Evolution(2009), ANR-10-BLAN-1726,IM-MODEL@CORALFISH,Modèle isolement-migration de l'histoire des communautés de poissons des récifs coralliens : théorie et données(2010), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-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)-Institut National de la Recherche Agronomique (INRA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE)
Subjects: bottleneck, Importance sampling, MESH: Mutation, Demographic history, MESH: Population Density, [SDV]Life Sciences [q-bio], Disequilibrium, Inference, Biology, [SHS.DEMO]Humanities and Social Sciences/Demography, Population structure, Coalescent theory, Statistics, Genetics, medicine, Animals, MESH: Animals, [MATH]Mathematics [math], Microsatellites, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Population Density, Likelihood Functions, Models, Genetic, Population size, Pongo, Robustness (evolution), Computational Biology, Confidence interval, Demographic inference, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, Population contraction, Mutation, Coalescent, MESH: Likelihood Functions, MESH: Microsatellite Repeats, medicine.symptom, Software, Maximum likelihood, Mutation processes, Microsatellite Repeats
Abstract: International audience; Understanding the demographic history of populations and species is a central issue in evolutionary biology and molecular ecology. In this work, we develop a maximum-likelihood method for the inference of past changes in population size from microsatellite allelic data. Our method is based on importance sampling of gene genealogies, extended for new mutation models, notably the generalized stepwise mutation model (GSM). Using simulations, we test its performance to detect and characterize past reductions in population size. First, we test the estimation precision and confidence intervals coverage properties under ideal conditions, then we compare the accuracy of the estimation with another available method (MSVAR) and we finally test its robustness to misspecification of the mutational model and population structure. We show that our method is very competitive compared with alternative ones. Moreover, our implementation of a GSM allows more accurate analysis of microsatellite data, as we show that the violations of a single step mutation assumption induce very high bias toward false contraction detection rates. However, our simulation tests also showed some limits, which most importantly are large computation times for strong disequilibrium scenarios and a strong influence of some form of unaccounted population structure. This inference method is available in the latest implementation of the MIGRAINE software package.
Published: 2014
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46. IBDSim: a computer program to simulate genotypic data under isolation by distance

Author: Raphaël Leblois, Arnaud Estoup, François Rousset, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-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), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Biologie Intégrative des Populations, École pratique des hautes études (EPHE)-Centre National de la Recherche Scientifique (CNRS), Centre de biologie et de gestion des populations, Institut National de la Recherche Agronomique (INRA), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE)
Subjects: 0106 biological sciences, coalescence, spatial and temporal heterogeneities, isolation by distance, Biology, Bioinformatics, 010603 evolutionary biology, 01 natural sciences, Coalescent theory, 03 medical and health sciences, Statistics, Genetics, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Isolation by distance, 0303 health sciences, Computer program, simulation, [SDE.BE.GP]Environmental Sciences/Biodiversity and Ecology/domain_sde.be.gp, [SDE]Environmental Sciences, microsatellite DNA, Biological dispersal, dispersal distribution, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Biotechnology, Test data
Abstract: COMPUTER PROGRAMS; International audience; IBDSim is a package for the simulation of genotypic data under isolation by distance. It is based on a backward 'generation by generation' coalescent algorithm allowing the consideration of various isolation by distance models with discrete subpopulations as well as continuous populations. Many dispersal distributions can be considered as well as heterogeneities in space and time of the demographic parameters. Typical applications of our program include (i) the study of the effect of various sampling, mutational and demographic factors on the pattern of genetic variation; and (ii) the production of test data sets to assess the influence of these factors on inferential methods available to analyse genotypic data.
Published: 2009
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47. Blacktip reef sharks, Carcharhinus melanopterus, have high genetic structure and varying demographic histories in their Indo-Pacific range: Blacktip reef sharks, Carcharhinus melanopterus, have high genetic structure and varying demographic histories in their Indo-Pacific range

Author: Eric Clua, Raphaël Leblois, Valentina Neglia, Johann Mourier, Jeffrey Maynard, Thomas Vignaud, Julia L.Y. Spaet, Serge Planes, Centre de recherches insulaires et observatoire de l'environnement (CRIOBE), Université de Perpignan Via Domitia (UPVD)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Department of Ecology and Evolutionary Biology, Cornell University [New York], 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), King Abdullah University of Science and Technology (KAUST), Ministère de l'Agriculture, de l'Alimentation, de la Pêche, de la ruralité et de l'Aménagement du territoire (MAAPRAT), Labex CORAIL, Ministère de l’Ecologie du Développement Durable et de l’Energie, Ministère de l’Outre Mer, Fonds Pacifique, IFRECOR, Délégation à la recherche de Polynésie, Agence Nationale de la Recherche, Institut National de Recherche en Agronomie, and Marie Curie Actions Fellowship
Subjects: Range (biology), [SDV]Life Sciences [q-bio], Population, Library science, French Polynesia, Biology, Pacific ocean, DNA, Mitochondrial, microsatellites, Polynesia, Marie curie, Evolution, Molecular, Genetics, genetic structure, Animals, 14. Life underwater, education, Indian Ocean, Ecology, Evolution, Behavior and Systematics, blacktip reef sharks, education.field_of_study, Pacific Ocean, Carcharhinus melanopterus, Coral Reefs, Australia, population genetics, Genetic Variation, Sequence Analysis, DNA, biology.organism_classification, demographic history, Fishery, Indian ocean, Genetics, Population, Haplotypes, Genetic structure, Sharks, Indo-Pacific, Microsatellite Repeats
Abstract: Times Cited: 0 0; International audience; For free-swimming marine species like sharks, only population genetics and demographic history analyses can be used to assess population health/status as baseline population numbers are usually unknown. We investigated the population genetics of blacktip reef sharks, Carcharhinus melanopterus; one of the most abundant reef-associated sharks and the apex predator of many shallow water reefs of the Indian and Pacific Oceans. Our sampling includes 4 widely separated locations in the Indo-Pacific and 11 islands in French Polynesia with different levels of coastal development. Four-teen microsatellite loci were analysed for samples from all locations and two mitochondrial DNA fragments, the control region and cytochrome b, were examined for 10 locations. For microsatellites, genetic diversity is higher for the locations in the large open systems of the Red Sea and Australia than for the fragmented habitat of the smaller islands of French Polynesia. Strong significant structure was found for distant locations with F-ST values as high as similar to 0.3, and a smaller but still significant structure is found within French Polynesia. Both mitochondrial genes show only a few mutations across the sequences with a dominant shared haplotype in French Polynesia and New Caledonia suggesting a common lineage different to that of East Australia. Demographic history analyses indicate population expansions in the Red Sea and Australia that may coincide with sea level changes after climatic events. Expansions and flat signals are indicated for French Polynesia as well as a significant recent bottleneck for Moorea, the most human-impacted lagoon of the locations in French Polynesia.
Published: 2014
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48. DIYABC v2.0: a software to make approximate Bayesian computation inferences about population history using single nucleotide polymorphism, DNA sequence and microsatellite data

Author: Arnaud Estoup, Raphaël Leblois, Pierre Pudlo, Julien Veyssier, Jean-Marie Cornuet, Jean-Michel Marin, Mathieu Gautier, Alexandre Dehne-Garcia, 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), Institut de Mathématiques et de Modélisation de Montpellier (I3M), Centre National de la Recherche Scientifique (CNRS)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM), Institut de Biologie Computationnelle (IBC), 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), Laboratoire de Mathématiques Appliquées de Bordeaux (MAB), Centre National de la Recherche Scientifique (CNRS)-Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1, Institut de biologie et chimie des protéines [Lyon] (IBCP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Mathématiques Appliquées (MAB), Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1-Centre National de la Recherche Scientifique (CNRS), 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), and Université Bordeaux Segalen - Bordeaux 2-Université Sciences et Technologies - Bordeaux 1 (UB)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Statistics and Probability, Theoretical computer science, Computer science, Population, Single-nucleotide polymorphism, Locus (genetics), computer.software_genre, Polymorphism, Single Nucleotide, Biochemistry, DNA sequencing, Software, [MATH.MATH-ST]Mathematics [math]/Statistics [math.ST], evolution, Genetics, Humans, education, Molecular Biology, education.field_of_study, business.industry, Dna polymorphism, Computational Biology, Bayes Theorem, Sequence Analysis, DNA, Computer Science Applications, Computational Mathematics, Genetics, Population, Computational Theory and Mathematics, Microsoft Windows, Microsatellite, Data mining, Approximate Bayesian computation, business, computer, Microsatellite Repeats, Model
Abstract: Motivation: DIYABC is a software package for a comprehensive analysis of population history using approximate Bayesian computation on DNA polymorphism data. Version 2.0 implements a number of new features and analytical methods. It allows (i) the analysis of single nucleotide polymorphism data at large number of loci, apart from microsatellite and DNA sequence data, (ii) efficient Bayesian model choice using linear discriminant analysis on summary statistics and (iii) the serial launching of multiple post-processing analyses. DIYABC v2.0 also includes a user-friendly graphical interface with various new options. It can be run on three operating systems: GNU/Linux, Microsoft Windows and Apple Os X. Availability: Freely available with a detailed notice document and example projects to academic users at http://www1.montpellier.inra.fr/CBGP/diyabc Contact: estoup@supagro.inra.fr Supplementary information: Supplementary data are available at Bioinformatics online.
Published: 2014
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49. Genetic structure of populations of whale sharks among ocean basins and evidence for their historic rise and recent decline

Author: Michael L. Berumen, Thomas Vignaud, Champak Reddy Beeravolu, Serge Planes, Simon J. Pierce, Sandra Baksay, Ricardo Vázquez-Juárez, Dení Ramírez-Macías, Raphaël Leblois, Mark G. Meekan, David Rowat, Jeffrey Maynard, Laboratoire d'excellence 'CORAIL', Centre de recherches insulaires et observatoire de l'environnement (CRIOBE), Université de Perpignan Via Domitia (UPVD)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Cornell University, Origine, structure et évolution de la biodiversité (OSEB), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Australian Institute of Marine Science [Perth] (AIMS Perth), Australian Institute of Marine Science (AIMS), centro de Investigaciones Biologicas Del Noroeste, Department of Plant Production (University of Milan), University of Milan, Marine Conservation Society Seychelles, Biology Department (WHOI), Woods Hole Oceanographic Institution (WHOI), Laboratoire d'Excellence CORAIL (LabEX CORAIL), Université des Antilles (UA)-Institut d'écologie et environnement-Université de la Nouvelle-Calédonie (UNC)-Université de la Polynésie Française (UPF)-Université de La Réunion (UR)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École des hautes études en sciences sociales (EHESS)-Université des Antilles et de la Guyane (UAG)-Institut de Recherche pour le Développement (IRD), Department of Ecology and Evolutionary Biology, Cornell University [New York], 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), The UWA Oceans Institute, Centro de Investigaciones Biologicas del Noroeste [Mexico] (CONACYT-CIBNOR), Consejo Nacional de Ciencia y Tecnología [Mexico] (CONACYT), Tiburon Ballena Mexico Proyecto Conciencia Mexico, Partenaires INRAE, Marine Megafauna Foundation, Wild Me, King Abdullah University of Science and Technology (KAUST), Labex CORAIL, Ministere de l'Ecologie du Developpement Durable et de l'Energie, Ministere de l'Outre Mer, Fonds Pacifique, IFRECOR, Delegation a la recherche de Polynesie, Agence Nationale de la Recherche, Institut National de Recherche en Agronomie, King Abdullah University of Science and Technology, Apache Energy Ltd, SeaWorld Research, Rescue Foundation Inc, Save our Seas Foundation, Australian Institute of Marine Science, Western Australian Department of Parks and Wildlife, EMARNAT-CONACYT, Whale Shark Mexico, Shark Foundation, Rufford Small Grant Foundation, and PADI Foundation
Subjects: molecular ecology mtDNA, Demographic history, Range (biology), Oceans and Seas, [SDV]Life Sciences [q-bio], Population, population expansion, Metapopulation, DNA, Mitochondrial, microsatellites, Genetic drift, biology.animal, Genetics, Animals, 14. Life underwater, education, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, education.field_of_study, biology, Ecology, Whale, Australia, Genetic Variation, Sequence Analysis, DNA, genetic diversity, demographic history, Fishery, Genetics, Population, Haplotypes, Rhincodon typus, Genetic structure, Sharks, Biological dispersal, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, human activities, Microsatellite Repeats
Abstract: International audience; This study presents genetic evidence that whale sharks, Rhincodon typus, are comprised of at least two populations that rarely mix and is the first to document a population expansion. Relatively high genetic structure is found when comparing sharks from the Gulf of Mexico with sharks from the Indo-Pacific. If mixing occurs between the Indian and Atlantic Oceans, it is not sufficient to counter genetic drift. This suggests whale sharks are not all part of a single global metapopulation. The significant population expansion we found was indicated by both microsatellite and mitochondrial DNA. The expansion may have happened during the Holocene, when tropical species could expand their range due to sea-level rise, eliminating dispersal barriers and increasing plankton productivity. However, the historic trend of population increase may have reversed recently. Declines in genetic diversity are found for 6 consecutive years at Ningaloo Reef in Australia. The declines in genetic diversity being seen now in Australia may be due to commercial-scale harvesting of whale sharks and collision with boats in past decades in other countries in the Indo-Pacific. The study findings have implications for models of population connectivity for whale sharks and advocate for continued focus on effective protection of the world's largest fish at multiple spatial scales.
Published: 2014
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50. Empirical likelihood for Bayesian inference in population genetics

Author: Pierre Pudlo, Raphaël Leblois, Christian Robert, Institut de Mathématiques et de Modélisation de Montpellier (I3M), Centre National de la Recherche Scientifique (CNRS)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM), 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, and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)
Subjects: [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], ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2012

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