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1. Effect of landscape structure on genetic structure of the Lesser horseshoe bat (Rhinolophus hipposideros) in Britanny colonies

Author

Eric J. Petit and Alexandra Rodriguez

Subjects
Geography, biology, Ecology, Rhinolophus hipposideros, Genetic structure, Biological dispersal, Population genetics, Landscape ecology, Hipposideros, biology.organism_classification, Horseshoe bat, Isolation by distance
Abstract

Some species are difficult to observe and others, need to be not disturbed because of their vulnerability. In response to the difficulty of studying the dispersal behaviors of these species, some areas of biology have been combined in order to access the information despite practical limitations. Here we present the combination of several methodologies from landscape ecology to non- invasive population genetics that allow us to obtain important information onRinolophus hipposideros, a vulnerable European bat. We genotyped 18 georeferrenced colonies in Brittany (France) from droppings collected in their refuges. We used 6 microsatellite markers in order to obtain the genetic distances between them. On the other hand we calculated Euclidian distances between the refuges occupied by these colonies and some ecological distances with the Pathmatrix module of ArcGis 3.2. We tested hypothesis about the difficulty of dispersal of the species in areas without forest cover or with a low density of hedges. Thanks to the Monmonier algorithm we could infer possible genetic barriers between the colonies and we could compare their location to the presence of landscape barriers (areas with little tree cover). We detected a pattern of isolation by distance that reveals limited dispersal capacities in the species but no pattern linked to ecological distances. We found that some of the neighboring colonies with greater genetic distances between them were located in areas with low density of hedges which could suggest an impact of this landscape element in their movements. Finer studies should allow us to conclude on the need or not of forest cover in the dispersal of this species.Abstract Figure

Published
2021

2. A multiscale analysis of landscape resistance reveals genetic isolates in an endangered forest-specialist species the Barbary macaque (Macaca sylvanus)

Author

Dominique Vallet, Eric J. Petit, Mohamed Qarro, Aude Ernoult, Yann Rantier, Pascaline Le Gouar, Stéphane Dréano, Nelly Ménard, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Station Biologique de Paimpont CNRS UMR 6653 (OSUR), Université de Rennes 1 (UR1), Écologie et santé des écosystèmes (ESE), AGROCAMPUS OUEST, 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), Institut de Génétique et Développement de Rennes (IGDR), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Ecole Nationale Forestière d'Ingénieurs du Maroc [Salé] (ENFI), contrat 'Service Provincial des Eaux et Forêts d'Ifrane(Maroc)/University of Rennes 1', Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-AGROCAMPUS OUEST, 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), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Université de Rennes (UR), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, and Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )

Subjects
0106 biological sciences, Primate conservation, Population, Endangered species, 010603 evolutionary biology, 01 natural sciences, Macaque, Landscape genetics, 03 medical and health sciences, biology.animal, Genetic erosion, education, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Nature and Landscape Conservation, Isolation by distance, Isolation by resistance, 0303 health sciences, education.field_of_study, biology, Ecology, Macaca sylvanus, Landscape heterogeneity, Dispersal, 15. Life on land, biology.organism_classification, Gene flow, Genetic structure, Biological dispersal, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract

International audience; In forest-specialist mammals, forest loss may induce resistance to animal movement and reduce gene flow between populations, and thereby increase genetic erosion and extinction risks for populations. Understanding how landscape features affect gene flow is of critical importance for conservation. Using landscape genetic tools at multiple spatial scales, we assessed the effects of landscape heterogeneity (in particular the presence of wide open or rural habitats) on gene flow in an endangered forest-specialist species – the Barbary macaque (Macaca sylvanus) –, in its major forest site in Morocco. We genotyped 248 individuals from 23 macaque groups using 11 microsatellite loci. We modelled different scenarios of isolation by landscape resistance. We further tested the relationships between genetic distance and isolation by resistance, after controlling for the effect of isolation by distance. Our results revealed a significant genetic structure and a disruption of gene flow even in geographic proximity. Whatever the spatial scale, remoteness from the forest edge beyond 1km acted as a barrier to macaque movements. In addition, at a fine scale, human-dominated areas were also detected as a barrier. The detection of private alleles in each population suggests an ongoing process of isolation. The preservation of the Barbary macaque implies 1) strictly avoiding all silvicultural practices (in particular clear-cutting of holm oak forests) that could contribute to increase distances between forest patches, 2) restoring corridors between forests, 3) and preserving key small forest patches as potential stepping stones facilitating macaque dispersal.

Published
2021

3. Genetic diversity in a long‐lived mammal is explained by the past’s demographic shadow and current connectivity

Author

Pierrette Nyssen, Sébastien J. Puechmaille, Damien Fourcy, Lisa Lehnen, Martin Biedermann, Wigbert Schorcht, Eric J. Petit, Gerald Kerth, Pierre-Loup Jan, Anne-Laure Besnard, Universität Greifswald - University of Greifswald, Écologie et santé des écosystèmes (ESE), AGROCAMPUS OUEST, 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), Interessengemeinschaft für Fledermausschutz und -forschung in Thüringen (IFT) e.V, Natagora (Association), Partenaires INRAE, Nachtaktiv Biologists Bat Res GbR, Erfurt, 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 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 de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, 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)-École Pratique des Hautes Études (EPHE)

Subjects
0106 biological sciences, bottleneck, Conservation of Natural Resources, Range (biology), Context (language use), Biology, 010603 evolutionary biology, 01 natural sciences, Bottleneck, 03 medical and health sciences, Genetics, Animals, Ecology, Evolution, Behavior and Systematics, Ecosystem, 030304 developmental biology, Isolation by distance, Mammals, Population Density, isolation-by-distance, 0303 health sciences, Genetic diversity, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Ecology, Population size, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], conservation, Genetic Variation, Global change, genetic diversity, 15. Life on land, respiratory system, Genetics, Population, 13. Climate action, connectivity, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Scale (map), human activities, Microsatellite Repeats
Abstract

International audience; Within-species genetic diversity is crucial for the persistence and integrity of populations and ecosystems. Conservation actions require an understanding of factors influencing genetic diversity, especially in the context of global change. Both population size and connectivity are factors greatly influencing genetic diversity; the relative importance of these factors can, however, change through time. Hence, quantifying the degree to which population size or genetic connectivity are shaping genetic diversity, and at which ecological time scale (past or present), is challenging, yet essential for the development of efficient conservation strategies. In this study, we estimated the genetic diversity of 42 colonies of Rhinolophus hipposideros, a long-lived mammal vulnerable to global change, sampling locations spanning its continental northern range. Here, we present an integrative approach that disentangles and quantifies the contribution of different connectivity measures in addition to contemporary colony size and historic bottlenecks in shaping genetic diversity. In our study, the best model explained 64% of the variation in genetic diversity. It included historic bottlenecks, contemporary colony size, connectivity and a negative interaction between the latter two. Contemporary connectivity explained most genetic diversity when considering a 65 km radius around the focal colonies, emphasizing the large geographic scale at which the positive impact of connectivity on genetic diversity is most profound and hence, the minimum scale at which conservation should be planned. Our results highlight that the relative importance of the two main factors shaping genetic diversity varies through time, emphasizing the relevance of disentangling them to ensure appropriate conservation strategies.

Published
2021

4. Genetic drift during the spread phase of a biological invasion

Author

Adrien Oger, Jean-Marc Paillisson, Nadège Bélouard, Anne-Laure Besnard, Eric J. Petit, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Écologie et santé des écosystèmes (ESE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, 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), Ministère de l'Education Nationale, de l'Enseignement Supérieur et de la Recherche, Agence française pour la biodiversité, Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Centre National de la Recherche Scientifique (CNRS), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), and Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Gene Flow, Male, 0106 biological sciences, 0301 basic medicine, Range (biology), range edge, Context (language use), Astacoidea, Biology, 010603 evolutionary biology, 01 natural sciences, Gene flow, 03 medical and health sciences, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Gene Frequency, Genetic drift, Effective population size, Genetics, Animals, 14. Life underwater, range expansion, Ecosystem, Ecology, Evolution, Behavior and Systematics, Genetic diversity, Ecology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Genetic Drift, landscape genetics, 15. Life on land, colonization, Genetics, Population, 030104 developmental biology, Wetlands, red swamp crayfish, Spatial ecology, Biological dispersal, Female, France, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, effective population size
Abstract

International audience; Recent theoretical and experimental models have revealed the role played by evolution during species spread, and in particular have questioned the influence of genetic drift at range edges. By investigating the spread of an aquatic invader in patchy habitats, we quantified genetic drift and explored its consequences for genetic diversity and fitness. We examined the interplay of gene flow and genetic drift in 36 populations of the red swamp crayfish, Procambarus clarkii, in a relatively recently invaded wetland area (30 years, Brière, northwest France). Despite the small spatial scale of our study (15 km ), populations were highly structured according to the strong barrier of land surfaces and revealed a clear pattern of colonization through watercourses. Isolated populations exhibited small effective sizes and low dispersal rates that depended on water connectivity, suggesting that genetic drift dominated in the evolution of allele frequencies in these populations. We also observed a significant decrease in the genetic diversity of isolated populations over only a 2-year period, but failed to demonstrate an associated fitness cost using fluctuating asymmetry. This study documents the possible strong influence of genetic drift during the spread of a species, and such findings provide critical insights into the current context of profound rearrangements in species distributions due to global change.

Published
2019

5. Longitudinal comparative transcriptomics reveals unique mechanisms underlying extended healthspan in bats

Author

Nicole M. Foley, Conor V. Whelan, Zixia Huang, Emma C. Teeling, David Jebb, Frédéric Touzalin, Sébastien J. Puechmaille, Eric J. Petit, School of Biology and Environmental Science, Science Centre West, University College Dublin [Dublin] (UCD), Brest, Bretagne Vivante - Société pour l'Etude et la Protection de la Nature en Bretagne (SEPNB), Écologie et santé des écosystèmes (ESE), AGROCAMPUS OUEST, 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), 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, Zoological Institute and Museum, Universität Greifswald - University of Greifswald, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-AGROCAMPUS OUEST, 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 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 de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, 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
0301 basic medicine, Candidate gene, [SDV]Life Sciences [q-bio], media_common.quotation_subject, defines, ved/biology.organism_classification_rank.species, Myotis myotis, Biology, Novel gene, Transcriptome, 03 medical and health sciences, 0302 clinical medicine, longevity, Chiroptera, microRNA, Animals, Humans, cancer, Longitudinal Studies, Model organism, database, Ecology, Evolution, Behavior and Systematics, media_common, Mammals, life-span, Ecology, ved/biology, Longevity, alignment, biology.organism_classification, gene-expression, pten, 030104 developmental biology, Evolutionary biology, Ageing, 030220 oncology & carcinogenesis, protein
Abstract

Bats are the longest-lived mammals, given their body size. However, the underlying molecular mechanisms of their extended healthspans are poorly understood. To address this question we carried out an eight-year longitudinal study of ageing in long-lived bats (Myotis myotis). We deep-sequenced ~1.7 trillion base pairs of RNA from 150 blood samples collected from known aged bats to ascertain the age-related transcriptomic shifts and potential microRNA-directed regulation that occurred. We also compared ageing transcriptomic profiles between bats and other mammals by analysis of 298 longitudinal RNA sequencing datasets. Bats did not show the same transcriptomic changes with age as commonly observed in humans and other mammals, but rather exhibited a unique, age-related gene expression pattern associated with DNA repair, autophagy, immunity and tumour suppression that may drive their extended healthspans. We show that bats have naturally evolved transcriptomic signatures that are known to extend lifespan in model organisms, and identify novel genes not yet implicated in healthy ageing. We further show that bats’ longevity profiles are partially regulated by microRNA, thus providing novel regulatory targets and pathways for future ageing intervention studies. These results further disentangle the ageing process by highlighting which ageing pathways contribute most to healthy ageing in mammals. RNA-Seq analysis of an 8-year longitudinal study of long-lived bats reveals unique transcriptomic signatures and novel candidate genes associated with healthy ageing.

Published
2019

6. Least cost path analysis for urban greenways planning: a test with moths and birds across two habitats and two cities

Author

Aude Ernoult, Luc Madec, Eric J. Petit, Romain Georges, Alain Butet, Solene Croci, Jean-Pierre Caudal, Manon Balbi, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Littoral, Environnement, Télédétection, Géomatique (LETG - Rennes), Littoral, Environnement, Télédétection, Géomatique UMR 6554 (LETG), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Université d'Angers (UA)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Brest (UBO)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut de Géographie et d'Aménagement Régional de l'Université de Nantes (IGARUN), Université de Nantes (UN)-Université de Nantes (UN)-Université de Caen Normandie (UNICAEN), Université de Nantes (UN)-Université de Nantes (UN), Écologie et santé des écosystèmes (ESE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, 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), Région Hauts‐de‐France, Région Bretagne, Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Normandie Université (NU)-Normandie Université (NU)-Université d'Angers (UA)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Brest (UBO)-Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Géographie et d'Aménagement Régional de l'Université de Nantes (IGARUN), AGROCAMPUS OUEST, 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), Littoral, Environnement, Télédétection, Géomatique (LETG - Nantes), 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 Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Université de Brest (UBO)-Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut de Géographie et d'Aménagement (IGARUN), and Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-AGROCAMPUS OUEST

Subjects
0106 biological sciences, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, Ecology, biology, Resistance (ecology), business.industry, Movement (music), Seven Management and Planning Tools, 010604 marine biology & hydrobiology, [SDV]Life Sciences [q-bio], Environmental resource management, Fragmentation (computing), 15. Life on land, 010603 evolutionary biology, 01 natural sciences, Passerine, Test (assessment), Geography, Habitat, biology.animal, 11. Sustainability, Green infrastructure, business
Abstract

International audience; 1.One of the major planning tools to respond to urban landscape fragmentation is the development of ecological corridors, that is, interconnected networks of urban green and blue spaces. Least‐cost paths (LCP) appear to be an easy and appropriate resistance‐based modelling method to respond to urban planners’ needs. However, the ecological validation of urban corridors using LCP is rarely performed and needs to be generalized to different species, habitats and cities.2.We developed an experimental design to test the efficiency of LCP predictions to detect highly connecting landscape contexts that facilitate individual movements compared to movements in less connecting landscape contexts. We deliberately assigned LCP analysis parameters based on the scientific literature and expert knowledge to test a method potentially easy to use for urban stakeholders. To extend the validation, we applied our LCP model to two biological taxa with different habitat requirements: grassland‐dwelling moths and forest‐dwelling passerines, and to two medium‐sized cities.3.We used mark–release–recapture (MRR) methods for moths and playback recall protocols for passerines to compare the patterns of individual movement between two contrasted connectivity contexts determined by the presence and absence of modelled LCPs. MRR protocol estimated movement rates between herbaceous patches and the two contrasted connectivity contexts. Playback recall protocol consisted in attracting individuals from wooded patches to the two contrasted connectivity contexts. A movement was considered facilitated, when displacement was rapidly engaged and individuals moved a long distance from their wooded patch.4.Moth and passerine movement patterns differed between the two connectivity contexts: moth recapture rates were higher in highly connecting contexts than in less connecting contexts. For passerine birds, responses to playback recalls were faster and movement distance longer in highly connecting contexts. All results support the hypothesis that both taxa were more prone to move in corridors modelled by LCP.5.Synthesis and applications. The convergence of the results for different biological models and across cities strengthens the relevance of LCP analysis for planning urban greenways and provides guidelines for landscape planners in the development of these corridors to favour the movement and survival of multiple urban species.

Published
2021

7. Complementarity and discriminatory power of genotype and otolith shape in describing the fine-scale population structure of an exploited fish, the common sole of the Eastern English Channel

Author

Thomas Le Berre, Elodie Réveillac, Bruno Ernande, Gilles Lassalle, Olivier Le Pape, Kelig Mahe, Marine Randon, Eric J. Petit, Filip Volckaert, Simon Fraser University (SFU.ca), Écologie et santé des écosystèmes (ESE), AGROCAMPUS OUEST, 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), Sclerochronology Centre, Laboratoire Ressources halieutiques, Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), International Institute for Applied Systems Analysis [Laxenburg] (IIASA), LIttoral ENvironnement et Sociétés - UMRi 7266 (LIENSs), and Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, Evolutionary Genetics, Single Nucleotide Polymorphisms, Population Dynamics, Population genetics, Marine and Aquatic Sciences, 01 natural sciences, Otolith, Mathematical and Statistical Techniques, Medicine and Health Sciences, Marine Fish, education.field_of_study, Multidisciplinary, biology, Fourier Analysis, Geography, Eukaryota, Discriminant Analysis, Multidisciplinary Sciences, medicine.anatomical_structure, Inner Ear, Vertebrates, Flatfishes, Medicine, Science & Technology - Other Topics, STOCK DISCRIMINATION, SPATIAL STRUCTURE, Anatomy, EMPIRICAL-EVALUATION, Research Article, Common sole, Genotype, NORTHEAST ATLANTIC, Science, Population, Metapopulation, Marine Biology, Research and Analysis Methods, 010603 evolutionary biology, Otolithic Membrane, medicine, Genetics, ATLANTIC COD, GENE FLOW, Animals, 14. Life underwater, education, MARINE FISHES, Probability, Evolutionary Biology, Analysis of Variance, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Science & Technology, Population Biology, Human evolutionary genetics, 010604 marine biology & hydrobiology, R-PACKAGE, Organisms, Biology and Life Sciences, biology.organism_classification, United Kingdom, Fish, Evolutionary biology, Ears, Complementarity (molecular biology), Spatial ecology, Earth Sciences, Genetic Polymorphism, FOURIER-ANALYSIS, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, LARVAL DRIFT, Head, Zoology, Population Genetics
Abstract

Marine organisms show population structure at a relatively fine spatial scale, even in open habitats. The tools commonly used to assess subtle patterns of connectivity have diverse levels of resolution and can complement each other to inform on population structure. We assessed and compared the discriminatory power of genetic markers and otolith shape to reveal the population structure on evolutionary and ecological time scales of the common sole (Solea solea), living in the Eastern English Channel (EEC) stock off France and the UK. First, we genotyped fish with Single Nucleotide Polymorphisms to assess population structure at an evolutionary scale. Then, we tested for spatial segregation of the subunits using otolith shape as an integrative tracer of life history. Finally, a supervised machine learning framework was applied to genotypes and otolith phenotypes to probabilistically assign adults to subunits and assess the discriminatory power of each approach. Low but significant genetic differentiation was found among subunits. Moreover, otolith shape appeared to vary spatially, suggesting spatial population structure at fine spatial scale. However, results of the supervised discriminant analyses failed to discriminate among subunits, especially for otolith shape. We suggest that the degree of population segregation may not be strong enough to allow for robust fish assignments. Finally, this study revealed a weak yet existing metapopulation structure of common sole at the fine spatial scale of the EEC based on genotypes and otolith shape, with one subunit being more isolated. Our study argues for the use of complementary tracers to investigate marine population structure. ispartof: PLOS ONE vol:15 issue:11 ispartof: location:United States status: published

Published
2020

8. Drivers of longitudinal telomere dynamics in a long‐lived bat species, Myotis myotis

Author

Nicole M. Foley, Eric J. Petit, Thomas Brazier, Sébastien J. Puechmaille, Graham M. Hughes, John A. Finarelli, Emma C. Teeling, Frédéric Touzalin, University College Dublin [Dublin] (UCD), Écologie et santé des écosystèmes (ESE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-AGROCAMPUS OUEST, 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), Ernst-Moritz-Arndt-Universität Greifswald, 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, AGROCAMPUS OUEST, 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, longitudinal data, Range (biology), Population, bats, Myotis myotis, Biology, Genus Myotis, heritability, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Chiroptera, Genotype, Genetics, telomere length, Animals, Humans, education, Child, Ecology, Evolution, Behavior and Systematics, Telomere Shortening, education.field_of_study, Infant, Newborn, conservation, Infant, Bayes Theorem, Heritability, Telomere, biology.organism_classification, 030104 developmental biology, Cross-Sectional Studies, climate change, Ageing, Evolutionary biology, Child, Preschool, [SDE]Environmental Sciences, France, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract

International audience; ge-related telomere shortening is considered a hallmark of the ageing process. However, a recent cross-sectional ageing study of relative telomere length (rTL) in bats failed to detect a relationship between rTL and age in the long-lived genus Myotis (M. myotis and M. bechsteinii), suggesting some other factors are responsible for driving telomere dynamics in these species. Here, we test if longitudinal rTL data show signatures of age-associated telomere attrition in M. myotis and differentiate which intrinsic or extrinsic factors are likely to drive telomere length dynamics. Using quantitative polymerase chain reaction, rTL was measured in 504 samples from a marked population, from Brittany, France, captured between 2013 and 2016. These represent 174 individuals with an age range of 0 to 7+ years. We find no significant relationship between rTL and age (p = .762), but demonstrate that within-individual rTL is highly variable from year to year. To investigate the heritability of rTL, a population pedigree (n = 1744) was constructed from genotype data generated from a 16-microsatellite multiplex, designed from an initial, low-coverage, Illumina genome for M. myotis. Heritability was estimated in a Bayesian, mixed model framework, and showed that little of the observed variance in rTL is heritable (h(2) = 0.01-0.06). Rather, correlations of first differences, correlating yearly changes in telomere length and weather variables, demonstrate that, during the spring transition, average temperature, minimum temperature, rainfall and windspeed correlate with changes in longitudinal telomere dynamics. As such, rTL may represent a useful biomarker to quantify the physiological impact of various environmental stressors in bats.

Published
2020

9. Population-level sensitivity to landscape variables reflects individual-based habitat selection in a woodland bat species

Author

Pierre-Loup Jan, Sébastien J. Puechmaille, Olivier Farcy, Damien Fourcy, Alice Baudouin, Josselin Boireau, Pascaline Le Gouar, Diane Zarzoso-Lacoste, and Eric J. Petit

Subjects
education.field_of_study, Habitat fragmentation, biology, Ecology, Population size, Rhinolophus hipposideros, Population, Foraging, Woodland, Horseshoe bat, biology.organism_classification, Geography, Habitat, education
Abstract

Understanding the relationship between habitat quality and population dynamics is fundamental for long-term management and range predictions in ecology. However, habitat quality is generally only investigated at the individual scale, as it is the case for the lesser horseshoe bat (Rhinolophus hipposideros), a species of conservation concern. Using a statistical modelling approach and census data of 94 lesser horseshoe bat colonies located in Brittany (France), we analysed the effect of landscape composition and configuration on the demographic components of surveyed maternity colonies (i.e. colony size, fecundity and growth rate), and compared our result to those provided by individual-based studies. Our results validated that the landscape in a 500-meter buffer around colonies (core foraging area) is crucial for population size and dynamics, and confirmed the positive influence of broadleaved woodland proportion on bat colony size. We revealed a positive effect of lakeshores and riverbanks on colony size and growth rate, underlying the importance of these habitats for the long-term conservation of this non-migratory forest species. Importantly, our results refine previous knowledge concerning the threat posed by the intensification of human activities (e.g. urbanization, agriculture, habitat fragmentation), and highlight the negative effect of large and regular patches of artificial and crop lands and of open land patches shape complexity on all demographic variables investigated. While our results support the dependence of population dynamics and associated conservation management to individual behaviour and sensitivity, environmental responses differed between the population metrics investigated, showing that efficient range prediction will require to fully grasp the complexity of the interaction between landscape and the different population dynamic parameters.

Published
2019

10. Exploring the causes of small effective population sizes in cyst nematodes using artificial Globodera pallida populations

Author

Josselin Montarry, Sylvain Fournet, Pierre-Loup Jan, Eric J. Petit, Eric Grenier, Romain Mabon, Sylvie Bardou-Valette, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, 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), Unité Mixte de Recherche sur les Herbivores - UMR 1213 (UMRH), Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Écologie et santé des écosystèmes (ESE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut National de la Recherche Agronomique (INRA)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), and Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST

Subjects
0106 biological sciences, Evolution, nematode, [SDV]Life Sciences [q-bio], Population, Zoology, selection, Potato cyst nematode, 010603 evolutionary biology, 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, [SHS]Humanities and Social Sciences, 03 medical and health sciences, Effective population size, Genetic drift, medicine, Animals, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Cyst, [INFO]Computer Science [cs], Tylenchoidea, Globodera pallida, education, Selection (genetic algorithm), Plant Diseases, Solanum tuberosum, 030304 developmental biology, General Environmental Science, Population Density, 0303 health sciences, education.field_of_study, General Immunology and Microbiology, biology, General Medicine, biology.organism_classification, medicine.disease, plant resistance, Nematode, [SDE]Environmental Sciences, genetic drift, General Agricultural and Biological Sciences, effective population size
Abstract

The effective size of a population is the size of an ideal population which would undergo genetic drift at the same rate as the real population. The balance between selection and genetic drift depends on the effective population size (Ne), rather than the real numbers of individuals in the population (N). The objectives of the present study were to estimateNein the potato cyst nematodeGlobodera pallidaand to explore the causes of a lowNe/Nratio in cyst nematodes using artificial populations. Using a temporal analysis of 24 independent populations, the medianNewas 58 individuals (minNe= 25 and maxNe= 228).Neis commonly lower thanNbut in the case of cyst nematodes, theNe/Nratio was extremely low. Using artificial populations showed that this low ratio did not result from migration, selection and overlapping generations, but could be explain by the fact thatG. pallidapopulations deviate in structure from the assumptions of the ideal population by having unequal sex ratios, high levels of inbreeding and a high variance in family sizes. The consequences of a lowNe, resulting in a strong intensity of genetic drift, could be important for their control becauseG. pallidapopulations will have a low capacity to adapt to changing environments.

Published
2019

11. Range expansion is associated with increased survival and fecundity in a long-lived bat species

Author

Anne-Laure Besnard, Wigbert Schorcht, Eric J. Petit, Gerald Kerth, Pierre-Loup Jan, Martin Biedermann, Lisa Lehnen, Sébastien J. Puechmaille, P. Le Gouar, Écologie et santé des écosystèmes (ESE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Ernst-Moritz-Arndt-Universität Greifswald, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Centre National de la Recherche Scientifique (CNRS), École pratique des hautes études (EPHE), Office National des Forets (ONF), PROCOPE/DAAD programme [57211773], PROCOPE/PHC programme [35454SB], DFG (RESPONSE exchange grant), Deutsche Forschungsgemeinschaft, German Science Foundation DFG, Interessengemeinschaft Fledermausschutz & Forsch, Bad Liebenstein, Nachtaktiv Biologists Bat Res GbR, Erfurt, Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL), 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 National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)

Subjects
0106 biological sciences, life history, capture-mark-recapture, Range (biology), media_common.quotation_subject, Rhinolophus hipposideros, Population, Longevity, Population Dynamics, Zoology, Trade-off, 010603 evolutionary biology, 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Feces, Chiroptera, Germany, Population growth, Animals, education, Population Growth, range expansion, 030304 developmental biology, General Environmental Science, media_common, trade-off, 0303 health sciences, education.field_of_study, General Immunology and Microbiology, biology, Ecology, Reproduction, General Medicine, DNA, 15. Life on land, Fecundity, biology.organism_classification, Fertility, Habitat, Female, France, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, General Agricultural and Biological Sciences, Animal Distribution
Abstract

The speed and dynamics of range expansions shape species distributions and community composition. Despite the critical impact of population growth rates for range expansion, they are neglected in existing empirical studies, which focus on the investigation of selected life-history traits. Here, we present an approach based on non-invasive genetic capture–mark–recapture data for the estimation of adult survival, fecundity and juvenile survival, which determine population growth. We demonstrate the reliability of our method with simulated data, and use it to investigate life-history changes associated with range expansion in 35 colonies of the bat species Rhinolophus hipposideros . Comparing the demographic parameters inferred for 19 of those colonies which belong to an expanding population with those inferred for the remaining 16 colonies from a non-expanding population reveals that range expansion is associated with higher net reproduction. Juvenile survival was the main driver of the observed reproduction increase in this long-lived bat species with low per capita annual reproductive output. The higher average growth rate in the expanding population was not associated with a trade-off between increased reproduction and survival, suggesting that the observed increase in reproduction stems from a higher resource acquisition in the expanding population. Environmental conditions in the novel habitat hence seem to have an important influence on range expansion dynamics, and warrant further investigation for the management of range expansion in both native and invasive species.

Published
2019

12. Variable effects of an invasive species on the reproduction and distribution of native species in pond networks

Author

Nadège Bélouard, Jean-Marc Paillisson, Eric J. Petit, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Écologie et santé des écosystèmes (ESE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, 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), Ministere de l'Education Nationale, de l'Enseignement Superieur et de la Recherche, Agence francaise pour la biodiversite, Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Centre National de la Recherche Scientifique (CNRS), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), and Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, Amphibian, species coexistence, Zoology, Introduced species, Aquatic Science, larval densities, 010603 evolutionary biology, 01 natural sciences, Swamp, Invasive species, Predation, biology.animal, breeding habitat, 14. Life underwater, Procambarus clarkii, geography, geography.geographical_feature_category, amphibians, biology, 010604 marine biology & hydrobiology, 15. Life on land, biology.organism_classification, Crayfish, Habitat, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract

International audience; The arrival of non-native species in a community can be deleterious for native species. The joint investigation of several descriptors of native populations susceptible to invaders, under different invasion contexts, may help in predicting the outcome of their co-occurrence with invasive species. Moreover, empirical studies seldom document the relative importance of the effects of invasive species on native species compared with other factors. Using survey data, we evaluated whether reproduction (larval density) and distribution of breeding sites of three amphibian species (Rana dalmatina, Lissotriton helveticus, and Triturus marmoratus) were related to the presence of invasive red swamp crayfish Procambarus clarkii, compared to other native predators, habitat, and landscape features, in two pond networks that differed in invasion intensity. The red swamp crayfish was only negatively associated with the larval density of one amphibian species studied. Its effect size was similar to that of some native predators, and much smaller than that of the canopy cover of ponds. Amphibians were widespread in the two pond networks. The occupancy of only one species in each network was negatively related to crayfish presence, while the occupancy of all species was negatively related to fish presence. The distribution of amphibian breeding sites was positively associated with aquatic vegetation cover. Negative associations between amphibians and red swamp crayfish were detected only in a few cases, even in the most invaded area, and thus results were less alarming than in previous studies. Differences in ecological traits of native amphibians and interactions with other environmental factors may explain the variable effects of red swamp crayfish on native amphibian populations.

Published
2019

13. Coexistence of two sympatric cryptic bat species in French Guiana: insights from genetic, acoustic and ecological data

Author

Corinne Régis, Guillaume Queney, Dominique Pontier, Jean-Baptiste Pons, Lina Muselet, Cécile Kaerle, Elodie Portanier, Eric J. Petit, Damien M. de Vienne, Ondine Filippi-Codaccioni, David Fouchet, Marie-Pauline Beugin, Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Ecoépidémiologie évolutionniste, Département écologie évolutive [LBBE], Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Bioinformatique, phylogénie et génomique évolutive (BPGE), Département PEGASE [LBBE] (PEGASE), Ecologie et évolution des populations, Antagene - Animal Genomics Laboratory, Écologie et santé des écosystèmes (ESE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, 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 Lyon, ANR-11-LABX-0048, and ANR-11-IDEX-0007

Subjects
0106 biological sciences, 0301 basic medicine, Population genetics, 01 natural sciences, Haplogroup, Chiroptera, Phylogeny, education.field_of_study, biology, Reproduction, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Reproductive isolation, Mitochondrial DNA, French Guiana, Pteronotus cf, Sympatry, Genetic structure, Pteronotus cf. parnellii, Research Article, Species complex, Neotropics, Genotype, Evolution, Population, Introgression, 010603 evolutionary biology, 03 medical and health sciences, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Species Specificity, Pteronotus, [SDV.BA.ZV]Life Sciences [q-bio]/Animal biology/Vertebrate Zoology, QH359-425, otorhinolaryngologic diseases, Animals, parnellii, Microsatellite, Echolocation, Asymmetric introgression, education, Ecosystem, Ecology, Evolution, Behavior and Systematics, Cell Nucleus, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Acoustics, biology.organism_classification, [SDV.BA.ZI]Life Sciences [q-bio]/Animal biology/Invertebrate Zoology, 030104 developmental biology, Evolutionary biology, Microsatellite Repeats, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract

Background The distinction between lineages of neotropical bats from the Pteronotus parnellii species complex has been previously made according to mitochondrial DNA, and especially morphology and acoustics, in order to separate them into two species. In these studies, either sample sizes were too low when genetic and acoustic or morphological data were gathered on the same individuals, or genetic and other data were collected on different individuals. In this study, we intensively sampled bats in 4 caves and combined all approaches in order to analyse genetic, morphologic, and acoustic divergence between these lineages that live in the same caves in French Guiana. Results A multiplex of 20 polymorphic microsatellite markers was developed using the 454-pyrosequencing technique to investigate for the first time the extent of reproductive isolation between the two lineages and the population genetic structure within lineages. We genotyped 748 individuals sampled between 2010 and 2015 at the 20 nuclear microsatellite loci and sequenced a portion of the cytochrome c oxydase I gene in a subset of these. Two distinct, non-overlapping haplogroups corresponding to cryptic species P. alitonus and P. rubiginosus were revealed, in accordance with previous findings. No spatial genetic structure between caves was detected for both species. Hybridization appeared to be quite limited (0.1–4%) using microsatellite markers whereas introgression was more common (7.5%) and asymmetric for mitochondrial DNA (mtDNA). Conclusions The extremely low rate of hybridization could be explained by differences in life cycle phenology between species as well as morphological and acoustical distinction between sexes in one or the other species. Taken together, these results add to our growing understanding of the nature of species boundaries in Pteronotus parnelli, but deserve more in-depth studies to understand the evolutionary processes underlying asymmetric mtDNA introgression in this group of cryptic species. Electronic supplementary material The online version of this article (10.1186/s12862-018-1289-8) contains supplementary material, which is available to authorized users.

Published
2018

14. Genetic isolation by distance and landscape connectivity in the American marten ( Martes americana )

Author

John M. Fryxell, Nicolas Ray, Françoise Burel, Thomas Broquet, Eric J. Petit, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Computational and Molecular Population Genetics (CMPG), Universität Bern [Bern] (UNIBE), Ethologie, éVolution, Ecologie (EVE), Ethologie animale et humaine (EthoS), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS), Zoology Department University of Guelph, University of Guelph, Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Université de Bern, Normandie Université (NU)-Normandie Université (NU)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Université de Caen Normandie (UNICAEN), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), and Normandie Université (NU)-Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, [SDV]Life Sciences [q-bio], Geography, Planning and Development, Isolation by distance, 010603 evolutionary biology, 01 natural sciences, Landscape genetics, 03 medical and health sciences, Genetic model, Martes americana, Boreal forest, [SDU.ENVI]Sciences of the Universe [physics]/Continental interfaces, environment, 030304 developmental biology, Nature and Landscape Conservation, ddc:599.9, 0303 health sciences, Connectivity, Ecology, biology, Dispersal, 15. Life on land, biology.organism_classification, American marten, Geography, Genetic structure, Biological dispersal, Effective distance, Landscape ecology, Genetic isolate, Landscape connectivity
Abstract

International audience; Empirical studies of landscape connectivity are limited by the difficulty of directly measuring animal movement. ‘Indirect' approaches involving genetic analyses provide a complementary tool to ‘direct' methods such as capture–recapture or radio-tracking. Here the effect of landscape on dispersal was investigated in a forest-dwelling species, the American marten (Martes americana) using the genetic model of isolation by distance (IBD). This model assumes isotropic dispersal in a homogeneous environment and is characterized by increasing genetic differentiation among individuals separated by increasing geographic distances. The effect of landscape features on this genetic pattern was used to test for a departure from spatially homogeneous dispersal. This study was conducted on two populations in homogeneous vs. heterogeneous habitat in a harvested boreal forest in Ontario (Canada). A pattern of IBD was evidenced in the homogeneous landscape whereas no such pattern was found in the near-by harvested forest. To test whether landscape structure may be accountable for this difference, we used effective distances that take into account the effect of landscape features on marten movement instead of Euclidean distances in the model of isolation by distance. Effective distances computed using least-cost modeling were better correlated to genetic distances in both landscapes, thereby showing that the interaction between landscape features and dispersal in Martes americana may be detected through individual-based analyses of spatial genetic structure. However, the simplifying assumptions of genetic models and the low proportions in genetic differentiation explained by these models may limit their utility in quantifying the effect of landscape structure.

Published
2018

15. 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

16. Growing old, yet staying young:The role of telomeres in bats' exceptional longevity

Author

Olivier Farcy, Emma C. Teeling, Mike Clarke, Nicole M. Foley, Roger D. Ransome, Gareth Jones, Hugo Rebelo, David Jebb, Joanna Kacprzyk, Conor V. Whelan, Luísa Rodrigues, Sébastien J. Puechmaille, Mary J. O'Connell, Graham M. Hughes, Zixia Huang, Gerald Kerth, Eric J. Petit, Frédéric Touzalin, University College Dublin [Dublin] (UCD), Écologie et santé des écosystèmes (ESE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Evolution et Diversité Biologique (EDB), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Bretagne Vivante, School of Biological Sciences [Bristol], University of Bristol [Bristol], University of Leeds, Ernst-Moritz-Arndt-Universität Greifswald, Universidade do Porto [Porto], Universidade de Lisboa (ULISBOA), Instituto de Conservaçao da natureza e das Florestas, Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Universidade do Porto = University of Porto, Universidade de Lisboa = University of Lisbon (ULISBOA), ERC-2012-StG311000, 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 National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, and Universidade do Porto

Subjects
0301 basic medicine, Telomerase, animal structures, DNA repair, DNA damage, media_common.quotation_subject, Longevity, Myotis myotis, 03 medical and health sciences, 0302 clinical medicine, Species Specificity, Chiroptera, [SDV.BA.ZV]Life Sciences [q-bio]/Animal biology/Vertebrate Zoology, Genetics, Animals, Selection, Genetic, Gene, Research Articles, media_common, Multidisciplinary, biology, Body Weight, Rhinolophus ferrumequinum, SciAdv r-articles, Telomere, biology.organism_classification, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, 030104 developmental biology, Evolutionary biology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, 030217 neurology & neurosurgery, Research Article
Abstract

Telomeres do not shorten with age in longest-lived bats., Understanding aging is a grand challenge in biology. Exceptionally long-lived animals have mechanisms that underpin extreme longevity. Telomeres are protective nucleotide repeats on chromosome tips that shorten with cell division, potentially limiting life span. Bats are the longest-lived mammals for their size, but it is unknown whether their telomeres shorten. Using >60 years of cumulative mark-recapture field data, we show that telomeres shorten with age in Rhinolophus ferrumequinum and Miniopterus schreibersii, but not in the bat genus with greatest longevity, Myotis. As in humans, telomerase is not expressed in Myotis myotis blood or fibroblasts. Selection tests on telomere maintenance genes show that ATM and SETX, which repair and prevent DNA damage, potentially mediate telomere dynamics in Myotis bats. Twenty-one telomere maintenance genes are differentially expressed in Myotis, of which 14 are enriched for DNA repair, and 5 for alternative telomere-lengthening mechanisms. We demonstrate how telomeres, telomerase, and DNA repair genes have contributed to the evolution of exceptional longevity in Myotis bats, advancing our understanding of healthy aging.

Published
2018

17. A cost-and-time effective procedure to develop SNP markers for multiple species: A support for community genetics

Author

Guillaume Evanno, Marie Massot, Erwan Guichoux, Marie-Agnès Coutellec, Raphaelle Rinaldo, Guillaume Longin, Elodie Réveillac, Dominique Barloy, Adrien Oger, Adline Delcamp, Jean-Marc Roussel, Patricia Le Quilliec, Clémence Genthon, Eric J. Petit, Sophie Launey, Olivier Lorvelec, Regis Vigouroux, Gilles Lassalle, Pierre-Yves Le Bail, Chrystelle Delord, Écologie et santé des écosystèmes (ESE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Laboratoire-Environnement de Petit Saut, Hydreco, Biodiversité, Gènes et Communautés, Institut National de la Recherche Agronomique (INRA), GeT PlaGe, Genotoul, Laboratoire de Physiologie et Génomique des Poissons (LPGP), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de la Recherche Agronomique (INRA), Parc Amazonien de Guyane, Association Nationale de la Recherche et de la Technologie, Agence de l’Eau Seine Normandie, DREAL, Office de l’Eau de Guyane, 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), Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), Génome et Transcriptome - Plateforme Génomique (GeT-PlaGe), Institut National de la Recherche Agronomique (INRA)-Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut National de la Recherche Agronomique (INRA)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3)

Subjects
0301 basic medicine, genetical analysis, [SDV]Life Sciences [q-bio], Computational biology, Biology, marqueur, 03 medical and health sciences, étude comparative, Snp markers, Guiana shield fish, 14. Life underwater, nonmodel organisms, Ecology, Evolution, Behavior and Systematics, comparative study, marker, SNP development, comparative genetic studies, écologie animale, Ecological Modeling, Community genetics, pipeline, Multiple species, Pipeline (software), RAD-Seq, 030104 developmental biology, MassArray, community genetics, guyane française, animal ecology, espèce animale, analyse génétique
Abstract

Multispecies population genetics is an emerging field that provides insight relevant to conservation biology and community ecology. However, to date, this approach is limited to species with available genetic resources. The use of thousands of single-nucleotide polymorphism (SNP) markers developed from recent genotyping-by-sequencing (GBS) technologies is a roadmap for the study of nonmodel species, but remains cost prohibitive when several, distantly related species are involved. We aimed to overcome this issue using a single HiSeq3000 run of restriction-site associated DNA sequencing (RAD-Seq) to retrieve SNP markers for 40 diverse species including plants, invertebrates, fish, and mammals. We developed a Python-based pipeline to isolate c. 100–500 high-quality SNP markers for each species that could be genotyped through classical PCR amplification methods. To assess the quality of these markers, we validated our approach on c. 160 of the characterized SNPs for each of 18 Neotropical fish species from the river Maroni (French Guiana, South America), using the MassARRAY iPLEX platform from Agena Bioscience (San Diego, CA, USA). A run of the pipeline applying stringent filtering parameters enabled the successful design of between 130 and 3,492 SNP markers for 30 of the 40 study species. Relaxing pipeline parameters allows for an increase in the number of detected SNPs. Across the 18 species from French Guiana, an average of 85% of markers were successfully amplified, polymorphic, and scored in ≥90% of individuals (c. 200 individuals per species). The great majority (>98%) of these markers were at Hardy–Weinberg equilibrium in each sampling site from the river Maroni. This SNP discovery was performed at the cost of c. $US110 for each of the 40 species. Genotyping was performed at the cost of c. $US6000 for each of the 18 fish species with an average of 200 individuals per species. This strategy was found cost-and-time efficient to develop hundreds of SNP markers for a large range of nonmodel species, which can be used to investigate ecological and evolutionary questions that do not require whole-genome coverage.

Published
2018

18. Effective population size and durability of plant resistances in the potato cyst nematode Globodera pallida

Author

Eric J. Petit, Pierre-Loup Jan, Josselin Montarry, Eric Grenier, Sylvain Fournet, Sylvie Bardou-Valette, and Romain Mabon

Subjects
education.field_of_study, biology, Genetic drift, Agronomy, Effective population size, Population size, Population, Potato cyst nematode, Globodera pallida, biology.organism_classification, education, Inbreeding, Selection (genetic algorithm)
Abstract

SummaryThe effective size of a population is the size of an ideal population which would drift at the same rate as the real population. The balance between selection and genetic drift depends on the population size expressed as the genetically effective population size (Ne), rather than the real numbers of individuals in the population (N).The objectives of the present study were to estimate Nein the potato cyst nematodeGlobodera pallidausing artificial populations and to explore the link between Neand the durability of plant resistances.Using a temporal method on 24 independent pairs of initial and final populations, the median Newas 58 individuals.Neis commonly lower than N but in our case the Ne/N ratio was extremely low becauseG. pallidapopulations deviate in structure from the assumptions of the ideal population by having unequal sex-ratios, high levels of inbreeding and a high variance in family sizes. The consequences of a low Necould be important for the control of phytoparasitic nematodes becauseG. pallidapopulations will have a low capacity to adapt to changing environments unless selection intensity is very strong, which could be greatly beneficial for long-term use of plant resistances.

Published
2017
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19. The downside of eDNA as a survey tool in water bodies

Author

Eric J. Petit, Jean-Marc Roussel, Anne Tréguier, Jean-Marc Paillisson, Écologie et santé des écosystèmes (ESE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Pôle Gest'Aqua, Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Office national de l'eau et des milieux aquatiques (ONEMA), Ministère de l'écologie, du développement durable et de l'énergie-Ministère de l'écologie, du développement durable et de l'énergie, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Centre National de la Recherche Scientifique (CNRS), Office national de l'eau et des milieux aquatiques (ONEMA), 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 la Recherche Agronomique (INRA)-Office national de l'eau et des milieux aquatiques (ONEMA), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), and Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS)

Subjects
survey tools, Ecology, aquatic ecosystem management, detection limit, species detectability, [SDV]Life Sciences [q-bio], Applied ecology, Aquatic ecosystem, DNA signal persistence, Survey tool, Biology, environmental DNA, 6. Clean water, Water sample, DNA signal transport, water sampling, false detection, False detection, Environmental DNA, 14. Life underwater, Relative species abundance, ComputingMilieux_MISCELLANEOUS, Invertebrate
Abstract

International audience; There is a growing literature on the detection of species-specific DNA fragments in water to reveal animals' presence in aquatic environments. Analysis of Rees etal. (Journal of Applied Ecology, 2014, 51, 1450) and additional publications highlight the downside of the method and suggest that some conclusions have to be toned down. Non-detection of species-specific DNA fragments in a water sample does not automatically imply the absence of the target species. A positive signal does not necessarily mean the species is present because the environmental DNA (eDNA) could have been transported or preserved after an animal's death. Detection of aquatic invertebrates is weakly documented. The effect of species abundance on detection efficiency is not always established.Synthesis and applications. Before successfully becoming an efficient tool to assist proper management policies for monitoring of aquatic species, eDNA surveys must implement sampling strategies that allow estimating detection rates and scaling up information from water samples to larger spatial areas. The effects of discharge variations and dendritic organization in running waters require particular consideration. Before successfully becoming an efficient tool to assist proper management policies for monitoring of aquatic species, eDNA surveys must implement sampling strategies that allow estimating detection rates and scaling up information from water samples to larger spatial areas. The effects of discharge variations and dendritic organization in running waters require particular consideration.

Published
2015

20. Female Bonds and Kinship in Forest Guenons

Author

Dominique Vallet, Karim Ouattara, Agnès Candiotti, Eric J. Petit, Camille Coye, Klaus Zuberbühler, Alban Lemasson, Ethologie animale et humaine (EthoS), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Zoologie et Biologie Animale, Université de Cocody, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Université de Neuchâtel (UNINE), Institut Universitaire de France (IUF), Ministère de l'Education nationale, de l’Enseignement supérieur et de la Recherche (M.E.N.E.S.R.), This research was funded by the French Ministry of Research, IUF, PICS-CNRS, ANR Orilang with additional support from the Wissenschaftskolleg zu Berlin, the EC FP6 programme (What It Means to Be Human) and ESF-Eurocores (The Origin of Man Language and Languages), the French Ministry of Foreign Affairs (Egide), and the Centre Suisse de Recherches Scientifiques (CSRS)., ANR-09-JCJC-0130,ORILANG,De la communication vocale animale au langage humain : approche comparative ' cétacé - singe - homme '(2009), Normandie Université (NU)-Normandie Université (NU)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)

Subjects
biology, Ecology, [SDV]Life Sciences [q-bio], Microsatellite, Cercopithecus, Cercopithecus diana, biology.organism_classification, Grooming, Female-bonded, Cercopithecus campbelli, Animal ecology, Sympatric speciation, Evolutionary biology, Kinship, biology.animal, Vocal exchange, Animal Science and Zoology, Primate, Social organization, Ecology, Evolution, Behavior and Systematics, Social behavior
Abstract

International audience; A general pattern in animal behavior is that group-living species tend to bias their sociopositive behavior toward genetic relatives. In nonhuman primates, kin-biased social bonds have been reported in large multimale, multifemale macaque and baboon groups, but little is known for other species. We addressed this with a comparative study on the genetic and social organization of two sympatric forest guenons, Diana (Cercopithecus diana) and Campbell’s monkeys (Cercopithecus campbelli). We conducted long-term observations of social interactions in two groups of each species in their natural West African forest habitat and collected fecal samples for subsequent microsatellite genetic analyses. We found that both formed female-bonded, egalitarian social organizations. We then compared patterns of genetic relatedness, spatial proximity, and key social behaviors and found that females consistently targeted individuals other than their closest relatives to form social bonds. The fact that females did not preferentially favor genetic relatives contributes to a growing literature showing that social bonds, or “friendships,” among unrelated individuals plays a key role in primate social organizations.

Published
2015

21. Strong matrilineal structure in common pipistrelle bats (Pipistrellus pipistrellus) is associated with variability in echolocation calls

Author

Zdeněk Řehák, Josef Bryja, Eric J. Petit, Alena Fornůsková, Peter Kaňuch, Alain Butet, and Tomáš Bartonička

Subjects
biology, Ecology, Evolutionary biology, Genetic structure, Maternal effect, Biological dispersal, Vocal learning, Philopatry, Human echolocation, Pipistrellus pipistrellus, biology.organism_classification, Ecology, Evolution, Behavior and Systematics, Intraspecific competition
Abstract

The ontogeny and heritability of echolocation, an important sense in echolocating bats, is still not completely understood. Intraspecific variation in echolocation calls can be high, although the importance of possible explanatory variables (e.g. age, sex, social groups) remains largely unknown. Echolocation pulse features may vary among maternity roosts and this can theoretically be caused either by intercolony genetic differences or by vocal dialects learned during ontogeny within a roost (or a combination of both). In the present study, we analyzed intraspecific variation in echolocation parameters in relation to genetic structure at bi-parentally inherited microsatellites and maternally inherited mitochondrial (mt)DNA in maternal colonies of Pipistrellus pipistrellus in Central Europe. We found that individual colonies differ significantly in mtDNA, whereas the structure on nuclear markers is almost absent. This suggests a typical temperate bat social structure pattern, with strong sex-biased dispersal (i.e. philopatric females and dispersing males) (up to 92% of males leave their birth place according to our results). However, we show for the first time that genetic differentiation among mtDNA matrilines is associated with significant intercolony echolocation parameter differences. Because the genetic component of echolocation is not likely to be encoded by mtDNA, the results support the hypothesis of maternal echolocation dialect transmission to offspring, and the role of learning in this process is discussed.

Published
2014

22. Which temporal resolution to consider when investigating the impact of climatic data on population dynamics? The case of the lesser horseshoe bat (Rhinolophus hipposideros)

Author

Erwan Le Texier, Olivier Farcy, Josselin Boireau, Pierre-Loup Jan, Sébastien J. Puechmaille, Alice Baudoin, Eric J. Petit, Pascaline Le Gouar, Écologie et santé des écosystèmes (ESE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Bretagne Vivante, Groupe Mammalogique Breton, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Centre National de la Recherche Scientifique (CNRS), Zoological Institute & Museum, Universität Greifswald - University of Greifswald, 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 National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), and Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, Rhinolophus hipposideros, Population, Population Dynamics, Horseshoe bat, 010603 evolutionary biology, 01 natural sciences, Temporal resolution, Chiroptera, Climatic variables, Animals, Precipitation, education, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, Demography, education.field_of_study, biology, Population demography, Ecology, 010604 marine biology & hydrobiology, biology.organism_classification, Fecundity, Taxon, 13. Climate action, Physical geography, France, [SDV.EE.BIO]Life Sciences [q-bio]/Ecology, environment/Bioclimatology, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Count data, Model averaging
Abstract

International audience; Climatic variables are often considered when studying environmental impacts on population dynamics of terrestrial species. However, the temporal resolution considered varies depending on studies, even among studies of the same taxa. Most studies interested in climatic impacts on populations tend to average climatic data across timeframes covering life cycle periods of the organism in question or longer, even though most climatic databases provide at least a monthly resolution. We explored the impact of climatic variables on lesser horseshoe bat (Rhinolophus hipposideros) demography based on count data collected at 94 maternity colonies from 2000 to 2014 in Britanny, France. Meteorological data were considered using different time resolutions (month, life cycle period and year) to investigate their adequacy. Model averaging was used to detect significant predictors for each temporal resolution. Our results show that the finest temporal resolution, e.g. month, was more informative than coarser ones. Precipitation predictors were particularly decisive, with a negative impact on colony sizes when rainfall occurred in October, and a positive impact for June precipitations. Fecundity was influenced by April weather. This highlights the strong impact of climatic conditions during crucial but short time periods on the population dynamics of bats. We demonstrate the importance of choosing an appropriate time resolution and suggest that analogous studies should consider fine-scale temporal resolution (e.g. month) to better grasp the relationship between population dynamics and climatic conditions.

Published
2016

23. La nageoire est un substitut pertinent et non-létal au muscle pour doser les isotopes stables chez les amphibiens

Author

Adrien Oger, Nadège Bélouard, Eric J. Petit, Dominique Huteau, Jean-Marc Paillisson, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Écologie et santé des écosystèmes (ESE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, 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), funded by the Agence Française pour la Biodiversité (research program supervised by J.M.P.) and the Ministère de l’Education Nationale, del’Enseignement Supérieur et de la Recherche (Ph.D. grant to N.B.) Ministère de l’Enseignement Supérieur et de la Recherche Scientifique, MESRS, Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut Ecologie et Environnement (INEE), and Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, Amphibian, Fin, Ecology (disciplines), tadpole, échantillonnage non-destructif, Zoology, Management, Monitoring, Policy and Law, Aquatic Science, Fin biopsy, 010603 evolutionary biology, 01 natural sciences, lcsh:Aquaculture. Fisheries. Angling, triton, biology.animal, newt, Lack of knowledge, 14. Life underwater, Taxonomic rank, Nature and Landscape Conservation, Water Science and Technology, Trophic level, lcsh:SH1-691, food web, Ecology, biology, Isotope, Stable isotope ratio, non-destructive sampling, 010604 marine biology & hydrobiology, Biopsie de nageoire, non destructive sampling, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, réseau trophique, têtard
Abstract

This study was funded by the Agence Francaise pour la Biodiversite (research program supervised by J.M.P.) and the Ministere de l'Education Nationale, de l'Enseignement Superieur et de la Recherche (Ph.D. grant to N.B.). This work was carried out under the licenses 08/2015 and 07/2016 delivered by the Prefecture de la Loire-Atlantique. We thank the Parc Natural Regional de Briere, notably J.P. Damien, for supporting our research activities on amphibian ecology. The authors declare that they have no conflict of interest. We are also grateful to two anonymous reviewers for their constructive comments on an earlier version of the manuscript.; International audience; Stable isotope analyses (SIA) are now widely used in ecology research to quantify the trophic implications of a large range of ecological processes. Non-destructive sampling methods have been successfully developed for most vertebrates, but the validation of such methods is missing in amphibians. Filling this methodological gap is critical to reduce the significant lack of knowledge on the trophic ecology of this imperilled group. The relevance of tail fin as a surrogate for muscle, a tissue routinely used for SIA, was assessed in four amphibian species, including tadpoles and adult newts, by (1) testing the link between the isotope ratios of carbon and nitrogen in fin and muscle, and addressing the additional practical issues of (2) the effects of a topical anaesthetic on isotope ratios, and (3) the minimum quantities of fin needed for SIA to limit the severity of sampling. The isotope ratios were highly correlated between the two tissues in all four species. Equations were provided to predict muscle estimates from fin values for each species separately and grouped by their taxonomic order (anurans or urodeles), which represent a valuable solution for any other species. Topical anaesthetics had little influence on isotope ratios, and the surface of tail fin needed for SIA was small. We conclude that the tail fin of amphibians can be used as a non-lethal surrogate for muscle in SIA, and this offers promising prospects for research on the trophic ecology of amphibians, and potentially on their conservation.; Les analyses d'isotopes stables (AIS) sont maintenant largement utilisées en recherche en écologie pour quantifier les implications trophiques d'une large gamme de processus écologiques. Des méthodes d'échantillonnage non-létales ont été développées chez la plupart des vertébrés, mais une telle validation est absente chez les amphibiens. Il est essentiel de combler cette lacune de façon à réduire le manque de connaissances sur l'écologie trophique de ce groupe menacé. La pertinence de la nageoire caudale comme substitut au muscle, un tissu régulièrement utilisé pour les AIS, a été évaluée chez quatre espèces d'amphibiens, incluant des têtards et des tritons, (1) en testant le lien entre les ratios isotopiques du carbone et de l'azote du muscle et de la nageoire, et en répondant à des questions pratiques comme (2) l'effet d'un anesthésique local sur les ratios isotopiques, et (3) les quantités minimales de nageoire nécessaires aux analyses isotopiques, dans le but de limiter la sévérité de l'échantillonnage. Les ratios isotopiques étaient hautement corrélés entre les deux tissus chez les quatre espèces. Des équations ont été fournies pour prédire les valeurs du muscle à partir de celles de la nageoire en considérant chaque espèce séparément et en les regroupant selon leur ordre taxonomique (anoures ou urodèles) ce qui représente une solution intéressante pour d'autres espèces. L'anesthésique topique a eu une faible influence sur les ratios isotopiques, et la surface de nageoire nécessaire pour les AIS était faible. Nous concluons que la nageoire caudale des amphibiens peut être utilisée en tant que substitut au muscle pour conduire des AIS, ce qui offre des perspectives prometteuses pour la recherche en écologie trophique des amphibiens, et potentiellement pour leur conservation.

Published
2019

24. Temporal sampling helps unravel the genetic structure of naturally occurring populations of a phytoparasitic nematode. 1. Insights from the estimation of effective population sizes

Author

Sylvain Fournet, Cécile Gracianne, Eric J. Petit, Catherine Porte, Eric Olivier, Jean-François Arnaud, Pierre-Loup Jan, Marie‐Christine Denis, Sylvie Bardou-Valette, Écologie et santé des écosystèmes (ESE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), AGROCAMPUS OUEST-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo), Université de Lille-Centre National de la Recherche Scientifique (CNRS), French Ministry of Agriculture, French Ministry of Education and Research, Institut Technique de la Betterave sucrière, Union Française des Semenciers, Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP)), 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 la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST

Subjects
0301 basic medicine, wild nematode populations, hetérodéra schachtii, Context (language use), plante hôte, Sea beet, Heterodera schachtii, 03 medical and health sciences, fréquence des allèles, Effective population size, genetique des populations, Genetics, Ecology, Evolution, Behavior and Systematics, nématode à kyste, 2. Zero hunger, Natural selection, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], biology, amaranthaceae, résistance aux parasites, Ecology, Population size, espèce végétale, fungi, food and beverages, Original Articles, 15. Life on land, biology.organism_classification, Beta vulgaris subsp. maritima, lutte contre les ravageurs, beta vulgaris spp. maritima, effective population size, heterodera schachtii, temporal sampling, betterave, 030104 developmental biology, Beta vulgaris spp. maritima, Genetic structure, plante, Original Article, General Agricultural and Biological Sciences, Inbreeding, mortalité
Abstract

International audience; The sustainability of modern agriculture relies on strategies that can control the ability of pathogens to overcome chemicals or genetic resistances through natural selection. This evolutionary potential, which depends partly on effective population size (Ne), is greatly influenced by human activities. In this context, wild pathogen populations can provide valuable information for assessing the long-term risk associated with crop pests. In this study, we estimated the effective population size of the beet cyst nematode, Heterodera schachtii, by sampling 34 populations infecting the sea beet Beta vulgaris spp. maritima twice within a one-year period. Only 20 populations produced enough generations to analyze the variation in allele frequencies, with the remaining populations showing a high mortality rate of the host plant after only one year. The 20 analyzed populations showed surprisingly low effective population sizes, with most having Ne close to 85 individuals. We attribute these low values to the variation in population size through time, systematic inbreeding, and unbalanced sex- ratios. Our results suggest that H. schachtii has low evolutionary potential in natural environments. Pest control strategies in which populations on crops mimic wild populations may help prevent parasite adaptation to host resistance.

Published
2016

25. Temporal sampling helps unravel the genetic structure of naturally occurring populations of a phytoparasitic nematode. 2. Separating the relative effects of gene flow and genetic drift

Author

Sylvain Fournet, Eric Olivier, Catherine Porte, Eric J. Petit, Cécile Gracianne, Sylvie Bardou-Valette, Marie‐Christine Denis, Jean-François Arnaud, Pierre-Loup Jan, VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), AGROCAMPUS OUEST-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA), Écologie et santé des écosystèmes (ESE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Ministère de l'Education Nationale, de l'Enseignement Superieur et de la Recherche, Delphine Eoche-Bosy and Didier Fouville (UMR IGEPP), French Ministry of Agriculture, Institut Technique de la Betterave sucrière, Union Française des Semenciers, Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, 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 la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP)), VetAgro Sup ( VAS ), Institut de Génétique, Environnement et Protection des Plantes ( IGEPP ), Institut National de la Recherche Agronomique ( INRA ) -Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -AGROCAMPUS OUEST, Écologie et santé des écosystèmes ( ESE ), Institut National de la Recherche Agronomique ( INRA ) -AGROCAMPUS OUEST, Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 ( Evo-Eco-Paléo ), and Université de Lille-Centre National de la Recherche Scientifique ( CNRS )

Subjects
0301 basic medicine, wild nematode populations, Population, marqueur génétique, assignment tests, hetérodéra schachtii, Biology, plante hôte, Sea beet, Gene flow, Heterodera schachtii, 03 medical and health sciences, Genetic drift, genetique des populations, Genetics, education, Ecology, Evolution, Behavior and Systematics, heterodera schachtii, gene flow, migration-drift equilibrium, nématode à kyste, 2. Zero hunger, education.field_of_study, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], amaranthaceae, Ecology, espèce végétale, fungi, food and beverages, Original Articles, 15. Life on land, biology.organism_classification, Beta vulgaris subsp. maritima, culture, lutte contre les ravageurs, [ SDV.GEN.GPO ] Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], betterave, 030104 developmental biology, Genetic marker, Evolutionary biology, Genetic structure, plante, Biological dispersal, Original Article, General Agricultural and Biological Sciences, migration–drift equilibrium
Abstract

International audience; Studying wild pathogen populations in natural ecosystems offers the opportunity to better understand the evolutionary dynamics of biotic diseases in crops and to enhance pest control strategies. We used simulations and genetic markers to investigate the spatial and temporal population genetic structure of wild populations of the beet cyst nematode Heterodera schachtii on a wild host plant species, the sea beet (Beta vulgaris spp. maritima), the wild ancestor of cultivated beets. Our analysis of the variation of eight microsatellite loci across four study sites showed that (i) wild H. schachtii populations displayed fine-scaled genetic structure with no evidence of substantial levels of gene flow beyond the scale of the host plant, and comparisons with simulations indicated that (ii) genetic drift substantially affected the residual signals of isolation-by-distance processes, leading to departures from migration–drift equilibrium. In contrast to what can be suspected for (crop) field populations, this showed that wild cyst nematodes have very low dispersal capabilities and are strongly disconnected from each other. Our results provide some key elements for designing pest control strategies , such as decreasing passive dispersal events to limit the spread of virulence among field nematode populations.

Published
2016

26. Social systems: demographic and genetic issues

Author

Nicolas Perrin, Eric J. Petit, and Nelly Ménard

Subjects
0106 biological sciences, 0303 health sciences, Kin recognition, media_common.quotation_subject, Inclusive fitness, Environmental ethics, Kin selection, Altruism (biology), Biology, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Social system, Reciprocity (social psychology), Evolutionary biology, Genetics, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Pace, Diversity (politics), media_common
Abstract

Animal societies certainly count among the most complex structures that emerged on earth, the latest of the 'major transitions' in evolution. Their study necessarily involves a wide panel of disciplines and a large diversity of approaches. The field is expanding at a rapid pace, which, however, is not going without some turbulence, as testified by recent fierce controversies regarding the concept of inclusive fitness. These battles elicited appeals for 'more cooperation among altruism researchers' (Okasha 2010). In this spirit, we recently organized at the University of Rennes (10-15 October 2010) a workshop on mammalian social systems. The idea was to bring together 'social scientists' working on a diversity of animal models (from bats to elephants and from hyenas to whales) and using a diversity of approaches (from demography to population genetics and from game-theoretical models to behavioural experiments), with the aim of evaluating how key processes (e.g. inclusive fitness and kin selection, versus cooperation and reciprocity, or the interplay between inbreeding, kin competition and kin recognition) might differently affect the emergence and evolution of social systems in a diversity of mammalian lineages, depending on ecological settings or other constraints. This diversity of complementary approaches explains why the several contributions to the workshop collected in the present Special Issue are not all 'pure' molecular ecology.

Published
2012

27. Social organization and genetic structure: insights from codistributed bat populations

Author

Matthew J. Struebig, Adura Mohd-Adnan, Thomas H. Kunz, Eric J. Petit, Sucharita Gopal, Akbar Zubaid, Tigga Kingston, and Stephen J. Rossiter

Subjects
0106 biological sciences, 0303 health sciences, education.field_of_study, Habitat fragmentation, Ecology, Ecology (disciplines), Foraging, Population, 15. Life on land, Biology, 010603 evolutionary biology, 01 natural sciences, Gene flow, 03 medical and health sciences, Habitat, Genetic structure, Genetics, Social organization, education, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology
Abstract

The impact of ecology and social organization on genetic structure at landscape spatial scales, where gene dynamics shape evolution as well as determine susceptibility to habitat fragmentation, is poorly understood. Attempts to assess these effects must take into account the potentially confounding effects of history. We used microsatellites to compare genetic structure in seven bat species with contrasting patterns of roosting ecology and social organization, all of which are codistributed in an ancient forest habitat that has been exceptionally buffered from radical habitat shifts. Over one thousand individuals were captured at foraging sites and genotyped at polymorphic microsatellite loci. Analyses of spatially explicit genotype data revealed interspecies differences in the extent of movement and gene flow and genetic structure across continuous intact forest. Highest positive genetic structure was observed in tree-roosting taxa that roost either alone or in small groups. By comparison, a complete absence of genetic autocorrelation was noted in the cave-roosting colonial species across the study area. Our results thus reveal measurable interspecies differences in the natural limits of gene flow in an unmodified habitat, which we attribute to contrasting roosting ecology and social organization. The consequences of ecology and behaviour for gene flow have important implications for conservation. In particular, tree-roosting species characterized by lower vagility and thus gene flow will be disproportionally impacted by landscape-scale forest clearance and habitat fragmentation, which are prevalent in the study region. Our method also highlights the usefulness of rapid sampling of foraging bats for assaying genetic structure, particularly where roosting sites are not always known.

Published
2011

28. Parallel declines in species and genetic diversity in tropical forest fragments

Author

Steven C. Le Comber, Tigga Kingston, Matthew J. Struebig, Akbar Zubaid, Eric J. Petit, Stephen J. Rossiter, and Adura Mohd-Adnan

Subjects
0106 biological sciences, 0303 health sciences, Genetic diversity, education.field_of_study, Habitat fragmentation, Ecological release, Ecology, Population, Biodiversity, Species diversity, 15. Life on land, Biology, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Alpha diversity, Species richness, education, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology
Abstract

The potential for parallel impacts of habitat change on multiple biodiversity levels has important conservation implications. We report on the first empirical test of the 'species-genetic diversity correlation' across co-distributed taxa with contrasting ecological traits in the context of habitat fragmentation. In a rainforest landscape undergoing conversion to oil palm, we show that depauperate species richness in fragments is mirrored by concomitant declines in population genetic diversity in the taxon predicted to be most susceptible to fragmentation. This association, not seen in the other species, relates to fragment area rather than isolation. While highlighting the over-simplification of extrapolating across taxa, we show that fragmentation presents a double jeopardy for some species. For these, conserving genetic diversity at levels of pristine forest could require sites 15-fold larger than those needed to safeguard species numbers. Importantly, however, each fragment contributes to regional species richness, with larger ones tending to contain more species.

Published
2011

29. Empirical evaluation of non-invasive capture-mark-recapture estimation of population size based on a single sampling session

Author

Sébastien J. Puechmaille and Eric J. Petit

Subjects
0106 biological sciences, Estimation, 0303 health sciences, Ecology, Population size, Bayesian probability, Sampling (statistics), Biology, 010603 evolutionary biology, 01 natural sciences, Mark and recapture, 03 medical and health sciences, Abundance (ecology), Statistics, Microsatellite, Genotyping, 030304 developmental biology
Abstract

Summary 1 Non-invasive genetic data analysed with capture–mark–recapture (CMR) models can be used to estimate population size, particularly for elusive and endangered species. Data generated from non-invasive genetic sampling are different, however, from conventional CMR data because individuals can be contacted several times within a single sampling session. Two methods have been proposed recently to accommodate this type of data, but no study has attempted to compare their estimates and evaluate their reliability compared with independent estimates of population size. 2 We investigated the reliability and accuracy of estimating the abundance of lesser horseshoe bats Rhinolophus hipposideros by genotyping DNA from droppings collected non-invasively at three colonies over 2 consecutive years. The number of times that each individual was ‘contacted’ (i.e. the number of droppings per individual) was used to estimate population size with two different published methods: a maximum likelihood and a Bayesian estimator. 3 Among the 586 samples extracted, 534 provided a complete genotype at six to eight microsatellite loci, which enabled a reliable discrimination of 165 individuals. Statistical estimates of colony sizes often included independent estimates obtained from visual counts, validating the method. Discrepancies appeared when capture heterogeneity was not taken into account while it occurred. 4 Synthesis and applications. We have taken a first step towards improving methods of estimating numbers of bats by demonstrating that genetic data produced from bat faecal DNA are of high quality and can provide accurate estimates of population size even when samples are taken during only one sampling session. Such protocols provide valuable management tools for elusive and rare species in general. The method is relatively easy and cost-efficient because only one sampling session is required.

Published
2007

30. SEX-BIASED DISPERSAL IN A MIGRATORY BAT: A CHARACTERIZATION USING SEX-SPECIFIC DEMOGRAPHIC PARAMETERS

Author

Francois Balloux, Jérôme Goudet, and Eric J. Petit

Subjects
Male, Nyctalus noctula, Animals, Chiroptera/genetics, Chiroptera/physiology, Computer Simulation, DNA, Mitochondrial/genetics, Europe, Female, Models, Biological, Population Dynamics, Sex Factors, Population, Population structure, Biology, DNA, Mitochondrial, Chiroptera, Genetic model, Genetics, education, Ecology, Evolution, Behavior and Systematics, Panmixia, education.field_of_study, Ecology, biology.organism_classification, Evolutionary biology, F-statistics, Biological dispersal, Philopatry, General Agricultural and Biological Sciences
Abstract

We studied the noctule bat (Nyctalus noctula), in which the mitochondrial F(ST) is about 10 times that revealed by nuclear markers, to address two questions. We first verified whether random dispersal of one sex is compatible with highly contrasted mitochondrial and nuclear population structures. Using computer simulations, we then assessed the power of multilocus population differentiation tests when the expected population structure departs only slightly from panmixia. Using an island model with sex-specific demographic parameters, we found that random male dispersal is consistent with the population structure observed in the noctule. However, other parameter combinations are also compatible with the data. We computed the minimum sex bias in dispersal (at least 69% of the dispersing individuals are males), a result that would not be available if we had used more classical population genetic models. The power of multilocus population differentiation tests was unexpectedly high, the tests being significant in almost 100% of the replicates, although the observed population structure infered from nuclear markers was extremely low (F(ST) = 0.6%).

Published
2007

31. Good DNA from bat droppings

Author

Gregory Mathy, Sébastien J. Puechmaille, and Eric J. Petit

Subjects
Genetics, Mitochondrial DNA, Rhinolophus hipposideros, Locus (genetics), Biology, biology.organism_classification, Horseshoe bat, chemistry.chemical_compound, chemistry, Microsatellite, Animal Science and Zoology, Multiplex, Allele, DNA
Abstract

Amplification of a mitochondrial DNA fragment was used to compare the efficiency of five methods for extracting DNA from bat droppings. The Qiagen DNA Stool Kit, which yielded > 90% mtDNA amplification success, was chosen to extract DNA from 586 samples taken over two years in three French colonies of the lesser horseshoe bat (Rhinolophus hipposideros). Samples, for which mtDNA amplification was successful, were subject to the multiplex amplification of eight microsatellite loci. This resulted in > 95% amplification success over 12,592 PCRs. Allelic dropout (ADO) and false allele (FA) rates were low, and consequently, sample and locus quality indexes (QI) were high. These results demonstrate that large scale noninvasive studies of bat colonies are possible.

Published
2007

32. Phylogeography and postglacial recolonization of Europe by Rhinolophus hipposideros: evidence from multiple genetic markers

Author

Serena E. Dool, Javier Juste, Andrea Viglino, Carlos F. Ibáñez, Stéphane G. Roué, Christian Dietz, Danilo Russo, Sébastien J. Puechmaille, Pavel Hulva, Emma C. Teeling, Stephen J. Rossiter, Gareth Jones, Eric J. Petit, Roberto Toffoli, Adriano Martinoli, University College Dublin, University College Dublin [Dublin] (UCD), Développement de l'enfant, Sensory Ecology Group [Seewiesen], Max Planck Institute for Ornithology, Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, Zoological Institut Tübingen University, Eberhard Karls Universität Tübingen = Eberhard Karls University of Tuebingen, Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Faculty of Science, Charles University [Prague] (CU), Dept Biol & Ecol, Techn Univ Ostrava, Technical University of Ostrava [Ostrava] (VSB), Stratégies évolutives et Dynamique spatiale des Populations, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS)-Station Biologique de Paimpont CNRS UMR 6653 (OSUR), Université de Rennes (UR)-Université de Rennes (UR), University of Bristol [Bristol], University of Naples Federico II = Università degli studi di Napoli Federico II, Consulenze Faunistiche, Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Department Environment-Health-Safety, Universitá degli Studi dell’Insubria = University of Insubria [Varese] (Uninsubria), School of Biological and Chemical Sciences [London], Queen Mary University of London (QMUL), Région Bretagne, IRCSET Marie Curie International Mobility Fellowship in Science, Engineering and Technology, Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Station Biologique de Paimpont CNRS UMR 6653 (OSUR), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES), Università degli studi di Napoli Federico II, Universitá degli Studi dell’Insubria, Serena E., Dool, Sébastien J., Puechmaille, Christian, Dietz, Javier, Juste, Carlos, Ibanez, Pavel, Hulva, Stéphane G., Roué, Eric J., Petit, Gareth, Jone, Russo, Danilo, Roberto, Toffoli, Andrea, Viglino, Adriano, Martinoli, Stephen J., Rossiter, and Emma C., Teeling

Subjects
Genetic Markers, 0106 biological sciences, Demographic history, Quaternary ice ages, Maghreb, Rhinolophus hipposideros, Western Palearctic, Horseshoe bat, Hipposideros, DNA, Mitochondrial, 010603 evolutionary biology, 01 natural sciences, Evolution, Molecular, 03 medical and health sciences, Gene Frequency, Chiroptera, Biglycan, Genetics, Animals, Anatolia, Glacial period, glacial refugia, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 0303 health sciences, Base Sequence, biology, Ecology, Genetic Variation, Last Glacial Maximum, Sequence Analysis, DNA, Cytochromes b, biology.organism_classification, Europe, Phylogeography, Haplotypes, Evolutionary biology, Microsatellite, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Microsatellite Repeats
Abstract

The demographic history of Rhinolophus hipposideros (lesser horseshoe bat) was recon- structed across its European, North African and Middle-Eastern distribution prior to, during and following the most recent glaciations by generating and analysing a multi- marker data set. This data set consisted of an X-linked nuclear intron (Bgn; 543 bp), mitochondrial DNA(cytb-tRNA-control region; 1630 bp) and eight variable microsatel- lite loci for up to 373 individuals from 86 localities. Using this data set of diverse markers, it was possible to determine the species’ demography at three temporal stages. Nuclear intron data revealed early colonization into Europe from the east, which pre-dates the Quaternary glaciations. The mtDNA data supported multiple glacial refugia across the Mediterranean, the largest of which were found in the Ibero- Maghreb region and an eastern location (Anatolia/Middle East)–that were used by R. hipposideros during the most recent glacial cycles. Finally, microsatellites provided the most recent information on these species’ movements since the Last Glacial Maxi- mumand suggested that lineages that had diverged into glacial refugia, such as in the Ibero-Maghreb region, have remained isolated. These findings should be used to inform future conservation management strategies for R. hipposideros and show the power of using a multimarker data set for phylogeographic studies.

Published
2013

33. Heterozygote deficits in cyst plant-parasitic nematodes: possible causes and consequences

Author

Sylvain Fournet, Andrew Overall, Eric J. Petit, Sylvie Bardou-Valette, Eric Olivier, Cécile Gracianne, Josselin Montarry, Pierre-Loup Jan, Eric Grenier, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Écologie et santé des écosystèmes (ESE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, School of Pharmacy and Biomedical Sciences, University of Brighton, 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 Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST

Subjects
0106 biological sciences, Heterozygote, microsatellite, Genotype, Wahlund effect, nematode, Consanguinity, Biology, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, consanguinity, Gene Frequency, Tobacco, Genetics, Animals, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Inbreeding, Tylenchoidea, Globodera pallida, Ecology, Evolution, Behavior and Systematics, Alleles, 030304 developmental biology, Solanum tuberosum, 0303 health sciences, Likelihood Functions, fungi, heterozygote deficit, Genetic Variation, food and beverages, Heterozygote advantage, biology.organism_classification, Null allele, Genetics, Population, null allele, Biological dispersal, Beta vulgaris, Heterodera schachtii, Microsatellite Repeats
Abstract

International audience; Deviations of genotypic frequencies from Hardy-Weinberg equilibrium (HWE) expectations could reveal important aspects of the biology of populations. Deviations from HWE due to heterozygote deficits have been recorded for three plant-parasitic nematode species. However, it has never been determined whether the observed deficits were due (i) to the presence of null alleles, (ii) to a high level of consanguinity and/or (iii) to a Wahlund effect. The aim of the present work was, while taking into the possible confounding effect of null alleles, to disentangle consanguinity and Wahlund effect in natural populations of those three economically important cyst nematodes using microsatellite markers: Globodera pallida, G. tabacum and Heterodera schachtii, pests of potato, tobacco and sugar beet, respectively. The results show a consistent pattern of heterozygote deficiency in the three nematode species sampled at the spatial scale of the host plant. We demonstrate that the prevalence of null alleles is weak and that heterozygote deficits do not have a single origin. Our results suggested that it is restricted dispersal that leads to heterozygote deficits through both consanguinity and substructure, which effects can be linked to soil movement, cyst density, and the number of generations per year. We discuss potential implications for the durability of plant resistances that are used to protect crops against parasites in which mating between relatives occur. While consanguineous mating leads to homozygosity at all loci, including loci governing avirulence/virulence, which favours the expression of virulence when recessive, the Wahlund effect is expected to have no particular effect on the adaptation of nematodes to resistances.

Published
2015

34. Molecular Phylogeny of Pheretimoid Earthworms (Haplotaxina: Megascolecidae) Based on Mitochondrial DNA in Hainan Island, China

Author

Andreas Prinzing, Qi Zhao, Charlène Briard, Eric J Petit, Daniel Cluzeau, Jiangping Qiu, Jing Sun, Jibao Jiang, Southwestern University of Finance and Economics [Chengdu, China], Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Station Biologique de Paimpont CNRS UMR 6653 (OSUR), Université de Rennes (UR), School of Agriculture and Biology, Shanghai, Shanghai Jiao Tong University [Shanghai], Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Université de Rennes 1 (UR1), and Briand, Valerie

Subjects
0106 biological sciences, 0303 health sciences, Phylogenetic tree, biology, Ecology, Amynthas, Earthworm, Biodiversity, biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, [SDE.BE] Environmental Sciences/Biodiversity and Ecology, 03 medical and health sciences, Geography, Genus, Megascolecidae, Molecular phylogenetics, General Materials Science, 14. Life underwater, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Molecular clock, 030304 developmental biology
Abstract

International audience; In the Chinese Hainan Island, Amynthas and Metaphire are two dominated pheretimoid earthworm species belonging to the family Megascolecidae. They differ from earthworms in the adjacent regions in their morphology and at the molecular level, which could have occurred due to the unique geography of Hainan Island. Hainan Island is made of two tectonic parts linked to South China and Indochina blocks, respectively. In addition, there is an apparent complicated link between Hainan Island and mainland China because of the different plate movements and sea level changes. In order to understand the evolution of pheretimoid earthworms in Hainan Island, we first investigated the earthworm biodiversity here. Bayesian phylogenetic tree was then constructed from 3511 base pairs from five mitochondrial genes: COI, COII, 16S, 12S, and ND1. Their divergent time was finally traced based on the molecular clock of 2.0-2.4% substitutions/Ma. The results showed three species differentiations between Hainan and Guangdong earthworm species. According to the paleogeography of Asiatic regions (including Hainan Island itself), we hypothesized that the Hainan pheretimoid earthworms might originate from Southeast Asia, and then they dispersed to the south and finally arrived at South China and Hainan Island. Meanwhile, due to the geology movement of the adjacent plates, there was also the migration of earthworms among adjacent regions. Furthermore, we also considered that the relationship between genera Metaphire and Amynthas might be re-considered as one genus.

Published
2015

35. Will reduced host connectivity curb the spread of a devastating epidemic?

Author

Sébastien J. Puechmaille, Eric J. Petit, Écologie et santé des écosystèmes (ESE), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Zoological Institute & Museum, Universität Greifswald - University of Greifswald, School of Biology and Environmental Science, University College Dublin [Dublin] (UCD), 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
chiroptera, Fauna, [SDV]Life Sciences [q-bio], Population, Disease free, Biology, Communicable Diseases, Emerging, Molecular ecology, Cave, Pseudogymnoascus destructans, Genetics, Animals, education, Ecology, Evolution, Behavior and Systematics, geography, education.field_of_study, geography.geographical_feature_category, Host (biology), Ecology, fungus, conservation, Fungal pathogen, biology.organism_classification, Genetics, Population, Mycoses, white-nose syndrome, epidemiology, predictive modelling
Abstract

The white-nose syndrome (WNS), caused by the fungal pathogen Pseudogymnoascus destructans, is threatening the cave-dwelling bat fauna of North America by killing individuals by the thousands in hibernacula each winter since its appearance in New York State less than ten years ago. Epidemiological models predict that WNS will reach the western coast of the USA by 2035, potentially eliminating most populations of susceptible bat species in its path (Frick et al. 2015; O'Regan et al. 2015). These models were built and validated using distributional data from the early years of the epidemic, which spread throughout eastern North America following a route driven by cave density and winter severity (Maher et al. 2012). In this issue of Molecular Ecology, Wilder et al. (2015) refine these findings by showing that connectivity among host populations, as assessed by population genetic markers, is crucial in determining the spread of the pathogen. Because host connectivity is much reduced in the hitherto disease free western half of North America, Wilder et al. make the reassuring prediction that the disease will spread more slowly west of the Great Plains.

Published
2015

36. Dispersal and genetic structure in the American marten, Martes americana

Author

Françoise Burel, Thomas Broquet, Eric J. Petit, C. A. Johnson, John M. Fryxell, and Ian D. Thompson

Subjects
0106 biological sciences, 0303 health sciences, education.field_of_study, biology, Ecology, Population, biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Geographical distance, biology.animal, Genetic structure, Martes americana, Genetic variation, Genetics, Biological dispersal, education, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Isolation by distance, Marten
Abstract

Natal dispersal in a vagile carnivore, the American marten (Martes americana), was studied by comparing radio-tracking data and microsatellite genetic structure in two populations occupying contrasting habitats. The genetic differentiation determined among groups of individuals using F(ST) indices appeared to be weak in both landscapes, and showed no increase with geographical distance. Genetic structure investigated using pairwise genetic distances between individuals conversely showed a pattern of isolation by distance (IBD), but only in the population occurring in a homogeneous high-quality habitat, therefore showing the advantage of individual-based analyses in detecting within-population processes and local landscape effects. The telemetry study of juveniles revealed a leptokurtic distribution of dispersal distances in both populations, and estimates of the mean squared parent-offspring axial distance (sigma2) inferred both from the genetic pattern of IBD and from the radio-tracking survey showed that most juveniles make little contribution to gene flow.

Published
2006

37. Colonization and dispersal in a social species, the Bechstein's bat (Myotis bechsteinii)

Author

Eric J. Petit and Gerald Kerth

Subjects
0106 biological sciences, 0303 health sciences, Mitochondrial DNA, Zoology, Metapopulation, Biology, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Genetic structure, Genetic model, Genetics, Biological dispersal, Philopatry, Colonization, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Isolation by distance
Abstract

Metapopulation genetic models consider that colonization and dispersal are distinct behaviours. However, whether colonization and dispersal indeed reflect different biological processes in nature is unclear. One possibility to test this assumption is to assess patterns of autosomal and mitochondrial genetic structure in species with strict female philopatry, such as the communally breeding Bechstein's bat. In this species, mitochondrial DNA can spread only when females establish new colonies, and autosomal DNA is transmitted among colonies only when females mate with solitary males born in foreign colonies. Investigating the genetic structure among 37 colonies, we found that autosomal genes followed an island model on a regional scale and a model of isolation by distance on a larger geographical scale. In contrast, mitochondrial genetic structure revealed no pattern of isolation by distance at a large scale but exhibited an effect of ecological barriers on a regional scale. Our results provide strong empirical evidence that colonization and dispersal do not follow the same behavioural rules in this bat, supporting the assumption of metapopulation genetic models.

Published
2005

38. Quantifying genotyping errors in noninvasive population genetics

Author

Thomas Broquet and Eric J. Petit

Subjects
0106 biological sciences, Selection bias, Genetics, 0303 health sciences, education.field_of_study, media_common.quotation_subject, Population, Population genetics, Biology, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Statistics, education, Estimation methods, Genotyping, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, media_common
Abstract

The use of noninvasively collected samples greatly expands the range of ecological issues that may be investigated through population genetics. Furthermore, the difficulty of obtaining reliable genotypes with samples containing low quantities of amplifiable DNA may be overcome by designing optimal genotyping schemes. Such protocols are mainly determined by the rates of genotyping errors caused by false alleles and allelic dropouts. These errors may not be avoided through laboratory procedure and hence must be quantified. However, the definition of genotyping error rates remains elusive and various estimation methods have been reported in the literature. In this paper we proposed accurate codification for the frequencies of false alleles and allelic dropouts. We then reviewed other estimation methods employed in hair- or faeces-based population genetics studies and modelled the bias associated with erroneous methods. It is emphasized that error rates may be substantially underestimated when using an erroneous approach. Genotyping error rates may be important determinants of the outcome of noninvasive studies and hence should be carefully computed and reported.

Published
2004

39. Mitochondrial DNA variation along an altitudinal gradient in the greater white-toothed shrew,Crocidura russula

Author

Nicolas Perrin, M. Ehinger, Eric J. Petit, and Pierre Fontanillas

Subjects
Mitochondrial DNA, biology, Ecology, Crocidura russula, Shrew, Haplotype, Zoology, Metapopulation, biology.organism_classification, Genetic drift, biology.animal, Genetic variation, Genetics, Biological dispersal, Ecology, Evolution, Behavior and Systematics
Abstract

The distribution of mitochondrial control region-sequence polymorphism was investigated in 15 populations of Crocidura russula along an altitudinal gradient in western Switzerland. High-altitude populations are smaller, sparser and appear to undergo frequent bottlenecks. Accordingly, they showed a loss of rare haplotypes, but unexpectedly, were less differentiated than lowland populations. Furthermore, the major haplotypes segregated significantly with altitude. The results were inconsistent with a simple model of drift and dispersal. They suggested instead a role for historical patterns of colonization, or, alternatively, present-day selective forces acting on one of the mitochondrial genes involved in metabolic pathways.

Published
2002

40. Molecular identification of an endemic Alpine mammal, Apodemus alpicola, using a PCR-based RFLP method

Author

Peter Vogel, Brigitte A. Reutter, and Eric J. Petit

Subjects
Genetics, Mitochondrial DNA, Apodemus alpicola, Cytochrome b, Apodemus, Mammal, Biology, Restriction fragment length polymorphism, biology.organism_classification, Ecology, Evolution, Behavior and Systematics, Molecular identification
Abstract

The ability of a PCR-based restriction fragment length polymorphism (RFLP) analysis of the cytochrome b (mtDNA) to distinguish Apodemus alpicola from two other Apodemus species was investigated. The partial sequencing of the cytochrome b allowed the identification of one enzyme as being potentially diagnostic. This was supported by an analysis of 131 specimens previously identified using morphometric and/or allozymic data, indicating that the PCR-based RFLP method provides a rapid and reliable tool for distinguishing A. alpicola from its two co-occurring congenerics. The method is applicable to samples taken in the field for ecological studies, and could easily be adapted to the identification of museum samples.

Published
2002

41. Performance of individual vs. group sampling for inferring dispersal under isolation-by-distance

Author

Thomas Broquet, Eric J. Petit, Natacha Luximon, Department of Ecology and Evolution, University of Lausanne, Université de Lausanne (UNIL), Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), DIVersité et COnnectivité dans le paysage marin côtier (DIVCO), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), 'Marine Aliens and Climate Change' Program funded by AXA Researcg Funds, Université de Lausanne = University of Lausanne (UNIL), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), and Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Spatial contextual awareness, Ecology, IBD, Sampling (statistics), Genetic Variation, dispersal kernel, Biology, Regression, Sampling Studies, individual-based simulations, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, Genetics, Population, Genetic drift, Geographical distance, dispersal inference, Statistics, Genetics, Spatial ecology, Biological dispersal, gene flow, Ecology, Evolution, Behavior and Systematics, Biotechnology, Isolation by distance, Demography
Abstract

International audience; Models of isolation-by-distance formalize the effects of genetic drift and gene flow in a spatial context where gene dispersal is spatially limited. These models have been used to show that, at an appropriate spatial scale, dispersal parameters can be inferred from the regression of genetic differentiation against geographic distance between sampling locations. This approach is compelling because it is relatively simple and robust and has rather low sampling requirements. In continuous populations, dispersal can be inferred from isolation-by-distance patterns using either individuals or groups as sampling units. Intrigued by empirical findings where individual samples seemed to provide more power, we used simulations to compare the performances of the two methods in a range of situations with different dispersal distributions. We found that sampling individuals provide more power in a range of dispersal conditions that is narrow but fits many realistic situations. These situations were characterized not only by the general steepness of isolation-by-distance but also by the intrinsic shape of the dispersal kernel. The performances of the two approaches are otherwise similar, suggesting that the choice of a sampling unit is globally less important than other settings such as a study's spatial scale.

Published
2014

42. Genetic Structure of Populations of the Mediterranean Mouflon (Ovis gmelini)

Author

Brigitte Crouau-Roy, Michel Dubois, Stéphane Aulagnier, Richard Bon, and Eric J. Petit

Subjects
education.field_of_study, Ecology, biology, Population, Zoology, Bovidae, biology.organism_classification, Mouflon, Genetic structure, Genetics, Microsatellite, Animal Science and Zoology, Philopatry, education, Ovis, Inbreeding, Ecology, Evolution, Behavior and Systematics, Nature and Landscape Conservation
Abstract

Genetic structure of a population of the Mediterranean mouflon ( Ovis gmelini ) in the Caroux-Espinouse Massif of southern France was investigated using six microsatellite loci. The population was subdivided into home-range groups of females that corresponded to sociospatial units. Males segregated from females outside rut, but they were faithful to the unit where they were born during rut. Both sexes were philopatric. A test for population differentiation and F -statistics was used to show that the sociospatial units corresponded to genetically differentiated units ( F ST = 0.043, P < 0.01). Pairwise comparisons between sociospatial units indicated that the amount of genetic differentiation coincided with their geographic distribution. Unexpectedly, no deficiencies in heterozygosity were found in the units. Lack of inbreeding is not well understood, but mechanisms of avoidance of incest and philopatry of the mouflon as a spatial attachment rather than a social attachment to relatives are discussed.

Published
1997

43. Rousettus madagascariensis (Chiroptera: Pteropodidae) shows a preference for native and commercially unimportant fruits

Author

Paul A. Racey, Radosoa A. Andrianaivoarivelo, Eric J. Petit, Richard K. B. Jenkins, Olga Ramilijaona, Noromampiandra Razafindrakoto, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Faculty of Sciences, Department of Animal Biology, Université d'Antananarivo, Madagasikara Voakajy [Antananarivo, Madagascar], Durrell Institute of Conservation and Ecology, University of Kent [Canterbury], Centre for Ecology and Conservation, Exeter, University of Exeter, Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), and Centre for Ecology and Conservation

Subjects
0106 biological sciences, food.ingredient, Fruit bat, Syzygium jambos, engineering.material, 010603 evolutionary biology, 01 natural sciences, Preference, Pteropodidae, Choice experiment, food, Botany, Madagascar, Nature and Landscape Conservation, Flight cage, Ecology, biology, 010604 marine biology & hydrobiology, Flesh, Pulp (paper), Diospyros kaki, food and beverages, 15. Life on land, biology.organism_classification, Rousettus madagascariensis, Syzygium, engineering, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract

International audience; Flight cage choice experiments carried out over 4 mo demonstrated that a Malagasy fruit bat, Rousettus madagascariensis G. Grandidier, 1928, prefers native or introduced fruit of no commercial value (Ficus polita, Syzygium jambos and S. malaccense) to commercially important fruits (Litchi chinensis and Diospyros kaki). We presented 10 fruit species to the bats: one native (F. polita) and the remainder introduced, 3 of which are commercially important. Most bats responded to fruit presented in a flight cage. Bats swallowed fruit juice and pulp and spat out the fibre of all fruit species provided except L. chinensis and Eugenia jambolana, the flesh of which was swallowed. Chemical composition was the most important determinant of selection by bats. Feeding preference was evidenced by large amounts of chewed pulp, repeated visits to the samefruits and more intensive feeding on lipid- and calcium-rich fruit species. Although commercially important fruit such as L. chinensis and D. kaki tended to have higher fructose content than other species, our results indicate that lipid and calcium content were more important in fruit selection. We suggest that maintaining natural food availability in humid forests and providing alternative sources of fruit (e.g. Syzygium spp.) may contribute to limiting the damage caused by R. madagascariensis to commercially important crops.

Published
2012

44. The evolution of sensory divergence in the context of limited gene flow in the bumblebee bat

Author

Iain Mackie, Eric J. Petit, Emma C. Teeling, Tin Nwe, Si Si Hla Bu, Meriadeg Ar Gouilh, Sébastien J. Puechmaille, Paul J. J. Bates, Medhi Yokubol, Piyathip Piyapan, Khin Mie Mie, Chutamas Satasook, Développement de l'enfant, University College Dublin [Dublin] (UCD), Center of Excellence for Vector and Vector-Borne Diseases, Faculty of Science Mahidol University at Salaya, Faculty of Science, Prince of Songkla University, Prince of Songkla University (PSU), Zoology Department, Yangon University, Yangon University, Harrison Institute, Centre for Systematics and Biodiversity Research, Harrison Institute, Hinthada University, Aberdeen Centre for Environmental Sustainability, University of Aberdeen, Stratégies évolutives et Dynamique spatiale des Populations, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Station Biologique de Paimpont CNRS UMR 6653 (OSUR), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES), Science Foundation Ireland (RFP GEN0056), Royal Irish Academy, Darwin Initiative (DEFRA), Royal Society International project, Thailande, Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS)-Station Biologique de Paimpont CNRS UMR 6653 (OSUR), and Université de Rennes (UR)-Université de Rennes (UR)

Subjects
0106 biological sciences, echolocation, General Physics and Astronomy, Myanmar, Craseonycteris thonglongyai, 01 natural sciences, Gene flow, Chiroptera, Phylogeny, 0303 health sciences, Multidisciplinary, Natural selection, Ecology, natural selection, Thailand, Adaptation, Physiological, Biological Evolution, Phenotype, Gene Flow, Genetic Speciation, drive, Molecular Sequence Data, Allopatric speciation, Human echolocation, Context (language use), Biology, DNA, Mitochondrial, 010603 evolutionary biology, Article, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Genetic algorithm, Sensory ecology, Animals, Amino Acid Sequence, capture, 030304 developmental biology, Local adaptation, bee bat, Genetic Drift, Genetic Variation, Bayes Theorem, population structure, General Chemistry, DNA Fingerprinting, Genetics, Population, hybrid incompatibilities, speciation, Evolutionary biology, Multilocus genotype data, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Microsatellite Repeats
Abstract

The sensory drive theory of speciation predicts that populations of the same species inhabiting different environments can differ in sensory traits, and that this sensory difference can ultimately drive speciation. However, even in the best-known examples of sensory ecology driven speciation, it is uncertain whether the variation in sensory traits is the cause or the consequence of a reduction in levels of gene flow. Here we show strong genetic differentiation, no gene flow and large echolocation differences between the allopatric Myanmar and Thai populations of the world's smallest mammal, Craseonycteris thonglongyai, and suggest that geographic isolation most likely preceded sensory divergence. Within the geographically continuous Thai population, we show that geographic distance has a primary role in limiting gene flow rather than echolocation divergence. In line with sensory-driven speciation models, we suggest that in C. thonglongyai, limited gene flow creates the suitable conditions that favour the evolution of sensory divergence via local adaptation., Populations of the same species living in different habitats can differ in sensory traits driving speciation, but it is not known if this variation limits gene flow. Here, a genetic and acoustic study of the bumblebee bat suggests that geographic distance, instead of echolocation divergence, limits gene flow.

Published
2011

45. Social learning of vocal structure in a nonhuman primate?

Author

Eric J. Petit, Karim Ouattara, Alban Lemasson, Klaus Zuberbühler, Institut Universitaire de France (IUF), Ministère de l'Education nationale, de l’Enseignement supérieur et de la Recherche (M.E.N.E.S.R.), Ethologie animale et humaine (EthoS), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS), Centre Suisse de Recherches Scientifiques, Laboratoire de zoologie et biologie animale, Université de Cocody-Abidjan, Université de Cocody-Abidjan, Stratégies évolutives et Dynamique spatiale des Populations, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Station Biologique de Paimpont CNRS UMR 6653 (OSUR), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES), School of Psychology and Neuroscience [University of St. Andrews], University of St Andrews [Scotland], PICS, University of St Andrews. School of Psychology and Neuroscience, University of St Andrews. Institute of Behavioural and Neural Sciences, University of St Andrews. Centre for Social Learning & Cognitive Evolution, Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS)-Station Biologique de Paimpont CNRS UMR 6653 (OSUR), and Université de Rennes (UR)-Université de Rennes (UR)

Subjects
Calls, Primates, 0106 biological sciences, Cercopithecus-campbelli, Evolution, QH301 Biology, Zoology, Monkeys, 010603 evolutionary biology, 01 natural sciences, Produce, QH301, biology.animal, Similarity (psychology), Captive group, QH359-425, otorhinolaryngologic diseases, Animals, Humans, Learning, Speech, Attention, 0501 psychology and cognitive sciences, Primate, SDG 14 - Life Below Water, 050102 behavioral science & comparative psychology, Chimpanzees, Social Behavior, Control (linguistics), Ecology, Evolution, Behavior and Systematics, Vocalizations, Structure (mathematical logic), biology, Repertoire, 05 social sciences, Haplorhini, Social learning, Biological Evolution, Nonhuman primate, Evolutionary biology, Convergence (relationship), Vocalization, Animal, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Research Article
Abstract

Background Non-human primate communication is thought to be fundamentally different from human speech, mainly due to vast differences in vocal control. The lack of these abilities in non-human primates is especially striking if compared to some marine mammals and bird species, which has generated somewhat of an evolutionary conundrum. What are the biological roots and underlying evolutionary pressures of the human ability to voluntarily control sound production and learn the vocal utterances of others? One hypothesis is that this capacity has evolved gradually in humans from an ancestral stage that resembled the vocal behavior of modern primates. Support for this has come from studies that have documented limited vocal flexibility and convergence in different primate species, typically in calls used during social interactions. The mechanisms underlying these patterns, however, are currently unknown. Specifically, it has been difficult to rule out explanations based on genetic relatedness, suggesting that such vocal flexibility may not be the result of social learning. Results To address this point, we compared the degree of acoustic similarity of contact calls in free-ranging Campbell's monkeys as a function of their social bonds and genetic relatedness. We calculated three different indices to compare the similarities between the calls' frequency contours, the duration of grooming interactions and the microsatellite-based genetic relatedness between partners. We found a significantly positive relation between bond strength and acoustic similarity that was independent of genetic relatedness. Conclusion Genetic factors determine the general species-specific call repertoire of a primate species, while social factors can influence the fine structure of some the call types. The finding is in line with the more general hypothesis that human speech has evolved gradually from earlier primate-like vocal communication.

Published
2011

46. Cross-amplified polymorphic microsatellites for Campbell's monkey

Author

Klaus Zuberbühler, Alban Lemasson, Karim Ouattara, Dominique Vallet, Eric J. Petit, Biologie des organismes et des populations appliquées à la protection des plantes (BIO3P), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Centre National de la Recherche Scientifique (CNRS), Centre de Recherches en Psychologie Cognition et Communication (CRPCC EA 1285), Université de Bretagne Sud (UBS)-Université de Brest (UBO)-MEN : EA1285-Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Université de Neuchâtel (UNINE), Ethologie, éVolution, Ecologie (EVE), Ethologie animale et humaine (EthoS), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Normandie Université (NU)-Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS), Institut Universitaire de France (IUF), Ministère de l'Education nationale, de l’Enseignement supérieur et de la Recherche (M.E.N.E.S.R.), AGROCAMPUS OUEST, 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 Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Université de Caen Normandie (UNICAEN), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Normandie Université (NU)-Normandie Université (NU)-Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS)-Université de Caen Normandie (UNICAEN), and Normandie Université (NU)-Normandie Université (NU)-Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, Genetic Markers, Male, Population, Endangered species, Captivity, Zoology, Animals, Wild, Cercopithecus, 010603 evolutionary biology, 01 natural sciences, Cross-amplification, 03 medical and health sciences, symbols.namesake, Cercopithecus campbelli, Old World monkeys, Animals, education, Ecology, Evolution, Behavior and Systematics, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Genetics, 0303 health sciences, Genetic diversity, education.field_of_study, Polymorphism, Genetic, biology, Gene diversity, Microsatellite, DNA, 15. Life on land, biology.organism_classification, Guenon, Catarrhines, Mendelian inheritance, symbols, Animal Science and Zoology, Animals, Zoo, Female, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Microsatellite Repeats
Abstract

Population genetic analyses are of considerable importance for conservation strategies to protect endangered primates. We tested microsatellites of human origin with an aim to understand the genetic diversity of a West African forest guenon, Campbell’s monkey, Cercopithecus campbelli. Twelve markers amplified successfully, were polymorphic and were inherited in a Mendelian fashion in a group of 4 individuals kept in captivity. These 12 markers were further amplified from 35 faecal samples collected in Taï National Park. These samples proved to originate from 18 free-ranging monkeys and showed that the 12 markers we developed for this species are polymorphic and suitable for future population genetic and parentage analyses.

Published
2009

47. Sex-biased dispersal patterns depend on the spatial scale in a social rodent

Author

Eric J. Petit, Bertrand Gauffre, Vincent Bretagnolle, S. Brodier, Jean-François Cosson, 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), Stratégies évolutives et Dynamique spatiale des Populations, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Biologie des organismes et des populations appliquées à la protection des plantes (BIO3P), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, 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 la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Centre d'études biologiques de Chizé (CEBC), Centre National de la Recherche Scientifique (CNRS), AGROCAMPUS OUEST, 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 Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, 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 la Recherche Agronomique (INRA), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS)-Biologie des organismes et des populations appliquées à la protection des plantes (BIO3P), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Centre d'Études Biologiques de Chizé (CEBC), Centre de biologie et de gestion des populations, Institut National de la Recherche Agronomique (INRA), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Centre National de la Recherche Scientifique (CNRS)-Biologie des organismes et des populations appliquées à la protection des plantes (BIO3P), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST

Subjects
Male, 0106 biological sciences, Aging, Ecology (disciplines), [SDE.MCG]Environmental Sciences/Global Changes, dispersal distances, 010603 evolutionary biology, 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, Microtus arvalis, 03 medical and health sciences, Research articles, genetic analyses, Animals, female kin clusters, Social Behavior, Microtus, Demography, 030304 developmental biology, General Environmental Science, Sex Characteristics, 0303 health sciences, General Immunology and Microbiology, biology, Arvicolinae, Ecology, natal and breeding dispersal, General Medicine, biology.organism_classification, colonization, [SDE.ES]Environmental Sciences/Environmental and Society, Evolutionary biology, Genetic structure, Spatial ecology, Biological dispersal, Female, Mammal, Evolutionary ecology, Vole, France, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, General Agricultural and Biological Sciences
Abstract

Dispersal is a fundamental process in ecology because it influences the dynamics, genetic structure and persistence of populations. Furthermore, understanding the evolutionary causes of dispersal pattern, particularly when they differ between genders, is still a major question in evolutionary ecology. Using a panel of 10 microsatellite loci, we investigated at different spatial scales the genetic structure and the sex-specific dispersal patterns in the common vole Microtus arvalis , a small colonial mammal. This study was conducted in an intensive agricultural area of western France. Hierarchical F ST analyses, relatedness and assignment tests suggested (i) that females are strongly kin-clustered within colonies; (ii) that dispersal is strongly male-biased at a local scale; and (iii) long-distance dispersal is not rare and more balanced between genders. We conclude that males migrate continuously from colony to colony to reproduce, whereas females may disperse just once and would be mainly involved in new colony foundation.

Published
2009

48. Molecular estimation of dispersal for ecology and population genetics

Author

Thomas Broquet, Eric J. Petit, Département d'écologie et évolution [Lausanne] (DEE), Université de Lausanne (UNIL), Stratégies évolutives et Dynamique spatiale des Populations, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Université de Lausanne = University of Lausanne (UNIL), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), and Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, 0303 health sciences, Ecology, Seed dispersal, Ecology (disciplines), Population genetics, backward dispersal, Context (language use), Biology, Ecology and Evolutionary Biology, 010603 evolutionary biology, 01 natural sciences, Variety (cybernetics), Gene flow, 03 medical and health sciences, Biological dispersal, migration rate, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, gene flow, genetic inference, Ecology, Evolution, Behavior and Systematics, dispersal distance, 030304 developmental biology
Abstract

International audience; The dispersal process, by which individuals or other dispersing agents such as gametes or seeds move from birthplace to a new settlement locality, has important consequences for the dynamics of genes, individuals, and species. Many of the questions addressed by ecology and evolutionary biology require a good understanding of species' dispersal patterns. Much effort has thus been devoted to overcoming the difficulties associated with dispersal measurement. In this context, genetic tools have long been the focus of intensive research, providing a great variety of potential solutions to measuring dispersal. This methodological diversity is reviewed here to help (molecular) ecologists find their way toward dispersal inference and interpretation and to stimulate further developments.

Published
2009

49. A new 2CTAB/PCI method improves DNA amplification success from faeces of Mediterranean (Barbary macaques) and tropical (lowland gorillas) primates

Author

Dominique Vallet, Florence Levréro, Nelly Ménard, Eric J. Petit, Sylvain Gatti, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Stratégies évolutives et Dynamique spatiale des Populations, Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Ethologie animale et humaine (EthoS), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Centre National de la Recherche Scientifique (CNRS), Ministère de l'Environnement AGRECO-GEIE (DG Environnement, EU) Programme ECOFAC, Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Université de Caen Normandie (UNICAEN), and Normandie Université (NU)-Normandie Université (NU)-Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, Gorillas, Zoology, Gorilla, Population biology, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 010603 evolutionary biology, 01 natural sciences, Macaque, Macaques, 03 medical and health sciences, Western lowland gorilla, biology.animal, Genetics, Primate, [SDU.ENVI]Sciences of the Universe [physics]/Continental interfaces, environment, DNA extraction, Ecology, Evolution, Behavior and Systematics, Feces, 030304 developmental biology, Faeces, 0303 health sciences, biology, Inhibitors, Macaca sylvanus, biology.organism_classification, genomic DNA
Abstract

International audience; Animal genomic DNA extracts of sufficient quality to address questions about population biology or behavioural ecology can be obtained from faeces when adequate extraction procedures are used. The presence of PCR inhibitors in extract products appears generally the main factor limiting DNA amplification success. We compared DNA amplification success from faeces of a tropical primate (western lowland gorilla, Gorilla g. gorilla) and a Mediterranean primate (Barbary macaque, Macaca sylvanus) between a standardized extraction technique widely used in animals (QIAamp(R) stool kit), a technique mainly used in plant species (CTAB) and a new protocol (2CTAB/PCI). Amplification success varied from 51% to 97%, the highest success being reached with the 2CTAB/PCI protocol in both species.

Published
2008

50. Noninvasive population genetics: a review of sample source, diet, fragment length and microsatellite motif effects on amplification success and genotyping error rates

Author

Thomas Broquet, Eric J. Petit, Nelly Ménard, Briand, Valerie, Département d'écologie et évolution [Lausanne] (DEE), Université de Lausanne (UNIL), Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Stratégies évolutives et Dynamique spatiale des Populations, Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Université de Lausanne = University of Lausanne (UNIL), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), and Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes (UR)-Institut Ecologie et Environnement (INEE)

Subjects
0106 biological sciences, Mitochondrial DNA, amplification success, Population genetics, Biology, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, chemistry.chemical_compound, noninvasive, Genetics, allelic dropout, Allele, Genotyping, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 0303 health sciences, Amplicon, genotyping errors, [SDE.BE] Environmental Sciences/Biodiversity and Ecology, chemistry, Genetic marker, Microsatellite, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, low DNA, DNA
Abstract

International audience; Noninvasive population genetics has found many applications in ecology and conservation biology. However, the technical difficulties inherent to the analysis of low quantities of DNA generally tend to limit the efficiency of this approach. The nature of samples and loci used in noninvasive population genetics are important factors that may help increasing the potential success of case studies. Here we reviewed the effects of the source of DNA (hair vs. faeces), the diet of focal species, the length of mitochondrial DNA fragments, and the length and repeat motif of nuclear microsatellite loci on genotyping success (amplification success and rate of allelic dropout). Locus-specific effects appeared to have the greatest impact, amplification success decreasing with both mitochondrial and microsatellite fragments' length, while error rates increase with amplicons' length. Dinucleotides showed best amplification success and lower error rates compared to longer repeat units. Genotyping success did not differ between hair- versus faeces-extracted DNA, and success in faeces-based analyses was not consistently influenced by the diet of focal species. While the great remaining variability among studies implies that other unidentified parameters are acting, results show that the careful choice of genetic markers may allow optimizing the success of noninvasive approaches.

Published
2007

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