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Modification of the Structure of Wild Boar Populations by Hunting and Influence on Reproductive Processes Thibault Gayet

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Modification of the Structure of Wild Boar Populations by Hunting and Influence on Reproductive Processes Thibault Gayet Modification of the structure of wild boar populations by hunting and influence on reproductive processes Thibault Gayet To cite this version: Thibault Gayet. Modification of the structure of wild boar populations by hunting and influence on reproductive processes. Animal genetics. Université de Lyon, 2018. English. NNT : 2018LYSE1125. tel-02314838 HAL Id: tel-02314838 https://tel.archives-ouvertes.fr/tel-02314838 Submitted on 14 Oct 2019 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. N° d’ordre NNT : 2018LYSE1125 THESE de DOCTORAT DE L’UNIVERSITE DE LYON opérée au sein de l’Université Claude Bernard Lyon 1 Ecole Doctorale N°341 Evolution, Ecosystèmes, Microbiologie, Modélisation Spécialité de doctorat : Ecologie Discipline : Biologie évolutive Soutenue publiquement le 13/07/2018, par : Thibault GAYET Modification of the structure of wild boar populations by hunting and influence on reproductive processes Devant le jury composé de : Albano BEJA-PEREIRA, Chercheur, Université de Porto Rapporteur Dustin J. PENN, Professeur adjoint, Université de Vienne Rapporteur Emmanuelle GILOT-FROMONT, Professeure, LBBE, Université Lyon 1 Examinatrice Nirmala SEON-MASSIN, Directrice adjointe DRE, ONCFS Examinatrice Ludovic SAY, Professeur, LBBE, Université Lyon 1 Directeur de thèse Eric BAUBET, Ingénieur chef de projet, ONCFS Co-directeur de thèse Sébastien DEVILLARD, MCU, LBBE, Université Lyon 1 Invité UNIVERSITE CLAUDE BERNARD - LYON 1 Président de l’Université M. le Professeur Frédéric FLEURY Président du Conseil Académique M. le Professeur Hamda BEN HADID Vice-président du Conseil d’Administration M. le Professeur Didier REVEL Vice-président du Conseil Formation et Vie Universitaire M. le Professeur Philippe CHEVALIER Vice-président de la Commission Recherche M. Fabrice VALLÉE Directrice Générale des Services Mme Dominique MARCHAND COMPOSANTES SANTE Faculté de Médecine Lyon Est – Claude Bernard Directeur : M. le Professeur G. RODE Faculté de Médecine et de Maïeutique Lyon Sud – Charles Directeur : Mme la Professeure C. BURILLON Mérieux Directeur : M. le Professeur D. BOURGEOIS Faculté d’Odontologie Directeur : Mme la Professeure C. VINCIGUERRA Institut des Sciences Pharmaceutiques et Biologiques Directeur : M. X. PERROT Institut des Sciences et Techniques de la Réadaptation Directeur : Mme la Professeure A-M. SCHOTT Département de formation et Centre de Recherche en Biologie Humaine COMPOSANTES ET DEPARTEMENTS DE SCIENCES ET TECHNOLOGIE Faculté des Sciences et Technologies Directeur : M. F. DE MARCHI Département Biologie Directeur : M. le Professeur F. THEVENARD Département Chimie Biochimie Directeur : Mme C. FELIX Département GEP Directeur : M. Hassan HAMMOURI Département Informatique Directeur : M. le Professeur S. AKKOUCHE Département Mathématiques Directeur : M. le Professeur G. TOMANOV Département Mécanique Directeur : M. le Professeur H. BEN HADID Département Physique Directeur : M. le Professeur J-C PLENET UFR Sciences et Techniques des Activités Physiques et Sportives Directeur : M. Y. VANPOULLE Observatoire des Sciences de l’Univers de Lyon Directeur : M. B. GUIDERDONI Polytech Lyon Directeur : M. le Professeur E. PERRIN Ecole Supérieure de Chimie Physique Electronique Directeur : M. G. PIGNAULT Institut Universitaire de Technologie de Lyon 1 Directeur : M. le Professeur C. VITON Ecole Supérieure du Professorat et de l’Education Directeur : M. le Professeur A. MOUGNIOTTE Institut de Science Financière et d'Assurances Directeur : M. N. LEBOISNE Modification of the structure of wild boar populations by hunting and influence on reproductive processes Thibault GAYET A thesis presented for the degree of Doctor of Philosophy A mon oncle Aimé, amateur de la bête noire Foreword My PhD grant was fund by the French Hunting and Wildlife Agency (Office National de la Chasse et de la Faune Sauvage, ONCFS), which is a public institution. Expenses related to my PhD were financially supported by both the Laboratory of Biometry and Evolutive Biology (Laboratoire de Biométrie et Biologie Evolutive, LBBE), which is an academic research laboratory, and the ONCFS. The ONCFS is divided in several departments with specific missions. I belonged to the Expertise and Research Department, whose missions are to acquire knowledge on wildlife species by conducting field studies and to provide expert counseling and technical support for field managers. Therefore, you will find two popularization articles (in French) in the last two appendices aiming to give feedbacks to partners involved and information to managers. Focusing a little closer, I was part of the Wild ungulates team, in the group Expertise and Management. My PhD was part of the project aiming to get information on wild boar biology. My original project was to investigate some of the mechanisms already proposed to explain the demography of wild boar currently observed. It included the disruption of the mating system, that I developed broadly in the thesis, and hybridization with the domestic pig. Initially, we wanted to study the impact of hybridization on the fitness of hybrids. Indeed, hybridization may give fitness advantages to hybrids and their offspring by introducing artificially selected genes of the pig in wild boar. It is suggested that hybrids and their descendant have increased the litter size and/or the individual growth rate for example. In contrary, artificially selected traits (by human) in the pig to increase productivity may be too maladaptive to be maintained in the wild, where resources are limited. Initially, we aimed to investigate if there is a link between the level of hybridization of an individual and its fitness. Sadly, detangling which scenario actually takes place was quickly abandoned because preliminary study of the diagnostic power of genetic tools available gave rather disappointing results. Due to the low level of genetic differentiation between wild boar and domestic pig, identifying hybrids beyond first generation hybrids (direct offspring of a wild boar and a pig) was not possible. However, this study lead to a publication available in first appendix. Also, the analytical skills obtained allowed me to take part of another project aiming to develop a new analytical technic to study hybridization which is in second appendix. Abstract The wild boar (Sus scrofa scrofa) is a peculiar species. It is an appreciated game species for hunters, a nightmare for farmers and a subject of debate for the society in general. The tenfold increase of the population over the last decades in France and all over Europe, despite increased hunting pressure, generated great human-wildlife conflict. The wild boar is responsible for great economic losses due to damaged crops, vehicle collision, diseases transmission and ecosystem disturbances. Improving management strategies becomes a prime interest to avoid such conflicts, or at least keep them under control. Obtaining information on the species is a first step toward good management strategies. The objective of my work is, in a first part, to characterize the mating system of the wild boar using genetic tools (microsatellite markers) and to identify some parameters influencing the reproductive processes, focusing especially on hunting. The second part focus on the investigation of the influence of the mating system on wild boar life history traits. My researches are based on the study of several populations contrasting in their hunting practices and on longitudinal data of a highly monitored population. The study is based on data collected on wild boars killed by hunting. Genotypes were obtained for pregnant females and their litter and paternity analyses were realized to measure the number of fathers in a litter and estimate multiple paternity rates (proportion of litter sired by more than one father). I was able to show that the mating system is mainly promiscuous (several males mate with several females) contrasting with the polygyny (a dominant male monopolizing a group of females) usually described in this species. Moreover, reproductive processes, estimated by the number of mates of a female and the multiple paternity rates, are influenced by hunting variations in a population. I also showed that number of fathers has positive effect on female fecundity. High rates of multiple paternity together with high genetic diversity were found in a heavily hunted population, suggesting multiple paternity may buffer yearly bottlenecks. However, the increase of number of fathers is not associated with increase of within-litter variation. Keywords: Harvesting, Mating system, Paternity analysis, Population genetic, Ungulate. Résumé Le sanglier (Sus scrofa scrofa) est une espèce à part entière. C'est une espèce de gibier particulièrement appréciée des chasseurs, un cauchemar pour les agriculteurs et un sujet de débat pour la société en général. La multiplication par dix des populations au cours des dernières décennies en France et dans toute l'Europe, malgré une pression de chasse accrue, a engendré de nombreux conflits entre les humains et la faune
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