Le campagnol terrestre, Arvicola terrestris, occasionne en France, lors de ses pullulations cycliques interannuelles, d’importants dégâts aux prairies de montagne. Un groupe de travail constitué des équipes de recherche de l’Université de Franche-Comté (UFC), de l’INRA (Centre de Biologie et de Gestion des Populations) et d’organismes agricoles (Fédération Régionale de Défense contre les Organismes Nuisibles de Franche-Comté, FREDON), ont privilégié une approche « systémique » dans laquelle les interactions entre les campagnols, leur habitat (paysage, prédateurs) et les pratiques agricoles sont analysées de façon hiérarchisées (spatialement et temporellement). Un des objectifs est de mettre en évidence le plus grand nombre possible de facteurs de contrôle sur lesquels il est possible d’agir, et l'échelle à laquelle ces actions sont pertinentes. Ces études ont permis d’initier une stratégie, expérimentée avec succès, notamment en Franche-Comté et en Auvergne, et qui privilégie la lutte raisonnée. Il subsiste néanmoins des zones d’ombre relatives à la compréhension du cycle, notamment concernant les déterminants de la phase de déclin. Le rôle du cortège de pathogènes (parmi lesquels certains peuvent être transmis à l’homme) reste pour l’instant sujet de débat dans la littérature scientifique. La compréhension des facteurs clés déterminant cette phase devrait permettre aux éleveurs de mieux anticiper les impacts économiques et adopter les stratégies de contrôles des population les plus adéquates. Objectifs de la thèse (1) Tester les hypothèses des pathogènes et de la sénescence pour expliquer le déclin démographique. (2) Rechercher des indicateurs biologiques (diversité des pathogènes et/ou indicateurs immunitaires) qui permettent de prédire les phases de déclin et d’anticiper des mesures agricoles appropriées pour restaurer les prairies. (3) Evaluer le rôle de la transition entre la phase de forte densité et de déclin démographique pour l’émergence de pathogènes circulants par les populations de campagnols et responsables de maladies humaines. Méthodologie générale Des suivis de populations avec des prélèvements réguliers (mensuels) seront réalisés sur plusieurs populations (répliquats) dans la période qui encadre le déclin démographique. Des méthodes fondées sur le séquençage à haut débit (NGS : Next Generation Sequencing) pour l’épidémiologie permettent d’établir des catalogues complets des pathogènes (virus, bactéries, parasites) hébergées par les populations, et d’en mesurer les prévalences. / Context In France, during cyclic population surges, water voles, Arvicola terrestri, cause extensive damage to mountain grassland. A working group consisting of researchers from the University of Franche-Comté (UFC), INRA (Centre de Biologie et de Gestion des Populations) agricultural organizations (Fédération Régionale de Défense contre les Organismes Nuisibles de Franche-Comté, FREDON) are working on systems approach in which interactions between voles, their habitat (landscape, predators) and agricultural practices are analysed hierarchically (in space and time). One of the objectives is to highlight the largest possible number of control factors on which it is possible to act, and the scale at which these actions are relevant. These studies have helped initiate a strategy, successfully tested in Franche-Comté and in Auvergne, which promotes the integrated control of water vole populations. Nevertheless, there are still grey areas in the understanding of the cycle, particularly on the determinants of the decline phase. The role of pathogen communities (some species may even be transmitted to humans) so far remains the subject of debate in the scientific literature. The understanding of the key factors determining this phase should allow farmers to better anticipate economic impacts and to adopt optimal strategies for vole population control Objectives: (1) To test the pathogens and senescence hypotheses in order to explain the population decline. (2) To look for biological indicators (diversity of pathogens and / or immune indicators) that may predict the decline phase in order to anticipate appropriate measures to restore grasslands. (3) To assess the role of the transition between high population density phase and the decline phase for the emergence of pathogens in vole populations that may cause human diseases.General Methodology Population monitoring with regular (monthly) sampling will be made on several populations (replicates) in the period that brackets the vole population declines. Methods based on Next Generation Sequencing (NGS) makes it possible to establish extensive catalogues of pathogens (viruses, bacteria, other parasites) hosted by vole populations and to measure the prevalence.

A ocorrência do ácaro vermelho das palmeiras (AVP), Raoiella indica Hirst (Acari: Tenuipalpidae), foi relatada no Novo Mundo em 2004 e desde então este ácaro tem colonizado várias espécies de aceráceas e musáceas, assim como plantas ornamentais de outras famílias nas ilhas do Caribe, Florida (USA), Venezuela, Brasil e Colômbia. Desde aquele primeiro relato, essa espécie tem produzido consideráveis perdas econômicas em coqueiro nos países onde foi encontrada, o que tem conduzido a um interesse cada vez maior em se conhecer o impacto da praga às plantas em que este ácaro tem sido encontrado. Com o objetivo de conhecer aspectos bioecológicos do AVP na Venezuela foram feitas amostragens para determinar a distribuição geográfica nesse país assim como as plantas hospedeiras e inimigos naturais com os quais a praga tem sido encontrada. A biologia da praga foi estudada em plantas ornamentais e em espécies de palmeiras nativas do Neotrópico, para avaliar o seu potencial em causar dano a estas plantas. Além disso, foi estudada sua distribuição intra-planta, sua flutuação populacional em plantios comerciais de coqueiro e também as variações na expressão das enzimas oxidativas (POD e PPO) e o grau de peroxidação de lipídeos em genótipos de coqueiro, como respostas à alimentação deste ácaro. Foram verificados altos níveis populacionais do AVP em plantios comerciais de coqueiro e em outras plantas crescendo naturalmente no litoral na Venezuela. Em apenas oito espécies de Arecaceae, uma de Musaceae e uma de Strelitziaceae foram verificados todos os estágios de desenvolvimento do AVP, sugerindo que este se desenvolve e se reproduz nestas plantas. O ácaro fitoseídeo Amblyseius largoensis (Muma) foi o predador mais frequentemente associado com o AVP em todos os locais estudados. Maiores densidades do AVP foram observadas nas regiões mediana e basal das folhas coletadas nos estratos mediano e basal da copa da planta. Em 2010, os níveis populacionais do AVP foram mais elevados que em 2011, aparentemente em função dos níveis menores de precipitação naquele ano. O AVP conseguiu se desenvolver sobre as espécies de plantas ornamentais, mas não nas espécies de arecáceas nativas do Novo Mundo. Com relação às enzimas oxidativas, as atividades das POD, PPO e a peroxidação de lipídeos foram maiores em plantas infestadas dos cultivares Anão Amarelo da Malásia (AAM) e Gigante do Caribe (GC) quando comparadas com os respectivos controles. Além disso, maiores atividades de POD e PPO foram detectadas no cultivar AAM que no cultivar GC, tanto em plantas infestadas quando não infestadas. Em contraste, maior peroxidação de lipídeos foi verificada em plantas do cultivar GC infestadas. Estes resultados sugerem que provavelmente esses genótipos de coqueiro possuim mecanismos de resistência ao AVP, porem estudos complementares precisam ser realizados. / Occurrence of the red palm mite, Raoiella indica Hirst (Acari: Tenuipalpidae), was related in the New World in 2004 and since then this mite species has colonized several arecaceaous and musaceous plant species, but also ornamental species in the Caribbean Islands, Florida (USA), Venezuela, Brazil and Colombia. Since firstly reported, this mite species has provoked considerable economic losses in coconut in countries where it has been found thus raising more interest to know pest impact on plant species on which mite has been found. In order to know biological aspects of R. indica samplings were made to determine geographical distribution, and also host plants and natural enemies which are found with it. Pest biology was assessed in ornamental plants and also on palms species native to Neotropical region in order to evaluated potential to cause damage on these plant species. Besides intra-plant distribution and population fluctuation was evaluated in coconut commercial plots and also variations in oxidative enzyme expression (POD and PPO) and extent of lipid peroxidation in coconut genotypes as response to R. indica feeding. Higher population levels of RPM were verified in coconut commercial plots but also in naturally growing plants in the coastal line in Venezuela. All developmental stages of the RPM were verified only on eight Arecaceae species, one Musaceae and one Strelitziaceae species thus suggesting that mite is able to develop and reproduce on these plant species. Phytoseiid mite Amblyseius largoensis (Muma) was the most frequent predator species associated to the RPM in all of the sampling areas. Higher mite densities were observed in middle and basal portions from leaf collected from middle and basal canopy. In 2010, RPM population levels were higher than in 2011, probably as function to lower rainfall levels in that year. The RPM completed development on ornamental plant species but did not on arecaeous native to New World. In regard to oxidative enzymes, POD and PPO activities and lipid peroxidation were higher in infested plants from Malaysian Yellow Dwarf (MYD) and Caribbean Tall (CT) as compared to respective controls. Besides higher POD or PPO activities were detected in MYD cultivar than in CT both in infested or no infested plants. In contrast, higher lipid peroxidation was verified in infested CT cultivar. Our results suggest that probably these coconut genotypes exhibit resistance mechanism to the RPM, however more detailed studies are required.

Made available in DSpace on 2015-03-04T18:51:19Z (GMT). No. of bitstreams: 1 TeseLeonardoGama.pdf: 673646 bytes, checksum: b1f31519bf1d9bd07a3dde2a7574423b (MD5) Previous issue date: 2010-04-01 / Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior / A food web comprises exchanges of matter and energy that occur among species and between biotic and abiotic environment. Given that abiotic components form the basal resources, the approach of this work consists of evaluating the effects of nutrients input in strategic models that describe food web and chain dynamics. Its focus lies on the determination of the nature of equilibrium populations as well as on their dynamics for different functional responses. Strategic models that describe the behavior of interactive populations under nutrient inputs are an important basis for outlining general phenomena that occur in community dynamics. / Uma rede trófica reúne as trocas de matéria e energia que ocorrem entre as espécies e entre o meio biótico e abiótico. Visto que os componentes abióticos formam a fonte de recursos basais, a abordagem deste trabalho consiste na avaliação dos efeitos da entrada de nutrientes alóctones em modelos estratégicos que descrevem a dinâmica de redes e cadeias tróficas, concentrando-se na determinação das características das populações de equilíbrio e das dinâmicas das espécies com diferentes respostas funcionais. Modelos estratégicos que contêm informações acerca do comportamento de populações interativas frente à entrada de nutrientes são uma base importante no delineamento de fenômenos gerais que podem ocorrer dentro da dinâmica de comunidades.

No ambiente agrícola, a possibilidade de prever eventos futuros para poder estabelecer prioridades e planejar atividades são indispensáveis para um manejo adequado. Modelos matemáticos têm se tornado ferramentas valiosas para o entendimento de fenômenos e simulação de soluções de um dado sistema de interesse para diferentes condições iniciais e valores de parâmetros. O crescimento das plantas obedece a certos princípios fisiológicos que podem ser descritos, em termos quantitativos em resposta ao meio ambiente, através de equações matemáticas. Nos agrosistemas, a dinâmica da população de plantas daninhas pode ser descrita por modelos matemáticos que relacionam as densidades de sementes produzidas e de plântulas em áreas de cultivo. Os valores dos parâmetros dos modelos podem ser inferidos diretamente de experimentação e análise estatística, ou extraídos da literatura. O presente trabalho tem por objetivo investigar as particularidades dos parâmetros de modelos dinâmicos para populações de plantas daninhas, a partir de um experimento conduzido em campo, usando inferência Bayesiana via método de Monte Carlo com cadeias de Markov e analisar situações que podem alterar a dinâmica do comportamento populacional por meio de simulações. / In the agricultural environment, the possibility to predict future events to establish priorities and to plan activities is indispensable for an appropriate management. Mathematical models have become precious tools for the understanding of phenomena and simulation of solutions of a given system for different initial conditions and values of parameters. The growth of plants obeys the certain physiological principles that can be described, in quantitative terms in reply to the environment, through mathematical equations. In agrosystems, the dynamics of weed populations can be described by mathematical models that relates the produced seeds density and seedlings density in areas of a crop. The parameter models can be either directly inferred from experimentation and statistics analysis, or can be extracted from literature. The goals of this work is to investigate the particularitities of the dynamic models parameters for weed populations, from field experiment, using Bayesian inference by Monte Carlo method with Markov chains and to analyze situations that can modify the population behavior by simulations.

O ácaro vermelho do tomateiro Tetranychus evansi Baker e Pritchard é uma importante praga exótica de solanáceas na Europa e na África. Sugere-se que este ácaro tenha originado na América do Sul, região onde este não é considerado uma praga importante. Um importante inimigo natural de T. evansi no Brasil é o fungo Neozygites floridana Weiser e Muma que tem como principais características: alta virulência, restrita gama de hospedeiros e difícil crescimento in vitro. A taxonomia das espécies de Neozygites ainda é incerta, sendo que algumas espécies não podem ser separadas por caracteres morfológicos. Estudos moleculares são necessários para separar espécies e isolados de Neozygites patogênicos a ácaros tetraniquídeos. Isolados de N. floridana provenientes de T. urticae apresentam baixa virulência a T. evansi, e isolados de T. evansi apresentam baixa virulência a T. urticae. Através do seqüenciamento parcial da região 18S do DNA ribossômico de N. floridana verificou-se que o isolado de T. evansi (LQ2) apresenta 98% de similaridade ao isolado de T. urticae (LQ3), mas estes dois isolados apresentam alta divergência com outros isolados patogênicos a outros ácaros tetraniquídeos. Por exemplo, a similaridade entre dois isolados coletados em T. urticae, LQ3 e ARSEF662, é de somente 90%, indicando que os fungos identificados como N. floridana possam pertencer a diferentes espécies. Embora N. floridana seja o principal inimigo natural associado a T. evansi na maioria das regiões brasileiras monitoradas até o momento, o papel deste patógeno na regulação populacional da praga ainda não havia sido determinado. Neste estudo, monitorou-se o impacto das epizootias do patógeno nas populações de T. evansi em experimentos de campo e ambiente protegido em quatro ciclos de cultivo em mariapreta e em tomateiro com e sem aplicação de pesticidas químicos. A densidade de T. evansi foi correlacionada com a incidência do fungo e às condições ambientais. O único inimigo natural encontrados nas folhas foi N. floridana e as observações feitas demonstraram que este é um importante fator de regulação das populações de T. evansi em tomateiro, especialmente em ambiente protegido. A sua introdução nos continentes onde esta praga foi recentemente introduzida pode contribuir para a redução do seu impacto nestes locais. / The tomato red spider mite, Tetranychus evansi Baker and Pritchard is an important exotic pest of Solanaceae in Europe and Africa. It is suggested that this mite could have originated from South America, a region where it is not considered as an important pest. An important natural enemy of T. evansi in Brazil is the fungus Neozygites floridana Weiser and Muma that is characterized by high virulence, restricted host range and fastidious in vitro growth. The taxonomy of Neozygites species is still uncertain given that some species cannot be distinguished by morphological characteristics. Molecular studies are usually necessary for discrimination of species and isolates of Neozygites pathogenic to tetranychid mites. Isolates of N. floridana from T. urticae have low virulence towards T. evansi and vice versa. Through partial sequencing of the 18S ribosomal DNA region of N. floridana, it was verified that the isolate of T. evansi (LQ2) had 98% similarity to the isolate of T. urticae (LQ3), but these two isolates had high divergence from other isolates pathogenic to tetranychid mites. For example, the similarity between two isolates collected on T. urticae, LQ3 and ARSEF662, was only 90%, indicating that the fungi identified as N. floridana may be a species complex. Although N. floridana is the principal natural enemy associated with T. evansi in most regions surveyed in Brazil up to date, the role of this pathogen in regulation of T. evansi population has not been determined. This study monitored the impact of the epizootics of the pathogen on populations of T. evansi in experiments both in the field and protected environments in four planting dates on nightshade and tomato with and without pesticide applications. The density of T. evansi was correlated with the prevalence of the fungus and the environmental conditions. The only natural enemy observed was N. floridana and the data revealed that is the fungus is an important factor in the regulation of T. evansi populations in tomato, especially in protected environment. Its introduction to continents where this pest was recently introduced may contribute to the reduction of its impact in these regions.

A merluza, Merluccius hubbsi Marini, 1933, é uma espécie demerso-pelágica típica da região Sudeste-Sul do Brasil, presente entre 21°S e 34°S. Capturada em pequenas quantidades pelas frotas de arrasto, a partir de 2001 tornou-se alvo de pescarias na plataforma externa e talude superior e, desde então, tem apresentado claros sinais de sobrepesca. Estudos sobre o crescimento, a mortalidade e a reprodução apontavam a necessidade de identificar os estoques de merluza na região Sudeste-Sul, visando o adequado ordenamento de sua pescaria, sendo este o objetivo do presente estudo. Com esta finalidade, exemplares da coleção do Museu de Zoologia da USP, otólitos de exemplares juvenis da coleção do Laboratório de Ictiofauna do Instituto Oceanográfico e exemplares coletados em 2004, junto às frotas pesqueiras no Rio de Janeiro, em Santos, em Itajaí e em Rio Grande, no verão e no inverno, foram utilizados para procurando identificar variações geográficas. Foram analisados dados sobre caracteres morfométricos e merísticos, sobre o crescimento de juvenis e de adultos e sobre a reprodução. Os caracteres morfométricos não variaram; os caracteres merísticos apresentaram maiores valores ao sul de 33°S; o crescimento de juvenis e adultos é diferencial entre as regiões, associado à diferentes épocas de desova, com pico no verão na região Sudeste e, no inverno na região Sul. Foram identificados dois estoques: um no sudeste, entre 21°S e 29°S, e outro no sul, entre 29°S e 34°S, este último compartilhado com o Uruguai e a Argentina. Para a gestão imediata da pescaria de M. hubbsi, sugere-se para os dois estoques, restringir a pesca de arrasto durante quatro meses, sendo nos dois primeiros entre 250 e 500 m e nos dois últimos entre 100 e 250 m. Para o estoque sudeste esta restrição deve ser aplicada, para a área entre 21°S e 25°S, de outubro a janeiro e, para a área entre 25°S e 29°S, de novembro a fevereiro. Para o estoque sul a restrição deve abranger a área entre 29°S e 34°S, e vigorar entre abril e julho. / The Argentine hake, Merluccius hubbsi Marini, 1933, is a demersal-pelagic fish inhabiting the South and the Southeast Brazilian area, between 21°S and 34°S. Since 2001, this species has been strongly targeted by trawlers operating at the external continental shelf and the slope. Previous studies about growth, mortality and reproduction pointed the necessity to identify stocks of this species which is the objective of this paper. Samples from the Museu de Zoologia USP collection, otoliths from juveniles fishes from the Ictiofauna Laboratory - IOUSP collection, and specimens collected during Summer and Winter of 2004 from fishing boats operanting in Rio de Janeiro, Santos, Itajaí and Rio Grande were used to analyze geographic variations. Morphometric and meristic data, juveniles and adults growth and reproduction characteristics were analysed. The morphometric characters did not present any variation, instead meristic counts tended to be larger in direction to south of 33°S. Juveniles and adults growth are different between the south and the southeast regions, and associated to different spawning periods, which is in the Summer and in the Winter, respectively. Two stocks were identified: one in the Southeast, between 21°S and 29°S, the other one in the south between 29°S and 34°S, the last one shared with Uruguay and Argentina. In order to manage these stocks, it is suggested the prohibition of the fishery activity during four months, the first two at depth between 250 and 500 m and the last two between 100 and 250 m. For the Southeast stock this restriction would be applied between 21°S and 25°S from October to January and between 25°S and 29°S from November to February. For the south stock the prohibition would be adopted in the area between 29°S and 34°S from April to July.

Composante importante de l’écosystème marin benthique, les bivalves exploités sont surtout situés dans la zone littorale dont les caractéristiques spatiales et temporelles engendrent des fluctuations populationnelles naturelles et contribuent à de fortes variations de biomasse et de structure démographique s’ajoutant aux effets d’activités anthropiques. La compréhension des interactions entre l’espèce, son environnement et son exploitation est cruciale. Leur formalisation, y compris pour la gestion, passe par le développement de modèles mathématiques qui visent à décrire le fonctionnement du système, expliquer des phénomènes observés en termes de cause à effet ou prédire l’effets de nouvelles causes. Espèce introduite en France dans les années 1980, la palourde japonaise (Venerupis philippinarum) constitue une ressource économique importante pour des zones littorales. Pour le bassin d’Arcachon, les pêcheurs à pied professionnels capturent quelques 600 tonnes par an. Outre la réglementation européenne qui fixe une taille minimale de capture, des mesures de gestion complémentaires sont établies par les structures professionnelles locales de la pêche dans un cadre de cogestion impliquant ces structures, scientifiques et administration.Ce travail de thèse s’inscrit dans ce contexte en intégrant les traits d’histoire de vie de la population dans le modèle de simulation utilisé à des fins de gestion. A l’échelle locale, l’analyse de forme conventionnelle basée sur des mesures métriques et pondérales établit des relations d’allométrie entre des paires de descripteurs avec un changement significatif de morphologie à partir d’une longueur de 16-20 mm. La variabilité phénotypique intra-site s’articule en trois patrons morphologiques. Dans le bassin d’Arcachon, le caractère globuleux, décrit pour la première fois ici, est associé à de faibles densités et à de fortes proportions d’individus affectés par la maladie du muscle marron, maladie émergente sur le bassin. A l’échelle de la façade atlantique française, trois ratios morphométriques (indices d’élongation, de densité de la valve et de poids de la valve sur sa longueur) discriminent les populations des sites nord (Banc du Guer, golfe du Morbihan) de celles des sites sud (Bellevue, bassin d’Arcachon). Une corrélation significative entre ces ratios et les conditions trophiques approchées par la concentration en chlorophylle a ainsi qu’un lien entre l’indice de densité de la valve et le pourcentage de températures comprises entre 12 et 20°C sont démontrés. La complexité des facteurs intervenant sur la morphologie intra et inter-sites laisse supposer l’intervention d’autres facteurs comme la nature du substrat, ce qui est conforté par des premières analyses de contours. Les travaux ont confirmé l’importance de la température sur les variables d’état du stock notamment lors de la période de reproduction. Pour ces mêmes variables, un rôle majeur des ressources trophiques a aussi été démontré avec des réponses différant selon les stades. Une partie de ces résultats a contribué à des modifications dans le modèle de simulation. Elles ont surtout concerné l’intégration de l’effet des ressources trophiques sur le recrutement, la révision de la production de juvéniles et des taux de croissance par classe de taille, la précision de données de captures et l’ajout d’un effet prix sur les stratégies de pêche. En parallèle à la validation du modèle, l’analyse de sensibilité a mis en évidence la sensibilité du modèle aux paramètres environnementaux et aux variables relatives aux stades les plus jeunes. Dans un contexte de cogestion, l’outil a été utilisé pour réaliser des projections sur le devenir de la population selon différents scénarios de gestion. Les différences de tendances d’évolution de la biomasse en réponse à ces dispositifs d’action ont servi aux gestionnaires pour la définition des mesures de gestion actuellement en vigueur. Au final, le modèle renforce la démarche participative engagée. / Significant component of the marine benthic ecosystem, exploited bivalves are mainly located inside the coastal area, which temporal and spatial features generate natural population fluctuations and contribute to considerable biomass and demographic structure changes added to anthropogenic activities’ effects (fishing, pollution,…). Understanding of the relationships between the species, its environment and its exploitation is crucial and their formalization, including for management purposes, requires development of mathematical models that aim at describing the functioning of the system, to explain the observed phenomenon in terms of cause and effect or predict effects of new causes. Originating from venerid culture trials carried out in France in the 80s, Manila clam (Venerupis philippinarum) is an important economic resource for coastal areas. Inside the Arcachon Bay, professional fishermen catch about 600 tonnes annually. Whereas the minimum legal harvest size is set by European legislation, complementary management measures are established by regional and departmental professional organizations in the framework of a co-management approach involving professional, scientists and administration. This doctoral thesis is part of this objective of co-management by integrating life history traits of the population in a simulation model used for management purposes. At local scale, conventional shape analysis methods using metric weights and measures establish allometric relationships between pairs of descriptors with a significant morphological change detected from a length of ca. 16-20 mm. Intra-site phenotypic variability is structured in three morphological patterns. Occurrence of globular character inside the Arcachon Bay, described here for the first time, is associated to low densities and to high proportions of individuals affected by brown muscle disease, an emerging disease in the Bay. At the scale of the French Atlantic coast, three morphological ratios (elongation, valve density and weight related to length indices) discriminate populations from northern (Banc du Guer and Morbihan Gulf) and southern sites (Bellevue and Arcachon Bay). Significant relationships between those ratios and trophic conditions expressed by chlorophyll a concentrations, as well as a link between weight surface ratios and percentage of seawater temperature ranging from 12 to 20°C are demonstrated. Complexity of factors involved in intrasite and intersite morphology suggests intervention of other factors such as sediment characteristics, which is supported by a first outlines analysis. This work confirmed the importance of seawater temperature on stock state variables particularly during the reproduction period. For those same variables, a major role of trophic conditions has also been demonstrated with answers depending on development stages. Part of this result contributed to modifications within the simulation model dedicated to this population. The modifications mainly concerned integration of trophic resources effect on recruitment level, juveniles’ production and growth rates per length class revision, accuracy of catches by professional fishermen and addition of a price effect on the fishing strategies. In conjonction with the model validation, the sensitivity analysis undertaken highlighted the sensitivity of the model to environmental parameters and to variables related to the younger stages. In a co-management context, this tool was used to perform projections on the future of the population according to various management scenarios. The differences in the patterns of biomass evolution in response to those action schemes were used by the stakeholders to identify management measures currently in force. In the end the model reinforces the engaged participatory process.

Les grands carnivores recolonisent l’Europe grâce à une augmentation des forêts et des populations d'ongulés sauvages ainsi que des mesures de conservation. Or, les carnivores entrent en interactions avec les activités humaines telles que l’élevage. Quantifier leur distribution peut aider à situer les impacts sur ces activités. Ces espèces sont très mobiles, difficiles à observer et vivent à de faibles densités. La modélisation de leur distribution présente plusieurs défis en raison 1) de leur détectabilité imparfaite, 2) de leur distribution dynamique dans le temps et 3) du suivi à grande échelle basé sur la collecte de données opportunistes sans mesure formelle de l'effort d'échantillonnage. Dans cette thèse, nous nous sommes concentrés sur deux espèces de grands carnivores, le loup et le lynx boréal, pour développer les méthodologies liées à la modélisation de la distribution d’espèces. Nous avons exploré l’application des modèles d’occupancy dans le contexte du suivi des grands carnivores en Europe. Ces modèles établissent le lien entre la présence d’une espèce et l’environnement dans le but d’établir la proportion d'une zone d'étude que l’espèce occupe, tout en prenant en compte une détectabilité imparfaite.Plus précisément, nous avons d'abord évalué la dynamique de la distribution des loups en France de 1994 à 2016, tout en prenant en compte leur détection imparfaite. Nous avons montré l'importance de prendre en compte l’effort d'échantillonnage variant dans le temps et dans l'espace à l’aide de de modèles d’occupancy dynamique.Deuxièmement, comme des faux positifs peuvent être présents lors de la surveillance d'espèces rares, nous avons développé un modèle dynamique d’occupancy qui tenait compte simultanément des faux négatifs et des faux positifs pour analyser conjointement des données qui contenaient à la fois des détections certaines et des détections incertaines. L'analyse des données sur le lynx boréal dans les pays alpins a suggéré que l'incorporation de détections incertaines produisait des estimations des paramètres écologiques plus précises.Troisièmement, nous avons développé un modèle qui prenait en compte l'hétérogénéité de la détection tout en traitant les faux positifs. En appliquant notre nouvelle approche au loup en France, nous avons démontré que l'hétérogénéité de la détection du loup était principalement due à un effort d'échantillonnage hétérogène dans l'espace.Quatrièmement, pour traiter des sources de données multiples, nous avons développé un modèle de processus ponctuel de Poisson qui permettait l'inclusion de différentes sources de données lors de la construction des SDMs. Nous avons montré comment la combinaison des données sur la distribution permettait d’optimiser un suivi en répondant à la question de savoir quelle(s) source(s) d'information apporterait l’essentiel de l’information lors du suivi du lynx en Norvège.Cinquièmement, pour comprendre les mécanismes sous-jacents de la colonisation des loups en France, nous avons développé un cadre statistique pour estimer l'occupation spatio-temporelle et la dynamique des effectifs en utilisant le cadre de diffusion écologique. Nous avons montré le potentiel de notre approche pour prédire la distribution future potentielle du loup à court terme, un élément qui pourrait contribuer à cibler des zones de gestion ou se concentrer sur des zones de conflit potentiel.Dans l'ensemble, nos travaux montrent que les données opportunistes peuvent être analysées à l'aide de modèles de distribution d’espèces qui prennent en compte les contraintes liées au type de suivi utilisé pour produire les données. Nos approches peuvent être utilisées par les gestionnaires pour optimiser la surveillance des grands carnivores, cibler des zones de présence potentielles et contribuer à proposer des mesures destinées à atténuer les conflits. / Large carnivores are recovering in Europe, due to an increasing forest cover, ungulate population and conservation measures. Tthis return poses challenges as carnivores can interact with livestock farming. Assessing their distributions can help to predict and mitigate conflicts with human activities. Because large carnivores are highly mobile, elusive and live at very low density, modeling their distributions presents several challenges due to 1) their imperfect detectability, 2) their dynamic ranges over time and 3) their monitoring at large scales consisting of opportunistic data without a formal measure of the sampling effort. In this thesis, we focused on two carnivore species, wolves (Canis lupus) and Eurasian lynx (Lynx lynx), to develop the methodological aspects related to the modelling of species distributions. We considered the application of occupancy models in the context of monitoring large carnivores in Europe. These models allow the establishment of a link between the species’ presence and environmental covariates while accounting for imperfect detectability, in order to establish the proportion of a study area occupied by the species.We first assessed wolf range dynamics in France from 1994 to 2016, while accounting for species imperfect detection and showed the importance of accounting for time- and space-varying sampling effort using dynamic site-occupancy models.Second, acknowledging that false positives may occur when monitoring rare species, we showcased a dynamic occupancy model that simultaneously accounts for false negatives and positives to jointly analyze data that include both unambiguous detections and ambiguous detections. The analysis of data on the Eurasian lynx in Alpine countries suggested that incorporating ambiguous detections produced more precise estimates of the ecological parameters.Third, we developed a model accounting for heterogeneity in detection while dealing with false positives. Applying our new approach to a case study with grey wolves in France, we demonstrated that heterogeneity in wolf detection was due to a heterogeneous sampling effort across space.Fourth, to deal with multiple data sources, we developed a Poisson point process approach which allows the inclusion of different data sources when building SDMs. By doing so, we also answered the question about which source(s) of information would provide most of the information when monitoring the lynx in Norway.Fifth and finally, to understand the underlying mechanisms of the colonization of wolves in France, we developed a statistical framework for estimating spatiotemporal occupancy and abundance dynamics using the ecological diffusion framework. We demonstrated the potential of our approach to predict the potential future distribution of wolves in the short term, an element that could contribute to target management areas or focus on areas of potential conflict.Overall our work shows that opportunistic data can be analyzed with species distribution models that control for issues linked to the type of monitoring used to produce the data. Our approaches have the potential for being used by decision-makers to optimize the monitoring of large carnivores and to target sites where carnivores are likely to occur and mitigate conflicts.

Em uma perspectiva evolutiva, a emergência e a manutenção de comportamentos altruísticos e de cooperação não é de fácil entendimento. O impulso por ajudar um indivíduo desconhecido não pode significar um prejuízo na capacidade reprodutiva, o que muitas vezes parece ser o mais óbvio. Muito se tem feito no sentido de compreender os ganhos indiretos da cooperação, ou o que se espera em retorno por este comportamento. A espera por reciprocidade é um dos modos de se tornar a cooperação atraente. Os seres humanos possuem uma capacidade singular de expandir a reciprocidade para interações organizadas em que não necessariamente se recebe a retribuição de um favor, mas sim o favor de um terceiro indivíduo. Para estes sistemas, de reciprocidade indireta, são necessários elaborados processos cognitivos que sustentam uma capacidade para linguagem, julgamentos morais e organização social. Entende-se que esta forma de cooperação é um fator essencial para a evolução do intelecto e da estrutura social atuais dos seres humanos. A teoria dos jogos evolucionária é uma ferramenta matemática muito utilizada na sistematização analítica dos problemas envolvendo cooperação e processos evolutivos no geral. A capacidade reprodutiva é traduzida em termos de funções matemáticas, sendo possível realizar dinâmicas populacionais que modelam a pressão seletiva. Neste trabalho, utilizamos métodos de teoria dos jogos evolucionária para explorar modelos de reciprocidade indireta, expandindo o tratamento de um modelo para interações opcionais envolvendo estratégias de cooperadores condicionais. Mostramos que a presença de cooperadores incondicionais ameaça a estabilidade da cooperação e que erros de execução podem ser uma solução. / At an evolutionary perspective, the emergence and maintenance of altruistic and cooperative behaviours is of no easy understanding. The impulse of helping an unrelated individual cannot mean a loss of reproductive fitness, as many times may seem the obvious. Much has been done in the way of knowing the indirect benefits of cooperation, or what to expect in retribution for this behaviour. To expect reciprocity is one way of looking at cooperation as more attractive. Human beings have a singular capacity of expanding reciprocity to organized interactions where retribution of a favour is not necessary, but one can expect the favour of a third-party. For these systems, of indirect reciprocity, elaborate cognitive processes are necessary, ones that maintain the capacity for language, moral judgements and social organization. One can understand this form of cooperation as an essential factor for the evolution of humans nowadays´ intellect and social structure. Evolutionary game theory is a mathematical tool that is largely used in the analytical systematization of problems involving cooperation and evolutionary processes in general. Reproductive fitness is understood in terms of mathematical functions, making possible the work on population dynamics that model selective pressure. In this work, we use methods in evolutionary game theory to explore models of indirect reciprocity, expanding the treatment of a model for optional interactions involving conditional cooperators strategies. We show that the presence of unconditional cooperators threatens the stability of cooperation and that execution errors might be a solution.

Made available in DSpace on 2016-12-23T14:20:38Z (GMT). No. of bitstreams: 1 Fabiano Boscaglia - Capitulo_I_e_II.pdf: 1956367 bytes, checksum: 65bf574f8e52dde89dae4cbc9ccd78d6 (MD5) Previous issue date: 2013-09-13 / O presente estudo discute a relação entre a dinâmica populacional e os recursos hídricos na área urbanizada do município da Serra-ES, a partir das modificações ocorridas na estrutura demográfica e no consumo de água residencial a partir da segunda metade do século XX. Assim, o objetivo da pesquisa consiste em caracterizar e analisar a dinâmica populacional e o consumo de água da Serra apontando as inter-relações atuais e futuras entre os componentes demográficos e o consumo de água residencial. Para alcançar o objetivo proposto delineamos um plano de trabalho que buscou inicialmente rastrear fundamentos teóricos em diversas áreas do conhecimento, almejando visualizar aproximações entre a população e os recursos hídricos. Na sequência, examinou-se com detalhes a evolução e o quadro atual demográfico, bem como o padrão de consumo de água no município, afim de, num esforço analítico encontrar pontos de confluência entre os aspectos demográficos e o consumo de água residencial. Dentre os resultados destacam-se às inter-relações entre o crescimento da população da área urbanizada da Serra e o consumo de água residencial, uma vez que se observa uma mesma tendência de evolução das taxas de crescimento e dos valores absolutos no período analisado entre outras. Os cenários futuros da dinâmica populacional e do consumo de água indicam que a população da Serra continuará crescendo nas próximas décadas, a taxas médias menores a cada período, sendo que após 2040 a população tende a atingir seu nível de saturação, ou seja, o crescimento se estabilizará. Os cenários do consumo se apresentam com tendência de crescimento até a década de 2040, com taxas superiores ao da população em ritmo de desaceleração / This dissertation aims to discuss the relationship between the populational dynamics and the use of water resourses in the urbanized area of the County of Serra, in Espírito Santo, focusing in the transformations that took place in the demographic structure and its relation to the water consumption. The analysis of such relation refers the second half of the twentieth century. Thus, the primary objective of the research consists in characterizing and analyzing the populational dynamic and the consumption of water in Serra, pointing out the current and future interrelationship between the demographic components and the domestic water use. In order to reach the proposed objective, our work plan has seeked, initially, to trace the theoretical framework in various areas of knowledge, trying to explore the theoretical approximations between both fields - Population and water resources. Then we have examined deeply the evolution and the current demographic frame, as well as the patterns of water consumption in the county, intending, in an analytical effort, find out similarities through the correlation of demographic aspects and the domestic water use. Among the outcomes, we would like to highlight the interrelationship between the population growth rate in the urbanized area of Serra County and the consumption of water in the domestic sphere, since it can be noticed the same trend of evolution in the population growth rates and the absolute values in water use in the period analyzed. The future scenario of population dynamic and the water consumption indicate that Serra population keep on growing in the next decades, although with lower rates in each period. Around 2040 the population of Serra must reach its level of saturation, that s to say, the growth will become stable. The scenario of water consumption, instead, will follow a trend of growth until the same decade, but with rates higher than those of the population, this one already in a slowdown