As abundâncias e identidades das espécies de qualquer comunidade biológica mudam tanto ao longo do espaço quanto do tempo. Não obstante, aspectos espaciais da biodiversidade têm sido muito mais explorados do que os temporais. Um dos motivos pelos quais padrões temporais têm recebido menos atenção é a escassez de estudos de longo prazo, especialmente na região neotropical, uma das mais biodiversas e ameaçadas do planeta. Estudar a dinâmica de populações e comunidades ao longo do tempo pode revelar processos ecológicos fundamentais, bem como descrever como pressões naturais e humanas afetam a biodiversidade. Entender a dinâmica das populações e comunidades envolve entender as histórias de vida dos organismos, como eles interagem com o ambiente, o papel de interações entre espécies, o papel de processos demográficos estocásticos, dentre outros fatores. Nesta tese investigamos a dinâmica temporal de populações e comunidades de borboletas e aves, e ao longo dos capítulos avaliamos o papel de diferentes processos na regulação dessas dinâmicas. No Capítulo 1 investigamos se um comportamento sazonal observado em borboletas Ithomiini (Nymphalidae, Danainae), supostamente adaptativo à seca - os \"bolsões de Ithomiini\"- seria uma simples resposta reativa à falta de chuvas ou se mecanismos endógenos (\"relógios biológicos\") estariam envolvidos. No Capítulo 2 realizamos um estudo de dinâmica populacional comparada de borboletas miméticas da tribo Ithomiini. Algumas evidências têm sugerido que além de convergir na morfologia, espécies co-miméticas tenderiam a convergir também no comportamento, no uso de microhabitats e possivelmente em suas dinâmicas populacionais. Testamos as hipóteses de que 1) pares de espécies co-miméticas (i.e., com a morfologia convergente) ou 2) pares de espécies mais próximas filogeneticamente teriam suas dinâmicas populacionais mais correlacionadas do que pares de espécies agrupados ao acaso. No Capítulo 3 descrevemos como a composição de espécies de assembleias de aves e borboletas de nove localidades tropicais e subtropicais na América do Sul e do Norte variou ao longo do tempo (anos a décadas), e se diferenças demográficas entre espécies (nicho) seriam importantes para explicar os padrões observados. No Capítulo 1 encontramos evidências de que a agregações seriam um comportamento endógeno sincronizado com o fotoperíodo, com plasticidade limitada para lidar com as alterações no regime de chuvas previstas para a região e para o continente. No Capítulo 2 encontramos que as dinâmicas populacionais de pares de espécies de Ithomiini de um mesmo anel mimético ou mais próximas filogeneticamente não tenderam a ser mais correlacionadas do que pares reunidos ao acaso, e que as espécies, anéis miméticos e subtribos estudadas tiveram suas dinâmicas temporais mais correlacionados do que seria esperado por acaso. Estes resultados e os do Capítulo 1 sugerem que na dinâmica desse sistema as pressões seletivas exercidas por fatores ambientais seriam mais importantes do que interações entre espécies. No Capítulo 3 mostramos que a composição de espécies de assembleias de aves na Amazônia, Cerrado, Mata Atlântica e Flórida se alterou ao longo dos anos, mesmo em assembleias de áreas bem preservadas. Sobreposta a essa rotatividade (turnover) interanual também encontramos rotatividade sazonal, previsível, na composição de espécies de assembleias de aves da Amazônia e da Mata Atlântica e na assembleia de borboletas Ithomiini. Padrões de rotatividade sazonal na composição de espécies podem ser mais comuns em comunidades neotropicais do que se imagina. As estratégias temporais dos organismos neotropicais, as quais parecem ser a base dos padrões sazonais observados nas comunidades, podem ser largamente determinadas por ritmos (\"relógios\") endógenos. Estudos sobre a regulação dos ritmos e estratégias temporais dos organismos, e dos efeitos das mudanças climáticas e do uso do solo sobre eles, são essenciais. Um importante passo nesse sentido é a disseminação de estudos de longo-prazo de populações e comunidades, contínuos, sistemáticos e com resolução para detectar padrões sazonais. Além disso, a interação das perspectivas, bases teóricas e abordagens da biologia molecular, fisiologia, cronobiologia e ecologia pode avançar nosso entendimento sobre os processos que moldam a dinâmica da biodiversidade e sobre as consequências das perturbações humanas sobre os ecossistemas / The species abundances and identities of any biological community change both over space and time. Nevertheless, Spatial biodiversity dimensions have been much more exploited than temporal ones. One of the reasons for which temporal patterns have received less attention is a scarcity of long-term studies, especially in the neotropical region, one of the most biodiverse and endangered on the planet. Studying the dynamics of populations and communities over time can reveal key ecological processes as well as describe how natural and human pressures affect biodiversity. Understanding the dynamics of populations and communities involves understanding organisms life histories, how they interact with the environment, the role of interactions among species, the role of stochastic demographic processes, and other factors. In this dissertation we investigated the temporal dynamics of butterflies and birds populations and assemblages, and throughout its chapters we evaluate the role of different processes in the regulation of dynamics. In Chapter 1 we investigated whether a seasonal behavior observed in butterflies Ithomiini (Nymphalidae, Danainae), supposedly adaptive to dissecation - the \"Ithomiini pockets \" - is a simple reactive response to drought or there is internal time-keeping mechanisms involved. In Chapter 2, we performed a comparative population dynamics study of mimetic butterflies of the Ithomiini tribe. Some evidence has suggested that besides the convergence in morphology, co-mimetic species would tend to converge also in behavior, in the use of microhabitats and possibly in their population dynamics. We hypothesized that (1) pairs of co-mimetic species or (2) pairs of species more phylogenetically related would have their population dynamics more correlated than pairs of species grouped at random. In Chapter 3 we described how species composition of bird and butterfly assemblages from nine tropical and subtropical locations in South and North America varied over time (years and decades), and if demographic differences between species (niche) are needed to explain observed patterns. In Chapter 1 we found evidence that Ithomiini pockets are regulated by internal time-keeping mechanisms synchronized to photoperiod, and that mechanism has limited plasticity to cope with rainfall regime changes predicted for the study region and for the continent as a whole. In Chapter 2 we found that the population dynamics of Ithomiini species pairs more phylogenetically related or belonging to the same mimetic ring did not tend to be more correlated than pairs assembled at random, and that the species, mimetic rings and subtribes had their temporal dynamics more correlated than would be expected By chance These results and those of Chapter 1 suggest that this system dynamics is more influenced by selective pressures exerted by environmental factors than by species interactions. In Chapter 3 we show that the composition of bird assemblages in the Amazon, Cerrado, Atlantic Rainforest, and Florida has changed over the years, even in assemblies of well-preserved areas. Superimposed to this interannual turnover we also found seasonal, predictable turnover in species composition of bird assemblages of the Amazon and Atlantic Forest and in the Ithomiini butterflies assembly. Patterns of seasonal turnover in species composition may be more common in neotropical communities than is imagined. The temporal strategies of neotropical organisms, which appear to be the basis of the seasonal patterns observed in communities, can be largely determined by endogenous rhythms (\"biological clocks\"). Studies on the regulation of organisms\' temporal rhythms and strategies, and the effects of climate change and land use on them, are essential. An important step in this direction is the dissemination of continuous, systematic, population and community long-term studies, with sampling resolution to detect seasonal patterns. In addition, the interaction of perspectives, theoretical basis, and approaches of molecular biology, physiology, chronobiology, and ecology can advance our understanding of the processes that shape biodiversity dynamics and the consequences of human disturbances on ecosystems

This thesis describes how life history characteristics of the varnish clam (Nuttallia obscurata), and interactions with the physical environment and other species, have contributed to its successful invasion in coastal British Columbia. Lab and field experiments were conducted to investigate varnish clam larval ecology (i.e. larval rearing experiments), adult population dynamics (i.e. annual population surveys, mark-recapture and length-frequency analysis, growth modeling) and ecological interactions with native species (i.e. predator/prey preference feeding trials). Using these results, a matrix demographic model was developed to determine which life history stage contributes the most to varnish clam population growth. Larval rearing experiments indicated that temperature and salinity tolerances of varnish clam larvae are comparable to native species, however the planktonic phase is slightly longer (3-8 weeks). Based on local oceanographic circulation, varnish clam larvae have the potential to disperse throughout their entire geographic range in just one reproductive season. Varnish clam population surveys revealed spatiotemporal variation in density and size. No relationships were evident between varnish clam density and the number or density of co-occurring bivalve species. Length-frequency analysis suggested that recruitment varies among sites, with high post-settlement mortality coinciding with high recruitment. The presence of similar recruitment pulses at geographically separate sites indicates regional scale processes may influence recruitment. Individual growth rates iii varied among sites, with higher growth corresponding to lower population densities and water temperature. Monthly survival rates ranged from 0.81 – 0.99 and were lower for clams 10-30 mm. Predator/prey preference feeding trials showed that crabs prefer varnish clams to local species when clam burial depth is limited. Crabs therefore have the potential to influence varnish clam distributions, particularly on beaches where the varnish clam is unable to bury deeply. Based on matrix demographic analysis, adult survival (e.g. clams ≥ 40 mm) is the most crucial factor for varnish clam population growth, and drives the observed population growth differences between sites. This study of the varnish clam invasion demonstrates that its success lies in both species (e.g. lengthy planktonic phase, high survival) and regional (e.g. favourable ocean circulation patterns for rapid dispersal) characteristics. Measures to reduce introductions should be targeted in areas where introductions are likely to have the furthest reaching impacts.

This thesis is presented as a collection of five papers and one report, each of which has been either published after peer review or submitted for publication. It covers a broad range of applied statistical methods, from deterministic modelling to integrated Bayesian modelling using MCMC, via bootstrapping and stochastic simulation. It also covers a broad range of subjects, from analysis of recreational fishing diaries, to genetic mark recapture for wombats. However, it focuses on practical applications of statistics to the management of wild populations. The first chapter (Hoyle and Jellyman 2002, published in Marine and Freshwater Research) applies a simple deterministic yield per recruit model to a fishery management problem: possible overexploitation of the New Zealand longfin eel. The chapter has significant implications for longfin eel fishery management. The second chapter (Hoyle and Cameron 2003, published in Fisheries Management and Ecology) focuses on uncertainty in the classical paradigm, by investigating the best way to estimate bootstrap confidence limits on recreational harvest and catch rate using catch diary data. The third chapter (Hoyle et al., in press with Molecular Ecology Notes) takes a different path by looking at genetic mark-recapture in a fisheries management context. Genetic mark-recapture was developed for wildlife abundance estimation but has not previously been applied to fish harvest rate estimation. The fourth chapter (Hoyle and Banks, submitted) addresses genetic mark-recapture, but in the wildlife context for estimates of abundance rather than harvest rate. Our approach uses individual-based modeling and Bayesian analysis to investigate the effect of shadows on abundance estimates and confidence intervals, and to provide guidelines for developing sets of loci for populations of different sizes and levels of relatedness. The fifth chapter (Hoyle and Maunder 2004, Animal Biodiversity and Conservation) applies integrated analysis techniques developed in fisheries to the modeling of protected species population dynamics - specifically the north-eastern spotted dolphin, Stenella attenuata. It combines data from a number of different sources in a single statistical model, and estimates parameters using both maximum likelihood and Bayesian MCMC. The sixth chapter (Hoyle 2002, peer reviewed and published as Queensland Department of Primary Industries Information Series) results directly from a pressing management issue: developing new management procedures for the Queensland east coast Spanish mackerel fishery. It uses an existing stock assessment as a starting point for an integrated Bayesian management strategy evaluation. Possibilities for further research have been identified within the subject areas of each chapter, both within the chapters and in the final discussion chapter.

As abundâncias e identidades das espécies de qualquer comunidade biológica mudam tanto ao longo do espaço quanto do tempo. Não obstante, aspectos espaciais da biodiversidade têm sido muito mais explorados do que os temporais. Um dos motivos pelos quais padrões temporais têm recebido menos atenção é a escassez de estudos de longo prazo, especialmente na região neotropical, uma das mais biodiversas e ameaçadas do planeta. Estudar a dinâmica de populações e comunidades ao longo do tempo pode revelar processos ecológicos fundamentais, bem como descrever como pressões naturais e humanas afetam a biodiversidade. Entender a dinâmica das populações e comunidades envolve entender as histórias de vida dos organismos, como eles interagem com o ambiente, o papel de interações entre espécies, o papel de processos demográficos estocásticos, dentre outros fatores. Nesta tese investigamos a dinâmica temporal de populações e comunidades de borboletas e aves, e ao longo dos capítulos avaliamos o papel de diferentes processos na regulação dessas dinâmicas. No Capítulo 1 investigamos se um comportamento sazonal observado em borboletas Ithomiini (Nymphalidae, Danainae), supostamente adaptativo à seca - os \"bolsões de Ithomiini\"- seria uma simples resposta reativa à falta de chuvas ou se mecanismos endógenos (\"relógios biológicos\") estariam envolvidos. No Capítulo 2 realizamos um estudo de dinâmica populacional comparada de borboletas miméticas da tribo Ithomiini. Algumas evidências têm sugerido que além de convergir na morfologia, espécies co-miméticas tenderiam a convergir também no comportamento, no uso de microhabitats e possivelmente em suas dinâmicas populacionais. Testamos as hipóteses de que 1) pares de espécies co-miméticas (i.e., com a morfologia convergente) ou 2) pares de espécies mais próximas filogeneticamente teriam suas dinâmicas populacionais mais correlacionadas do que pares de espécies agrupados ao acaso. No Capítulo 3 descrevemos como a composição de espécies de assembleias de aves e borboletas de nove localidades tropicais e subtropicais na América do Sul e do Norte variou ao longo do tempo (anos a décadas), e se diferenças demográficas entre espécies (nicho) seriam importantes para explicar os padrões observados. No Capítulo 1 encontramos evidências de que a agregações seriam um comportamento endógeno sincronizado com o fotoperíodo, com plasticidade limitada para lidar com as alterações no regime de chuvas previstas para a região e para o continente. No Capítulo 2 encontramos que as dinâmicas populacionais de pares de espécies de Ithomiini de um mesmo anel mimético ou mais próximas filogeneticamente não tenderam a ser mais correlacionadas do que pares reunidos ao acaso, e que as espécies, anéis miméticos e subtribos estudadas tiveram suas dinâmicas temporais mais correlacionados do que seria esperado por acaso. Estes resultados e os do Capítulo 1 sugerem que na dinâmica desse sistema as pressões seletivas exercidas por fatores ambientais seriam mais importantes do que interações entre espécies. No Capítulo 3 mostramos que a composição de espécies de assembleias de aves na Amazônia, Cerrado, Mata Atlântica e Flórida se alterou ao longo dos anos, mesmo em assembleias de áreas bem preservadas. Sobreposta a essa rotatividade (turnover) interanual também encontramos rotatividade sazonal, previsível, na composição de espécies de assembleias de aves da Amazônia e da Mata Atlântica e na assembleia de borboletas Ithomiini. Padrões de rotatividade sazonal na composição de espécies podem ser mais comuns em comunidades neotropicais do que se imagina. As estratégias temporais dos organismos neotropicais, as quais parecem ser a base dos padrões sazonais observados nas comunidades, podem ser largamente determinadas por ritmos (\"relógios\") endógenos. Estudos sobre a regulação dos ritmos e estratégias temporais dos organismos, e dos efeitos das mudanças climáticas e do uso do solo sobre eles, são essenciais. Um importante passo nesse sentido é a disseminação de estudos de longo-prazo de populações e comunidades, contínuos, sistemáticos e com resolução para detectar padrões sazonais. Além disso, a interação das perspectivas, bases teóricas e abordagens da biologia molecular, fisiologia, cronobiologia e ecologia pode avançar nosso entendimento sobre os processos que moldam a dinâmica da biodiversidade e sobre as consequências das perturbações humanas sobre os ecossistemas / The species abundances and identities of any biological community change both over space and time. Nevertheless, Spatial biodiversity dimensions have been much more exploited than temporal ones. One of the reasons for which temporal patterns have received less attention is a scarcity of long-term studies, especially in the neotropical region, one of the most biodiverse and endangered on the planet. Studying the dynamics of populations and communities over time can reveal key ecological processes as well as describe how natural and human pressures affect biodiversity. Understanding the dynamics of populations and communities involves understanding organisms life histories, how they interact with the environment, the role of interactions among species, the role of stochastic demographic processes, and other factors. In this dissertation we investigated the temporal dynamics of butterflies and birds populations and assemblages, and throughout its chapters we evaluate the role of different processes in the regulation of dynamics. In Chapter 1 we investigated whether a seasonal behavior observed in butterflies Ithomiini (Nymphalidae, Danainae), supposedly adaptive to dissecation - the \"Ithomiini pockets \" - is a simple reactive response to drought or there is internal time-keeping mechanisms involved. In Chapter 2, we performed a comparative population dynamics study of mimetic butterflies of the Ithomiini tribe. Some evidence has suggested that besides the convergence in morphology, co-mimetic species would tend to converge also in behavior, in the use of microhabitats and possibly in their population dynamics. We hypothesized that (1) pairs of co-mimetic species or (2) pairs of species more phylogenetically related would have their population dynamics more correlated than pairs of species grouped at random. In Chapter 3 we described how species composition of bird and butterfly assemblages from nine tropical and subtropical locations in South and North America varied over time (years and decades), and if demographic differences between species (niche) are needed to explain observed patterns. In Chapter 1 we found evidence that Ithomiini pockets are regulated by internal time-keeping mechanisms synchronized to photoperiod, and that mechanism has limited plasticity to cope with rainfall regime changes predicted for the study region and for the continent as a whole. In Chapter 2 we found that the population dynamics of Ithomiini species pairs more phylogenetically related or belonging to the same mimetic ring did not tend to be more correlated than pairs assembled at random, and that the species, mimetic rings and subtribes had their temporal dynamics more correlated than would be expected By chance These results and those of Chapter 1 suggest that this system dynamics is more influenced by selective pressures exerted by environmental factors than by species interactions. In Chapter 3 we show that the composition of bird assemblages in the Amazon, Cerrado, Atlantic Rainforest, and Florida has changed over the years, even in assemblies of well-preserved areas. Superimposed to this interannual turnover we also found seasonal, predictable turnover in species composition of bird assemblages of the Amazon and Atlantic Forest and in the Ithomiini butterflies assembly. Patterns of seasonal turnover in species composition may be more common in neotropical communities than is imagined. The temporal strategies of neotropical organisms, which appear to be the basis of the seasonal patterns observed in communities, can be largely determined by endogenous rhythms (\"biological clocks\"). Studies on the regulation of organisms\' temporal rhythms and strategies, and the effects of climate change and land use on them, are essential. An important step in this direction is the dissemination of continuous, systematic, population and community long-term studies, with sampling resolution to detect seasonal patterns. In addition, the interaction of perspectives, theoretical basis, and approaches of molecular biology, physiology, chronobiology, and ecology can advance our understanding of the processes that shape biodiversity dynamics and the consequences of human disturbances on ecosystems

Submitted by Fabio Sobreira Campos da Costa (fabio.sobreira@ufpe.br) on 2017-02-20T13:51:05Z No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) Dissertação CD Biblioetca Denise Moraes 2016 FINAL.pdf: 2561125 bytes, checksum: 30370d4b25d98afe00850c78927ba185 (MD5) / Made available in DSpace on 2017-02-20T13:51:05Z (GMT). No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) Dissertação CD Biblioetca Denise Moraes 2016 FINAL.pdf: 2561125 bytes, checksum: 30370d4b25d98afe00850c78927ba185 (MD5) Previous issue date: 2016-08-19 / FACEPE / O conhecimento dos parâmetros de crescimento e mortalidade em braquiúros é fundamental para a compreensão da sua dinâmica e para o manejo de suas populações. Neste sentido, foram estimados os parâmetros de crescimento e mortalidade para Cardisoma guanhumi Latreille, 1825 (guaiamum), uma espécie com elevada importância socioeconômica no nordeste brasileiro e atualmente considerada pelo Ministério do Meio Ambiente como Criticamente em Perigo de extinção. As amostragens foram efetuadas durante um ano, entre abril de 2015 a março de 2016, na margem superior do mangue do CMA/ICMBio/CEPENE na ilha de Itamaracá, Pernambuco, Brasil. Foram capturados, medidos e pesados 1078 indivíduos (572 machos e 506 fêmeas). Destes, 291 indivíduos foram marcados com microchips PIT ("Passive Integrated Transponder"), para determinação dos parâmetros de crescimento através dos incrementos de peso e tamanho e do crescimento individual. Para a análise dos dados, foram utilizados o método ELEFAN I (baseado na distribuição de frequência de largura de carapaça de 1078 indivíduos), inserido no pacote computacional Fisat II e através da função GrowthTraject (baseada em incrementos individuais de 291 indivíduos marcados com PITs, utilizando o pacote fishmethods (Ambiente de programação “R”). Os indivíduos de C.guanhumi apresentaram largura da carapaça entre 20,9 e 70,0 mm (média: 43,45 mm, desvio padrão: 8,53 mm, mediana: 44,05 mm) o peso total entre 4 e 162 g (média: 45,85 g, desvio padrão: 25,34 g, mediana: 44,0 g). Não houve diferenças significativas, em tamanho médio e peso médio, entre machos e fêmeas. Os parâmetros de crescimento estimados com a função GrowthTraject para 130 incrementos (machos e fêmeas) foram: Linf (tamanho assintótico) = 108,03 mm (largura da carapaça); K (coeficiente de crescimento) = 0,145 ano-1. A Mortalidade total (Z) da população, estimada pelo método Length – converted Catch Curve (pacote FISAT II) usando os parâmetros de crescimento do GrowthTraject foi de = 2,39 ano-1. Não ocorrem capturas comerciais nesta área fechada, portanto, este valor equivale à mortalidade total e natural (Z=M). A idade dos indivíduos capturados variou de 1,49 anos (20,9mm) a 7,02 anos (70,0mm). O recrutamento, calculado no pacote FISAT II e estimado através da presença de juvenis, mostrou-se contínuo durante todo o ano. Os métodos de análises de frequência e comprimento inseridos no pacote FISAT (Bhattacharya, ELEFAN I e Shepherd’s) não foram capazes de determinar os parâmetros de crescimento, provavelmente devido ao crescimento lento e recrutamento contínuo durante todo ano. O tamanho total da população no manguezal do CMA foi estimado em 1262 indivíduos (+- 401ind.), baseado nos dados de marcação e recaptura. / Knowledge on the growth parameters and mortality in brachyuran is fundamental to the understanding of the dynamics and management of their populations. Growth and mortality parameters were estimated for Cardisoma guanhumi Latreille, 1825 (locally known as”guaiamum”), a species with high socio-economic importance in northeastern Brazil and currently considered by the Ministry of the Environment as Critically Endangered of Extinction. The samples were taken over one year, from April 2015 to March 2016, at the upper margin of a small, isolated mangrove patch at CMA-ICMBio-CEPENE on Itamaracá Island, Pernambuco, Brazil. A total of 1078 individuals (572 males and 506 females) were captured, measured and weighed. Of these, 291 individuals were marked with PIT tags (Passive Integrated Transponder tags), as to determine the growth parameters through the analysis of the increments in weight and size and individual growth. For the data analysis, we used the ELEFAN I method (based on the frequency distribution of carapace width 1078 individuals), inserted into the computer package FISAT II and through the GrowthTraject function (based on individual increments of 291 individuals marked with PIT tags, using the fishmethods package ("R” Environment). C. guanhumi showed carapace widths between 20.9 and 70.0 mm (mean: 43,45 mm, standard deviation: 8,53 mm, median: 44,05 mm) and total weight between 4 and 162 g (mean: 45,85 g, standard deviation: 25,34 g, median: 44,0 g). There were no significant differences in average size and average weight between males and females. Growth parameters estimated with the fishmethods package, based on 130 increments (males and females), were: L∞ (asymptotic carapace width) = 108.03 mm; K (coefficient growth) = 0.145 y-1. Total mortality (Z) of the population, estimated through the Length-converted catch Curve method (FISAT II package), using the fishmethods growth parameters, was 2.39 y-1. Since this is a restricted area without regular commercial catches, so this value is roughly equivalent to the total and natural mortality (Z = M). The age of the individuals captured ranged from 1.49 years (20,9 mm) to 7.02 years (70,0 mm). Recruitment, calculated in FISAT II package and estimated by the presence of juveniles, showed to be continuous throughout the year. The methods of length-frequency analysis inserted in the FISAT package (Bhattachary of protective measures for this species.

La fragmentation des paysages et des habitats induite par les infrastructures linéaires de transport terrestres est une des principales causes de la perte de biodiversité actuelle. Parmi ces infrastructures, la route est un acteur majeur de fragmentation, d’autant plus qu’elle possède des effets propres dus au trafic circulant qui induit des collisions véhicule-faune et une pollution des paysages. Afin de diminuer ces effets négatifs, des mesures de réduction sont mises en place, notamment des passages à faune permettant de faire traverser la faune de part et d’autre des voies. La route crée aussi de nouveaux habitats potentiels pour les espèces de la petite faune dans des paysages anthropisés et fragmentés. Dans ce mémoire sont démontrées (1) la potentialité d’habitat de différents éléments routiers ; (2) la possibilité de prédire les collisions véhicule-faune afin de positionner au mieux les mesures de réduction ; (3) l’importance de la méthodologie dans l’évaluation de l’efficacité des passages à faune ; et (4) la possibilité d’améliorer les passages à faune existants. Ces résultats permettront d’améliorer les stratégies de défragmentation des paysages. / Habitats and landscape fragmentation, caused by linear land transports infrastructures, is one of the major cause for the current loss of biodiversity. Among those infrastructures, road is a major cause of fragmentation, especially as it possess specific traffic-linked effects, which induces wildlife-vehicles collisions and landscape pollution. In order to decrease those negative effects, mitigation measures are taken, among which wildlife crossings, enabling wildlife to cross the road. Road also creates new potential habitats for small wildlife species in anthropogenic and fragmented landscapes. In this essay are shown (1) the potential as habitat of different road-linked elements; (2) the possibility to anticipate wildlife-vehicles collisions in order to improve the position of mitigation measures; (3) the importance of methodology in the evaluation of wildlife crossings effectiveness; and (4) the possibility to improve existing wildlife crossings. Those results will allow improving landscape defragmentation strategies.

Pour limiter l'impact des activités humaines sur la biodiversité, les populations animales sont gérées dans de nombreux contextes. La gestion des populations animales comprend la conservation des espèces menacées, comme l’exploitation/régulation des espèces gibiers ou considérées nuisibles. Elle consiste à modifier la dynamique des populations soit en favorisant leur croissance, soit en réduisant leur abondance. Face à l’urgence d’agir dans un contexte de ressources financières limitées, une gestion efficiente des populations animales requiert une bonne compréhension de leur dynamique en réponse aux actions mises en œuvre. Durant mon doctorat, j’ai travaillé en partenariat avec des gestionnaires agissant sur deux systèmes biologiques : la conservation de rapaces méditerranéens (aigles de Bonelli et vautours percnoptères) et la régulation des densités de renards en paysage rural. Pour chaque système, mon travail a consisté i) en l’analyse des suivis de populations qui sont réalisés pour ii) évaluer l’effet de la gestion sur la dynamique des espèces gérées. Dans les deux contextes, j’ai pu iii) mettre en évidence la contribution de l’immigration à la croissance des populations menacées, comme à l’atténuation des effets de la régulation. Après iv) avoir extrait des recommandations pouvant améliorer l’efficience de la gestion en tenant compte de ces processus d’immigration, mon travail s’est conclu par v) une réflexion en retour sur l’optimisation des suivis de populations, afin qu’ils génèrent le plus d’informations pour un investissement moindre. Dans l’ensemble, ce travail aboutit à une réflexion sur les moyens favorisant une gestion efficiente des populations animales. / Due to the multiple interactions linking species together, human activities and animal species influence each other. Animal populations are therefore managed to favour long-term cohabitation. Wildlife management includes the conservation of endangered species, the harvest of game species and the control of species considered as pest. It consists in impacting population dynamics (density variation in a territory) either by favouring or limiting population growth. Faced with the complexity of ecological processes and the urgent need for acting in a context of decreasing allocated resources, an efficient management requires a precious understanding of population dynamics in response to actions. During my PhD, I collaborated with managers supervising two contrasted biological systems: the conservation of endangered Mediterranean raptors (Bonelli’s eagles and Egyptian vultures) and the control of fox densities in French rural landscapes. For each case of study, my work consisted in i) analysing data from population monitoring designed to ii) evaluate the management impact on population dynamics. In both systems, I highlighted iii) the crucial importance of immigration either in boosting endangered population or compensating for fox regulation. After having iv) derived concrete guidelines to improve management facing with immigration. I concluded my PhD by v) searching in turn for cost-effective designs of population monitoring. Overall, I questioned the contrasted systems I studied to understand pitfalls and solutions favouring an efficient management of animal populations.

During the past century the Swedish otter (Lutra lutra) population showed a rapid decline in abundance and genetic diversity. Among the most affected areas was the southern province of Skåne. After prohibiting hunting of otters and banning harmful pollutants like PCB, Swedish populations slowly recovered. To some areas the otter returned late, like Kristianstad in north-eastern Skåne. Here, the River Helge å enters Kristianstad’s Vattenrike, Biosphere Reserve and forms a biodiverse wetland. By 2011, otters had established once more along the river. In recent years, a female otter with cubs have appeared outside Vattenriket visitor’s centre “naturum”, to the joy of inhabitants and visitors. In Kristianstad, otters have become a recurring winter attraction. However, not much is known about this new population. For assessment of abundance and genetic diversity, microsatellite variation was investigated among now-living individuals from eleven sites in the Biosphere reserve, and stored museum samples from ten otters with origins in North-eastern Skåne. Using a non-invasive methodology, investigated DNA was extracted from faeces and muscle tissue from dead individuals. Multiple replicate screening was performed to detect errors in genotyping procedures. Results show the presence of three now-living individuals (two males and one female). Now-living otters and museum specimens from north-eastern Skåne were not closely related. Sampled individuals show Hardy-Weinberg Equilibrium, but their heterozygosity is very low. Results suggest that, even though some individuals may remain undetected, low admixture of new genes may be a cause for concern. For long-term protection and management in Kristianstad’s Vattenrike, Biosphere Reserve, further knowledge is needed about our new and precious otter population. / Den svenska utterstammen (Lutra lutra) genomgick drastiska populationsminskningar under mitten av 1900-talet. Minskningen ledde till en förlust av genetisk diversitet i många områden, och bland de värst drabbade var Skåne. Uttern blev fredad från jakt och ett förbud mot det skadliga miljögiftet PCB infördes, vilket skapade förutsättningar för utterpopulationen i Sverige att långsamt återhämta sig i antal. Men uttern återvände sent till vissa områden, som Kristianstad i Nordöstra Skåne. Genom staden Kristianstad rinner Helge å, som formar vidsträckta, artrika våtmarker i Biosfärområde Kristianstads Vattenrike. Uttern visade inga tecken på återkomst till området förrän 2011. De senaste åren har en utterhona med ungar regelbundet visat sig vid besökscentret ”naturum”, till glädje för stadens invånare och besökare. Uttrarna har blivit en återkommande vinterattraktion i Kristianstad. Men kunskapen om den nya populationen är begränsad. För uppskattning av antal och genetisk diversitet, undersöktes mikrosatellitvariationer hos nu levande individer från elva lokaler i Vattenriket. För jämförelse inkluderades arkiverade prover från Naturhistoriska Riksmuseets ”Miljöprovbank”, från tio döda uttrar med ursprung i Nordöstra Skåne. Med icke-invasiva metoder undersöktes DNA som extraherats från avföring- och muskelvävnad. Multipel replikatanalys gjordes för detektering av eventuella fel i genotypningsproceduren. Resultaten visar förekomsten av tre nu levande individer i Vattenriket (två hanar och en hona). Det är dock troligt att en- eller flera nu levande individer kan ha undkommit identifiering. Individerna var inte nära släkt med museiexemplaren från Nordöstra Skåne. Studerade individer är i Hardy-Weinberg jämvikt, men heterozygositeten är låg. Låg heterozygositet kan bero på en låg genomblandning i populationen, vilket kan vara en anledning till oro och bör undersökas närmre. Det behövs ytterligare kunskap och studier för att långsiktigt skydda och förvalta den nya, värdefulla utterpopulationen i Kristianstads Vattenrike.

Please read the abstract in the section 00front of this document. / Dissertation (MSc)--University of Pretoria, 2010. / Zoology and Entomology / unrestricted

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