Orientador: Sergio Nascimento Stampar / Resumo: O estudo da conectividade entre as populações é de grande relevância para entender como variantes ambientais podem afetar estes eventos, reconhecendo os padrões de estrutura genética e filogeográficos. Grande parte das espécies marinhas possuem, ao menos, uma fase larval com alto potencial de dispersão, onde possivelmente possa resultar numa população homogênea e com maior conectividade, comparado a outros grupos de animais. Para a compreensão dos padrões variáveis, as análises moleculares trazem informações importantes sobre a variabilidade genética, evolução e mudanças demográficas na história. Por este motivo torna-se cada vez mais importante o uso destes dados em pesquisas que abordam conceitos populacionais. Os acompanhamentos dos cenários em organismos planctônicos ainda são escassos, mesmo com sua grande abundância no ambiente marinho. Sob o cenário da representativa espécie de medusa, endêmica do Atlântico Sul Ocidental, Lychnorhiza lucerna Haeckel 1880 (Scyphozoa; Rhizostomeae) diante de lacunas ainda existentes sobre a estrutura populacional foi analisado como as populações estão se comportando geneticamente ao longo de toda sua distribuição e para isto foram utilizados os marcadores COI, ITS-1 e 2 para inferir a divergência intra e inter-populacional. Os resultados obtidos indicaram um padrão histórico de alta conectividade entre as subpopulações de Lychnorhiza lucerna evidenciando a existência de uma Metapopulação em grande escala. / Abstract: The study of connectivity between populations is relevant to understand the environmental diversity impact on the populations, acknowledging both genetic structural and phylogeographic patterns. Most of the marine species exhibit at least one larval stage with a high dispersal potential that possibly results in a homogeneous population with a wide connectivity when compared to other groups of animals. Molecular analysis provide essential informations concerning the genetic variability, evolution and demographic changes along the history supporting the recognition of variable patterns. Thus, it is essential the use of these data in researches approaching population concepts. Even though planktonic organisms are very abundant in the marine environment, studies regarding the scenario comprising these organisms are scarce. Owing to existing gaps about that, populations of the remarkable medusa specie endemic in the South Western Atlantic, Lychnorhiza lucerna Haeckel 1880 (Scyphozoa; Rhizostomeae), were genetically assessed along the geographic distribution known . For this were used COI and ITS 1-2 molecular markers to conclude about intrapopulation/ interpopulation divergence. The results obteined indicated a historic pattern of high connectivity between subpopulations of Lychnorhiza lucerna evidencing a metapopulation existence on a large scale. / Mestre

O presente trabalho teve como objetivo conhecer os fatores que propiciam as grandes densidades ecológicas de capivaras, através da comparação das dinâmicas populacionais de dois agrupamentos, em diferentes localidades do município de Pirassununga, SP (Campus Administrativo da Universidade de São Paulo – USP/Pirassununga e o Centro de Pesquisa e Gestão de Recursos Pesqueiros e Continentais – CEPTA/Ibama), para que futuramente seja possível propor uma metodologia de manejo que promova o controle populacional dessa espécie no Estado de São Paulo. Para tanto, foi realizado o monitoramento populacional de ambos agrupamentos durante 15 meses, através da contagem direta dos animais, constituindo na principal fonte de informação para determinar as dinâmicas populacionais. Adicionalmente realizaram-se as capturas dos indivíduos de ambas populações pelo uso de bretes fixos, para que fossem feitas as pesagens, sexagens e marcações eletrônicas pelo uso de microchips e assim, conhecer a distribuição etária, bem como a proporção entre sexos. O uso de ceva no interior dos bretes, para a atração dos animais, possibilitou a realização das contagens diretas e das capturas e recapturas. Para a análise das dinâmicas populacionais foram realizadas as comparações descritivas e estatísticas das densidades ecológicas das populações e das respectivas classes etárias, além do cálculo da taxa de crescimento das mesmas. A alimentação em ceva apresentou-se influenciada pela hierarquia de dominância social, o que fez com que apenas as parcelas dominantes fossem capturadas. Percebeu-se, através das capturas, que o número de fêmeas apreendidas foi superior ao de machos nas parcelas dominantes das duas populações. Por meio das observações foram detectados indivíduos satélites e subagrupamentos, cuja ocorrência pode caracterizar um sistema biológico de metapopulação. A comparação descritiva e estatística das densidades ecológicas das populações, bem como a comparação das taxas de crescimento revelaram superioridade populacional do agrupamento do CEPTA/Ibama em relação ao Campus da USP/Pirassununga, provavelmente pelo maior número de picos de acasalamentos observados, os quais possivelmente são influenciados pelo tipo de habitat antropizado e abundante em recursos hídricos presente no CEPTA/Ibama. / The present research aimed the knowledge of the factors that allow the high ecological densities of capybaras through the population dynamics comparison of two capybara groups in the district of Pirassununga, SP (Campus Administrativo da Universidade de São Paulo – USP/Pirassununga and Centro de Pesquisa e Gestão de Recursos Pesqueiros e Continentais – CEPTA/Ibama), intending to propose forward a management methodology for capybara population control in the State of São Paulo. The populations monitoring was carried out through direct count of animals during 15 months, which played the main role to determine the population dynamics. Fixed traps were used to allow the weightings, sex definitions and identification through microchips, and also to know the age distribution and sex ratios. It was used bait inside the traps to attract animals and thus make direct counting and capture possible. To analyze population dynamics it was used the population ecological densities comparisons (statistically and descriptively) and also their rates of increase. It was detected social dominance hierarchy inside the traps, thus only the dominant part of population could be caught. Females represented the majority among captured animals. Satellites individuals and new groups were seen during observations and their existence might characterize a biological system of metapopulation. The descriptive and statistic comparisons of population ecological densities, as well as their rates of increase showed population superiority of CEPTA/Ibama’s group probably for its bigger reproduction effort detected, which possibly receives influence of anthropogenic and water abundant habitats of CEPTA/Ibama.

Submitted by Stefany Archangelo de Angelis null (stefany.archangelis@hotmail.com) on 2018-03-13T14:41:37Z No. of bitstreams: 1 VERSÃO ficha catalografica_DISSERTAÇÃO STEFANY_OK.pdf: 2022875 bytes, checksum: 3f24d2ef22761a31bf2d4ab1b1d18584 (MD5) / Rejected by Disleide Silvia Valerio Gounella null (disleide@clp.unesp.br), reason: Boa tarde. Favor corrigir e completar os itens: - O nome do arquivo deve ser o título do trabalho; - Incluir palavras-chaves em inglês; - Incluir abstract; - Folha de aprovação com data. - As referência bibliográficas foram feitas baseadas nas Normas da ABNT? ABS. Disleide Silvia Valerio Gounella Bibliotecária CLP - São Vicente Fone: (13)3569-7154 Mailto: disleide@clp.unesp.br skype: disleidesilviavaleriogounella on 2018-03-15T18:32:55Z (GMT) / Submitted by Stefany Archangelo de Angelis null (stefany.archangelis@hotmail.com) on 2018-03-16T01:25:44Z No. of bitstreams: 1 Conectividade Populacional de Lychnorhiza lucerna (Cnidaria; Scyphozoa) no Atlântico Sul.pdf: 3463809 bytes, checksum: 5c128c22ffece0245d8284e53a0c5430 (MD5) / Rejected by Disleide Silvia Valerio Gounella null (disleide@clp.unesp.br), reason: xxxxxxxxxxxxxxxxxxxx on 2018-03-19T20:05:54Z (GMT) / Submitted by Stefany Archangelo de Angelis null (stefany.archangelis@hotmail.com) on 2018-03-19T20:07:48Z No. of bitstreams: 1 Conectividade Populacional de Lychnorhiza lucerna (Cnidaria; Scyphozoa) no Atlântico Sul.pdf: 3463809 bytes, checksum: 5c128c22ffece0245d8284e53a0c5430 (MD5) / Approved for entry into archive by Disleide Silvia Valerio Gounella null (disleide@clp.unesp.br) on 2018-03-19T20:26:56Z (GMT) No. of bitstreams: 1 angelis_sa_me_svic.pdf: 3463809 bytes, checksum: 5c128c22ffece0245d8284e53a0c5430 (MD5) / Made available in DSpace on 2018-03-19T20:26:56Z (GMT). No. of bitstreams: 1 angelis_sa_me_svic.pdf: 3463809 bytes, checksum: 5c128c22ffece0245d8284e53a0c5430 (MD5) Previous issue date: 2018-02-19 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / O estudo da conectividade entre as populações é de grande relevância para entender como variantes ambientais podem afetar estes eventos, reconhecendo os padrões de estrutura genética e filogeográficos. Grande parte das espécies marinhas possuem, ao menos, uma fase larval com alto potencial de dispersão, onde possivelmente possa resultar numa população homogênea e com maior conectividade, comparado a outros grupos de animais. Para a compreensão dos padrões variáveis, as análises moleculares trazem informações importantes sobre a variabilidade genética, evolução e mudanças demográficas na história. Por este motivo torna-se cada vez mais importante o uso destes dados em pesquisas que abordam conceitos populacionais. Os acompanhamentos dos cenários em organismos planctônicos ainda são escassos, mesmo com sua grande abundância no ambiente marinho. Sob o cenário da representativa espécie de medusa, endêmica do Atlântico Sul Ocidental, Lychnorhiza lucerna Haeckel 1880 (Scyphozoa; Rhizostomeae) diante de lacunas ainda existentes sobre a estrutura populacional foi analisado como as populações estão se comportando geneticamente ao longo de toda sua distribuição e para isto foram utilizados os marcadores COI, ITS-1 e 2 para inferir a divergência intra e inter-populacional. Os resultados obtidos indicaram um padrão histórico de alta conectividade entre as subpopulações de Lychnorhiza lucerna evidenciando a existência de uma Metapopulação em grande escala. / The study of connectivity between populations is relevant to understand the environmental diversity impact on the populations, acknowledging both genetic structural and phylogeographic patterns. Most of the marine species exhibit at least one larval stage with a high dispersal potential that possibly results in a homogeneous population with a wide connectivity when compared to other groups of animals. Molecular analysis provide essential informations concerning the genetic variability, evolution and demographic changes along the history supporting the recognition of variable patterns. Thus, it is essential the use of these data in researches approaching population concepts. Even though planktonic organisms are very abundant in the marine environment, studies regarding the scenario comprising these organisms are scarce. Owing to existing gaps about that, populations of the remarkable medusa specie endemic in the South Western Atlantic, Lychnorhiza lucerna Haeckel 1880 (Scyphozoa; Rhizostomeae), were genetically assessed along the geographic distribution known . For this were used COI and ITS 1-2 molecular markers to conclude about intrapopulation/ interpopulation divergence. The results obteined indicated a historic pattern of high connectivity between subpopulations of Lychnorhiza lucerna evidencing a metapopulation existence on a large scale.

abstract: This work is an assemblage of three applied projects that address the institutional and spatial constraints to managing threatened and endangered (T & E) terrestrial species. The first project looks at the role of the Endangered Species Act (ESA) in protecting wildlife and whether banning non–conservation activities on multi-use federal lands is socially optimal. A bioeconomic model is used to identify scenarios where ESA–imposed regulations emerge as optimal strategies and to facilitate discussion on feasible long–term strategies in light of the ongoing public land–use debate. Results suggest that banning harmful activities is a preferred strategy when valued species are in decline or exposed to poor habitat quality. However such a strategy cannot be sustained in perpetuity, a switch to land–use practices characteristic of habitat conservation plans is recommended. The spatial portion of this study is motivated by the need for a more systematic quantification and assessment of landscape structure ahead of species reintroduction; this portion is further broken up into two parts. The first explores how connectivity between habitat patches promotes coexistence among multiple interacting species. An agent–based model of a two–patch metapopulation is developed with local predator–prey dynamics and density–dependent dispersal. The simulation experiment suggests that connectivity levels at both extremes, representing very little risk and high risk of species mortality, do not augment the likelihood of coexistence while intermediate levels do. Furthermore, the probability of coexistence increases and spans a wide range of connectivity levels when individual dispersal is less probabilistic and more dependent on population feedback. Second, a novel approach to quantifying network structure is developed using the statistical method of moments. This measurement framework is then used to index habitat networks and assess their capacity to drive three main ecological processes: dispersal, survival, and coexistence. Results indicate that the moments approach outperforms single summary metrics and accounts for a majority of the variation in process outcomes. The hierarchical measurement scheme is helpful for indicating when additional structural information is needed to determine ecological function. However, the qualitative trend between network indicator and function is, at times, unintuitive and unstable in certain areas of the metric space. / Dissertation/Thesis / Ph.D. Applied Mathematics for the Life and Social Sciences 2013

abstract: Mathematical modeling of infectious diseases can help public health officials to make decisions related to the mitigation of epidemic outbreaks. However, over or under estimations of the morbidity of any infectious disease can be problematic. Therefore, public health officials can always make use of better models to study the potential implication of their decisions and strategies prior to their implementation. Previous work focuses on the mechanisms underlying the different epidemic waves observed in Mexico during the novel swine origin influenza H1N1 pandemic of 2009 and showed extensions of classical models in epidemiology by adding temporal variations in different parameters that are likely to change during the time course of an epidemic, such as, the influence of media, social distancing, school closures, and how vaccination policies may affect different aspects of the dynamics of an epidemic. This current work further examines the influence of different factors considering the randomness of events by adding stochastic processes to meta-population models. I present three different approaches to compare different stochastic methods by considering discrete and continuous time. For the continuous time stochastic modeling approach I consider the continuous-time Markov chain process using forward Kolmogorov equations, for the discrete time stochastic modeling I consider stochastic differential equations using Wiener's increment and Poisson point increments, and also I consider the discrete-time Markov chain process. These first two stochastic modeling approaches will be presented in a one city and two city epidemic models using, as a base, our deterministic model. The last one will be discussed briefly on a one city SIS and SIR-type model. / Dissertation/Thesis / Ph.D. Applied Mathematics for the Life and Social Sciences 2014

Orientador: Ana Maria Lima de Azeredo-Espin / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-07T07:13:58Z (GMT). No. of bitstreams: 1 Torres_TatianaTeixeira_D.pdf: 5404919 bytes, checksum: 33cdb805f7c8934dd855ce4d3d6ea798 (MD5) Previous issue date: 2006 / Resumo: A importância cultural e econômica da produção animal na América Latina tem suas raízes na era colonial. Este continente possui uma das maiores populações de gado do mundo e países como o Brasil, a Argentina e o Uruguai têm um papel importante no cenário mundial como produtores e exportadores de uma grande variedade de produtos pecuários. Doenças parasitárias afetam profundamente a produtividade animal e a venda de animais vivos ou derivados e, conseqüentemente, representam um grande impacto no desenvolvimento do setor agropecuário nos países sul americanos. A mosca da bicheira, Cochliomyia hominivorax (Coquerel) é um dos principais agentes causadores de miíases traumáticas na região Neotropical. Larvas da mosca da bicheira alimentam-se de tecidos vivos de animais de sangue quente. Esta espécie foi erradicada da América do Norte e parte da América Central através da técnica do inseto estéril (SIT). Na América do Sul, no entanto, esta peste continua causando um grande prejuízo à pecuária e um projeto internacional está em andamento para se avaliar a execução de um programa de controle da mosca da bicheira neste continente. Neste sentido, o principal objetivo deste estudo foi gerar informações sobre padrões de variabilidade, estrutura genética e fluxo gênico de populações sul americanas de C. hominivorax. Estas são importantes informações para o investimento em programas de controle de insetos-praga. Os microssatélites são uma classe especial de marcadores moleculares tipicamente codominantes e multi-alélicos altamente polimórficos e com uma alta heterozigosidade esperada. Estas características fazem com estes marcadores sejam cada vez mais empregados para investigar questões acerca da variabilidade genética, fluxo gênico e sistemas de acasalamento, até mesmo em espécies com baixos níveis de variabilidade em outros marcadores. A principal limitação dos microssatélites é a necessidade de se desenvolver marcadores microssatélites de novo para cada nova espécie a ser estudada, o que pode ser uma tarefa cara e demorada, mas indispensável na maioria dos casos. Para investigar padrões de variabilidade genética e diferenciação populacional na atual distribuição de C. hominivorax, duas abordagens foram empregadas para isolar marcadores microssatélites a partir de bibliotecas genômicas. Inicialmente, 10 locos foram isolados a partir de uma biblioteca enriquecida em repetições (AC)n. A amplificação destes locos em 30 indivíduos de C. hominivorax, revelou uma média de 6,9 alelos por loco, com heterozigosidades esperadas variando de 0,3831 a 0,8022. Na segunda abordagem, sete novos marcadores polimóficos foram desenvolvidos utilizando uma estratégia diferente, na qual uma sonda (AG)n foi usada em vez de (GT)n na etapa de enriquecimento. A média de alelos encontrados nos sete novos locos foi de 7,8 alelos por loco, com heterozigosidades esperadas variando de 0,4220 to 0,9045. Os "primers" desenvolvidos para C. hominivorax foram utilizados com sucesso na amplificação heteróloga em outras espécies da família Calliphoridae, sugerindo que os locos caracterizados poderão ser úteis em estudos nessas espécies após a avaliação do conteúdo de polimorfismo. Estas duas abordagens também motivaram o desenvolvimento de um conjunto de ferramentas de bioinformática para a análise de seqüências contendo microssatélites, o FiRe ("Find Repeats"). Esta iniciativa representa uma importante contribuição para facilitar o isolamento e caracterização destes marcadores. Doze, dos 17 marcadores desenvolvidos, foram selecionados para caracterizar a variabilidade genética e a estrutura populacional de amostras de C. hominivorax da América do Sul. Em uma análise da estrutura espacial e temporal de populações geográficas do Uruguai, desvios significativos do equilíbrio de Hardy-Weinberg foram observados em todas as subpopulações. Vários pares de locos também apresentaram desequilíbrio de ligação independentemente nas subpopulações. Um baixo, mas significativo, nível de diferenciação foi observado entre as subpopulações, mas não foi detectado isolamento por distância. A análise temporal indicou um aumento na diferenciação populacional global após um ano e foi observada uma diferenciação populacional significativa entre subpopulações da mesma localidade em períodos diferentes. As diferenças observadas entre as populações locais são, provavelmente, um resultado de alterações demográficas em populações da mosca da bicheira. A análise conjunta de 21 populações geográficas da América do Sul (distantes de 15 a 5180 km entre si) revelou uma alta variabilidade genética. Desvios significativos do equilíbrio de Hardy-Weinberg e desequilíbrio de ligação entre pares de locos foram freqüentes nas amostras analisadas. Foi observada uma diferenciação populacional baixa, mas significativa, indicando uma homogeneidade entre as amostras analisadas. A correlação entre as distâncias genéticas e geográficas das amostras não foi significativa. As evidências encontradas apontam para uma expansão populacional recente da espécie no continente sul americano, mas as observações também podem ser uma evidência de uma dinâmica populacional envolvendo eventos freqüentes de extinção e recolonização, na qual cada subpopulação de C. hominivorax se comportaria como uma metapopulação. Independentemente de qual seja o cenário que melhor descreva a história evolutiva desta espécie, fica evidente o potencial de dispersão e adaptação desta espécie, o que terá profundas implicações em programas de controle da espécie. Estudos futuros poderão fornecer um quadro mais completo sobre a dinâmica das populações da mosca da bicheira, gerando informações fundamentais para a tomada de decisões no que concerne à erradicação desta importante praga da pecuária / Abstract: The cultural and economic importance of animal production in South America dates back to the colonial era. This continent has one of the largest percentages of the world's total cattle population and countries like Brazil, Argentina and Uruguay play a major role as exporters of a variety of livestock products. Diseases affecting livestock can have a significant impact on animal productivity, on trade of live animais, meat and other animal products, which, consequently, affects the overall process of the economic development of South American countries. The New World screw-worm (NWS), Cochliomyia hominivorax (Coquerel), is an important parasitic insect pest in Neotropical regions. NWS myiasis is caused by the larval stage of the fly infesting tissues of warm-blooded vertebrates. This species has been successfully eradicated from North and most of Central America by the sterile insect technique. In South America, however, this pest continues to affect the development of the livestock sector and an international effort is underway to evaluate the feasibility of eradicating the NWS from endemic areas of Central and South America. Therefore, the aim of this study was to provide some insight into the patterns of genetic variation, structure and gene flow of C. hominivorax populations from South America. Those are valuable information required prior to an investment on large-scale efforts aiming at controlling insect pests. Microsatellites stand out as co-dominant markers with a high number of alleles per locus, high polymorphism and high-expected heterozygosities. Due to those features, these markers have been increasingly used to investigate questions regarding population structure, gene flow and mC!ting system even in populations that have low levels of allozyme and mitochondrial variation. The major drawback of microsatellites is that they must often be isolated de novo for each species. In order to investigate patterns of genetic differentiation of C. hominivorax from its current distribution using microsatellite loci, two efforts were made to isolate these markers from enriched genomic libraries. Initially, a set of 10 polymorphic microsatellite loci was isolated from an AC-enriched genomic library. Amplification of the reported loci in 30 screw-worms revealed an average of 6.9 alleles per locus with expected heterozygosities ranging from 0.3831 to 0.8022. In the second effort, seven new pOlymorphic microsatellite markers were developed using a different protocol. An (AG)n probe was used instead of (GT)n in the enrichment step. The number of alleles found in the seven new loci ranged from 3 to 13 per locus, with the expected heterozygosities ranging from 0.4220 to 0.9045. Cross-species amplifications of the 17 microsatellite markers were successful in other Calliphoridae species, suggesting that these loci may be useful in those species after evaluating the extent of polymorphism. These efforts have also motivated the development of a web-based, user-friendly toolkit for microsatellite sequence characterization, the FiRe (Find Repeats). This initiative represents an important contribution to other efforts aimed at isolating and characterizing microsatellite markers. Twelve of the 17 isolated loci were used to characterize genetic variability and population structure across NWS South American populations. In the spatio-temporal analysis of C. hominivorax populations from Uruguay, significant departures from Hardy-Weinberg equilibrium were observed for ali populations. Linkage disequilibrium was also detected for severa I locus pairs. Low, but significant, levels of subdivision were recorded between populations, but no evidence of isolation by distance was observed. The temporal analysis indicated a population differentiation increase over time and ali pairwise comparisons between temporal subpopulations yielded significant estimates of population differentiation. The observed differences between local populations are probably a result of the occurrence of demographic changes that affected NWS populations. Analysis of populations from 21 geographical sites in South America (distances ranging from 15 to 5180 km) revealed a high genetic variability within NWS populations. Deviations from Hardy-Weinberg equilibrium and linkage disequilibrium were frequent. A strikingly low, but significant, genetic differentiation was observed, indicating a broad-scale genetic homogeneity in the continent. This low differentiation was coupled with a lack of isolation by distance. These results are consistent with the patterns expected from a species that has undergone range expansion. The pattern of genetic variation among populations could also be an evidence of colonization-extinction dynamics, where subpopulations of this species might usefully be viewed as a metapopulation. Whichever scenario best describes the population structure of NWS, it will have deep implications in contrai strategies. Further studies should complement these findings and provide support for decision makers in the planning and implementation of new area-wide contrai programs of this important livestock pest / Doutorado / Genetica Animal e Evolução / Doutor em Genetica e Biologia Molecular

Halimeda (Chlorophyta, Bryopsidales) (Lamouroux 1812) is a genus of calcareous green algae that has become abundant on coral reefs of the tropics and subtropics. Though they serve biologically and geologically important roles in these ecosystems, their presence may be an indicator of declining environmental conditions. This study focused on a population of Halimeda in the shallow coastal waters of Tavernier, Florida. Three species were encountered: Halimeda discoidea, Halimeda opuntia, and Halimeda incrassata; Halimeda discoidea was the most abundant. The study was conducted in two parts. Part one involved the observation and quantification of the life history characteristics (e.g. fertility rate, growth rate, mortality rate) of the collected specimens in an artificial environment. Population numbers increased throughout the five week study as new individuals were added through vegetative reproduction. Sexual reproduction was not observed. In Part two the life history characteristics of H. discoidea were used in the construction of a size-classified transition matrix model. Sensitivity and elasticity analyses suggested that the population is most sensitive to changes in the survival rate of reproductive juveniles, and least sensitive to the survival of post-reproductive adults. A standard Chi-square test was used to examine the accuracy of the population distribution predicted by the model against the observed distribution during each week of the study. The test results confirmed the validity of the model; however further analysis of the matrix revealed that without the input of sexual recruits the population will go extinct. A random sexual component was then added to the matrix. Environmental stochasticity can have a direct affect on sexual recruitment in Halimeda. Recruitment interval and recruitment success influence the ability of the population to maintain itself. These factors were manipulated in the matrix. With a 25% recruitment interval of 50 recruits the simulated population was able to avoid extinction over a 25 year period. These results implicate that Halimeda populations require both sexual and asexual recruitment. Additionally, the patchy distribution of Halimeda on and near coral reefs of south Florida indicates that the population may actually be a metapopulation. Recommendations for further studies include an investigation of additional sub-populations within the metapopulation. A mortality analysis would also be useful for gaining a better understanding of the population dynamics and sediment contributions of Halimeda in south Florida.

La connectivité est supposée influencer fortement la dynamique et la pérennité des populations d’organismes marins. Ainsi, étudier l’évolution et le maintien des patrons de connectivité au sein des populations marines semble essentiel pour la planification spatiale, la création et la gestion des Aires Marines Protégées (AMP). Cependant, comprendre la complexité des processus régissant la connectivité entre les populations marines nécessite l’utilisation d’outils, qui associent des modèles biophysiques et des informations caractérisant les relations entre démographie et génétique, résultant des échanges larvaires entre les populations. L’objectif de cette thèse de doctorat est donc, d’évaluer les patrons de connectivité génétique au sein des populations de gorgones à une échelle régionale et d'explorer les processus induisant la connectivité observée, grâce à des simulations de modèles prenant en compte les connectivités hydrologique, démographique et génétique. Le premier chapitre présente un modèle de métapopulation spatialement explicite qui, grâce à l’utilisation de matrices de connectivité stochastique, permet d’évaluer l’effet de la démographie sur la fréquence des allèles dans une métapopulation d’espèces marines benthiques sessiles. Le modèle est alors utilisé pour déterminer l’effet des traits démographiques et de la structure de connectivité sur la diversité génétique de la métapopulation. Le deuxième chapitre présente une analyse des patrons de connectivité génétique de deux espèces communes et largement répandues de gorgones, à une échelle régionale : Paramuricea clavata en mer de Ligure et Eunicella singularis dans le Golfe du Lion. Les deux espèces présentent de forts patrons de structure génétique à l’échelle régionale, bien que leur capacité de dispersion ne semble pas limitante (>100m). Le troisième chapitre vise à tester si la dispersion larvaire seule permet d'expliquer la connectivité réalisée d’E. singularis dans le Golfe du Lion, en appliquant le modèle présenté dans le Chapitre 1, et en comparant les patrons de structure génétique modélisés, aux résultats obtenus dans le Chapitre 2, par les méthodes empiriques d’analyse de données génétiques. Les patrons de structure génétique modélisés en ne prenant en compte que la structure spatiale de dispersion sont similaires à ceux observés entre les populations d’E. singularis dans cette région, suggérant le rôle prépondérant de la connectivité hydrologique dans la distribution régionale de l'espèce, tant au niveau démographique que génétique. La capacité d’évaluer le développement des structures génétiques entre populations, sous différents scénarios démographiques et hydrologiques, avec le modèle de paysage sous-marin présenté dans le Chapitre 1 s'avère donc un outil efficace pour la planification spatiale et la pérennité des populations marine. / Connectivity is expected to strongly influence the dynamics and persistence of marine populations. Studying the development and maintenance of connectivity patterns among marine populations is, thus, essential for spatial planning and the proper design and management of Marine Protected Areas (MPAs). However, understanding the complex processes driving marine population connectivity requires the use of tools that integrate bio-physical models with information regarding the demographic and genetic linkages resulting from the larval exchange among populations. Therefore, the aim of this PhD dissertation is to evaluate the patterns of genetic connectivity among gorgonian populations at a regional scale, and disentangle the processes that shape the observed connectivity by using model simulations accounting for hydrological, demographic and genetic connectivity. The first chapter presents a spatially explicit metapopulation model that, using stochastic connectivity matrices, assesses the effect of demography on allele frequencies in a marine metapopulation of sessile benthic species. The model is then used to evaluate the effect of demographic traits and connectivity structure on the genetic diversity of a marine metapopulation. The second chapter examines the patterns of genetic connectivity of two common and widely distributed gorgonian species at a regional scale: Paramuricea clavata in the Ligurian Sea, and Eunicella singularis in the Gulf of Lions. Both species exhibit strong patterns of genetic structure at a regional scale, although the dispersal capacity of each species does not seem limited (>100 m). The third chapter discerns among the potential processes shaping the realized connectivity of E. singularis in the Gulf of Lions by applying the model presented in Chapter 1, and comparing the modeled patterns of genetic structure to the results obtained from empirical genetic data in Chapter 2. Modeled and empirical results show similar patterns of genetic structure among populations of E. singularis in the region. Genetic and demographic differentiation among populations is demonstrated to result from the spatial structure of dispersal alone. The ability to evaluate the expected development of genetic structure among populations under different demographic and hydrological scenarios using the seascape model presented in Chapter 1 provides a useful tool with relevance for marine spatial planning and the persistence of marine populations.

Abstract Plants in riparian environments have to tolerate disturbances like floods and erosion. In the absence of disturbances, habitats will gradually become unfavorable for early-successional species. This can have fundamental consequences not only for adaptation at the individual level, but also for the viability of local populations as well as for the persistence of the species on a regional scale. Silene tatarica is a rare perennial plant exposed to annual floods of the Oulanka River. After sand burial most plants formed vertical rhizomes and new meristems by bud ramification. The special anatomical features of these fleshy underground structures seemed to allow the plants to be very resilient against fast-flowing water. Seed structure may enhance long-distance dispersal by water. Selection gradients for plant height were positive at the individual and group levels, but for the number of stems they were in opposition, as selection at the group level favored a smaller number of stems. This can be associated with pollination and herbivory, since taller and larger plants often attract more pollinators and mammalian herbivores. At the local level, population growth was most sensitive to the survival and growth of juvenile individuals. The populations showed different fates, and according to stochastic simulations some of them will disappear in the near future. Their colonization and extinction rates varied between the years, but their balance over the study period was positive. Small patches had the highest risk of extinction and recolonization of extinct patches was very rare. Elasticity analysis indicated that the survival of patches made a much greater contribution to patch dynamics than did the production of new patches. The short-term dynamics of S. tatarica depend primarily on local dynamics but, in the long run, the species will track the availability of habitat, and its persistence will depend on successful colonizations. The amount of suitable habitat depends on river disturbance. Conservation of this species requires the creation of new suitable open sites for colonization, a dispersal process leading to successful colonizations, and favorable habitats for survival. These conditions can be maintained either by natural processes of river disturbance or by active conservation management.

The species–area relationship (SAR) has been applied to predict species richness declines as area is converted to human-dominated land covers.In many areas of the world, however, many species persist in human-dominated areas, including threatened species. Because SARs are decelerating nonlinear, small extents of natural habitat can be converted to human use with little expected loss of associated species, but with the addition of more species that are associated with human land uses. Decelerating SARs suggest that, as area is converted to human-dominated forms, more species will be added to the rare habitat than are lost from the common one. This should lead to a peaked relationship between richness and natural area. I found that the effect of natural area on avian richness across Ontario was consistent with the sum of SARs for natural habitat species and human-dominated habitat species, suggesting that almost half the natural area can be converted to human-dominated forms before richness declines. However, I found that this spatial relationship did not remain consistent through time: bird richness increased when natural cover was removed (up to 4%), irrespective of its original extent. The inclusion of metapopulation processes in predictive models of species presence improves predictions of diversity change through time dramatically. Variability in site occupancy was common among bird species evaluated in this study, likely resulting from local extinction-colonization dynamics. Likelihood of species presence declined when few neighbouring sites were previously occupied by the species. Site occupancy was also less likely when little suitable habitat was present. Consistent with expectations that larger habitats are easier targets for colonists, habitat area was more important for more isolated sites. Accounting for the effect of metapopulation dynamics on site occupancy predicted change in richness better than land cover change and increased the strength of the regional richness–natural area relationship to levels observed for continental richness–environment relationships suggesting that these metapopulation processes “scale up” to modify regional species richness patterns making them more difficult to predict. It is the existence of absences in otherwise suitable habitat within species’ ranges that appears to weaken regional richness–environment relationships.