Orientadores: Fernando José Von Zuben, Leandro Nunes de Castro Silva / Tese (doutorado) - Universidade Estadual de Campinas, Faculdade de Engenharia Elétrica e de Computação / Made available in DSpace on 2018-08-22T19:55:45Z (GMT). No. of bitstreams: 1 Pasti_Rodrigo_D.pdf: 4931504 bytes, checksum: 28f0e5bc0f2210db1cfb2cd2fc4c7f15 (MD5) Previous issue date: 2013 / Resumo: Existem muitas formas de se entender e descrever a natureza, sendo que a Computação Natural parte do princípio de que sistemas naturais são processadores de informação, ou seja, realizam computação. Esta tese recorre aos mecanismos da Computação Natural para o entendimento das computações realizadas em um sistema natural específico: os ecossistemas. O primeiro passo está fundamentado na ciência da Biogeografia, que estuda os ecossistemas e seus padrões emergentes. Na Biogeografia, é possível identificar elementos, relações entre eles e processos. A principal contribuição desta tese está na formalização computacional da Biogeografia, dando origem à Computação Biogeográfica. A proposta da Computação Biogeográfica é desenvolvida em várias frentes. A primeira delas promove a formalização do metamodelo, definido como uma estrutura conceitual que busca contextualizar a existência de ecossistemas artificiais e seus processos espaço temporais. Em seguida, para ilustrar a aplicação do metamodelo, são propostas definições de computação de ecossistemas em superfícies adaptativas fenotípicas. Essas definições resultam em um conjunto de relações e processos, os quais são aplicáveis à construção de ecossistemas artificiais. Estes, por sua vez, permitem o entendimento de dinâmicas e padrões de ecossistemas e também podem contribuir para a resolução de problemas computáveis. Na etapa final da tese, será proposto um algoritmo de radiação adaptativa que exibe padrões similares aos encontrados em ecossistemas reais e que se mostra competitivo para otimização multimodal em espaços contínuos. Por fim, perspectivas futuras são apresentadas visando indicar caminhos para se consolidar a Computação Biogeográfica como um novo ramo da Computação Natural / Abstract: There are several attempts to understand and describe nature, and Natural Computing is founded on the principle that natural systems are information processors, in the sense that they perform computation. This thesis makes use of Natural Computing mechanisms for the understanding of the computation taking place in a specific natural system: the ecosystems. The first step is based on the science of Biogeography, devoted to the study of ecosystems and their emerging patterns. In Biogeography, it is possible to identify elements, relations among them, and processes. The main contribution of this thesis resides in the computational formalization of Biogeography, thus establishing the research area of Biogeographic Computation. The proposal of Biogeographic Computation is introduced in several fronts. The first front promotes the metamodel formalism, which defines a conceptual framework focused on contextualizing the existence of artificial ecosystems and their spatio-temporal processes. After that, aiming at illustrating the application of the metamodel, definitions of ecosystems computing in phenotypic adaptive surfaces is proposed. These definitions proceed to a set of relations and processes directly applicable to the proposition of artificial ecosystems. These artificial ecosystems promote the understanding of natural ecosystems dynamics and patterns, and can also contribute to the resolution of computable problems. At the final stage of the thesis, it is presented an adaptive radiation algorithm exhibiting patterns which are similar to the ones found in real ecosystems, and also proving to be competitive for multimodal optimization in continuous spaces. To conclude, some perspectives for the further steps of the research are outlined with the purpose of indicating some routes to consolidate Biogeographic Computation as a new branch of Natural Computing / Doutorado / Engenharia de Computação / Doutor em Engenharia Elétrica

In this thesis I describe fine-scale spatial patterns in rain forest termites, from the colony to the assemblage level, sampled from one hectare plots in Central African and South East Asian lowland rain forest. By so doing the ecological interactions that structure this functionally important and abundant soil community were identified. The African termite assemblage, dominated by soil-feeding termites, saturated the upper soil profile (collected from 90% of soil pits). In contrast termites were collected from <50% of soil pits in Asia, with this difference reflecting the lower species densities and abundances of soil-feeding termites in Asian forests. Territoriality and inter-specific competition was shown to be important between colonies of soil-feeding species in the African plot. The termite assemblages were spatially associated with several environmental properties. However these could not explain the spatial patterns in the functional components of the assemblages. Wood-feeding termites were highly patchily distributed, due to the heterogeneous nature of their food material, but also due to possible competitive interactions for this. Humus-feeding termites were homogenously structured, due to the continuous nature of soil as their feeding and nesting material. True soil-feeding termites, unique to the African assemblage, were heterogeneously distributed despite the equally continuous nature of their feeding and nesting material. This structure may arise from facilitative interactions, such as co-operative defence against ant predation which may be intense in African systems, or through the transfer of soil material at different stages of decomposition. Competition for space is apparent in both regions, both at the colony level among soil-feeding genera, and between aggregations of functional groups. Positive and negative biotic interactions, operating at various spatial and functional scales, appear to be important in influencing how assemblage composition is spatially structured. If indeed facilitation is important in maintaining the taxonomic and functional diversity in termite assemblages, it would be valuable to confirm the mechanism(s) that drives this (i.e. predation and/or food transfer), as these may then influence ecosystem stability.

Biogeographers have long searched for common processes responsible for driving diversification in the Holarctic region. Although terrestrial flora and fauna have been well studied, much of the marine biogeographic work addresses patterns and processes occurring over a relatively recent timescale. A prerequisite to comparative biogeographic analysis requires well-resolved phylogenies of similarly distributed taxa that diverged over a similar timeframe. The overall aim of my Ph.D. thesis was to address fundamental questions in the systematics and biogeography of a family of Holarctic fish (Osmeridae) and place these results in a broad comparative biogeographic framework. With eight conflicting morphological hypotheses, the northern hemisphere smelts have long been the subjects of systematic disagreement. In addition to the uncertainty in the interrelationships within this family, the relationship of the Osmeridae to several other families remains unclear. Using DNA sequence data from three mitochondrial and three nuclear genes from multiple individuals per species, I reconstructed the phylogenetic relationships among the 6 genera and 15 osmerid species. Phylogenetic reconstruction and divergence dating yielded a well-resolved phylogeny of the osmerid genera and revealed several interesting evolutionary patterns within the family: (1) Hypomesus chishimaensis and H. nipponensis individuals are not reciprocally monophyletic, suggesting that they are conspecific and H. chishimaensis is a recently evolved freshwater ecotype that invaded the Kuril Islands following the last glaciation, (2) The trans-Pacific sister relationships in Hypomesus based on lateral line scale counts are not supported, implying that this phenotype evolved in parallel on each side of the North Pacific Ocean, (3) The Plecoglossidae are the Osmeridae sister group, (4) Over half of the characters from previous studies show evidence of parallel evolution; however, 27 traits reflect ancestral relationships, (5) Multiple divergences within the Osmeridae date to both the mid-Miocene cooling period and the Pliocene Bering Seaway opening, suggesting these events were important in the evolution of these fishes, and (6) Divergences in many marine taxa for which dated phylogenies are available are also correlated with these time periods. Future research should target additional Holarctic marine taxa for further comparative analysis.

Biogeographers have long searched for common processes responsible for driving diversification in the Holarctic region. Although terrestrial flora and fauna have been well studied, much of the marine biogeographic work addresses patterns and processes occurring over a relatively recent timescale. A prerequisite to comparative biogeographic analysis requires well-resolved phylogenies of similarly distributed taxa that diverged over a similar timeframe. The overall aim of my Ph.D. thesis was to address fundamental questions in the systematics and biogeography of a family of Holarctic fish (Osmeridae) and place these results in a broad comparative biogeographic framework. With eight conflicting morphological hypotheses, the northern hemisphere smelts have long been the subjects of systematic disagreement. In addition to the uncertainty in the interrelationships within this family, the relationship of the Osmeridae to several other families remains unclear. Using DNA sequence data from three mitochondrial and three nuclear genes from multiple individuals per species, I reconstructed the phylogenetic relationships among the 6 genera and 15 osmerid species. Phylogenetic reconstruction and divergence dating yielded a well-resolved phylogeny of the osmerid genera and revealed several interesting evolutionary patterns within the family: (1) Hypomesus chishimaensis and H. nipponensis individuals are not reciprocally monophyletic, suggesting that they are conspecific and H. chishimaensis is a recently evolved freshwater ecotype that invaded the Kuril Islands following the last glaciation, (2) The trans-Pacific sister relationships in Hypomesus based on lateral line scale counts are not supported, implying that this phenotype evolved in parallel on each side of the North Pacific Ocean, (3) The Plecoglossidae are the Osmeridae sister group, (4) Over half of the characters from previous studies show evidence of parallel evolution; however, 27 traits reflect ancestral relationships, (5) Multiple divergences within the Osmeridae date to both the mid-Miocene cooling period and the Pliocene Bering Seaway opening, suggesting these events were important in the evolution of these fishes, and (6) Divergences in many marine taxa for which dated phylogenies are available are also correlated with these time periods. Future research should target additional Holarctic marine taxa for further comparative analysis.

Biogeographers have long searched for common processes responsible for driving diversification in the Holarctic region. Although terrestrial flora and fauna have been well studied, much of the marine biogeographic work addresses patterns and processes occurring over a relatively recent timescale. A prerequisite to comparative biogeographic analysis requires well-resolved phylogenies of similarly distributed taxa that diverged over a similar timeframe. The overall aim of my Ph.D. thesis was to address fundamental questions in the systematics and biogeography of a family of Holarctic fish (Osmeridae) and place these results in a broad comparative biogeographic framework. With eight conflicting morphological hypotheses, the northern hemisphere smelts have long been the subjects of systematic disagreement. In addition to the uncertainty in the interrelationships within this family, the relationship of the Osmeridae to several other families remains unclear. Using DNA sequence data from three mitochondrial and three nuclear genes from multiple individuals per species, I reconstructed the phylogenetic relationships among the 6 genera and 15 osmerid species. Phylogenetic reconstruction and divergence dating yielded a well-resolved phylogeny of the osmerid genera and revealed several interesting evolutionary patterns within the family: (1) Hypomesus chishimaensis and H. nipponensis individuals are not reciprocally monophyletic, suggesting that they are conspecific and H. chishimaensis is a recently evolved freshwater ecotype that invaded the Kuril Islands following the last glaciation, (2) The trans-Pacific sister relationships in Hypomesus based on lateral line scale counts are not supported, implying that this phenotype evolved in parallel on each side of the North Pacific Ocean, (3) The Plecoglossidae are the Osmeridae sister group, (4) Over half of the characters from previous studies show evidence of parallel evolution; however, 27 traits reflect ancestral relationships, (5) Multiple divergences within the Osmeridae date to both the mid-Miocene cooling period and the Pliocene Bering Seaway opening, suggesting these events were important in the evolution of these fishes, and (6) Divergences in many marine taxa for which dated phylogenies are available are also correlated with these time periods. Future research should target additional Holarctic marine taxa for further comparative analysis. / Science, Faculty of / Zoology, Department of / Graduate

Estudo da termitofauna (Insecta, Isoptera) da região do alto Rio Madeira, Rondônia. Na região conhecida como alto Rio Madeira, no município de Porto Velho, Rondônia, estão sendo criadas as Usinas Hidrelétricas (UHEs) de Santo Antônio e Jirau. As construções das represas das UHEs estão inundando grandes porções de floresta ao longo das duas margens do rio Madeira. Desta forma o conhecimento da biota local, especialmente de sua distribuição no espaço, é extremamente importante, ainda mais porque o alinhamento dos rios Amazonas-Madeira-Mamoré separa a região Neotropical em duas áreas de endemismo para diversos grupos de animais. Essa tese tem por objetivo apresentar os resultados gerais obtidos ao longo de três anos de monitoramento de cupins nas áreas de influência da UHE de Jirau e dois anos nas áreas de influência da UHE de Santo Antônio, assim como desenvolver um estudo de comunidades e análise da distribuição espacial dos cupins presentes nas áreas de influência da UHE de Jirau (Capítulo 1). Outro objetivo é o estudo da estrutura genética das populações de Heterotermes tenuis (Rhinotermitidae) ao longo das áreas de influência das duas UHEs, visando investigar a existência de fluxo gênico entre as populações de cada margem do Rio Madeira (Capítulo 2). Foram amostrados doze módulos, sete na margem esquerda do rio e cinco na margem direita. Cada um era compostos por transectos de 3 ou 4 km e parcelas perpendiculares a cada 1km, e as amostragens foram realizadas em subparcelas de 5x2m dentro das parcelas. Durante um total de 20 campanhas foram investigadas 1121 subparcelas, totalizando 7875 amostras de cupins e pelo menos 169 espécies. Esse é provavelmente o trabalho com maior esforço amostral já empregado e também o que registrou o maior número de espécies de cupins até hoje. Para o estudo de comunidades, foram aleatorizadas 20 subparcelas nos seis módulos da UHE de Jirau, sendo cinco subparcelas dentro das parcelas marcadas nas seguintes distâncias em relação à margem do rio: P1 - 50 m, P2 - 1 km, P3 - 2 km e P4 - 3 km. A composição de cupins não está relacionada com o lado do rio. O estimador que mais se aproximou do provável número real de espécies foi o Jackknife 2. Como resultado das análises de diversidade beta utilizando a composição de espécies de cupins houve um agrupamento dos módulos com o mesmo tipo de solo, sugerindo que algumas espécies de cupins estejam distribuídas de acordo com esta variável. Em relação à distância para o rio, a parcela mais próxima do rio foi a mais singular, tanto em relação à composição de espécies quanto à riqueza e abundância, sendo que existem espécies restritas à P1 e outras praticamente ausentes nessas parcelas. Das dez variáveis ambientais analisadas, a riqueza de cupins se mostrou correlacionada com a altitude, concentração de argila e silte no solo e estratificação vegetal entre 1 e 5 m. Para o estudo da estrutura genética das populações de H. tenuis foram utilizadas 84 sequências dessa espécie dos 12 módulos de monitoramento, seis de colônias do Cerrado e três do GenBank (de Manaus, Guiana Francesa, e Equador), além de uma de H. longiceps como grupo externo. Nas análises iniciais, foi encontrada uma forte estruturação genética entre as sequências: todas as análises filogenéticas (máxima parcimônia, máxima verossimilhança e inferência bayesiana), assim como a rede de haplótipos, formaram dois grupos consistentes, mas sem qualquer relação espacial. A partir disso, passou-se a trabalhar com a hipótese de que há duas espécies crípticas (chamadas Ht. A e Ht. B). Desta forma, todas as análises para testar se o Rio Madeira funcionava como barreira biogeográfica foram testadas separadamente para cada uma das supostas duas espécies crípticas, entretanto, não foi constatada qualquer influência do rio como barreira ao fluxo gênico entre as populações de cada margem. / The Santo Antônio and Jirau hydroelectrics plants (HP) are being built in the Madeira River region, in Porto Velho, RO, Brazil. The HPs will flood large portions of native forest, and thus knowledge of the local biota and its distribution in space is extremely important for the formulation of management plans for creation of protected areas. This region in particular is unique, since the alignment of Amazonas-Madeira-Mamoré Rivers divides the Neotropical region into two areas of endemism for a diversity of taxa. The main objective of this thesis was to monitor termites for three years in areas near the Jirau HP and two years in areas near the Santo Antônio HP. As well as conduct a community level study and analyze the spatial distributions of termites from the areas influenced by Jirau HP (Chapter 1); and investigate the population genetic structure of Heterotermes tenuis (Rhinotermitidae), for the two areas influenced by the HPs, to test whether there is genetic flow between the populations on either bank of the Madeira River (Chapter 2). Twelve modules were marked, seven on the left bank of the river and five on the right bank. Each module was composed of 3 or 4 km transects and perpendicular parcels every 1 km. The sampling was conducted in sub parcels of 5 x 2 m inside each main parcels. During 20 expeditions, 1121 subparcels were investigated and a total of 7875 samples were collected and identified to 169 species. This study incorporates greater sampling effort than already employed by other published studies to date and also registered the highest number of termites species of any similar study. For the community study, 20 subparcels were randomized in the six modules of the Jirau HP, with five subparcels marked in relation to distance from the river margin (P1 - 50 m, P2 - 1 km, P3 - 2 km, and P4 - 3 km). The termite species composition was not related to side of the river bank. The richness estimator Jackknife 2 was the best estimator of the real number of species diversity. The beta diversity analysis with termite species composition clustered for modules with the same soil type, suggesting that some termite species may be distributed according to the soil type. Parcels closest to the river were the most unique, both in terms of termite species composition and abundance patterns, with some species restricted to the P1 and others absent. Of the ten environmental variables measured, termite species richness was correlated with altitude, clay and silt concentration in the soil, and vegetation stratification between 1 and 5 m, among. For the study of the genetic structure of Heterotermes tenuis, 84 sequences of this species were used from the 12 monitoring modules, six from colonies from the Cerrado (Brazilian Savanna), three from GeneBank (from Manaus, French Guiana and Ecuador), and one of H. longiceps as outgroup. In the initial analysis, relatively strong genetic structure within the samples was found: all phylogenetic analysis (maximum parsimony and likelihood, and Bayesian inference), and haplotype networks, consistently clustered two groups of haplotypes, but without any spatial relationships. Thus was assumed that there were two cryptic species (here called Ht. A and Ht. B), and all the analysis to test whether the Madeira River was a biogeographic barrier were conducted separately for each putative species. However, it was not possible to detect any influence of the river to genetic flow between the populations from either side of the river.

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No. of bitstreams: 1 TeseABS.pdf: 3646095 bytes, checksum: 69cc4a94c2c83a237f373c83a0febc9d (MD5) Previous issue date: 2015-06-08 / Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / The populations of Neotropical inland fishes have the distribution of their genetic diversity influenced by historical and recent biogeographic factors. Natural barriers such as the formation of waterfalls can disrupt gene flow between populations upstream and downstream. In addition, river fragmentation by hydroelectric dams also impacts on gene connectivity and, moreover, it exposes population to more intense evolutionary forces, such as genetic drift. The effects of habitat fragmentation are more pronounced in migratory species, which move large distances to reproduce. Among these species, Pseudoplatystoma corruscans, a piscivorous catfish, plays an important ecological role as top predator. In addition, this fish represents the main income for thousands of riverine families. Understanding the influence of historical factors on the population structuring is important for species conservation, because it helps in decision making, such as the determination of management units and guidelines for conducting restocking. On the other hand, analysis of recent factors such as river fragmentation can indicate the impact of habitat fragmentation on the population viability, since smaller populations show greater effects of genetic drift and inbreeding. Having said that, we have analyzed the influence of historical and recent events on the genetic diversity distribution of P. corruscans. For historical events, we collected samples of P. corruscans in all basins of its natural occurrence (São Francisco, Paraná, Paraguay and Uruguay) and used markers with slow mutational rates (S7-íntron1, CITB and D-loop). For recent events, we used microsatellite markers, with high mutational rates. We collected samples in four sections of different sizes of rivers bordered by dams (Grande, Verde, Paraná and Paraguay). The mitochondrial markers indicated the existence of two groups, one in the São Francisco basin and another in the Prata basin (Paraná, Paraguay and Uruguay). The three genes analyzed showed private haplotypes for populations in the São Francisco basin, although S7-íntron1 marker has indicated the existence of only one clade for all basins. These results indicate that the geographical separation between San Francisco and Upper Paraná promoted genetic differentiation between populations of the two basins. On the other hand, the “Sete Quedas” fall, which historically separated the Upper Paraná and Paraguay basins, was not enough to promote population structuring. Probably the two basins were connected by headwaters. Thus, we suggest that conservation efforts are earmarked for two large basins (São Francisco and Prata), with a special look to Prata basin, since the species is threatened with extinction in the Uruguay basin, addition to the large number dams present in the Paraná basin. Regarding the river fragmentation caused by dams, smaller river stretches had lower genetic diversity and greater kinship between their individuals, which can result in lower population viability, since there is an increase of inbreeding depression and loss of adaptive genetic diversity. We therefore suggest that studies with other species are performed to determine the stretch minimum size in which the populations of migratory fish are viable, providing guidelines for the construction of new dams. / As populações de peixes continentais neotropicais têm a distribuição de sua diversidade genética influenciada por fatores biogeográficos históricos e recentes. Barreiras naturais, como a formação de cachoeiras, podem interromper o fluxo gênico entre populações a montante e a jusante. Além disso, o barramento de rios por usinas hidrelétricas (UHE) também causam impacto sobre a conectividade gênica e ainda expõe as populações a forças evolutivas mais intensas, como a deriva genética. Os efeitos dessa fragmentação do habitat são mais pronunciados em espécies migradoras, que se deslocam grandes distâncias para se reproduzir. Entre essas espécies, encontra-se Pseudoplatystoma corruscans, um bagre piscívoro que exerce um importante papel ecológico como predador de topo, além de representar a principal fonte de renda para milhares de famílias ribeirinhas. Compreender como os fatores históricos determinam a estruturação populacional da espécie é importante para sua conservação, visto que auxiliam em tomadas de decisões, como determinação de unidades de manejo e orientações para a realização do repovoamento de rios. Já a análise de fatores recentes, como o barramento de rios, pode nos indicar o impacto da fragmentação de habitat sobre a viabilidade de populações, visto que quanto menor a população, maior o efeito da deriva genética e da endogamia. Nesse contexto, o objetivo neste estudo foi analisar a influência de eventos históricos e recentes sobre a distribuição da diversidade genética de P. corruscans. Para os eventos históricos, coletamos amostras de P. corruscans em todas as bacias de sua ocorrência (São Francisco, Paraná, Paraguai e Uruguai) e utilizamos marcadores com taxas mutacionais mais lentas (S7-íntron1, CitB e D-loop). Para os eventos recentes, coletamos amostras em quatro trechos de rios de tamanhos diferentes delimitados por UHE (Grande, Verde, Paraná e Paraguai). Neste caso, utilizamos marcadores microssatélites, com taxas mutacionais elevadas. Os marcadores mitocondriais indicaram a existência de dois grupos, um da bacia do São Francisco e outro da bacia do Prata (Paraná, Paraguai e Uruguai). Os três marcadores analisados apresentaram haplótipos exclusivos para populações da bacia do São Francisco, embora o marcador S7-íntron1 tenha indicado a existência de apenas um clado com indivíduos de todas as bacias. Esses resultados indicam que a separação geográfica entre a bacia do São Francisco e do Alto Paraná promoveu a diferenciação genética entre as populações das duas bacias. Por outro lado, a presença do Salto de Sete Quedas, que separou historicamente as bacias do Alto-Paraná e do Paraguai, não foi suficiente para promover a estruturação populacional. Provavelmente as duas bacias foram conectadas por capturas de cabeceiras. Dessa forma, sugerimos que os esforços de conservação sejam destinados às duas grandes bacias (São Francisco e Prata), com um olhar especial à bacia do Prata, visto que a espécie encontra-se ameaçada de extinção na bacia do Uruguai, além da grande quantidade de usinas hidrelétricas presentes na bacia do Paraná. Em relação à fragmentação dos rios por UHE, trechos de rios menores apresentaram menor diversidade genética e maior parentesco entre seus indivíduos, o que pode acarretar em menor viabilidade populacional, visto que pode haver depressão endogâmica e perda de diversidade genética adaptativa. Sugerimos, portanto, que estudos com outras espécies sejam realizados para determinar o tamanho mínimo do trecho em que as populações de peixes migradores são viáveis, fornecendo diretrizes para a construção de novas barragens.

Estudo da termitofauna (Insecta, Isoptera) da região do alto Rio Madeira, Rondônia. Na região conhecida como alto Rio Madeira, no município de Porto Velho, Rondônia, estão sendo criadas as Usinas Hidrelétricas (UHEs) de Santo Antônio e Jirau. As construções das represas das UHEs estão inundando grandes porções de floresta ao longo das duas margens do rio Madeira. Desta forma o conhecimento da biota local, especialmente de sua distribuição no espaço, é extremamente importante, ainda mais porque o alinhamento dos rios Amazonas-Madeira-Mamoré separa a região Neotropical em duas áreas de endemismo para diversos grupos de animais. Essa tese tem por objetivo apresentar os resultados gerais obtidos ao longo de três anos de monitoramento de cupins nas áreas de influência da UHE de Jirau e dois anos nas áreas de influência da UHE de Santo Antônio, assim como desenvolver um estudo de comunidades e análise da distribuição espacial dos cupins presentes nas áreas de influência da UHE de Jirau (Capítulo 1). Outro objetivo é o estudo da estrutura genética das populações de Heterotermes tenuis (Rhinotermitidae) ao longo das áreas de influência das duas UHEs, visando investigar a existência de fluxo gênico entre as populações de cada margem do Rio Madeira (Capítulo 2). Foram amostrados doze módulos, sete na margem esquerda do rio e cinco na margem direita. Cada um era compostos por transectos de 3 ou 4 km e parcelas perpendiculares a cada 1km, e as amostragens foram realizadas em subparcelas de 5x2m dentro das parcelas. Durante um total de 20 campanhas foram investigadas 1121 subparcelas, totalizando 7875 amostras de cupins e pelo menos 169 espécies. Esse é provavelmente o trabalho com maior esforço amostral já empregado e também o que registrou o maior número de espécies de cupins até hoje. Para o estudo de comunidades, foram aleatorizadas 20 subparcelas nos seis módulos da UHE de Jirau, sendo cinco subparcelas dentro das parcelas marcadas nas seguintes distâncias em relação à margem do rio: P1 - 50 m, P2 - 1 km, P3 - 2 km e P4 - 3 km. A composição de cupins não está relacionada com o lado do rio. O estimador que mais se aproximou do provável número real de espécies foi o Jackknife 2. Como resultado das análises de diversidade beta utilizando a composição de espécies de cupins houve um agrupamento dos módulos com o mesmo tipo de solo, sugerindo que algumas espécies de cupins estejam distribuídas de acordo com esta variável. Em relação à distância para o rio, a parcela mais próxima do rio foi a mais singular, tanto em relação à composição de espécies quanto à riqueza e abundância, sendo que existem espécies restritas à P1 e outras praticamente ausentes nessas parcelas. Das dez variáveis ambientais analisadas, a riqueza de cupins se mostrou correlacionada com a altitude, concentração de argila e silte no solo e estratificação vegetal entre 1 e 5 m. Para o estudo da estrutura genética das populações de H. tenuis foram utilizadas 84 sequências dessa espécie dos 12 módulos de monitoramento, seis de colônias do Cerrado e três do GenBank (de Manaus, Guiana Francesa, e Equador), além de uma de H. longiceps como grupo externo. Nas análises iniciais, foi encontrada uma forte estruturação genética entre as sequências: todas as análises filogenéticas (máxima parcimônia, máxima verossimilhança e inferência bayesiana), assim como a rede de haplótipos, formaram dois grupos consistentes, mas sem qualquer relação espacial. A partir disso, passou-se a trabalhar com a hipótese de que há duas espécies crípticas (chamadas Ht. A e Ht. B). Desta forma, todas as análises para testar se o Rio Madeira funcionava como barreira biogeográfica foram testadas separadamente para cada uma das supostas duas espécies crípticas, entretanto, não foi constatada qualquer influência do rio como barreira ao fluxo gênico entre as populações de cada margem. / The Santo Antônio and Jirau hydroelectrics plants (HP) are being built in the Madeira River region, in Porto Velho, RO, Brazil. The HPs will flood large portions of native forest, and thus knowledge of the local biota and its distribution in space is extremely important for the formulation of management plans for creation of protected areas. This region in particular is unique, since the alignment of Amazonas-Madeira-Mamoré Rivers divides the Neotropical region into two areas of endemism for a diversity of taxa. The main objective of this thesis was to monitor termites for three years in areas near the Jirau HP and two years in areas near the Santo Antônio HP. As well as conduct a community level study and analyze the spatial distributions of termites from the areas influenced by Jirau HP (Chapter 1); and investigate the population genetic structure of Heterotermes tenuis (Rhinotermitidae), for the two areas influenced by the HPs, to test whether there is genetic flow between the populations on either bank of the Madeira River (Chapter 2). Twelve modules were marked, seven on the left bank of the river and five on the right bank. Each module was composed of 3 or 4 km transects and perpendicular parcels every 1 km. The sampling was conducted in sub parcels of 5 x 2 m inside each main parcels. During 20 expeditions, 1121 subparcels were investigated and a total of 7875 samples were collected and identified to 169 species. This study incorporates greater sampling effort than already employed by other published studies to date and also registered the highest number of termites species of any similar study. For the community study, 20 subparcels were randomized in the six modules of the Jirau HP, with five subparcels marked in relation to distance from the river margin (P1 - 50 m, P2 - 1 km, P3 - 2 km, and P4 - 3 km). The termite species composition was not related to side of the river bank. The richness estimator Jackknife 2 was the best estimator of the real number of species diversity. The beta diversity analysis with termite species composition clustered for modules with the same soil type, suggesting that some termite species may be distributed according to the soil type. Parcels closest to the river were the most unique, both in terms of termite species composition and abundance patterns, with some species restricted to the P1 and others absent. Of the ten environmental variables measured, termite species richness was correlated with altitude, clay and silt concentration in the soil, and vegetation stratification between 1 and 5 m, among. For the study of the genetic structure of Heterotermes tenuis, 84 sequences of this species were used from the 12 monitoring modules, six from colonies from the Cerrado (Brazilian Savanna), three from GeneBank (from Manaus, French Guiana and Ecuador), and one of H. longiceps as outgroup. In the initial analysis, relatively strong genetic structure within the samples was found: all phylogenetic analysis (maximum parsimony and likelihood, and Bayesian inference), and haplotype networks, consistently clustered two groups of haplotypes, but without any spatial relationships. Thus was assumed that there were two cryptic species (here called Ht. A and Ht. B), and all the analysis to test whether the Madeira River was a biogeographic barrier were conducted separately for each putative species. However, it was not possible to detect any influence of the river to genetic flow between the populations from either side of the river.

The Florida Reef Tract (FRT) extends from the tropical Caribbean northward along the Florida coast into a warm temperate environment where tropical reef communities diminish with increasing latitude. This study was designed to map the nearshore benthic habitats including coral reefs and evaluate how the benthic communities differ between habitats and along the coast. Benthic communities across the northern FRT from Key Biscayne to Hillsboro Inlet (25.5°-26.3° N) were digitized from aerial photography taken in 2013 at a 1:1,000 scale. Three main hard-bottom habitat types were identified that ran parallel to shore and consecutively further away from shore: Colonized Pavement, Ridge, and Inner Reef. Five 1-km wide cross-shelf corridors (numbered 1-5, south to north) were designated and spaced as evenly as possible throughout the region. Five sites per habitat per corridor (70 total) were randomly selected and quantitative data collected within 4,200 m2. Significant differences in percent benthic cover among habitats were found in all corridors and within habitat types between corridors, indicating cross-shelf and latitudinal variation. Mean stony coral density increased with depth, with the Inner Reef habitat being significantly higher than both the Colonized Pavement and Ridge. Mean stony coral species richness also increased with depth, with all habitats significantly different from one another. A total of 22 stony coral species were identified within the mapped region, the three most abundant being Porites astreoides, Siderastrea siderea, and Acropora cervicornis. Results from this study support the ecosystem regions denoted in the Walker (2012) study. Corridor 1, located in the Biscayne Region, was the only corridor to contain any seagrass. In addition, Corridor 1 Inner Reef had significantly higher values for mean stony coral density, mean stony coral species richness, mean gorgonian density of the plume morphotype, and mean density of stony corals infected with Cliona spp. Corridors 2-4, located in the Broward-Miami Region, had some variability associated with them, but were generally similar in benthic composition. Corridor 5, likewise located in the Broward-Miami Region but in close proximity to the Deerfield Region, also had differences associated with it. Both the Colonized Pavement and Ridge habitats in Corridor 5 had the lowest mean coral species richness, as well as total absence of both sponge species noted in this study. Corridor 5 Inner Reef also had significantly lower mean stony coral densities compared to Corridors 1, 2, and 4. As such, these results support the idea of different biogeographic regions occurring off the southeastern Florida coast. This study produced two key findings. It discovered over 110 large (>2 m) resilient coral colonies, of which 50 were alive in various conditions. This study also found 38 acres of dense Acropora cervicornis patches, tripling the previously known area within the study region. These are the largest dense patches in the continental United States.

Several studies have found separation of biogeographic provinces on the West Florida Shelf (WFS), but the location of this separation differs depending on different organisms with faunal boundaries proposed at Apalachicola, Cedar Key, Anclote Key. Tampa Bay, Charlotte Harbor, Cape Romano, or Cape Sable. Biogeographic boundaries can be gradual over a given space and are often species-specific. Analyses of marine benthic mapping and community characterization of Florida’s West-central coast shallow water (depth) hardbottom habitats indicate a major shift in the benthos across Tampa Bay. Quantitative benthic surveys of 29 sites yielded a total of 4,079 individuals of nine stony coral species and 1,918 soft coral colonies. Populations were dominated by four species of corals: Siderastrea radians, Oculina robusta, Solenastrea hyades, and Cladacora arbuscula. Most corals were less than 10 cm in diameter. Cluster analyses of coral density and major functional group percent cover showed distinct differences in hard and soft coral densities and species demographics from south to north with clear spatial patterns between regions. These benthic hardbottom coral communities change over a relatively small spatial scale (10’s of km), indicating a biogeographical province or ecosystem region boundary in marine benthic communities at, or very near, the mouth of Tampa Bay. Broader studies are needed to identify the shifts in benthic community biogeography along the West Florida Shelf.