O objetivo desta tese é identificar e descrever variações espacial, sazonal e multidecadal, com dados históricos, e padrões ecológicos locais na ictiofauna do estuário Cananéia-Iguape (ECI) em relação a fatores ecológicos naturais e/ou aqueles induzidos pelo aporte exógeno do rio Ribeira de Iguape (RI) através do canal artificial Valo Grande (VG). Demonstrou-se a relação de atributos hidrológicos, sazonalidade e espacialidade com a estruturação da diversidade da assembléia no infralitoral inconsolidado em escala local (i.e. dentro de um setor estuarino do ECI, a baía do Trapandé) utilizando delineamento amostral espacial e sazonalmente estratificado com amostragens mensais (julho/2009 junho/2010) com rede otter-trawl. Identificaram-se dois padrões locais na estrutura da assembleia: persistência sazonal de maior riqueza e abundância no interior (ambientalmente favorável) do que foz da baía (hidrodinamicamente instável) e variabilidade dessa estrutura espacial pelo efeito da interação entre profundidade, temperatura e ritmos sazonais populacionais. O ECI abrigou 246 espécies entre 1962 e 2010 e 214 entre 1993 e 2010. De acordo com extrapoladores matemáticos, há mais de 173 espécies no habitat demersal do eixo sul. Durante o período chuvoso, riqueza e abundância na ictiofauna do eixo sul aumentam com o incremento do recrutamento e agregações reprodutivas, estimuladas pelo pico de produtividade no ECI, e das migrações massivas à jusante, devido à forte redução das condições estuarinas no eixo norte. Propõe-se uma metacomunidade organizada por efeitos de massa entre a assembleia da baía do Trapandé e o pool regional de populações marinhas. A degradação das condições estuarinas pelo aporte do RI limitou a dispersão de espécies estuarino-residentes e marinho-migrantes no ECI. Isso determinou um gradiente espacial de perda generalizada de abundância, riqueza e diversidade funcional acompanhando consistentemente o gradiente espacial de impacto. O sinal desse efeito antrópico foi suficientemente elevado para ser detectado mesmo sob interferência de outras fontes de variabilidade espacial, temporal e ambiental. A redução da vazão do RI ao ECI para sua recuperação ecológica, estabelecida pelas autoridades governamentais, é uma medida que também restaurará a dispersão multiespecífica e, assim, a funcionalidade ecossistêmica da ictiofauna / The aim of the present thesis is to identify and describe spatial, seasonal, and multidecadal variations, by using historical data, and local ecological patterns in the fish fauna of the Cananéia-Iguape Estuary (ECI) in relation to ecological factors and/or factors derived from the exogenous discharge of the Ribeira de Iguape River (RI) flowing through the Valo Grande artificial channel. It was demonstrated the relation of hydrological attributes, seasonality, and spatiality with the beta diversity of the soft bottom infralitoral fish assemblage in local scale (i.e. within an ECI estuarine sector, the Trapandé Bay) with a seasonally and spatially stratified sampling design and monthly sampling (July/2009 June/2010) using otter-trawl net. Two patterns were identified: (I) fish species richness and abundance were higher and seasonally persistent in inner (environmentally favorable habitat) than in outer sector of bay; and (II) a variability of this fish faunas spatial structure induced by the effect of the interaction among depth, water temperature, and seasonal rhythms of fish populations. ECI hold 246 fish species between 1962 and 2010 and 214 species between 1993 and 2010. Mathematic extrapolators estimated > 173 species in the south axis of ECI. In rainy season, fish species richness and abundance in south axis increase with increasing (I) massive immigration of individuals from north axis of ECI due to the highest RI discharge and lowest salinity; (II) massive recruitments and reproductive aggregations and activities, which are coupled with the peak of primary and secondary productivity in ECI. It is proposed the existence of a metacommunity ruled by mass effect between assemblage of Trapandé bay and regional pool of marine populations. The degradation of ECIs estuarine conditions due to RI inflow limited multispecific dispersion among resident estuarine and marine species. This resulted in a spatial gradient of generalized loss in abundance, richness, and function in the fish fauna structure that strongly follow the spatial gradient of impact. The signal of this anthropogenic effect was enough high to be revealed even under interference from other sources of environmental, spatial, and temporal variability. The reduction of RI inflow to ECI in order to recover its ecological estuarine conditions is a governmental authorities correct decision to also recover the fish dispersion and, thus, the ecosystem functionality of fish fauna

Este trabalho enfatizou as escalas espaciais de microhabitat e de mesohabitat para investigar como a fauna de macroinvertebrados aquáticos é influenciada pelas variáveis ambientais e espaciais. O primeiro capítulo trás uma visão geral da aplicabilidade das escalas de microhabitat e de mesohabitat ao avaliar a estrutura da fauna e, também, demonstra que a composição do substrato influencia a composição faunística. No segundo capítulo, realizamos uma avaliação da suficiência amostral e comparamos a diversidade alfa e beta entre métodos de coleta e entre diferentes mesohabitats. No terceiro capítulo avaliamos diferentes variáveis hidráulicas e suas relações com a abundância de indivíduos e a riqueza de táxons considerando as escalas espaciais de microhabitat e mesohabitat. Observamos que as condições hidráulicas foram importantes na estruturação da comunidade de macroinvertebrados, influenciando positivamente a abundância de indivíduos e negativamente a riqueza de táxons nos microhabitats. No quarto capítulo nos baseamos na teoria de metacomunidades para compreender a influência das variáveis ambientais e espaciais na estruturação da fauna em uma perspectiva de microescala. Além da esperada importância do ambiente para a microdistribuição dos organismos, identificamos uma forte influência do espaço na estruturação da fauna. Nossos resultados demonstraram que a fauna de macroinvertebrados aquáticos é estruturada pela composição do substrato, condições hidráulicas e fatores espaciais, todas estas condições perceptíveis na escala do microhabitat. Deste modo, a microescala pode ser considerada como uma perspectiva válida para o estudo de ecologia de riachos. / We focused on the microhabitat and the mesohabitat spatial scales to investigate the environmental and spatial features influence on aquatic macroinvertebrate fauna. The first chapter brings an overview about the microhabitat and mesohabitat applicability to evaluate the fauna structure. Likewise, it shows the substrate influence on the fauna composition. In the second chapter, we evaluate the sampling sufficiency and compare the alpha and beta diversity among the sampling methods and mesohabitats. In the third chapter we evaluated the hydraulic features and its relationships with abundance and richness considering the microhabitat and mesohabitat spatial scales. Our results show that the hydraulic conditions have influence on macroinvertebrate community structure, showing a positive relationship with abundance and negative with microhabitat richness. In the fourth chapter, we applied the metacommunity theory in the microhabitat scale to understand the hole of environmental and spatial features on the community structure. Further than the expected environmental influence on organisms microdistribution, we identified a strong spatial influence on the fauna structure. Our results showed that the aquatic macroinvertebrate fauna was structured by the substrate composition, hydraulic conditions and spatial features. All this conditions are noticeable on microhabitat spatial scale. Accordingly, the microhabitat scale can be considered as an effectual perspective to the stream ecology.

O objetivo desta tese é identificar e descrever variações espacial, sazonal e multidecadal, com dados históricos, e padrões ecológicos locais na ictiofauna do estuário Cananéia-Iguape (ECI) em relação a fatores ecológicos naturais e/ou aqueles induzidos pelo aporte exógeno do rio Ribeira de Iguape (RI) através do canal artificial Valo Grande (VG). Demonstrou-se a relação de atributos hidrológicos, sazonalidade e espacialidade com a estruturação da diversidade da assembléia no infralitoral inconsolidado em escala local (i.e. dentro de um setor estuarino do ECI, a baía do Trapandé) utilizando delineamento amostral espacial e sazonalmente estratificado com amostragens mensais (julho/2009 junho/2010) com rede otter-trawl. Identificaram-se dois padrões locais na estrutura da assembleia: persistência sazonal de maior riqueza e abundância no interior (ambientalmente favorável) do que foz da baía (hidrodinamicamente instável) e variabilidade dessa estrutura espacial pelo efeito da interação entre profundidade, temperatura e ritmos sazonais populacionais. O ECI abrigou 246 espécies entre 1962 e 2010 e 214 entre 1993 e 2010. De acordo com extrapoladores matemáticos, há mais de 173 espécies no habitat demersal do eixo sul. Durante o período chuvoso, riqueza e abundância na ictiofauna do eixo sul aumentam com o incremento do recrutamento e agregações reprodutivas, estimuladas pelo pico de produtividade no ECI, e das migrações massivas à jusante, devido à forte redução das condições estuarinas no eixo norte. Propõe-se uma metacomunidade organizada por efeitos de massa entre a assembleia da baía do Trapandé e o pool regional de populações marinhas. A degradação das condições estuarinas pelo aporte do RI limitou a dispersão de espécies estuarino-residentes e marinho-migrantes no ECI. Isso determinou um gradiente espacial de perda generalizada de abundância, riqueza e diversidade funcional acompanhando consistentemente o gradiente espacial de impacto. O sinal desse efeito antrópico foi suficientemente elevado para ser detectado mesmo sob interferência de outras fontes de variabilidade espacial, temporal e ambiental. A redução da vazão do RI ao ECI para sua recuperação ecológica, estabelecida pelas autoridades governamentais, é uma medida que também restaurará a dispersão multiespecífica e, assim, a funcionalidade ecossistêmica da ictiofauna / The aim of the present thesis is to identify and describe spatial, seasonal, and multidecadal variations, by using historical data, and local ecological patterns in the fish fauna of the Cananéia-Iguape Estuary (ECI) in relation to ecological factors and/or factors derived from the exogenous discharge of the Ribeira de Iguape River (RI) flowing through the Valo Grande artificial channel. It was demonstrated the relation of hydrological attributes, seasonality, and spatiality with the beta diversity of the soft bottom infralitoral fish assemblage in local scale (i.e. within an ECI estuarine sector, the Trapandé Bay) with a seasonally and spatially stratified sampling design and monthly sampling (July/2009 June/2010) using otter-trawl net. Two patterns were identified: (I) fish species richness and abundance were higher and seasonally persistent in inner (environmentally favorable habitat) than in outer sector of bay; and (II) a variability of this fish faunas spatial structure induced by the effect of the interaction among depth, water temperature, and seasonal rhythms of fish populations. ECI hold 246 fish species between 1962 and 2010 and 214 species between 1993 and 2010. Mathematic extrapolators estimated > 173 species in the south axis of ECI. In rainy season, fish species richness and abundance in south axis increase with increasing (I) massive immigration of individuals from north axis of ECI due to the highest RI discharge and lowest salinity; (II) massive recruitments and reproductive aggregations and activities, which are coupled with the peak of primary and secondary productivity in ECI. It is proposed the existence of a metacommunity ruled by mass effect between assemblage of Trapandé bay and regional pool of marine populations. The degradation of ECIs estuarine conditions due to RI inflow limited multispecific dispersion among resident estuarine and marine species. This resulted in a spatial gradient of generalized loss in abundance, richness, and function in the fish fauna structure that strongly follow the spatial gradient of impact. The signal of this anthropogenic effect was enough high to be revealed even under interference from other sources of environmental, spatial, and temporal variability. The reduction of RI inflow to ECI in order to recover its ecological estuarine conditions is a governmental authorities correct decision to also recover the fish dispersion and, thus, the ecosystem functionality of fish fauna

In the Midwestern US, forested and other woody plant habitats are embedded in a matrix of agricultural and urban landcover that alters configurations of “natural” habitats and creates novel habitat types. Variation in the type and juxtaposition of landcover in the matrix between habitats can profoundly impact the spatial and temporal distributions of insects. Intense urban and agricultural development alters habitats, increases fragmentation, and may decouple trophic interactions if plants or animals cannot disperse to needed resources. Specialist insects represent a substantial proportion of global biodiversity and their fidelity to discrete microhabitats provides a powerful framework for investigating organismal responses to human land use. Specialist herbivores and parasitoids that depend on discrete plant habitats simplify assessment of how trophic interactions, local demographic traits, and dispersal processes affect responses to landcover heterogeneity. Herbivore responses to landcover change are highly idiosyncratic and not well characterized. Parasitoid wasps are predicted to be more prone than their herbivore hosts to local extinction in response to increased habitat fragmentation, but often respond differently to similar landcover contexts. Understanding and predicting idiosyncratic spatial population dynamics of simple host-parasitoid communities and other insect systems requires integration of metacommunity-level ecological paradigms with spatial analyses across multiple spatial scales. We sampled site occupancy and densities for two plant-herbivore-parasitoid systems from 250 sites across a 360 km2 urban/ agricultural landscape across three study years to ask whether and how human development decouples interactions between trophic levels. We first performed a single year analysis to investigate broad scale patterns. We compared patterns of site occupancy, host plant density, herbivory and parasitism rates of insects at two trophic levels with respect to landcover at multiple spatial scales. Geospatial analyses were used to identify landcover characters predictive of insect distributions. We found that herbivorous insect densities were decoupled from host tree densities in urban landcover types at several spatial scales. This effect was amplified for the third trophic level in one of the two insect systems: despite being abundant regionally, a parasitoid species was absent from all urban/ suburban landcover even where its herbivore host was common. Our results indicate that human land use patterns limit distributions of specialist insects. Dispersal constraints associated with urban built development are specifically implicated as a limiting factor. Our multi-year analysis of trophic interactions in urban versus agricultural landcover showed that important results from our single-year study are consistent over time and provided useful insights into the factors mediating spatial distributions of specialist insects in altered landscapes. While we observed that insect species responded to landcover at consistent local- and landscape-scale spatial extents, we observed that coarse grain landcover categories (i.e. urban versus agricultural) at low spatial resolution yielded the most consistent patterns of organismal response. Our results indicate that agricultural versus urban landcover contexts can mediate distinct spatial population structuring across linked trophic levels. This finding has important implications for conservation and pest management strategies in heterogeneous landscapes and is an important consideration when translating heuristics regarding metacommunity dynamics from one broad spatial context to another.

<p>Biological diversity is controlled by an array of factors and processes all active at different spatial and temporal scales. Regional factors control what species are available to occur locally, whereas the local factors determine what species are actually capable of colonizing the locality.</p><p>I have investigated how these local and regional factors affect species richness and diversity, mainly of fish in Swedish lakes and in order to assess the impact of dispersal mode one study on bacteria was also performed. In addition, potential first steps towards speciation were investigated in perch (<i>Perca fluviatilis</i>) from two different habitats. </p><p>Fish species richness and diversity were found to be regulated by history, dispersal limitation and the local environment. In addition, striking similarities were found in the control of community composition for fish and bacteria. Both were regulated by nearly equal parts regional and local factors. The study of morphological and genetical variation in perch (<i>Perca fluviatilis</i>) revealed genetic differentiation at small spatial scales, suggesting that genetic differences can evolve between groups at strikingly small spatial scales, which might have implications for speciation in a long time perspective. </p><p>Based on these findings I conclude that space and time matter. Space has the potential to isolate sites. And both dispersal and local extinctions, it seems, might take a long time, as effects of the last ice-age can still be seen on the contemporary fish community richness and composition.</p>

Loss of biodiversity is one of the most severe threats to the ecosystems of the world. The major causes behind the high population and species extinction rates are anthropogenic activities such as overharvesting of natural populations, pollution, climate change and destruction and fragmentation of natural habitats. There is an urgent need of understanding how these species losses affect the ecological structure and functioning of our ecosystems. Ecological communities exist in a landscape but the spatial aspects of community dynamics have until recently to large extent been ignored. However, the community’s response to species losses is likely to depend on both the structure of the local community as well as its interactions with surrounding communities. Also the characteristics of the species going extinct do affect how the community can cope with species loss. The overall goal of the present work has been to investigate how both local and regional processes affect ecosystem stability, in the context of preserved biodiversity and maintained ecosystem functioning. The focus is particularly on how these processes effects ecosystem’s response to species loss. To accomplish this goal I have formulated and analyzed mathematical models of ecological communities. We start by analyzing the local processes (Paper I and II) and continue by adding the regional processes (Paper III, IV and V). In Paper I we analyze dynamical models of ecological communities of different complexity (connectance) to investigate how the structure of the communities affects their resistance to species loss. We also investigate how the resistance is affected by the characteristics, like trophic level and connectivity, of the initially lost species. We find that complex communities are more resistant to species loss than simple communities. The loss of species at low trophic levels and/or with high connectivity (many links to other species) triggers, on average, the highest number of secondary extinctions. We also investigate the structure of the post-extinction community. Moreover, we compare our dynamical analysis with results from topological analysis to evaluate the importance of incorporating dynamics when assessing the risk and extent of cascading extinctions. The characteristics of a species, like its trophic position and connectivity (number of ingoing and outgoing trophic links) will affect the consequences of its loss as well as its own vulnerability to secondary extinction. In Paper II we characterize the species according to their trophic/ecological uniqueness, a new measure of species characteristic we develop in this paper. A species that has no prey or predators in common with any other species in the community will have a high tropic uniqueness. Here we examine the effect of secondary extinctions on an ecological community’s trophic diversity, the range of different trophic roles played by the species in a community. We find that secondary extinctions cause loss of trophic diversity greater than expected from chance. This occurs because more tropically unique species are more vulnerable to secondary extinctions. In Paper III, IV and V we expand the analysis to also include the spatial dimension. Paper III is a book chapter discussing spatial aspects of food webs. In Paper IV we analyze how metacommunities (a set of local communities in the landscape connected by species dispersal) respond to species loss and how this response is affected by the structure of the local communities and the number of patches in the metacommunity. We find that the inclusion of space reduces the risk of global and local extinctions and that lowly connected communities are more sensitive to species loss. In Paper V we investigate how the trophic structure of the local communities, the spatial structure of the landscape and the dispersal patterns of species affect the risk of local extinctions in the metacommunity. We find that the pattern of dispersal can have large effects on local diversity. Dispersal rate as well as dispersal distance are important: low dispersal rates and localized dispersal decrease the risk of local and global extinctions while high dispersal rates and global dispersal increase the risk. We also show that the structure of the local communities plays a significant role for the effects of dispersal on the dynamics of the metacommunity. The species that are most affected by the introduction of the spatial dimension are the top predators.

One of ecology’s primary goals is to comprehend biodiversity and its patterns of distribution over space and time. Since microorganisms play a pivotal role in key ecological processes, the diversity of microbial communities may have important implications for the stability and functioning of Earth’s ecosystems. Thus, it is of utmost importance to develop a theoretical foundation but also a conceptual understanding for the mechanisms that generate and maintain microbial diversity. The aim of this thesis is to investigate to what extent local freshwater bacterioplankton diversity, i.e. richness and community composition, is structured by local environmental interactions and/or regional processes. The key objective is to identify ecological linkages between lake bacterioplankton and bacterial communities in connected streams and the surrounding terrestrial landscape, thereby applying a metacommunity approach. To do so, I studied several natural lake bacterioplankton assemblies within different regions of Sweden and assessed both local environmental properties and regional parameters (e.g. dispersal, landscape position). The genetic composition of freshwater bacterioplankton diversity was determined by means of terminal-restriction fragment length polymorphism or 454 pyrosequencing. From the review on the biogeography of bacterioplankton in inland waters it became clear that microbial diversity and its spatial distribution are governed by a complex interplay of both local and regional drivers. In one case, freshwater bacterioplankton communities were structured by local environmental conditions rather than by regional dispersal processes. These local environmental conditions seemed to be equally important in controlling both the total bacterioplankton community and its active fraction. In a study of bacterioplankton communities from five different regions, locally abundant aquatic bacteria were shown to be also regionally widespread, a pattern predicted by neutral theory. Yet, this degree of similarity decreased with increasing environmental heterogeneity. In another study, bacterioplankton richness was controlled mostly by nutrient content, indicating that productivity exerted influence on bacterioplankton richness. However, landscape position and productivity covaried, suggesting that the landscape dictates environmental properties, which then directly structure local bacterioplankton richness. Finally, a review synthesising results from empirical metacommunity approaches and comparing these to theory showed that yet a gap between empirics and theory exists. To conclude, local bacterioplankton diversity appeared to be mainly structured by local environmental properties. However, signatures of neutral processes driving local bacterioplankton community assembly were also recorded.

Bacterial diversity and ecosystem functioning (BEF) relationships have received considerable attention during the last three decades and tend to be positive in most cases. However, most studies were done in closed systems and largely ignored the importance of placing local communities into the metacommunity context, in which dispersal can be a crucial factor modifying community diversity and composition and ecosystem functioning. The aim of this study was to investigate the effects of both diversity and dispersal on the responses of bacterial community to a starvation perturbation. To achieve this, we implemented a batch culture experiment using the dilution-to-extinction approach to create a diversity gradient of local bacterial community richness. Different dispersal rates were manipulated by transferring cells in different quantities from a regional source to the cultures, and they were then exposed to a perturbation by transferring them into water from another lake which differed in organic carbon content and quality. We evaluated the BEF relationship by measuring the bacterial community composition using t-RFLP and multiple ecosystem functions. Generally, our results demonstrated that diversity and dispersal have an interactive and positive effect on ecosystem functioning. In particular, dispersal had a stronger and more pronounced effect on ecosystem functioning when bacterial diversity was low. When evaluating the responses of bacterial community respiration, no significant difference was observed among different treatments, however, there were clear differences in substrate utilization patterns, implying that specific functions, such as decomposing certain substrates, are more sensitive to a perturbation than general functions, such as respiration. Therefore it is important to include multiple functional parameters when studying BEF relationships and, in particular, when applying our knowledge to the conservation of natural environments.

Biodiversity is distributed unevenly across geographic space and the tree of life. A key task of biology is to understand the ecological and evolutionary processes that generate these patterns. I investigate how the structure and geometry of a landscape, for example the sizes and arrangements of islands in an archipelago, affects processes contributing to the generation and conservation of biodiversity patterns. In the first chapter, I integrate two disparate bodies of theory, ecological neutral theory and network theory into a powerful new framework for investigating patterns of biodiversity in a complex landscape. I examine the consequences of network structure, such as size, topology, and connectivity, for diversity patterning across the metacommunity. The second chapter focuses on how the position of a node within a network controls local community (node) diversity. Network statistics, such as node centrality, are found to predict diversity patterns with more central nodes accumulating the most diversity. In the third chapter, I use the theory to evaluate how well fundamental concepts in conservation biology perform when neutral metacommunity processes generate diversity patterns. I find that contemporary diversity patterns are poor predictors of the long-term capacity of a network to support diversity, challenging a host of conservation concepts and applications. In the fourth chapter, I consider biodiversity dynamics in a network with a different model of speciation, where spatial structure is needed for divergence. In this case, speciation hotspots form where the dispersal properties of an organism and the spatial structure of the landscape coincide. In the final chapter I study the biodiversity of a natural structured metacommunity, the ants of the Fijian archipelago. I used a variety of collecting techniques to inventory the ant species occurring across a system of islands in the southwest Pacific. Approximately 50 new species were discovered, and the distributions of the ant species across the islands are firmly established. Radiations are observed in the genera Pheidole, Camponotus, Lordomyrma, Leptogenys, Cerapachys, Strumigenys, Poecilomyrma, and Hypoponera. / text

In the Oueme River, a lowland river in Benin, Africa, artificial ponds constructed in the floodplain (whedos) are colonized during the high-water period by a presumably random sample of fishes from the river channel. As water slowly recedes from the floodplain, fishes are isolated in whedos until they are harvested near the end of the dry season. I surveyed fishes in whedos and adjacent main-channel and floodplain habitats during two low-water (2008 and 2009) and one falling-water (2010-2011) periods, and measured a suite of physicochemical variables including dissolved oxygen, temperature, specific conductivity, and percent cover of aquatic vegetation in the falling-water period to investigate if fish assemblage structure of whedos resulted from stochastic or deterministic processes. I also investigated food web structure of whedos by analyzing carbon (delta13C) and nitrogen (delta15N) stable isotope ratios of fish and primary producer tissue samples, and samples of net primary production, soluble reactive phosphorus (SRP), NH4+, NO2-, and NO3- collected during the falling-water period. Whedos were covered with dense growth of aquatic vegetation, and dissolved oxygen concentrations were lower in whedos compared to a natural floodplain depression and the main channel. Multivariate analyses revealed that habitat types were distinct with regard to fish assemblage structure and abiotic conditions. Assemblages in whedos and natural floodplain depressions were differentiated from those of the river channel, with the floodplain habitats being dominated by piscivorous fishes that tolerate aquatic hypoxia. These results indicate that fish assemblage structure of whedos was influenced by deterministic processes during the falling- and low-water periods when these water bodies were isolated. Floodplain habitats were more nutrient-rich than the river channel, and whedos were net heterotrophic. Microphytobenthos and C3 macrophytes accounted for a large fraction of fish biomass in whedos, compared with the river channel, which was mainly supported by seston. Whedo food webs had fewer trophic transfers compared to the food web of the river channel.