Master of Science / Department of Biology / Keith B. Gido / Stream networks provide complex habitats for fish assemblages that can vary gradually along a gradient of stream size or abruptly at transition zones between large rivers and their tributaries. We evaluated the relative importance of these gradual and abrupt habitat transitions in regulating stream fish assemblages by quantifying roles of stream size and spatial position within a drainage network as a determinant of fish assemblage structure within the Kansas River basin, KS. We predicted fish assemblage structure to generally be dependent on stream size and that smaller streams would be influenced by their connectance to larger mainstem rivers. Fishes in the Kansas River basin varied along a gradient of stream size and longitude, and after controlling for these effects, there was evidence that connectivity to a larger river influenced species richness and assemblage structure. In 1st order streams there was an increase in species richness with increasing distance from a mainstem confluence and species composition in larger tributaries (i.e., 4th order streams) varied with proximity to the mainstem river. We also found an increase in species richness at sites located on smaller tributaries connected to a larger downstream mainstem. Species composition in 1st and 4th order streams also varied with connectance to the mainstem river. Within three intensively sampled tributaries, there was an abrupt change in fish fauna between the Kansas River and sample sites above the confluence, but only gradual change in assemblage structure within each tributary with a high degree of seasonal variation. In the first 20 stream km of these three mainstem tributaries adult fishes were more structured along a gradient away from the mainstem river than juveniles, potentially suggesting more generalized habitat needs of juvenile fishes. At the spatial and temporal scale of our analysis, it appeared the effects of large rivers on tributary streams were generally localized. However, the documented influence of spatial position suggests movements between habitats could regulate community level dynamics as well as individual species over longer temporal scales.

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.

Analysing ecological communities as complex networks of interactions has become an important tool for ecologists. Understanding how these networks change through time, over landscapes, or in response to disturbances is a primary goal of community ecology. The number of interactions and the way in which those interactions organise themselves as individuals, small groups, and the whole community can play an important role in predicting how ecological communities will respond to disturbances. In this thesis, we investigated variation in network structure at several scales both empirically and in a theoretical context. Our first hypothesis was that the structural role of species in a variable system would show little variation, despite high levels of species turnover and a fragmented landscape. In a collaboration with Riikkaa Kaartinen and Tomas Roslin, we studied the distribution of species’ roles at three scales in host-parasitoid networks collected from a fragmented forest in Finland. We found that species’ roles were remarkably consistent through time and in the presence of species turnover. These results suggest that species’ roles may be an intrinsic property of species and may be predictable over spatial and temporal scales. Our second study investigated the structural variation of simulated ecological networks and the relationship between structural variation and whole-network measures of network organization, such as connectance, nestedness, and modularity. We quantified structural variation of networks at three scales, macro-scale, motif-scale, and participation scale. These scales represent whole-network measures (macro-scale), sub-network measures (motifs – small groups of interacting species), and individual measures (motif participation). We compared the variation in these structures to connectance, nestedness, and modularity. We found that at fixed levels of connectance, nestedness, and modularity, the motif profiles of networks and the distribution of species across those profiles showed remarkable dissimilarity. This result suggests that networks displaying similar macro-scale structural measures can be composed of vastly different motif- and participation-scale structures. Together, the work that makes up this thesis suggests that we should give more attention to the meso-scale structures of ecological networks. As the more detailed perspective of motifs can capture additional detail about the structure of empirical networks, and as a result, provide a clearer picture of ecological communities. In addition, we found that the particular species themselves can have a significant impact on the meso-scale structure and, in some cases, may impose strict limitations on what interactions can occur within a community. This has important implications for our understanding of how ecological networks are built and maintained, and thereby for our understanding of the stability and resilience of ecological communities.

Orientador: Prof. Dr. Danilo da Cruz Centeno / Dissertação (mestrado) - Universidade Federal do ABC, Programa de Pós-Graduação em Biotecnociência, 2018. / A recalcitrância da parede celular, associada à presença da lignina nos tecidos vegetais, dificulta e torna mais oneroso o uso da biomassa para a produção de etanol de segunda geração. Para driblar este obstáculo, muitos estudos têm sido realizados para compreender o metabolismo da lignina e encontrar formas alternativas de tratamento da biomassa. Recentemente, o ozônio vem sendo aplicado como uma alternativa de pré-tratamento do material lignocelulósico, devido à ação específica sobre a lignina. O presente trabalho possui dois capítulos independentes, e teve como objetivo principal estudar as alterações no conteúdo de lignina em cana-de-açúcar dado as características inerentes aos colmos das variedades estudadas e ao efeito causado pela fumigação aguda com ozônio. No capítulo I, além da quantificação de lignina, determinamos a concentração de açúcares solúveis totais para quatro variedades ¿ RB72454, RB855156, RB867515 e RB9257. Estes dados foram submetidos a análises de correlação e conectância com dados de metabolismo primário previamente obtidos por nosso grupo de pesquisa. A influência da variação da concentração do ácido chiquímico sobre o conteúdo de lignina não pôde ser confirmada através da correlação encontrada entre os dois compostos. Porém, a análise de rede de conectância mostrou que a lignina e o ácido chiquímico estão mais fortemente conectados nas variedades de colheita tardia RB72454 e RB92579. Estas conexões revelam a influência das fases do desenvolvimento vegetal no metabolismo da lignina. No capítulo II, avaliamos as alterações no conteúdo de lignina de folhas de cana-de-açúcar após exposições sucessivas à fumigação com ozônio. Os resultados mostraram uma reação das plantas (despolimerização) aos danos causados pelo estresse oxidativo quando submetidas a um ciclo de fumigação, e um aumento no conteúdo de lignina como uma resposta de memória ao estresse, amplificando suas defesas contra este estresse. O metabolismo da lignina e sua relação com o metabolismo primário é complexo e, no presente estudo, os resultados mostraram que alterações nesta relação podem ser observadas tanto constitutivamente (i.e., inerentes ao desenvolvimento da planta), quanto induzidas por estresse. Ademais, reportamos que, entre as técnicas utilizadas neste trabalho, a rede de conectância e o FT-Raman mostraram-se importantes ferramentas no estudo da lignina. / The recalcitrance of the cell wall is associated with the presence of lignin in the vegetal tissues, making it difficult and more expensive to use biomass for the production of second-generation ethanol. To overcome this obstacle many studies have been carried out to understand the lignin metabolism and to find alternative forms of biomass treatment. Recently, ozone has been applied as an alternative pretreatment of the lignocellulosic material, due to its specific action on lignin. The present work has two independent chapters, in which the main objective was to study the changes in lignin content in sugarcane due to the inherent characteristics of the stems of the studied varieties and the effect caused by the acute fumigation with ozone. In chapter I, in addition to the quantification of lignin we determined the total soluble sugars of four varieties RB72454, RB855156, RB867515 and RB9257. These data were submitted to correlation analysis and the network connectance analysis with data of primary metabolism, previously obtained in our group. The influence of the variation of the shikimate concentration on the lignin content was not confirmed by the correlation found between the two compounds. However, the network connectance analysis showed that lignin and shikimate are more strongly connected in late harvest varieties RB72454 and RB92579. These connections revealed the influence of plant development phases over lignin metabolism. In chapter II, changes in the lignin content of leaf blades of sugarcane were evaluated after multiple exposures to ozone fumigation. The results showed a reaction of the plants (depolymerization) to the damage caused by oxidative stress when submitted to one fumigation exposure, and an increase in lignin content as a memory response to stress, amplifying their defenses against ozone. The metabolism of lignin and its relation to the primary metabolism is complex and our results showed that alterations in this relationship may be constitutive (i.e., inherent to the plant development), and induced by abiotic stress. In addition, we reported that among the techniques applied in this work, the network connectance and the FT-Raman showed to be useful tools in the study of lignin.