Because of the scarcity of information for bird communities at the major mainland rivers of southeastern Alaska, the main objective of this study was to provide baseline information including distribution, status, and habitat associations of breeding birds. I conducted a meta-analysis of all known reports (including the current study) conducted at major mainland rivers during the breeding season. I described bird species composition, distribution, abundance estimates, status, habitat associations, and guild membership for all birds recorded at 11 major mainland rivers. Based on incidental observations, 170 species were recorded by all studies. Of these, 134 species were known or suspected to breed, accounting for 50% of all birds known from Alaska and 80% of all birds known from southeastern Alaska. In addition, I provided information on species of management concern as well as management implications and recommendations. I used point counts to survey birds within deciduous riparian vegetation at 6 major mainland rivers during 2000-2002. I compared bird species composition, abundance, richness, and diversity among four main vegetation types of deciduous riparian vegetation: shrubland, young deciduous forest, mature deciduous forest, and mixed deciduous-coniferous forest. Species richness was similar among all habitat types; however, relative abundance and diversity of birds was highest in mixed forest stands. Mature forests had the greatest number of species associated with the Canadian interior. I also used point counts to compare bird species composition, abundance, richness, and diversity among 6 major mainland rivers consisting of three trans-mountain and three coastal rivers. Latitude, connectivity, and availability of mature and mixed forests were the major factors thought to cause differences in bird communities among rivers. Contrary to our predictions, coastal rivers had higher bird species richness, diversity, point abundance , and point richness than trans-mountain rivers. Of the 10 species associated with the Canadian interior recorded during point counts, 8 occurred at both trans-mountain and coastal rivers.

The effects of fire on vernal herbs of the mesic forests of eastern North America are poorly understood. I studied the influence of prescribed fire on species richness, abundance of rare and common species, and density of exotics in the vernal herbaceous layer. To determine these effects, three sites in central Kentucky were surveyed prior to and following one of three treatments: spring burn, winter burn, or negative control. I conducted low-intensity spring burns in April 2010 and winter burns in February 2011. I used chi square analyses to test for changes in species richness, abundance of rare species, abundance of common species, and abundance of Glechoma hederacea, an exotic herb. I used multiple logistic regressions to test for the effect of burn severity on the abundance of two of the most common herbs, Erythronium americanum and Viola sororia sensu lato. The abundance of rare species increased significantly after fire treatment, with a 2% greater increase on burned plots than control plots (p < 0.05), and showed a 40% greater increase in plots burned in winter than plots burned in spring. However, there was no significant difference in overall species richness due to fire or to the season in which the prescribed fire was conducted. There were no significant differences in the density of common species or Glechoma hederacea due to fire treatment or due to fire season. There were also no significant differences in the abundances of Erythronium americanum or Viola sororia sensu lato due to burn severity. Changes in the abundance of rare species due to fire might suggest that prescribed burns may slightly increase the diversity of vernal herbs in eastern mesic forests. Changes in the abundance of rare species due to fire season might suggest that prescribed fires conducted prior to emergence may further increase the diversity of vernal herbs in the eastern mesic forest.

As distribuições de abundância das espécies (SADs) são consideradas uma maneira informativa e sintética de descrever a diversidade biológica, e revelam um dos padrões mais bem estabelecidos da ecologia, que é a predominância de espécies raras nas comunidades biológicas. A generalidade deste padrão o torna relevante para a análise de outros parâmetros das comunidades. Além disso, ele levou ao desenvolvimento dos modelos teóricos de SAD. Os modelos estatísticos de SAD, por sua vez, passaram a ocupar um papel central na biologia, como principio empírico que sustenta várias teorias ecológicas. Preston sugeriu em 1948 que as SADs das comunidades naturais teriam uma distribuição aproximadamente Lognormal, porém apareciam truncadas devido ao efeito do tamanho amostral, cuja forma real só seria revelada, portanto, em amostras grandes. Esta ideia vai de encontro à propriedade estatística da consistência, que implica que o acúmulo de evidência causado pelo aumento do tamanho amostral favorece a aproximação ao modelo verdadeiro, bem como às estimativas de seus parâmetros. Além do efeito do tamanho amostral, os padrões de distribuição de abundância podem diferir dependendo da medida de abundância utilizada. Estudos sugerem que a biomassa seria uma medida de abundância mais adequada para revelar a distribuição subjacente de uma comunidade biológica em amostras ou escalas menores (differential veiling). Neste contexto, nosso objetivo principal neste trabalho foi investigar e discutir a vantagem de considerarmos a biomassa como medida de abundância nos modelos teóricos de distribuição de abundância das espécies. Avaliamos, então, o efeito do tamanho da amostra sobre a qualidade dos ajustes dos modelos sob duas diferentes medidas de abundância: biomassa e número de indivíduos. Simulamos amostras de diferentes tamanhos a partir de amostragens aleatórias de uma base de dados empírica e as ajustamos a diferentes modelos de SADs . Com isso, pudemos avaliar a eficiência das amostras - com cada medida de abundância - em revelar o modelo correto, bem como a acurácia e precisão das estimativas dos parâmetros desses modelos. Para o presente estudo, utilizamos um grupo com reconhecido potencial indicador e relevância para estudos ecológicos, os besouros Scarabaeinae. Os resultados encontrados neste estudo mostram que a maior eficiência da biomassa para revelar a distribuição subjacente não é tão geral quanto sugerem os trabalhos anteriores Os critérios de análise utilizados não favoreceram consistentemente a biomassa como medida mais eficiente em revelar o modelo correto e apresentar maior acurácia e precisão nas estimativas de seus parâmetros. Assim, a afirmativa de que a SAD de biomassa não é oculta (veiled) em escalas e amostra menores não parece ser geral. Os resultados obtidos no presente estudo também indicam que o padrão de differential veiling entre as SADs de biomassa e número de indivíduos podem variar dependendo da escolha do modelo e do conjunto de dados avaliados. No entanto, se a causa do differential veiling entre as SADs de biomassa e número de indivíduos for principalmente devido ao efeito de escala, uma explicação alternativa é que a escala do presente estudo teria que ser ampliada para podermos demonstrá-lo. Considerando então, os efeitos de amostragem apontados pelos nossos resultados sobre a medida de diversidade, destacamos que, apesar da importância do assunto, há uma escassez de estudos que investiguem o uso da biomassa como medida de abundância nas SADs, cujas implicações de diferentes efeitos sobre esta medida destacam a necessidade de estudos adicionais que possibilitem isolar o efeito de escala do efeito de tamanho amostral / The species abundance distributions (SADs) are considered an informative way to describe the biological diversity revealling one of the most wellestablished patterns in ecology: the predominance of rare species in biological communities. The generality of such pattern made it relevant to the analysis of other biodiversity parameters an to induce the development of theoretical models of SAD. On the other hand statistical models of SAD occupied a central role in biology as an empirical principle that underlies many ecological theories. Preston suggested in 1948 that SADs follow an approximately lognormal distribution, but that may appear truncated by the effect of sample size, being completely revealed only in large samples. This idea is associated with the statistical property of consistency, which implies that the accumulation of evidence - represented by the increase in sample size - approaches the samples distribution to the true model, as well as the estimates of the parameters to their real values. Beyond the effect of sample size, the SADs may differ depending on the measure of abundance adopted. Studies suggest that biomass could be a more efficient measure of abundance to reveal the underlying distribution of biological communities in smaller samples or scales (differential veiling). In this context, our aim in this study was to investigate and discuss the advantage of considering biomass in theoretical models of SAD. Thus we evaluated the effect of sample size on the quality of models fitness under two different measures of species abundance: biomass and number of individuals. We simulated samples of different sizes taken from an empirical database of Scarabaeinae beetles - recognized as a potential and relevant indicator in ecological studies. Further we adjusted the simulated samples to different SAD models and evaluated the efficiency of each kind of abundance index to reveal the correct model, as well as the accuracy and precision of the parameters estimates. Our results show that the efficiency of biomass to reveal the underlying distribution is not as general as suggested by previous works. According to our analysis criteria, biomass was not consistently as far more efficient in revealing the correct model or in providing greater accuracy and precision in parameters estimates than the number of individuals. Thus, the statement that the SAD biomass is not veiled on small scales or samples does not seem to be general. Moreover our results also indicate that the effect of differential veiling on SADs using biomass and number of individuals depends on the choice of the evaluated model and data set. However, if the cause of the differential veiling - between the biomass and number of individuals SADs - is mainly due to scale effects. An alternative explanation is that the scale of this study was not wide enough to show it. Considering the sampling effects studied here in biodiversity evaluation we highlight the lack of studies investigating the use of biomass as a measure of abundance in SADs which the implications of different effects on this measure indicate the urgent call by further studies on this subject, enablying us to isolate the effect of scale from the sample size

Orientadores: Fernando Roberto Martins, Roque Cielo Filho / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-22T19:33:19Z (GMT). No. of bitstreams: 1 Azevedo_MarioJoseMarques_M.pdf: 1374222 bytes, checksum: 6cfc592a0f568c5e7abef9efd6a9adeb (MD5) Previous issue date: 2013 / Resumo: O padrão de utilização de recursos e a teoria de nichos ecológicos constituem elementos importantes na compreensão de como comunidades ecológicas são estruturadas. A maneira como os recursos são partilhados entre as espécies é refletida na sua distribuição de abundância. Abundância e diversidade de espécie são resultantes de processos que determinam as comunidades. Um padrão frequentemente observado é a relação unimodal entre diversidade e produtividade. Processos competitivos são inferidos na determinação da diversidade ao longo do gradiente de produtividade. Devido à abundância das espécies serem resultantes de interações biológicas, os modelos de distribuição de abundância de espécies (DAE) permitem inferir na maneira como o espaço de nicho é partilhado. Utilizamos os modelos de DAE proposto por Tokeshi e índices de concentração de dominância e equabilidade para testar por meio de regressões como a riqueza, biomassa e equabilidade variam ao longo de um gradiente de estresse nutricional definido pela concentração de alumínio no solo. Verificamos um padrão linear negativo entre a riqueza e gradiente de estresse nutricional com fragmentos de floresta estacional semidecídua no extremo de menor estresse e cerradão no extremo oposto do gradiente. A biomassa apresentou um padrão em forma de "U" quando relacionado ao mesmo gradiente. Os índices e os modelos foram condizentes na verificação da concentração de dominância por poucas espécies nos extremos do gradiente, porém somente o índice Evar verificou a maior equabilidade nos valores intermediários do gradiente. Nossos resultados permitiram inferir que tal gradiente foi importante na determinação da riqueza e biomassa das comunidades. Os modelos e índices permitiram verificar o padrão de partilha de nicho, porém não foi possível afirmar o processo que resultou tal partilha / Abstract: The resource utilization patterns and ecological niche theory are important in understand how communities are assembled. The way how resources are apportioned between species are showed in its abundance distribution. Abundance and diversity are outcome of process that structure communities. The pattern frequently found is a "hump-back" relationship between diversity and productivity. Competitive processes are inferred in determination of diversity along productivity gradient. Due to species abundance are outcome of biological interaction, models of species abundance distribution (SAD) allow us to infer how niche are apportioned. We use Tokeshi's SADs models and dominance and evenness index to test, using regression, how richness, biomass and evenness change along stress nutrition gradient defined by aluminium concentration in soil. We verified a negative linear pattern between richness and nutrition stress gradient with semideciduous forest fragment at extreme of lesser stress gradient and cerradão at opposite extreme gradient. The biomass showed a "U" shape pattern along the same gradient. The index and SADs models showed similar result measuring dominance of few species at extremes of gradient, however only Evar index measured more evenness between extremes of gradient. Our results allow inferring that such gradient war important to define community richness and biomass. The models and index allowed testing the patterns of niche apportionment, however its do not allowed us confirm the process of niche apportionment / Mestrado / Ecologia / Mestre em Ecologia

Dans les applications modernes des statistiques et de l'apprentissage, il est courant que les données récoltées présentent un certain nombre d'imperfections. En particulier, les données sont souvent hétérogènes, c'est-à-dires qu'elles contiennent à la fois des informations quantitatives et qualitatives, incomplètes, lorsque certaines informations sont inaccessibles ou corrompues, et multi-sources, c'est-à-dire qu'elles résultent de l'agrégation de plusieurs jeux de données indépendant. Dans cette thèse, nous développons plusieurs méthodes pour l'analyse de données hétérogènes, incomplètes et multi-source. Nous nous attachons à étudier tous les aspects de ces méthodes, en fournissant des études théoriques précises, ainsi que des implémentations disponibles au public, et des évaluations empiriques. En particulier, nous considérons en détail deux applications issues de l'écologie pour la première et de la médecine pour la seconde. / In modern applications of statistics and machine learning, one often encounters many data imperfections. In particular, data are often heterogeneous, i.e. combine quantitative and qualitative information, incomplete, with missing values caused by machine failure or nonresponse phenomenons, and multi-source, when the data result from the compounding of diverse sources. In this dissertation, we develop several methods for the analysis of multi-source, heterogeneous and incomplete data. We provide a complete framework, and study all the aspects of the different methods, with thorough theoretical studies, open source implementations, and empirical evaluations. We study in details two particular applications from ecology and medical sciences.

A descrição de padrões, i.e., tendências ou arranjos não aleatórios em comunidades, possui um longo histórico em ecologia vegetal. Comumente, a estrutura e diversidade de comunidades vegetais são descritas a partir de sua distribuição em classes de tamanho (SDD), distribuição espacial (SSD) e de sua distribuição abundância de espécies (SAD). Isto porque há um pressuposto de que padrões existentes nestes descritores de comunidades são assinaturas de processos fundamentais na sua organização e funcionamento. Assim, a descrição de padrões é com frequência o primeiro passo para gerar ou testar hipóteses sobre esses processos que regulam a estrutura e diversidade de comunidades. Organizada em diferentes capítulos, esta tese teve como objetivo central descrever e comparar padrões em diferentes comunidades arbóreas Neotropicais, buscando gerar hipóteses sobre os processos que regulam sua organização e funcionamento. Para tanto, buscou-se utilizar uma abordagem de inferência baseada no ajuste e seleção de modelos, que foi realizado usando máxima verossimilhança estatística. Em todos os capítulos, os dados sobre as comunidades arbóreas são oriundos de diferentes parcelas florestais permanentes, quatro delas com 10,24 hectares, localizadas no Brasil, e outra com 50 hectares, localizada no Panamá. Além da introdução geral sobre os conceitos e técnicas utilizadas nesta tese (Capítulo 1), foram avaliados e comparados: (i) os descritores básicos da estrutura florestal (i.e. abundância, área basal e riqueza de espécies por sub-parcela - Capítulo 2); (ii) a SAD e como ela varia com o aumento da escala e tamanho amostral (Capítulo 3); (iii) a SDD e como ela se relaciona com a demografia das espécies (Capítulo 4.1 e 4.2); e, por fim, (iv) a SSD e como ela varia entre parcelas permanentes (Capítulo 5). Apenas a relação entre a SDD e a demografia das espécies foi realizada como os dados da parcela panamenha, enquanto que os demais capítulos se referem as quatro parcelas brasileiras. Cada capítulo utilizou métodos e modelos probabilísticos distintos para a descrição e comparação das variáveis de interesse. O Capítulo 2 mostrou que os descritores básicos florestais foram muito diferentes entre as quatro parcelas brasileiras. Estes descritores foram raramente normais nas escalas estudadas e as diferenças entre as parcelas foram mais evidentes quando a variância é considerada, fornecendo informações extras sobre os processos geradores de variabilidade dentro das parcelas. O Capítulo 3 mostrou que a mudança no formato da SAD com o aumento da escala é predominantemente um efeito indireto do tamanho da amostra. Assim, pode haver um efeito de escala, mas esse efeito é pequeno e parece depender do grau de similaridade de espécies entre amostras. No capítulo 4.1, foi necessária uma combinação de quatro diferentes distribuições de probabilidade para descrever a ampla gama de SDD, visto que os modelos candidatos raramente foram adequados para a maioria das espécies. No capítulo 4.2, verificou-se que o crescimento e recrutamento determinam o formato da SDD, o que não aconteceu com a mortalidade. No geral, curvas decrescentes de crescimento por diâmetro (i.e., maior crescimento juvenil) levaram à SDD menos íngremes, enquanto que taxas altas de recrutamento estiveram relacionadas à SDD mais íngremes. Apesar das previsões da teoria de equilíbrio demográfico terem apresentado relações positivas com as SDD observadas, houve muita variação, fazendo com que as previsões fossem pouco confiáveis. No capítulo 5, confirmou-se que a grande maioria das espécies se distribui de maneira agregada no espaço. No entanto, as parcelas apresentaram diferentes padrões de intensidade e tamanho de agregação. As diferenças nestes padrões entre parcelas foram, em geral, similares àquelas encontradas ao comparar populações de uma mesma espécie entre parcelas. Assim, as parcelas permanentes brasileiras apresentaram padrões bem distintos umas das outras, tanto em termos de estrutura quanto de diversidade de espécies, padrões estes que provavelmente foram determinados pelas condições ambientais as quais estas comunidades estão sujeitas. Diferentes padrões também foram encontrados em relação à distribuição espacial das espécies (i.e. frequência, intensidade e tamanho de agregação). Contudo, os resultados sugeriram que estes padrões estiveram mais ligados a heterogeneidade ambiental interna das parcelas do que com condições de clima e solo as quais estas comunidades estão sujeitas. Por outro lado, os padrões de distribuição espacial das espécies parecem ter influenciado os padrões de diversidade das comunidades. Não houve, entretanto, um número suficiente de parcelas sob as diferentes combinações de condições ambientais para testar estas sugestões ou para fazer generalizações para cada formação florestal, sendo necessário o confronto destas sugestões com outros estudos realizados em condições similares. Já na parcela panamenha, foi confirmada a expectativa teórica de que distribuições diamétricas refletem a demografia das espécies, em especial os padrões de crescimento e recrutamento. Mas, houve grande variação entre as espécies, dificultando a inferência precisa de padrões demográficos passados das espécies a partir de SDD atuais. Por fim, a abordagem analítica baseada no ajuste e seleção de modelos por máxima foi uma alternativa viável, flexível e apropriada, principalmente em relação à comparação simultânea de diferentes modelos e à busca de processos por trás dos padrões encontrados. Apesar de algumas limitações de cunho operacional, a abordagem baseado em modelos é uma alternativa adequada para a descrição de comunidades arbóreas, podendo ser utilizada de maneira consorciada com outras abordagens (e.g. testes de hipóteses) para descrever padrões e para gerar ou testar hipóteses sobre esses processos fundamentais que regulam a estrutura e diversidade destas comunidades. / Pattern description - search for trends or non-random arrangements in communities, has a long history in plant ecology. Commonly, the structure and diversity of plant communities are described based on their size class distribution (SDD), spatial distribution (SSD) and species abundance distribution (SAD). This is because there is an underlying assumption that the existing patterns in these community descriptors are signatures of key processes determining their organization and functioning. Thus, pattern description is often the first step to generate or test hypotheses about the processes governing community structure and diversity. Organized in different chapters, the main goal of this thesis was to describe and compare different patterns in Neotropical tree communities and to generate hypotheses about the processes that regulate them. To do so we used an approach based on model selection, which was performed using maximum likelihood. In all chapters the data on tree communities came from different permanent forest plots, four of them of 10.24 ha located in Brazil and another 50 ha located in Panama. In addition to the general introduction of key concepts and techniques used along the thesis (Chapter 1), it was evaluated and compared: (i) the basic forest descriptors (i.e. abundance, basal area and species richness per subplot - Chapter 2), (ii) the SAD and how it varies with increasing sample size and scale (Chapter 3), (iii) the SDD and how it relates to species demography (Chapter 4.1 and 4.2) and, finally, (iv) the SSD and how it varies between plots (Chapter 5). Only the relationship between SDD and species demography o was performed using the Panama plot data, while the remaining chapters relate the four Brazilian plots. Each chapter used different methods and probabilistic models for the description and comparison of the variables of interest. In Chapter 2, it was found that basic forest descriptors were very different between the four Brazilian plots. These descriptors were rarely normal at the studied scales and differences between plots were more evident when variance is accounted for, which seems to provide information on processes generating within-plot variability. Chapter 3 showed that the change in shape of the SAD due to increasing scale is predominantly an indirect effect of sample size. Thus, there may be an effect of the scale, but this effect is minor and seems to depend on the degree of species turnover between samples. In Chapter 4.1, it was shown that the combination of four different probability distributions was necessary to describe the wide range of SDD, since models were rarely appropriate for the majority of tree species. In Chapter 4.2, it was found that growth and recruitment, but not mortality, shape the SDD. On average, decreasing growth-diameter curves (i.e. higher juvenile growth) were associated to less steep SDD, whereas high recruitment rates were related to steeper SDD. Although the predictions of demographic equilibrium theory were positively related to the observed SDD, there was lots of variation, making predictions quite unreliable. In Chapter 5, it was confirmed that the great majority of species had clumped spatial distributions. However, the results of intensity and size of clumps showed that the patterns of aggregation were different among plots. Species shared between two plots generally showed patterns of spatial distribution that matched the patterns found for individual plots. Therefore, the Brazilian plots presented very distinct patterns, both in terms of structure and species diversity, which were most probably determined by the environmental conditions to which these communities are subjected. Different patterns among plots were also found in respect to species spatial distribution (i.e. frequency, intensity and size of aggregation). However, the results suggested that these patterns were more connected to within-plot environmental heterogeneity than with climate and soil conditions. On the other hand, the spatial distribution of the species seems to have influenced the patterns of diversity of communities. There was not, however, a sufficient number of plots under different combinations of environmental conditions to test these suggestions or to make generalizations for each forest type, being necessary to confront these suggestions with other studies conducted in similar conditions. In the Panamanian plot, it was confirmed the theoretical expectation that diameter distributions reflect the demographics of the species, in particular the patterns of growth and recruitment. But there was great variability among species, making it difficult to infer past demographic patterns from current SDD. Finally, the analytical approach based on model fit and selection by maximum likelihood was a viable, flexible and appropriate approach, particularly in respect to the simultaneous comparison of different models and to the search for mechanisms underlying patterns. Despite some more operational limitations, the model-based approach is an appropriate alternative for the description of tree communities and can be jointly used with other approaches (e.g. hypothesis testing) for pattern description and to generate and test hypotheses on the fundamental processes that determine the structure and diversity of these communities.

Biodiversity is determined by a myriad of complex processes acting at different scales. Given the current rates of biodiversity loss and change, it is of paramount importance that we improve our understanding of the underlying structure of ecological communities. In this thesis, I focused on Species Abundance Distributions (SAD), as a synthetic measure of biodiversity and community structure, and on Beta (β) diversity patterns, as a description of the spatial variation of species composition. I systematically assessed the effect of scale on both these patterns, analysing a broad range of community data, including different taxa and habitats, from the terrestrial, marine and freshwater realms. Knowledge of the scaling properties of abundance and compositional patterns must be fully integrated in biodiversity research if we are to understand biodiversity and the processes underpinning it, from local to global scales. SADs depict the relative abundance of the species present in a community. Although typically described by unimodal logseries or lognormal distributions, empirical SADs can also exhibit multiple modes. However, the existence of multiple modes in SADs has largely been overlooked, assumed to be due to sampling errors or a rare pattern. Thus, we do not know how prevalent multimodality is, nor do we have an understanding of the factors leading to this pattern. Here, I provided the first global empirical assessment of the prevalence of multimodality across a wide range of taxa, habitats and spatial extents. I employed an improved method combining two model selection tools, and (conservatively) estimated that ~15% of the communities were multimodal with strong support. Furthermore, I showed that the pattern is more common for communities at broader spatial scales and with greater taxonomic diversity (i.e. more phylogenetically diverse communities, since taxonomic diversity was measured as number of families). This suggests a link between multimodality and ecological heterogeneity, broadly defined to incorporate the spatial, environmental, taxonomic and functional variability of ecological systems. Empirical understanding of how spatial scale affects SAD shape is still lacking. Here, I established a gradient in spatial scale spanning several orders of magnitude by decomposing the total extent of several datasets into smaller subsets. I performed an exploratory analysis of how SAD shape is affected by area sampled, species richness, total abundance and taxonomic diversity. Clear shifts in SAD shape can provide information about relevant ecological and spatial mechanisms affecting community structure. There was a clear effect of area, species richness and taxonomic diversity in determining SAD shape, while total abundance did not exhibit any directional effect. The results supported the findings of the previous analysis, with a higher prevalence of multimodal SADs for larger areas and for more taxonomically diverse communities, while also suggesting that species spatial aggregation patterns can be linked to SAD shape. On the other hand, there was a systematic departure from the predictions of two important macroecological theories for SAD across scales, specifically regarding logseries distributions being selected only for smaller scales and when species richness and number of families were proportionally much smaller than the total extent. β diversity quantifies the variation in species composition between sites. Although a fundamental component of biodiversity, its spatial scaling properties are still poorly understood. Here, I tested if two conceptual types of β diversity showed systematic variation with scale, while also explicitly accounting for the two β diversity components, turnover and nestedness (species replacement vs species richness differences). I provided the first empirical analysis of β diversity scaling patterns for different taxa, revealing remarkably consistent scaling curves. Total β diversity and turnover exhibit a power law decay with log area, while nestedness is largely insensitive to scale changes. For the distance decay of similarity analysis, while area sampled affected the overall dissimilarity values, rates of similarity were consistent across large variations in sampled area. Finally, in both these analyses, turnover was the main contributor to compositional change. These results suggest that species are spatially aggregated across spatial scales (from local to regional scales), while also illustrating that substantial change in community structure might occur, despite species richness remaining relatively stable. This systematic and comprehensive analysis of SAD and community similarity patterns highlighted spatial scale, ecological heterogeneity and species spatial aggregation patterns as critical components underlying the results found. This work expanded the range of scales at which both theories deriving SAD and community similarity studies have been developed and tested (from local plots to continents). The results here showed strong departures from two important macroecological theories for SAD at different scales. In addition, the overall findings in this thesis clearly indicate that unified theories of biodiversity (or assuming a set of synthetic minimal assumptions) are unable to accommodate the variability in SADs shape across spatial scales reported here, and cannot fully reproduce community similarity patterns across scales. Incorporating more realistic assumptions, or imposing scale dependent assumptions, may prove to be a fruitful avenue for ecological research regarding the scaling properties of SAD and community similarity patterns. This will allow deriving new predictions and improving the ability of theoretical models to incorporate the variability in abundance and similarity patterns across scales.

A descrição de padrões, i.e., tendências ou arranjos não aleatórios em comunidades, possui um longo histórico em ecologia vegetal. Comumente, a estrutura e diversidade de comunidades vegetais são descritas a partir de sua distribuição em classes de tamanho (SDD), distribuição espacial (SSD) e de sua distribuição abundância de espécies (SAD). Isto porque há um pressuposto de que padrões existentes nestes descritores de comunidades são assinaturas de processos fundamentais na sua organização e funcionamento. Assim, a descrição de padrões é com frequência o primeiro passo para gerar ou testar hipóteses sobre esses processos que regulam a estrutura e diversidade de comunidades. Organizada em diferentes capítulos, esta tese teve como objetivo central descrever e comparar padrões em diferentes comunidades arbóreas Neotropicais, buscando gerar hipóteses sobre os processos que regulam sua organização e funcionamento. Para tanto, buscou-se utilizar uma abordagem de inferência baseada no ajuste e seleção de modelos, que foi realizado usando máxima verossimilhança estatística. Em todos os capítulos, os dados sobre as comunidades arbóreas são oriundos de diferentes parcelas florestais permanentes, quatro delas com 10,24 hectares, localizadas no Brasil, e outra com 50 hectares, localizada no Panamá. Além da introdução geral sobre os conceitos e técnicas utilizadas nesta tese (Capítulo 1), foram avaliados e comparados: (i) os descritores básicos da estrutura florestal (i.e. abundância, área basal e riqueza de espécies por sub-parcela - Capítulo 2); (ii) a SAD e como ela varia com o aumento da escala e tamanho amostral (Capítulo 3); (iii) a SDD e como ela se relaciona com a demografia das espécies (Capítulo 4.1 e 4.2); e, por fim, (iv) a SSD e como ela varia entre parcelas permanentes (Capítulo 5). Apenas a relação entre a SDD e a demografia das espécies foi realizada como os dados da parcela panamenha, enquanto que os demais capítulos se referem as quatro parcelas brasileiras. Cada capítulo utilizou métodos e modelos probabilísticos distintos para a descrição e comparação das variáveis de interesse. O Capítulo 2 mostrou que os descritores básicos florestais foram muito diferentes entre as quatro parcelas brasileiras. Estes descritores foram raramente normais nas escalas estudadas e as diferenças entre as parcelas foram mais evidentes quando a variância é considerada, fornecendo informações extras sobre os processos geradores de variabilidade dentro das parcelas. O Capítulo 3 mostrou que a mudança no formato da SAD com o aumento da escala é predominantemente um efeito indireto do tamanho da amostra. Assim, pode haver um efeito de escala, mas esse efeito é pequeno e parece depender do grau de similaridade de espécies entre amostras. No capítulo 4.1, foi necessária uma combinação de quatro diferentes distribuições de probabilidade para descrever a ampla gama de SDD, visto que os modelos candidatos raramente foram adequados para a maioria das espécies. No capítulo 4.2, verificou-se que o crescimento e recrutamento determinam o formato da SDD, o que não aconteceu com a mortalidade. No geral, curvas decrescentes de crescimento por diâmetro (i.e., maior crescimento juvenil) levaram à SDD menos íngremes, enquanto que taxas altas de recrutamento estiveram relacionadas à SDD mais íngremes. Apesar das previsões da teoria de equilíbrio demográfico terem apresentado relações positivas com as SDD observadas, houve muita variação, fazendo com que as previsões fossem pouco confiáveis. No capítulo 5, confirmou-se que a grande maioria das espécies se distribui de maneira agregada no espaço. No entanto, as parcelas apresentaram diferentes padrões de intensidade e tamanho de agregação. As diferenças nestes padrões entre parcelas foram, em geral, similares àquelas encontradas ao comparar populações de uma mesma espécie entre parcelas. Assim, as parcelas permanentes brasileiras apresentaram padrões bem distintos umas das outras, tanto em termos de estrutura quanto de diversidade de espécies, padrões estes que provavelmente foram determinados pelas condições ambientais as quais estas comunidades estão sujeitas. Diferentes padrões também foram encontrados em relação à distribuição espacial das espécies (i.e. frequência, intensidade e tamanho de agregação). Contudo, os resultados sugeriram que estes padrões estiveram mais ligados a heterogeneidade ambiental interna das parcelas do que com condições de clima e solo as quais estas comunidades estão sujeitas. Por outro lado, os padrões de distribuição espacial das espécies parecem ter influenciado os padrões de diversidade das comunidades. Não houve, entretanto, um número suficiente de parcelas sob as diferentes combinações de condições ambientais para testar estas sugestões ou para fazer generalizações para cada formação florestal, sendo necessário o confronto destas sugestões com outros estudos realizados em condições similares. Já na parcela panamenha, foi confirmada a expectativa teórica de que distribuições diamétricas refletem a demografia das espécies, em especial os padrões de crescimento e recrutamento. Mas, houve grande variação entre as espécies, dificultando a inferência precisa de padrões demográficos passados das espécies a partir de SDD atuais. Por fim, a abordagem analítica baseada no ajuste e seleção de modelos por máxima foi uma alternativa viável, flexível e apropriada, principalmente em relação à comparação simultânea de diferentes modelos e à busca de processos por trás dos padrões encontrados. Apesar de algumas limitações de cunho operacional, a abordagem baseado em modelos é uma alternativa adequada para a descrição de comunidades arbóreas, podendo ser utilizada de maneira consorciada com outras abordagens (e.g. testes de hipóteses) para descrever padrões e para gerar ou testar hipóteses sobre esses processos fundamentais que regulam a estrutura e diversidade destas comunidades. / Pattern description - search for trends or non-random arrangements in communities, has a long history in plant ecology. Commonly, the structure and diversity of plant communities are described based on their size class distribution (SDD), spatial distribution (SSD) and species abundance distribution (SAD). This is because there is an underlying assumption that the existing patterns in these community descriptors are signatures of key processes determining their organization and functioning. Thus, pattern description is often the first step to generate or test hypotheses about the processes governing community structure and diversity. Organized in different chapters, the main goal of this thesis was to describe and compare different patterns in Neotropical tree communities and to generate hypotheses about the processes that regulate them. To do so we used an approach based on model selection, which was performed using maximum likelihood. In all chapters the data on tree communities came from different permanent forest plots, four of them of 10.24 ha located in Brazil and another 50 ha located in Panama. In addition to the general introduction of key concepts and techniques used along the thesis (Chapter 1), it was evaluated and compared: (i) the basic forest descriptors (i.e. abundance, basal area and species richness per subplot - Chapter 2), (ii) the SAD and how it varies with increasing sample size and scale (Chapter 3), (iii) the SDD and how it relates to species demography (Chapter 4.1 and 4.2) and, finally, (iv) the SSD and how it varies between plots (Chapter 5). Only the relationship between SDD and species demography o was performed using the Panama plot data, while the remaining chapters relate the four Brazilian plots. Each chapter used different methods and probabilistic models for the description and comparison of the variables of interest. In Chapter 2, it was found that basic forest descriptors were very different between the four Brazilian plots. These descriptors were rarely normal at the studied scales and differences between plots were more evident when variance is accounted for, which seems to provide information on processes generating within-plot variability. Chapter 3 showed that the change in shape of the SAD due to increasing scale is predominantly an indirect effect of sample size. Thus, there may be an effect of the scale, but this effect is minor and seems to depend on the degree of species turnover between samples. In Chapter 4.1, it was shown that the combination of four different probability distributions was necessary to describe the wide range of SDD, since models were rarely appropriate for the majority of tree species. In Chapter 4.2, it was found that growth and recruitment, but not mortality, shape the SDD. On average, decreasing growth-diameter curves (i.e. higher juvenile growth) were associated to less steep SDD, whereas high recruitment rates were related to steeper SDD. Although the predictions of demographic equilibrium theory were positively related to the observed SDD, there was lots of variation, making predictions quite unreliable. In Chapter 5, it was confirmed that the great majority of species had clumped spatial distributions. However, the results of intensity and size of clumps showed that the patterns of aggregation were different among plots. Species shared between two plots generally showed patterns of spatial distribution that matched the patterns found for individual plots. Therefore, the Brazilian plots presented very distinct patterns, both in terms of structure and species diversity, which were most probably determined by the environmental conditions to which these communities are subjected. Different patterns among plots were also found in respect to species spatial distribution (i.e. frequency, intensity and size of aggregation). However, the results suggested that these patterns were more connected to within-plot environmental heterogeneity than with climate and soil conditions. On the other hand, the spatial distribution of the species seems to have influenced the patterns of diversity of communities. There was not, however, a sufficient number of plots under different combinations of environmental conditions to test these suggestions or to make generalizations for each forest type, being necessary to confront these suggestions with other studies conducted in similar conditions. In the Panamanian plot, it was confirmed the theoretical expectation that diameter distributions reflect the demographics of the species, in particular the patterns of growth and recruitment. But there was great variability among species, making it difficult to infer past demographic patterns from current SDD. Finally, the analytical approach based on model fit and selection by maximum likelihood was a viable, flexible and appropriate approach, particularly in respect to the simultaneous comparison of different models and to the search for mechanisms underlying patterns. Despite some more operational limitations, the model-based approach is an appropriate alternative for the description of tree communities and can be jointly used with other approaches (e.g. hypothesis testing) for pattern description and to generate and test hypotheses on the fundamental processes that determine the structure and diversity of these communities.

This thesis is the first of its kind that evaluates the species composition, species richness and species abundance of zooplankton in littoral samples of 90 Tatras lakes (Western and High Tatras of Slovakia and Poland) collected in September 2004 in the context of environmental parameters of lakes and spatial relationships of individual lakes. The most frequently occurring species in the Tatras lakes in 2004 were also evaluated in terms of their occurrence in the lakes a century ago (Minkiewicz 1914, 1917 and Lityński 1913, 1917), during the period of acidification (Ertl & Vranovský 1964, Ertl et al. 1965, Hrbáček et al. 1974, Stuchlík et al. 1985) and during the period of recovery of the lakes from acidification (Hořická et al. 2006, Sacherová et al. 2006). Relationships between variables were analysed using Poisson regression, cluster analysis with multinomial regression, canonical correspondence analysis, Mantel tests and multiple negative binomial regression. Using analyses, lakes were divided into four clusters (A, B, C, D). Each cluster consisted of lakes with the same environmental and spatial factors and similar species composition. Thirteen zooplankton species (Acanthocyclops vernalis, Acroperus harpae, Alona affinis, Arctodiaptomus alpinus, Ceriodaphnia quadrangula, Cyclops abyssorum...

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