Seed dispersal is crucial for plants to colonize new habitats and facilitate gene flow between populations. However, Pleistocene extinctions of large-bodied fruit-eating and seed-dispersing animals, known as ‘megafrugivores’, may have hindered the dispersal of plants with large fruits (> 4cm fruit length – ‘megafruits’). Plants with megafruits are common across the flora of Madagascar, especially within the palm (Arecaceae) family. This dissertation investigates the macro-ecological and micro-evolutionary consequences of dispersal limitation on palms with megafruits in Madagascar. Specifically, I investigated three key aspects: (i) turnover or beta-diversity of palms on Madagascar and the distribution of their dispersal-related traits, (ii) the genetic diversity and genetic structure of three palms with megafruits compared to one palm with small fruits, and (iii) population size and migration rate changes over time of several Malagasy palm species with different ecological characteristics. To address these questions, historical ranges of extinct megafrugivores were reconstructed based on fossil sites, and data on extant frugivores, human activities, and climate were collected. Fieldwork in Madagascar provided genetic data for 12 palm species across 46 populations, from which I generated double digest restriction-site associated DNA sequencing data. Various interdisciplinary methods were employed, including redundancy analyses, variation partitioning, linear mixed effect models, species distribution models, and demographic modelling. The findings indicate that the current turnover of palms in Madagascar is primarily influenced by extant frugivores and climate, with limited impact from extinct frugivores. Surprisingly, there is no evidence of decreased genetic diversity or increased genetic differentiation in megafruited palms due to the loss of their megafrugivore dispersers. Genetic diversity is positively associated with human population density but negatively influenced by road densities, possibly reflecting habitat fragmentation by humans. Connectivity between populations is linked to the number of shared extinct and extant (mega)frugivore species, for megafruited and small-fruited palm populations, respectively. This highlights the importance of past long-distance dispersal events by megafrugivores and human-mediated dispersal possibly maintaining connectivity for megafruited palms. Population declines are observed across palms since the Last Glacial Maximum, particularly in humid forest species rarely used by humans, while humid forest species with megafruits show recent migration disruption. In contrast, palm species with smaller fruits that are highly used by humans show less pronounced declines and more stable historical migration rates. Overall, this dissertation illustrates that while the role of megafrugivores as seed dispersers is still evident in the genome of megafruited palms, other factors such as human-mediated dispersal and climate have an influence over the distribution, genetics and demographic histories of palms in Madagascar. It further shows how integrating genetic data with ecological data on species distributions, climate, human activities, can provide novel insights into the drivers of different facets of biodiversity of such a diverse group of plants such as palms.:Chapter 1 - General introduction ....................................................................................... 7 Background and problem statement...................................................................................... 7 Plant seed dispersal, fleshy fruits and frugivory ............................................................ 7 Megafauna and megafruits ............................................................................................ 9 Thesis scope .......................................................................................................................... 12 Madagascar as a model system .................................................................................... 12 Palms as a model system .............................................................................................. 16 Thesis aims and importance ................................................................................................. 19 Overview of methodologies used ......................................................................................... 19 Field data collection ..................................................................................................... 19 Double digest restriction-site associated DNA (ddRAD) .............................................. 21 Outline of the thesis ............................................................................................................. 22 Chapter 2 - Megafrugivores as fading shadows of the past: extant frugivores and the abiotic environment as the most important determinants of the distribution of palms in Madagascar .................................................................................................................... 25 Chapter 3 - Genomic signatures of past megafrugivore-mediated dispersal in Malagasy palms ............................................................................................................................. 39 Chapter 4 - Insights into the demographic history of Malagasy palms: exploring the role of global change and species-specific characteristics ........................................................... 57 Chapter 5 – General discussion ....................................................................................... 73 Summary and key findings.................................................................................................... 73 The fate of megafruited plants in the post-megafrugivore era ........................................... 74 Vulnerability and resilience in megafruited plants .............................................................. 76 Understanding the complex role of humans in the distribution and genetics of megafruited plants ……………………………………………………………………………………………………………………………..77 The influence of abiotic factors over the distribution and genetics of Malagasy palms ..... 78 Outlook ................................................................................................................................. 79 References ...................................................................................................................... 83 Appendix ...................................................................................................................... 101 Appendix Chapter 2 ............................................................................................................ 101 Appendix Chapter 3 ............................................................................................................ 123 6 Appendix Chapter 4 ............................................................................................................ 145 Summary ...................................................................................................................... 159 Zusammenfassung ........................................................................................................ 163 Acknowledgments ........................................................................................................ 169 Curriculum Vitae ..................................................................................................................... 171 List of publications and scientific presentations .................................................................... 171 Selbstständigkeitserklärung……………………………………………………………………………………….……..168

L’objectif de ce mémoire est de déterminer si l’unicité écologique des communautés végétales est un critère approprié pour prioriser l’allocation des efforts de conservation dans les milieux humides lacustres. Pour répondre à cette question, j’ai utilisé des données d’inventaire végétal dans deux emplacements géographiques situés dans le sud du Québec et pour trois types de milieux humides (i.e., frênaies, aulnaies, tourbières). J’ai d’abord identifié les milieux humides statistiquement uniques en calculant leur contribution locale à la diversité bêta (LCBD). J’ai ensuite mesuré le degré d’association relatif entre les valeurs d’unicité écologique et plusieurs autres critères couramment employés pour déterminer les priorités de conservation, et ce, à l’aide de corrélations de Pearson et de partitionnements hiérarchiques. Les tourbières uniques avaient une grande valeur de conservation dans les deux régions étudiées, alors que les aulnaies et frênaies uniques montraient des signes d’altération de leur composition en espèces. La composition en espèces des sites uniques devrait donc être examinée pour en déterminer la valeur de conservation, puisqu’elle pourrait être affectée par le niveau d’intégrité du paysage. La proportion d’espèces rares ainsi que la présence d’espèces spécialistes sensibles aux perturbations étaient corrélées de façon importante et congruentes avec l’unicité dans les deux régions étudiées. Au contraire, la richesse spécifique était négativement corrélée avec l’unicité, ce qui suggère la nécessité d’un compromis. Une combinaison de critères complémentaires devrait donc être utilisée en plus de l’unicité afin d’identifier l’ensemble optimal de sites à protéger dans un contexte donné. / This study aimed to determine whether plant composition uniqueness is an adequate criterion for assessing conservation priorities in lake-edge wetlands. To answer this question, I used vegetation data from two large datasets of lake-edge wetlands located in southern Québec, which encompassed three wetland types (i.e., ash-dominated swamps, alder-dominated swamps, peatlands). I first identified statistically unique wetlands by computing their local contribution to beta diversity (LCBD). I then measured the relative association between ecological uniqueness values and other criteria commonly used to assess conservation priorities using Pearson correlations and hierarchical partitioning. Unique peatlands had a high conservation value in both study regions, while ash- and alder-dominated swamps showed more signs that their species composition had been altered. The species composition of unique sites should thus be examined closely to determine its conservation value, as it could be affected by the overall integrity of the landscape. The proportion of rare species and the presence of disturbance-sensitive specialist species were appreciably correlated and congruent with uniqueness in both study regions. On the other hand, species richness was negatively correlated with uniqueness, suggesting that there was a trade-off. A combination of complementary criteria should therefore be used in conjunction with uniqueness in order to identify the optimal set of sites to protect in a given context.

La diversité bêta est une mesure essentielle pour décrire l'organisation de la biodiversité dans l'espace. Le calcul des contributions locales à la diversité bêta (LCBD), en particulier, permet d'identifier des sites à forte unicité écologique montrant une diversité exceptionnelle au sein d'une région d'intérêt. Jusqu’à présent, l'utilisation des LCBD s'est restreinte à des échelles locales ou régionales avec un petit nombre de sites. Dans ce mémoire, j'ai examiné si les modèles de répartition d'espèces (SDM) permettent d'évaluer l'unicité écologique sur de plus grandes étendues spatiales. J'ai également étudié l’effet des changements d’échelle sur la quantification de la diversité bêta. Pour ce faire, j'ai utilisé la base de données eBird et des arbres de régression additifs bayésiens pour prédire la répartition des parulines en Amérique du Nord. J'ai ensuite calculé les LCBD sur ces prédictions, ce qui permet de couvrir de plus grandes étendues spatiales et un nombre de sites plus élevé. Mes résultats ont montré que les SDM fournissent des estimations d'unicité fortement corrélées avec les données observées et montrant une association spatiale statistiquement significative. Ils ont également montré que la relation entre la richesse et les LCBD varie selon la région et l'étendue spatiale et qu'elle est influencée par la proportion d'espèces rares dans les communautés. Ainsi, les sites identifiés comme uniques peuvent varier selon les caractéristiques de la région étudiée. Ces résultats montrent que les SDM peuvent être utilisés pour prédire l'unicité écologique, ce qui pourrait permettre d'identifier d'importantes cibles de conservation au sein de régions non échantillonnées. / Beta diversity is an essential measure to describe the organization of biodiversity through space. The calculation of local contributions to beta diversity (LCBD), specifically, allows the identification of sites with high ecological uniqueness and exceptional diversity within a region of interest. To this day, LCBD indices have primarily been used on regional and smaller scales, with relatively few sites. Furthermore, their use is typically restricted to strictly sampled sites with known species composition, leading to gaps in spatial coverage on broad extents. Here, I examined whether species distribution models (SDMs) can be used to assess ecological uniqueness over broader spatial extents and investigated the effect of scale changes on beta diversity quantification. To this aim, I used observations recorded in the eBird database and Bayesian additive regression trees to model warbler species composition in North America, then computed LCBD indices on the predictions, thus covering a broader spatial extent and a higher number of sites. My results showed that SDMs provide uniqueness estimates highly correlated with observed data with a statistically significant spatial association. They also showed that the relationship between richness and LCBD values varies according to the region and the spatial extent and that it is affected by the proportion of rare species in communities. Sites identified as unique may therefore vary according to regional characteristics. These results show that SDMs can be used to predict ecological uniqueness over broad spatial extents, which could help identify beta diversity hotspots and important targets for conservation purposes in unsampled locations.

Whether species interactions are static or change over time has wide-reaching ecological and evolutionary consequences. However, species interaction networks are typically constructed from temporally aggregated interaction data, thereby implicitly assuming that interactions are fixed. This approach has advanced our understanding of communities, but it obscures the timescale at which interactions form (or dissolve) and the drivers and consequences of such dynamics. We address this knowledge gap by quantifying the within-season turnover of plant-pollinator interactions from weekly censuses across 3years in a subalpine ecosystem. Week-to-week turnover of interactions (1) was high, (2) followed a consistent seasonal progression in all years of study and (3) was dominated by interaction rewiring (the reassembly of interactions among species). Simulation models revealed that species' phenologies and relative abundances constrained both total interaction turnover and rewiring. Our findings reveal the diversity of species interactions that may be missed when the temporal dynamics of networks are ignored.

Orientador: Massanori Takaki / Resumo: Grandes iniciativas mundiais no esforço de alavancar um aumento na restauração ecológica surgiram recentemente, como a Iniciativa 20 x 20 e a Bonn Challenge, que apresentam como meta conjunta restaurar 500 milhões de hectares até 2030. Assim, uma das metas da ecologia aplicada à restauração é buscar compreender as distintas maneiras pelas quais a vegetação varia durante o processo de restauração e quais fatores influenciam o aumento da riqueza de espécies regenerantes. Este trabalho teve como objetivos: (1) Compreender como variam a abundância relativa e riqueza rarefeita, quando se comparam a regeneração natural total e específica (espécies que ocorreram apenas na área de referência), nas áreas em restauração com diferentes idades. (2) Avaliar como variam a diversidade alfa e beta nas áreas em restauração com idades distintas. (3) Observar a variação na abertura do dossel nas áreas com idades distintas. (4) Analisar se as variáveis da abertura do dossel e a idade são fatores importantes no que tange à influência com o aumento da riqueza de espécies regenerantes. Nove áreas em processo de restauração, localizadas no município de Extrema (Minas Gerais), foram selecionadas com 4, 7 e 10 anos de idade e um fragmento de referência, onde ao todo, 360 parcelas foram instaladas. Em cada parcela foram mensurados todos os regenerantes entre 20 cm e 2 m de altura (ervas, trepadeiras, arbustos, arbóreas e pteridófitas). Resultados: Foram encontrados 6788 regenerantes. As herbáceas e arb... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Major global initiatives in an effort to leverage an increase in the ecological restoration areas have recently emerged, such as the 20 x 20 Initiative and the Bonn Challenge, which aim to restore together 500 million hectares by 2030. Thus, one of the goals of ecology applied to restoration is to look at the different ways in which vegetation varies during the restoration process and what factors influence the increase of regenerating species richness. This work has as objectives: (1) To understand how the relative abundance and rarefied richness vary, when comparing the total and specific natural regeneration (species that occurred only in the reference area) in restoration areas having varying ages. (2) To evaluate how alpha and beta diversity varies in areas of restoration of different ages. (3) To observe the variation in canopy opening in areas of different ages. (4) To analyze whether the variable canopy opening and age are important factors in the influence or relation with the increase of the richness of regenerating species. Nine areas aged 4,7 and 10 under restoration process were selected and a reference fragment, in which a total of 360 parcels were installed. All the areas are located in the Municipality of Extrema, Minas Gerais. In each plot was measured all regenerants between 20 cm and 2 m in height (herbs, climbers, shrubs, trees and pteridophytes). Results: 6788 regenerants were found. Herbs and trees had the highest relative abundances, general and specifi... (Complete abstract click electronic access below) / Doutor

Uma grande parte das florestas secundárias ao redor do mundo é resultado da regeneração natural de áreas agrícolas abandonadas, localizadas em paisagens altamente modificadas pelo homem. O conhecimento sobre a composição funcional dessas florestas ainda é escasso, sendo urgentes pesquisas que contribuem para esse entendimento, pois os atributos funcionais das plantas são condutores da dinâmica florestal e, portanto, importantes para a manutenção da biodiversidade e dos serviços ecossistêmicos. Nesse contexto, escolhemos como modelo uma bacia hidrográfica no sudeste do Brasil, com matriz agrícola e florestas sob diferentes condições ambientais, para responder a duas perguntas: 1) Como fatores temporais, locais e de paisagem afetam a composição funcional de florestas secundárias (regenerando sob plantios de eucalipto e pastos abandonados) em paisagens agrícolas e 2) Como se comportam as diversidades taxonômica e funcional em tipos florestais com diferentes históricos de vida (florestas remanescentes conservadas, florestas remanescentes degradadas, florestas secundárias regenerando sob plantios de eucalipto abandonados e florestas secundárias regenerando sob pastos abandonados). Para responder as duas perguntas utilizamos o valor médio por espécie de dados primários (área foliar, área foliar específica, conteúdo de matéria seca da folha e espessura da folha) e secundários (densidade da madeira). A partir disso, usamos modelos generalizados mistos, média ponderada pela comunidade para cada atributo funcional e três índices de diversidade funcional para responder a primeira pergunta e testes de dissimilaridade para responder a segunda. Ao todo foram avaliadas 59 parcelas, 43 de florestas secundárias, 10 de florestas remanescentes degradadas e seis de florestas remanescentes conservadas, totalizando 6.089 indivíduos levantados e 284 espécies identificadas. Concluímos que 1) área foliar, área foliar específica e riqueza funcional de florestas secundárias são afetadas, ao mesmo tempo e de formas diferentes, por idade, declividade, teor de argila do solo, área basal de eucaliptos, cobertura florestal média, diferença na cobertura florestal e proximidade com cana- de-açúcar; e 2) florestas secundárias tendem a ter maior riqueza funcional e taxonômica que florestas conservadas, sendo que dentro dos tipos florestais existe uma diversidade beta taxonômica maior que a funcional, com comunidades apresentando, em geral, espécies abundantes diferentes com atributos funcionais similares. Nossos resultados demonstram que as florestas secundárias são afetadas tanto por fatores naturais quanto por fatores antrópicos, os quais devem ser levados em consideração tanto em pesquisas que visam compreender os condutores da regeneração natural quanto em projetos que visam utilizar esse processo como estratégia para conservar a biodiversidade e prover serviços ecossistêmicos. Adicionalmente, demonstramos que florestas remanescentes degradadas e secundárias são importantes fontes de biodiversidade e, portanto, potenciais provedoras de serviços ecossistêmicos / Large part of the secondary forests across the world is the result of the natural regeneration in abandoned agricultural areas located in landscapes highly human-modified. Knowledge about the functional composition of these forests is still scarce, and research contributing to this understanding results urgent since the functional traits may be important drivers of the forest ecological dynamics and therefore are important for the maintenance of biodiversity and ecosystem services the forest provides. In this context, we chose as a study case a watershed in the Atlantic Forest in Southeastern Brazil, with an agricultural matrix and patches of secondary forests regenerating under different environmental conditions, to answer the following two questions: 1) How temporal, local and landscape factors affect the functional composition of secondary forests regenerating in Eucalyptus plantations and abandoned pastures and (2) how taxonomic and functional diversity behave in forest types under different land-use histories (i.e. conserved remnant forest, degraded remnant forest, secondary forests regenerating in abandoned Eucalyptus plantations and secondary forests regenerating in abandoned pastures). In order to answer the two questions we used the mean value per species of primary data (leaf area, specific leaf area, leaf dry matter content and leaf thickness) and secondary data (wood density). We use mixed generalized models, the community weighted mean with species mean traits and three diversity indexes to answer the first question and dissimilarity tests to answer the second question. Overall, 59 plots were evaluated, including 43 secondary forests, 10 degraded remnant forests and 6 conserved remnant forest, where we registered totaling total of 6.089 individuals and 284 species. We conclude that: 1) leaf area, specific leaf area and functional richness of secondary forests is affected, at the same time and in different ways, by age, slope, soil clay content, basal area of Eucalyptus, average native forest cover , difference in surrounding native forest cover and proximity to sugarcane plantations; and 2) secondary forests tend to have higher functional and taxonomic richness than conserved forests, and within the forest types taxonomic beta diversity results higher than functional, with communities presenting, in general, different abundant species with similar functional traits. Our results demonstrate that secondary forests are affected by both natural and anthropogenic factors, which should be taken into account both in research aimed at understanding the drivers of natural regeneration and in projects that use this process as a strategy to conserve biodiversity and provide ecosystem services. In addition, we show that degraded remnants and secondary forests are important sources of biodiversity and therefore potential providers of ecosystem services.

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

Submitted by Liliane Ferreira (ljuvencia30@gmail.com) on 2018-04-16T15:52:11Z No. of bitstreams: 2 Dissertação - Carolina Ramos Caiado Gomes - 2014.pdf: 1331727 bytes, checksum: 59847313ee21fdd7bb1bffc8147d497d (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Approved for entry into archive by Luciana Ferreira (lucgeral@gmail.com) on 2018-04-17T10:55:24Z (GMT) No. of bitstreams: 2 Dissertação - Carolina Ramos Caiado Gomes - 2014.pdf: 1331727 bytes, checksum: 59847313ee21fdd7bb1bffc8147d497d (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Made available in DSpace on 2018-04-17T10:55:24Z (GMT). No. of bitstreams: 2 Dissertação - Carolina Ramos Caiado Gomes - 2014.pdf: 1331727 bytes, checksum: 59847313ee21fdd7bb1bffc8147d497d (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Previous issue date: 2014-05-23 / Conselho Nacional de Pesquisa e Desenvolvimento Científico e Tecnológico - CNPq / Nestedness is a particular pattern of species distribution in metacommunities in which a group of species found in poorer sites is a subset of the group of species found in richer sites. In the beta diversity partition context, nestedness is considered one of beta diversity components, jointly with species turnover. However, it is clear now that this term has been used in a wrong way instead of beta diversity due to richness differences. In specific cases that such richness differences reflect an ordered gain or loss of species between sites, then the nested pattern emerges. In the present work I used the beta diversity partition approach, focusing on the richness differences component, combined with a specific metric of nestedness, the NODF, to explore situations in which the richness differences between sites occur in a nested way considering different systems and scales of study. In the first chapter I use aquatic macroinvertebrates communities to show the importance of spatial position of patches of the same microhabitat in generating nestedness in riffles. I found that patches and riffle sites located in the beginning of the riffles are poorer then patches and riffle sites at the end of the same riffles, and that initial sites are nested in final sites in a same riffle. In the second chapter I use birds and mammals communities in the New World to assess how nestedness varies in latitudinal and longitudinal gradients. Nestedness emerged in several regions in both gradients, and it is always related to richness differences in such gradients combined with directional processes that cause an ordered loss or gain of species. / O aninhamento é um padrão ecológico particular de distribuição de espécies em metacomunidades em que o grupo de espécies encontradas em sítios menos ricos é subconjunto daquele encontrado em sítios mais ricos. No contexto de partição de diversidade beta, o aninhamento era considerado, juntamente com a substituição de espécies, um componente da diversidade beta. Porém, atualmente está claro que este termo estava sendo equivocadamente utilizado para se referir à diversidade beta devido a diferenças de riqueza. Em casos específicos em que tais diferenças de riqueza refletem uma perda ou ganho ordenado de espécies entre sítios emerge, então, o aninhamento. No presente trabalho utilizei a abordagem de partição de diversidade beta, focando no componente das diferenças de riqueza, combinada com o uso de uma métrica específica de aninhamento, o NODF, a fim de explorar situações em que a diferença de riqueza entre sítios ocorre de maneira aninhada, considerando diferentes sistemas e escalas de estudo. No primeiro capítulo utilizo comunidades de macroinvertebrados aquáticos para evidenciar a importância da posição espacial de um mesmo micro-habitat na geração de aninhamento em corredeiras. Encontrei que manchas e trechos no início de corredeiras são menos ricos do que no final de corredeiras, e que para trechos há aninhamento da fauna encontrada no trecho inicial em relação à fauna encontrada no trecho final de uma mesma corredeira. No segundo capítulo utilizo comunidades de aves e mamíferos considerando uma escala que abrange todo o Novo Mundo para avaliar como o aninhamento varia ao longo de gradientes latitudinais e longitudinais. O padrão aninhado emergiu em várias regiões de ambos os gradientes, e está sempre relacionado a diferenças de riquezas existentes nesses gradientes combinada com processos direcionais que levam a perda ou ganho ordenado de espécies.

Submitted by Marlene Santos (marlene.bc.ufg@gmail.com) on 2014-10-10T21:20:05Z No. of bitstreams: 2 Tese - Bruno de souza Barreto - 2012.pdf: 2817636 bytes, checksum: 84c30327e24d85125e1faf1207b4bb14 (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) / Approved for entry into archive by Jaqueline Silva (jtas29@gmail.com) on 2014-10-13T20:46:53Z (GMT) No. of bitstreams: 2 Tese - Bruno de souza Barreto - 2012.pdf: 2817636 bytes, checksum: 84c30327e24d85125e1faf1207b4bb14 (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) / Made available in DSpace on 2014-10-13T20:46:53Z (GMT). No. of bitstreams: 2 Tese - Bruno de souza Barreto - 2012.pdf: 2817636 bytes, checksum: 84c30327e24d85125e1faf1207b4bb14 (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) Previous issue date: 2012-12-19 / Conselho Nacional de Pesquisa e Desenvolvimento Científico e Tecnológico - CNPq / Increasingly biodiversity has lost diversity around the globe because of the way the human population have used natural resources. To reduce the impacts caused by human activity, conservation units (CU) have been created to ensure the maintenance of biodiversity. However, many conservation units were not established following scientific criteria and its efficiency can therefore be questioned. In this study we tried to evaluate the efficiency of conservation of the Cerrado based on species richness and beta diversity of mammals currently and in accord to climate change expected for 2080. We show through gap analyzes that species are represented in the current system both in the current climate and in the future. However, they have become rarer within CUs with climate change. We show that CUs do not capture a greater diversity than expected by chance. It is expected a larger number of species within the CUs in 2080, however, the number of species outside them will also be greater. As for beta diversity, there will be a reduction of the index in 2080 and both outside and within the UCs expected on average the same value. Climate change became UC’s Cerrado more inefficient, there will be an increase in the number of threatened species because of climate change interfering in the spatial arrangement of species on the Cerrado. This draws attention to the evaluation of systems of protected areas consider the spatial-temporal dynamics of the species. / Cada vez mais a biodiversidade tem perdido diversidade ao redor do planeta em razão do modo como a população humana têm utilizado os recursos naturais. Para reduzir os impactos causados pela atividade humana, unidades de conservação (UC) têm sido criadas para garantir a manutenção da biodiversidade. Contudo, muitas unidades de conservação criadas não seguem critérios científicos e sua eficiência pode ser, portanto, questionada. No presente trabalho buscou-se avaliar a eficiência das unidades de conservação do Cerrado com base na riqueza de espécies e a diversidade beta dos mamíferos atualmente e em consonância com as mudanças climáticas esperadas para 2080. Nós mostramos por meio de análises de lacunas, as espécies estão representadas no atual sistema tanto no clima atual quanto no futuro. Contudo, elas tornaram-se mais raras dentro das UC’s com as mudanças climáticas. Mostramos que as UC’s não capturam uma diversidade maior que o esperado ao acaso. Espera-se um número maior de espécies dentro das UC’s em 2080, contudo, o número de espécies fora delas será também maior. Quanto a diversidade beta, haverá uma redução do índice em 2080 e tanto fora das UC’s quanto dentro espera-se, em média o mesmo valor. As mudanças climáticas tornaram as UC’s do Cerrado mais ineficientes, haverá um aumento do número de espécies ameaçadas em razão das mudanças climáticas interferirem no arranjo espacial das espécies sobre o Cerrado. Isto chama a atenção para a avaliação de sistemas de unidades de conservação considerem a dinâmica espaço-temporal das espécies.

Human-induced alterations of the environment are causing biotic changes worldwide, including the extinction of species and a mixing of once disparate floras and faunas. One type of biological communities that is expected to be particularly affected by environmental alterations are herb layer plant communities of fragmented forests such as those in the west European lowlands. However, our knowledge about current changes in species diversity and composition in these communities is limited due to a lack of adequate long-term studies. In this thesis, I resurveyed the herb layer communities of ancient forest patches in the Weser-Elbe region (NW Germany) after two decades using 175 semi-permanent plots. The general objectives were (i) to quantify changes in plant species diversity considering also between-community (β) and functional diversity, (ii) to determine shifts in species composition in terms of species’ niche breadth and functional traits and (iii) to find indications on the most likely environmental drivers for the observed changes. These objectives were pursued with four independent research papers (Chapters 1-4) whose results were brought together in a General Discussion. Alpha diversity (species richness) increased by almost four species on average, whereas β diversity tended to decrease (Chapter 1). The latter is interpreted as a beginning floristic homogenization. The observed changes were primarily the result of a spread of native habitat generalists that are able to tolerate broad pH and moisture ranges. The changes in α and β diversity were only significant when species abundances were neglected (Chapters 1 and 2), demonstrating that the diversity changes resulted mainly from gains and losses of low-abundance species. This study is one of the first studies in temperate Europe that demonstrates floristic homogenization of forest plant communities at a larger than local scale. The diversity changes found at the taxonomic level did not result in similar changes at the functional level (Chapter 2). The likely reason is that these communities are functionally “buffered”. Single communities involve most of the functional diversity of the regional pool, i.e., they are already functionally rich, while they are functionally redundant among each other, i.e., they are already homogeneous. Independent of taxonomic homogenization, the abundance of 30 species decreased significantly (Chapter 4). These species included 12 ancient forest species (i.e., species closely tied to forest patches with a habitat continuity > 200 years) and seven species listed on the Red List of endangered plant species in NW Germany. If these decreases continue over the next decades, local extinctions may result. This biotic impoverishment would seriously conflict with regional conservation goals. Community assembly mechanisms changed at the local level particularly at sites that experienced disturbance by forest management activities between the sampling periods (Chapter 3). Disturbance altered community assembly mechanisms in two ways: (i) it relaxed environmental filters and allowed the coexistence of different reproduction strategies, as reflected by a higher diversity of reproductive traits at the time of the resurvey, and (ii) it enhanced light availability and tightened competitive filters. These limited the functional diversity with respect to canopy height and selected for taller species. Thirty-one winner and 30 loser species, which had significantly increased or decreased in abundance, respectively, were characterized by various functional traits and ecological performances to find indications on the most likely environmental drivers for the observed floristic changes (Chapter 4). Winner species had higher seed longevity, flowered later in the season and had more often an oceanic distribution compared to loser species. Loser species tended to have a higher specific leaf area, to be more susceptible to deer browsing and to have a performance optimum at higher soil pH values compared to winner species. Multiple logistic regression analyses indicated that disturbances due to forest management interventions were the primary cause of the species shifts. As one of the first European resurvey studies, this study provides indications that an enhanced browsing pressure due to increased deer densities and increasingly warmer winters are important drivers. The study failed to demonstrate that eutrophication and acidification due to atmospheric deposition substantially drive herb layer changes. The restriction of the sample to the most base-rich sites in the region is discussed as a likely reason. Furthermore, the decline of several ancient forest species is discussed as an indication that the forest patches are still paying off their “extinction debt”, i.e., exhibit a delayed response to forest fragmentation. / Umweltveränderungen beeinträchtigen weltweit die Artenvielfalt. Die Lebensgemeinschaften fragmentierter Lebensräume gelten als besonders anfällig für Veränderungen. In dieser Arbeit wurden Untersuchungen an Krautschichtgemeinschaften historisch alter Waldfragmente im Elbe-Weser-Dreieck nach zwei Jahrzehnten wiederholt. Ziel war es anhand von 175 semi-permanenten Aufnahmeflächen (i) die Veränderungen der Pflanzenartendiversität zu quantifizieren, (ii) Artenverschiebungen in Bezug auf Nischenbreite und funktionale Merkmale festzustellen und (iii) Hinweise auf die verantwortlichen Umweltveränderungen zu finden. Die α-Diversität (Artenzahl) stieg durchschnittlich um vier Arten an. Die β-Diversität (Artenturnover zwischen den Flächen) nahm tendenziell ab. Letzteres wird als Beginn einer floristischen Homogenisierung interpretiert. Diese Studie ist eine der ersten im gemäßigten Europa, die eine floristische Homogenisierung von Waldpflanzengemeinschaften auf einer größeren als der lokalen Ebene aufzeigt. Die Diversitätsveränderungen auf taxonomischer Ebene führten nicht zu ähnlichen Veränderungen auf funktionaler Ebene. Bereits einzelne Gemeinschaften wiesen den Großteil der funktionalen Vielfalt des regionalen Artenpools, also ein Maximum an funktionaler Diversität auf. Gleichzeitig waren sie untereinander funktional redundant, also bereits homogen. Die mit der beginnenden taxonomischen Homogenisierung verbundene floristische Verarmung wird als gering eingestuft, da die Homogenisierung primär das Ergebnis der Zuwanderung häufig vorkommender Standortgeneralisten war. Unabhängig von der Homogenisierung gingen 30 Arten signifikant in ihrer Abundanz zurück, darunter 12 an historisch alte Wälder gebundene Arten sowie sieben Rote-Liste-Arten. Ein weiterer Rückgang oder ein lokales Aussterben dieser Arten stünde im Widerspruch zu regionalen Naturschutzzielen. Nullmodelltests und der Vergleich funktionaler und taxonomischer Diversitätskomponenten lassen auf regionaler Ebene auf eine zeitliche Konstanz der grundlegenden Mechanismen der Artenvergesellschaftung schließen. Auf der lokalen Ebene veränderten sich die Vergesellschaftungsmechanismen erheblich, insbesondere auf forstwirtschaftlich gestörten Standorten. Einerseits ermöglichte dort eine Abschwächung der Umweltfilter die Koexistenz von Arten mit unterschiedlichen Reproduktionsstrategien. Andererseits führte die erhöhte Lichtverfügbarkeit zu einer Verstärkung der Konkurrenzfilter und einer Selektion hochwüchsiger Arten. Gewinner- und Verliererarten wurden anhand funktionaler Merkmale und ihres ökologischen Verhaltens charakterisiert, um Hinweise auf die verantwortlichen Umweltveränderungen zu finden. Gewinnerarten wiesen eine höhere Langlebigkeit der Samen auf, blühten später in der Vegetationsperiode und hatten öfter eine ozeanische Verbreitung. Verliererarten hatten eine höhere spezifische Blattfläche, einen höheren Attraktivitätswert als Wildäsung und ein ökologisches Optimum bei höheren pH-Werten. Logistische Regressionsanalysen zeigen, dass Störung durch forstwirtschaftliche Eingriffe hauptverantwortlich für die Artenverschiebungen war. Zusätzlich liefert diese Wiederholungsstudie als eine der ersten in Europa Hinweise darauf, dass ein erhöhter Äsungsdruck sowie zunehmend mildere Winter entscheidende Einflussfaktoren darstellen. Der Rückgang mehrerer an historisch alte Wälder gebundener Arten wird als Anzeichen für eine verspätete Reaktion auf die Waldfragmentierung diskutiert.