Phylogenetic diversity (PD) is a measure of species biodiversity quantified by how much of an evolutionary tree is spanned by a subset of species. In this thesis, we study optimization problems that aim to find species sets with maximum PD in different scenarios, and examine random extinction models under various assumptions to predict the PD of species that will still be present in the future. Optimizing PD with Dependencies is a combinatorial optimization problem in which species form an ecological network. Here, we are interested in selecting species sets of a given size that are ecologically viable and that maximize PD. The NP-hardness of this problem is proved and it is established which special cases of the problem are computationally easy and which are computationally hard. It is also shown that it is NP-complete to decide whether the feasible solution obtained by the greedy algorithm is optimal. We formulate the optimization problem as an integer linear program and find exact solutions to the largest food web currently in the empirical literature. In addition, we give a generalization of PD that can be used for example when we do not know the true evolutionary history. Based on this measure, an optimization problem is formulated. We discuss the complexity and the approximability properties of this problem. In the generalized field of bullets model (g-FOB), species are assumed to become extinct with possibly different probabilities, and extinction events are independent. We show that under this model the distribution of future phylogenetic diversity converges to a normal distribution as the number of species grows. When extinction probabilities are influenced by some binary character on the tree, the state-based field of bullets model (s-FOB) represents a more realistic picture. We compare the expected loss of PD under this model to that under the associated g-FOB model and find that the former is always greater than or equal to the latter. It is natural to further generalize the s-FOB model to allow more than one binary character to affect the extinction probabilities. The expected future PD obtained for the resulting trait-dependent field of bullets model (t-FOB) is compared to that for the associated g-FOB model and our previous result is generalized.

Submitted by bruna ortiz (brunaortiz.f@gmail.com) on 2016-07-04T13:23:51Z No. of bitstreams: 1 Dissertação-Gisiane R. Lima.pdf: 2658393 bytes, checksum: ad7192984a0e2312329813835b3b2a1d (MD5) / Approved for entry into archive by Divisão de Documentação/BC Biblioteca Central (ddbc@ufam.edu.br) on 2016-07-21T13:17:41Z (GMT) No. of bitstreams: 1 Dissertação-Gisiane R. Lima.pdf: 2658393 bytes, checksum: ad7192984a0e2312329813835b3b2a1d (MD5) / Approved for entry into archive by Divisão de Documentação/BC Biblioteca Central (ddbc@ufam.edu.br) on 2016-07-21T13:21:38Z (GMT) No. of bitstreams: 1 Dissertação-Gisiane R. Lima.pdf: 2658393 bytes, checksum: ad7192984a0e2312329813835b3b2a1d (MD5) / Made available in DSpace on 2016-07-21T13:22:14Z (GMT). No. of bitstreams: 1 Dissertação-Gisiane R. Lima.pdf: 2658393 bytes, checksum: ad7192984a0e2312329813835b3b2a1d (MD5) Previous issue date: 2016-01-22 / FAPEAM - Fundação de Amparo à Pesquisa do Estado do Amazonas / Riverine forests, locally known as varzeas, represent the second main habitat in terms of area of the Amazon basin. The varzeas are directly influenced by the seasonal flooding caused by raise of the level of the rivers, and reveal a series of different riverine habitats which have specific avifaunas and are directly influenced by a flooding gradient. In the rio Branco basin, these habitats include the rivers themselves, as well as beaches, sandbars, riverine florests, flooded and transitional forests. On the upper rio Branco, flooded forests are replaced by gallery forests. The main goal of this study was to describe the association between those different habitats and the avifauna, and understand how these animal assemblages are functionally and phylogenetically structured. Specifically, I aimed to i) describe patterns of species richness across different riverine habitats; ii) describe how the structural complexity of habitats found along a flooding gradient determines patterns of functional and phylogenetic diversity; iii) compare and relate different diversity metrics (species richness, and functional and phylogenetic diversity); and iv) identify which functional traits are selected by the different habitats. To reach these goals, we conducted three expeditions into the rio Branco from 2012 to 2014. Where we conducted systematic avian surveys across the entire length of the river. Overall, we detected 315 bird species during our surveys, and these were used for all the analyses. To define the list of bird species that occur in each habitat, we complemented the result of our surveys with mist-nets and specimen collections. These specimens were used to obtain morphological measurements related to different functional traits of each species, including measurements of mass, bill length, height, and width, lenght of the tarsus, tail, and nail, and the kipp index, a measurement of flying capacity. To describe phylogenetic diversity, I used data from Jetz et al. (2012) to built a tree with all the 315 species. Our results showed that forest habitats presented higher species richness than relatively simpler habitats, such as rivers, beaches and sand banks.However, bird assemblages associated to rivers and beaches presented higher levels of functional and phylogenetic diversity, showing no correlation between species richness and other diversity metrics. Some functional traits were clearly associated to different habitats; for ex., larger birds with longer bills and tarsi were clearly associated to rivers and beaches, likely related to the life style of aquatic birds and shorebirds. On the other hand, taller and wider bills, typical of granivorous birds, dominated sandbar scrubs. Smaller birds with shorter bills and tarsi were associated to forested environments. This study shows that habitats affect bird species composition, filtering morphologic traits and selecting which species can leave in each habitat. In general, we found a high degree of species especialization, given that 1/3 of the species were exc;usive of certain habitats. This habitat especificity turns riverine birds vulnerable to changes in river hydrology, and changes in riverine habitats due to human interventions can affect dramaticaly the avifauna of the varzeas. / As várzeas amazônicas representam o segundo principal habitat da bacia em termos de área, e se caracterizam por serem alagadas anualmente pelo pulso de inundação resultante do padrao de chuvas da região. As várzeas revelam uma série de ambientes ribeirinhos que são diretamente influencidos por um gradiente de alagamento, e que possuem avifaunas específicas, muitas vezes exclusivas de cada ambiente. Na bacia do Rio Branco, estes ambientes incluem os proprios rios, as praias, bancos de areia com gramíneas e arbustos, embaubais, florestas de várzea, e florestas de transição. Na região do alto rio Branco, as florestas de várzea são substituidas pela florestas de galeria. O principal objetivo deste estudo foi descrever a relação entre as espécies de aves e os ambientes ribeirinhos na bacia do rio Branco, e estudar como as comunidades de aves desses diferentes ambientes se estruturam funcional e filogeneticamente. Especificamente, procurou-se i) avaliar a riqueza de espécies de aves associadas aos diferentes ambientes ribeirinhos do rio; ii) descrever como a complexidade estrutural dos ambientes de várzea encontrados ao longo do gradiente de alagamento determina a diversidade filogenética e funcional das assembleias de aves; iii)_comparar e relacionar diferentes métricas de diversidade de aves (riqueza de espécies, diversidade filogenética e funcional) nos ambientes sucessionais de várzea; e iv) identificar as características funcionais que mais se relacionam aos diferentes ambientes. Para atingir esses resultados, foram realizadas três expedições onde foram realizados inventários padronizados de aves na bacia do rio Branco entre 2012 e 2014. Ao todo, foram registradas 315 espécies de aves durante os censos, as quais foram usadas para as análises. Para definir a lista de espécies que ocorre em cada um dos habitats, os dados obtidos dos censos foram complemantados com capturas com redes de neblina e coleta de especimes. Estes especimes foram usados para obter medidas da morfologia, as quais estariam ligadas às características funcionais de cada espécie, incluindo medidas de peso, comprimento, largura, e altura do bico, comprimento do tarso, cauda e unha, e o índice de kipp, um medida relacionada com a capacidade de voo. Para descrever a diversidade filogenética, foi gerada uma ávore filogenética com dados de terceiros, incluindo as 315 espécies. Os ambientes florestais apresentaram maior riqueza de espécies do que ambientes relativamente mais simples, como ambientes aquáticos, as praias e os bancos de areia. Entretanto, as assembleias de aves associadas aos rios e praias apresentaram maior diversidade filogenética e funcional, mostrando que não existe uma correlação clara entre a riqueza de espécies e a diversidade funcional e filogenética. Alguns atributos funcionais estao claramente associados com os diferentes ambientes da várzea; por ex., aves maiores, bicos e tarsos mais compridos estão associados com os ambintes aquáticos e as praias, diretamente relacionados com o estilo de vida das aves piscívoras ou limícolas, que constituem em sua maioria estes ambientes. Por outro lado, bicos mais altos e largos, típicos de aves granívoras, ocorrem principalmente nos bancos de areia com gramíneas. Aves menores, com bicos e tarsos curtos estão claramente associados com os ambientes florestais. Este trabalho mostra que os ambientes afetam a composição de espécies e filtram dimensões morfológicas funcionais das aves, selecionando espécies. Em termos gerais, este estudo aponta um elevado grau de especializacao da avifauna da várzea, pois cerca de 1/3 das espécies são exclusivas de pelo menos um tipo de ambiente. Esta especificidade de ambiente torna as aves ribeirinhas vulneráveis a mudanças na hidrologia dos rios, que pode afetar de forma drástica a avifauna dos ambientes ribeirinhos.

Subalpine ecosystems are experiencing rapid changes in snow pack, temperature, and precipitation regime as a result of anthropogenic climate forcing. These changes in climate can have a profound effect on subalpine ecosystem structure and functioning, which may ultimately feed back to climate change. In this study, I examined the response of the subalpine meadow plant communities at the Rocky Mountain Biological Laboratory to natural and simulated climate change. First, I looked at whether changes in growing season precipitation or temperature regime would have the larger effect on subalpine ecosystem carbon flux. In a simulated warming experiment, changes in growing season precipitation had a tenfold larger effect on cumulative carbon flux than did the warming treatment. Along a natural climatic and elevational gradient, precipitation stimulates carbon uptake, particularly at higher elevations. Given projected decreases in summer precipitation in the high elevation Rockies, we predict a 20% decrease in carbon uptake from subalpine meadows. Second, I compared the taxonomic, phylogenetic and functional structure of plant communities along an elevational gradient to infer which climatic and biotic factors influence community assembly at each elevation. Floral and phenology traits become overdispersed at high elevation, mirroring phylogenetic relatedness, and suggesting pressure to diversify to attract pollinators during the abbreviated growing season. At the same time, leaf functional traits become clustered at high elevation, indicating multiple opposing assembly mechanisms in subalpine communities. Finally, I studied the natural history of sagebrush, Artemisia tridentate ssp. vaseyana, at its elevational range limit in subalpine meadows. In particular, I focused on the importance of warming and species interactions in elevational advance of the species. I found that facilitation by neighboring forbs was critical for sagebrush seedling survival, decreasing mortality by 75%. Seedling mortality was overwhelmingly due to desiccation of seedlings; therefore, neighboring forbs moderate temperature and water stress for seedlings. Despite the extremely limited growing season at high elevation caused by subfreezing temperatures, subalpine ecosystem structure and function are closely tied to water availability during the growing season. Therefore, improved predictions of future precipitation regimes over the Rocky Mountains will be our best tool for conservation of these fragile habitats.

Abordagens integrativas considerando diferentes dimensões da diversidade (p.ex., taxonômica, funcional, ou filogenética) cada vez mais estão sendo utilizadas para (1) avançar o nosso conhecimento sobre os mecanismos que criam e mantém a biodiversidade, e (2) elucidar a distribuição da biodiversidade tanto em áreas geográficas de interesse como dentro de áreas protegidas. De fato, entender como a biodiversidade se distribui no espaço e como ela é mantida ao longo do tempo é fundamental para embasar o planejamento de áreas protegidas e corredores ecológicos, assim como auxiliar no manejo de espécies invasoras, restauração de habitats degradados e manejo de ecossistemas. Nessa perspectiva, os objetivos centrais desta tese foram: (1) avaliar os mecanismos ecológicos e evolutivos, que potencialmente influenciam a diversidade beta taxonômica e filogenética de árvores nas florestas Atlânticas do sul do Brasil, e (2) avaliar como os componentes taxonômicos e filogenéticos se distribuem ao longo destas florestas, e como eles são representados dentro da rede regional de áreas protegidas. Para tal, utilizei modelagem de equações estruturais (capítulo 1) para testar a validade de uma rede de hipóteses ligando dados e teoria. No capítulo 1, avaliei a relação entre a diversidade beta taxonômica e filogenética, e como elas se relacionam com a riqueza de espécies, filtragem ambiental, espaço geográfico e estrutura filogenética (agrupamento filogenético). Nesse capítulo, concluí que a diversidade beta taxonômica é influenciada principalmente pelos gradientes altitudinais e climáticos, enquanto que a diversidade beta filogenética é determinada também pelo grau de agrupamento filogenético, em nível local, que provavelmente reflete o conservadorismo de nicho dentro das linhagens e distúrbio humano, que historicamente tem conduzido as florestas estudadas a um processo de homogeneização biótica. Em relação ao segundo objetivo, utilizei uma abordagem integrativa para predizer e mapear os componentes taxonômicos e filogenéticos da diversidade de árvores e, em seguida, avaliar a efetividade da rede de áreas protegidas em representar tais componentes nas florestas Atlânticas do sul Brasil. Nesse capítulo, concluí que as áreas protegidas são insuficientes para preservar adequadamente a biodiversidade de árvores nestas florestas. Sugeri que a expansão da rede em direção as áreas de alta singularidade taxonômica e filogenética, como definidas aqui, poderia aumentar, ao mesmo tempo, a representação da riqueza de espécies, da diversidade beta e da história evolutiva das espécies estudadas. Sugeri também que a inclusão de áreas de alta insubstituibilidade, em termos de história evolutiva, poderia ajudar a aumentar a proteção da diversidade de características e do potencial evolutivo das espécies. / Integrative approaches considering different dimensions of biodiversity are increasingly being used in ecology and conservation to (1) advance our knowledge about the mechanisms underlying current patterns of biological diversity, and (2) elucidate the distribution of biodiversity in geographical areas of interest, and within the protected areas. Indeed, understanding how biodiversity is distributed in space and how it is maintained over time is critical to support the planning of protected areas and ecological corridors as well as assist the management of invasive species, the restoration of degraded areas and ecosystem management. In this perspective, the central goals of this thesis were: (1) to evaluate the ecological and evolutionary mechanisms that potentially influence the tree taxonomic and phylogenetic beta diversity in Atlantic forests located in southern Brazil, and (2) to evaluate how the taxonomic and phylogenetic diversity components are distributed across these forests, and how they are represented within the regional network of protected areas. For this, I used structural equation modeling (chapter 1) to test the validity of a network of hypotheses linking data and theory. In the chapter 1, I evaluate the relationship between taxonomic and phylogenetic beta diversity, and how they are related to species richness, environmental filtering, geographical space and phylogenetic structure (phylogenetic clustering). In this chapter, I conclude that taxonomic beta diversity (at the study scale) is mainly driven by the altitudinal and climatic gradients, while phylogenetic beta diversity is also determined by the degree of phylogenetic clustering at local level, more likely reflecting niche conservatism within lineages and human disturbance that has historically conducted the studied forests to a process of biotic homogenization. In relation to the second goal, I used an integrative approach to predict and map the taxonomic and phylogenetic components of tree diversity, and to assess the effectiveness of the protected areas network in representing these components in the Atlantic forests. In this chapter, I conclude that protected areas are insufficient to adequately preserve the tree biodiversity in these forests. I suggest that expanding the network towards the areas of taxonomic and phylogenetic uniqueness, as defined here, could increase the representation of species richness, beta diversity and evolutionary history of angiosperm trees at the same time. Furthermore, the inclusion of areas of high irreplaceability in terms of evolutionary history could help to improve the protection of feature diversity and evolutionary potential of species.

Habitat loss and fragmentation have been identified as the main drivers of biodiversity loss. These drivers increase the proportion of habitat edges and change the configuration of landscapes. Habitat edges are known to affect ecological patterns and processes, however, is still unknown how these boundaries affect the assemblage of interactions among species within a community, and particularly its structure. Food webs depict not only the composition of the community, but also the feeding links, which represent a measure of energy flow. Therefore, they can inform about the relationships among community diversity, stability, and ecosystem functions. This thesis explores the effects of habitat edges across native vs. managed forests on the food web of a tri-trophic system comprising plants, herbivores (Lepidoptera larvae) and predators (parasitoids). Particularly, it addresses three main objectives: 1) how food webs at habitat edges are assembled from the species and interactions present in the adjoining habitats; 2) how phylogenetic diversity and the coevolutionary signal among interacting species change across a habitat edge gradient; and 3) whether the mechanisms driving community-wide consumption rates and the ecosystem service of pest control are related to structural characteristics of the food webs. The key findings of this thesis are that, despite the composition of species and interactions of native and managed habitats merging at their interface, food-web structure did not arise as a simple combination of its adjacent habitat webs, potentially due to differential responses of organisms to habitat edges. Moreover, beyond taxonomic composition, the phylogenetic diversity and signal of coevolution among interacting species also change between habitat types, even though this did not translate to changes in consumption rates. Consumption rates and their stability increased with complementarity and redundancy in resource-use among predators. This reflects how environmental changes such as habitat fragmentation can have an effect beyond composition per se, affecting the assemblage of species interactions and even potentially interfering with natural evolutionary processes. Therefore, using interaction-network approaches for determining the impacts of changes may shed light on the underlying mechanisms driving such changes, and help to develop landscape management plans that reduce negative effects on species assemblages.

O florestamento dos campos do sul da América do Sul incluindo os campos do Pampa estão mudando a paisagem local e levando a mudanças nas populações de aves. O conhecimento sobre o efeito do florestamento sobre a avifauna dos campos do sul da América do Sul é bastante limitado à riqueza e composição de espécies. Além de preencher lacunas considerando diferentes índices para avaliar respostas das comunidades de aves ao florestamento dos campos (Capítulos 2 e 3), nesta tese nós também avaliamos se Áreas de Preservação Permanente localizadas dentro de plantações de eucalipto são funcionais para a avifauna local, fazendo uma comparação com áreas de campo pastejado (Capítulo 1). No capítulo 1 nós registramos uma diferença na composição de espécies entre as áreas devido principalmente às mudanças na altura e densidade da vegetação. Nos capítulos 2 e 3 nós avaliamos diferentes componentes da diversidade (taxonômica, filogenética e funcional) considerando possíveis efeitos do florestamento dos campos sobre estes Nossos resultados demonstram respostas diferenciadas entre os componentes, enquanto o florestamento leva a uma redução na diversidade taxonômica, diversidade filogenética e funcional não demonstram respostas negativas. No capítulo 2 no entanto, nós observamos que o florestamento dos campos conduz a uma perda de distintividade evolutiva, beneficiando desta forma linhagens que se diversificaram recentemente. No capítulo 3 apesar da redução na diversidade taxonômica não houve uma redução na diversidade funcional em áreas plantadas. Já a associação de alguns atributos funcionais com as áreas pós-corte, indica a plasticidade de algumas espécies que retornam para essas áreas logo após o corte dos plantios.De modo geral nossos resultados indicam que a manutenção de mosaicos de campo de diferentes alturas maximiza a biodiversidade local de aves e destaca a importância da proteção de áreas campestres. Além disso, vimos que considerar diferentes componentes da diversidade que incorporam informações sobre as espécies são importantes pois podem informar por exemplo, quantas extinções uma comunidade pode suportar até que funções importantes sejam perdidas, afetando assim a estabilidade dos ecossistemas. / The afforestation of southern grasslands of South America including the Pampa grasslands are changing the local landscape and leading to reduction of bird populations. Knowledge about the effect of afforestation on the avifauna of the southern South American grasslands is limited to richness and composition of species. In addition to filling gaps considering different indices to evaluate responses of the bird communities to the afforestation of the grasslands (Chapters 2 and 3), in this thesis we also evaluated whether Permanent Preservation Areas located within eucalyptus plantations are functional for the local avifauna, making a comparison with grazed grasslands areas (Chapter 1). In Chapter 1 we recorded a difference in species composition between areas due mainly to changes in height and density of vegetation. In chapters 2 and 3 we evaluated different components of diversity (taxonomic, phylogenetic, and functional), considering possible effects of grasslands afforestation on them. Our results demonstrate differentiated responses among components, while afforestation leads to a reduction in taxonomic diversity, phylogenetic and functional diversity do not demonstrate negative responses In chapter 2 however, we observe that grasslands afforestation leads to a loss of evolutionary distinctiveness, thus benefiting species that have diversified recently. In chapter 3, despite the reduction in taxonomic diversity, there was no reduction in functional diversity in planted areas. Furthermore, the association of some functional traits with the post-cut areas indicates the plasticity of some species that return to these areas soon after cut the plantations. In general our results indicate that the maintenance of grasslands mosaics of different heights maximize the local biodiversity of birds and highlight the importance of the protection of grasslands areas. In addition, we have seen that considering different components of diversity that incorporate information on species is important because they can tell, for example, how many extinctions a community can support until important functions are lost.

O florestamento dos campos do sul da América do Sul incluindo os campos do Pampa estão mudando a paisagem local e levando a mudanças nas populações de aves. O conhecimento sobre o efeito do florestamento sobre a avifauna dos campos do sul da América do Sul é bastante limitado à riqueza e composição de espécies. Além de preencher lacunas considerando diferentes índices para avaliar respostas das comunidades de aves ao florestamento dos campos (Capítulos 2 e 3), nesta tese nós também avaliamos se Áreas de Preservação Permanente localizadas dentro de plantações de eucalipto são funcionais para a avifauna local, fazendo uma comparação com áreas de campo pastejado (Capítulo 1). No capítulo 1 nós registramos uma diferença na composição de espécies entre as áreas devido principalmente às mudanças na altura e densidade da vegetação. Nos capítulos 2 e 3 nós avaliamos diferentes componentes da diversidade (taxonômica, filogenética e funcional) considerando possíveis efeitos do florestamento dos campos sobre estes Nossos resultados demonstram respostas diferenciadas entre os componentes, enquanto o florestamento leva a uma redução na diversidade taxonômica, diversidade filogenética e funcional não demonstram respostas negativas. No capítulo 2 no entanto, nós observamos que o florestamento dos campos conduz a uma perda de distintividade evolutiva, beneficiando desta forma linhagens que se diversificaram recentemente. No capítulo 3 apesar da redução na diversidade taxonômica não houve uma redução na diversidade funcional em áreas plantadas. Já a associação de alguns atributos funcionais com as áreas pós-corte, indica a plasticidade de algumas espécies que retornam para essas áreas logo após o corte dos plantios.De modo geral nossos resultados indicam que a manutenção de mosaicos de campo de diferentes alturas maximiza a biodiversidade local de aves e destaca a importância da proteção de áreas campestres. Além disso, vimos que considerar diferentes componentes da diversidade que incorporam informações sobre as espécies são importantes pois podem informar por exemplo, quantas extinções uma comunidade pode suportar até que funções importantes sejam perdidas, afetando assim a estabilidade dos ecossistemas. / The afforestation of southern grasslands of South America including the Pampa grasslands are changing the local landscape and leading to reduction of bird populations. Knowledge about the effect of afforestation on the avifauna of the southern South American grasslands is limited to richness and composition of species. In addition to filling gaps considering different indices to evaluate responses of the bird communities to the afforestation of the grasslands (Chapters 2 and 3), in this thesis we also evaluated whether Permanent Preservation Areas located within eucalyptus plantations are functional for the local avifauna, making a comparison with grazed grasslands areas (Chapter 1). In Chapter 1 we recorded a difference in species composition between areas due mainly to changes in height and density of vegetation. In chapters 2 and 3 we evaluated different components of diversity (taxonomic, phylogenetic, and functional), considering possible effects of grasslands afforestation on them. Our results demonstrate differentiated responses among components, while afforestation leads to a reduction in taxonomic diversity, phylogenetic and functional diversity do not demonstrate negative responses In chapter 2 however, we observe that grasslands afforestation leads to a loss of evolutionary distinctiveness, thus benefiting species that have diversified recently. In chapter 3, despite the reduction in taxonomic diversity, there was no reduction in functional diversity in planted areas. Furthermore, the association of some functional traits with the post-cut areas indicates the plasticity of some species that return to these areas soon after cut the plantations. In general our results indicate that the maintenance of grasslands mosaics of different heights maximize the local biodiversity of birds and highlight the importance of the protection of grasslands areas. In addition, we have seen that considering different components of diversity that incorporate information on species is important because they can tell, for example, how many extinctions a community can support until important functions are lost.

Submitted by Luciana Ferreira (lucgeral@gmail.com) on 2018-09-25T12:11:34Z No. of bitstreams: 2 Dissertação - Lucas Lacerda Caldas Zanini Jardim - 2014.pdf: 1922668 bytes, checksum: 8ba35cacc2f1d99252124085bf81a549 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Approved for entry into archive by Luciana Ferreira (lucgeral@gmail.com) on 2018-09-26T11:42:18Z (GMT) No. of bitstreams: 2 Dissertação - Lucas Lacerda Caldas Zanini Jardim - 2014.pdf: 1922668 bytes, checksum: 8ba35cacc2f1d99252124085bf81a549 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Made available in DSpace on 2018-09-26T11:42:18Z (GMT). No. of bitstreams: 2 Dissertação - Lucas Lacerda Caldas Zanini Jardim - 2014.pdf: 1922668 bytes, checksum: 8ba35cacc2f1d99252124085bf81a549 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Previous issue date: 2014-03-28 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / We have been describing species for a long time and we have been asking about how many of them are left on the Earth. Species are evolutionary lineages and the answer to that question maybe is not in richness estimates, but in how much of the evolutionary tree was already described. Here, we studied how richness and phylogenetic diversity have been accumulated in Tetrapods and how those metrics differ from each other. We also tested if there were biases for particular clades in species describing process, it would mean non-random description along the phylogeny. We found Amphibia and Squamata have ascendant curves for both metrics, Mammals are beginning its stabilization and Birds are stabilizing for about 60 years. Nonetheless, phylogenetic diversity trends to stabilize firstly than richness, due to the convex relationship between them. We also founde that description has been at random about clades. Thus, more efforts are necessary to improve our phylogenetic resolution of Amphibia, Squamata and Mammals. Once we have an ample sample size in Birds and a random sample along phylogeny, we need to resolve Darwinian and Wallacean shortfalls, taking into consideration the phylogenetic relationship among species, the evolutionary model of their traits and where those species occur. Understanding species as lineages permits us to stabilize early the number of species and to infer which species could have been extinct before description, such as what would be their impacts in conservation, community ecology and ecosystem function. / Nós temos descrito espécies há muito tempo e nos perguntamos sobre quantas delas existem na Terra. Espécies são linhagens evolutivas e a resposta à essa pergunta talvez não esteja na estimativa de riqueza, mas em quanto da árvore evolutiva já foi descrita. Aqui nós estudamos como tem sido o acúmulo de riqueza e diversidade filogenética desde 1758 nos Tetrápodas e como essas duas métricas se diferem. Também testamos se havia vieses para descrições de espécies em determinados clados, indicando descrição não aleatória na filogenia. Nós encontramos que Anfíbios e Squamata possuem curvas ascendentes, Mamíferos estão começando a estabilizar e Aves estão estabilizando nos últimos 60 anos. No entanto, apesar de riqueza e diversidade filogenética serem correlacionadas, a segunda tende a estabilizar primeiro que riqueza, devido a relação convexa entre elas, parecida com as relações espécie-área. Nós também encontramos que o processo de amostragem (descrição) ao longo da filogenia tem sido aleatório. Assim, mais esforços são necessários para melhorarmos nossa resolução filogenética de Anfíbio, Squamata e Mamíferos. Já Aves, uma vez que temos grande tamanho amostral necessitamos focar agora nas suas lacunas Darwinianas e Wallaceanas, resolvendo as incerteza sobre a relação de parentesco entre as espécies, quais são os modelos evolutivos que explicam a evolução de suas características e onde essas espécies ocorrem. Entender espécies como linhagens permite-nos estabilizar o número de espécies mais cedo e inclusive inferir quais espécies poderiam ter sido extintas antes de descritas e quais seriam seus impactos em conservação, ecologia de comunidades e funcionamento de ecossistemas.

O florestamento dos campos do sul da América do Sul incluindo os campos do Pampa estão mudando a paisagem local e levando a mudanças nas populações de aves. O conhecimento sobre o efeito do florestamento sobre a avifauna dos campos do sul da América do Sul é bastante limitado à riqueza e composição de espécies. Além de preencher lacunas considerando diferentes índices para avaliar respostas das comunidades de aves ao florestamento dos campos (Capítulos 2 e 3), nesta tese nós também avaliamos se Áreas de Preservação Permanente localizadas dentro de plantações de eucalipto são funcionais para a avifauna local, fazendo uma comparação com áreas de campo pastejado (Capítulo 1). No capítulo 1 nós registramos uma diferença na composição de espécies entre as áreas devido principalmente às mudanças na altura e densidade da vegetação. Nos capítulos 2 e 3 nós avaliamos diferentes componentes da diversidade (taxonômica, filogenética e funcional) considerando possíveis efeitos do florestamento dos campos sobre estes Nossos resultados demonstram respostas diferenciadas entre os componentes, enquanto o florestamento leva a uma redução na diversidade taxonômica, diversidade filogenética e funcional não demonstram respostas negativas. No capítulo 2 no entanto, nós observamos que o florestamento dos campos conduz a uma perda de distintividade evolutiva, beneficiando desta forma linhagens que se diversificaram recentemente. No capítulo 3 apesar da redução na diversidade taxonômica não houve uma redução na diversidade funcional em áreas plantadas. Já a associação de alguns atributos funcionais com as áreas pós-corte, indica a plasticidade de algumas espécies que retornam para essas áreas logo após o corte dos plantios.De modo geral nossos resultados indicam que a manutenção de mosaicos de campo de diferentes alturas maximiza a biodiversidade local de aves e destaca a importância da proteção de áreas campestres. Além disso, vimos que considerar diferentes componentes da diversidade que incorporam informações sobre as espécies são importantes pois podem informar por exemplo, quantas extinções uma comunidade pode suportar até que funções importantes sejam perdidas, afetando assim a estabilidade dos ecossistemas. / The afforestation of southern grasslands of South America including the Pampa grasslands are changing the local landscape and leading to reduction of bird populations. Knowledge about the effect of afforestation on the avifauna of the southern South American grasslands is limited to richness and composition of species. In addition to filling gaps considering different indices to evaluate responses of the bird communities to the afforestation of the grasslands (Chapters 2 and 3), in this thesis we also evaluated whether Permanent Preservation Areas located within eucalyptus plantations are functional for the local avifauna, making a comparison with grazed grasslands areas (Chapter 1). In Chapter 1 we recorded a difference in species composition between areas due mainly to changes in height and density of vegetation. In chapters 2 and 3 we evaluated different components of diversity (taxonomic, phylogenetic, and functional), considering possible effects of grasslands afforestation on them. Our results demonstrate differentiated responses among components, while afforestation leads to a reduction in taxonomic diversity, phylogenetic and functional diversity do not demonstrate negative responses In chapter 2 however, we observe that grasslands afforestation leads to a loss of evolutionary distinctiveness, thus benefiting species that have diversified recently. In chapter 3, despite the reduction in taxonomic diversity, there was no reduction in functional diversity in planted areas. Furthermore, the association of some functional traits with the post-cut areas indicates the plasticity of some species that return to these areas soon after cut the plantations. In general our results indicate that the maintenance of grasslands mosaics of different heights maximize the local biodiversity of birds and highlight the importance of the protection of grasslands areas. In addition, we have seen that considering different components of diversity that incorporate information on species is important because they can tell, for example, how many extinctions a community can support until important functions are lost.

A robust ecosystem requires a functionally heterogeneous community of organisms with a wide range of traits that permits broad resource partitioning. Understanding community diversity patterns can help investigate drivers of community assembly and how different metrics reflect the success of restoration in grassland or weed control in cropland. The objectives of my study were to identify assembly drivers influencing community taxonomic, phylogenetic, and functional diversity. The first study examined the effect of different ecotypes of dominant species on grassland community diversity along a spatial aridity gradient during restoration. This study showed that ecotype significantly affected species richness and shaped taxonomic, phylogenetic, and functional diversity. Accordingly, restorations should consider ecotypic variation as a critical biological filter to community assembly in grassland ecosystems. Given the community response across the tallgrass prairie, restoration practitioners should draw attention to regional sources of dominant species because ideal ecotypic sources can affect species richness and even sustain the phylogenetic and functional patterns. The restoration efficacy of existing ecosystems should be evaluated to large-scale diversity patterns to detect gaps and limitations that will reveal which diversity components to highlight for further restoration investment. The second study investigated temporal variations in diversity metrics among dominant species ecotypes and a drought treatment on the importance of external and internal filters in shaping the assembly of grassland communities. In this study, species richness decreased significantly during the early stages of restoration while phylogenetic and functional diversity was maintained over eight years. I also found no significant effect of experimental drought treatment on community biodiversity. Moreover, ecotypic variation as an internal filter played a key role in grassland assembly but the external filter was less strong because of high trait overlap among species within a community. In general, this study highlighted the consequence of integrating both interspecific and intraspecific trait variabilities and the value of concentrating on functional traits to comprehend better how trait variability is coupled with species coexistence. Future investigations are necessary to examine the distinctive origins of variability in plant traits and how they contribute to grassland community assembly. The third study focused on whether weed management tactics such as a glyphosate-resistant (GR) cropping system were beneficial to control weed diversity in the soil seedbank of the agroecosystem. Both phylogenetic and functional diversity of the soil seedbank was relatively stable with different GR cropping systems across six years. The neutral assembly of the soil seedbank may imply that the belowground weed community could be restrained by stochastic mechanisms, such as dispersal and demographic stochasticity of seeds, during agricultural activities. Therefore, I recommend integrated weed management with a sustainable perspective to fight against the evolutionary feedback due to weed herbicide resistance. While the GR cropping system still seems beneficial, future weed control cannot overlook the extensive impact of GR systems on biodiversity variations, the shifts in weed composition, and the resistance evolution of weed species to herbicides in the agroecosystem.