Doctor of Philosophy / Department of Biology / Samantha Wisely / Habitat fragmentation and destruction are the most ubiquitous and serious environmental threats confronting the long-term survival of plant and animal species worldwide. However, some native or exotic species can take advantages of these alterations and expand their range, placing endemic species at risk of extinction by changing the composition of biotic communities and altering ecosystem. Capybara (Hydrochoerus hydrochaeris) are a widely distributed rodent throughout most of South and Central America, but restricted to areas of standing water. As the Gran Chaco ecosystem of Paraguay has been converted from dry tropical forest to pastureland, I hypothesized that this habitat alteration created potential for invasion by capybara into newly fragmented areas. I used ecological niche modeling to generate hypotheses about how the distribution of capybara has been affected by land use change, and tested those hypotheses with phylogeographic analyses. To understand the mechanisms that have allowed the invasion, I investigated home range, habitat use and thermoregulation of capybara via radiotelemetry in a deforested area in which capybara had recently invaded. Genetic analyses confirm a rapid range expansion scenario with evidence of secondary contact between two distinct phylogroups which had previously been disjunct. Modeling results indicated that conversion of forest to pastureland allowed the expansion to occur. Capybara selected water significantly more than it was available to them, and avoided shrub forest. I found a significant positive correlation between body temperature and distance from water, and a significant negative correlation between distance from water and Chaco ambient temperature. Capybara proximity to water appeared to be tightly linked to body thermoregulation. These results suggest that although capybara have expanded into the Chaco forest as it is converted to pastureland, the presence of permanent water sources in those pastures are the mechanism that allow capybara to persist in this habitat. This is the first study to characterize capybara in a xeric habitat without a year round water source, and scarce natural grasslands. My results show how anthropogenic habitat modification has allowed capybara to thrive. Understanding how capybara invade and utilize the deforested Central Dry Chaco will provide valuable information for the future management of the species and the Chaco ecosystem.

Environmentally related selective pressures and community interactions are well-documented drivers for niche differentiation, as natural selection acts on adaptive traits best fit for survival. Here, we investigated niche evolution between and within Pinus taeda, Pinus rigida, and Pinus pungens and sought to identify which climate variables contributed to species divergence. We also sought to describe niche differentiation across genetic groupings previously identified for P. taeda and P. rigida. Ecological niche models were produced using Maximum Entropy followed by statistical testing based on a measure of niche overlap, Schoener’s D. Both niche conservatism and niche divergence were detected, thus leading us to conclude that directional or disruptive selection drove divergence of the P. taeda lineage from its ancestor with P. rigida and P. pungens, while stabilizing selection was associated with the divergence of P. rigida and P. pungens. The latter implies that factors beyond climate are important drivers of speciation within Pinus.

Orientador: Ananda Virginia de Aguiar / Resumo: Myracrodruon urundeuva é uma espécie madeireira natural com grande potencial de uso comercial no Brasil, principalmente nas regiões do Pantanal, do Cerrado e da Caatinga, onde ocorre a exploração de espécies nativas. A exploração intensiva tem causado grande perda de indivíduos e o isolamento de populações em ilhas, devido à fragmentação do habitat da espécie. Assim, a adoção de estratégias para conservação ex situ de espécie nativas torna-se indispensável. Duas propostas foram idealizadas neste trabalho. A primeira foi estimar a variabilidade genética e ganho genético com a seleção de um teste de progênies. O teste de progênie consorciado com as espécies Myracrodruon urundeuva, Terminalia argentea e Astronium fraxinifolium, foi instalado em 12 de julho de 1994 na Fazenda de Ensino, Pesquisa e Extensão (FEPE), do campus de Ilha Solteira (FEIS/UNESP) na cidade Selvíria – MS. O delineamento utilizado foi o de blocos completos casualizados, contendo 28 progênies, seis plantas por parcela e quatro repetições para as espécies instaladas. Os caracteres altura e diâmetro a altura do peito (DAP) foram mensurados aos 24 anos após o plantio. Verificou-se a existência de variação genética significativa entre as progênies para os caracteres analisados. A alta taxa de sobrevivência indica boa adaptação da espécie em testes consorciados. As estimativas do coeficiente de variação genética tiveram resultados de 19,41% e 17,26% para DAP e altura, em nível de indivíduo, e de 9,7% e 8,63%, entr... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Myracrodruon urundeuva is a natural timber species with great potential for commercial use in Brazil, especially in the Pantanal, Cerrado and Caatinga regions, where native species are exploited. Intensive exploitation has caused great loss of individuals and the isolation of populations on islands due to the fragmentation of the species' habitat. Thus, the adoption of strategies for ex situ conservation of native species becomes indispensable. Two proposals were conceived in this work. The first was to estimate the genetic variability and genetic gain with the selection of a progeny test. The progeny test consortium with the species Myracrodruon urundeuva, Terminalia argentea and Astronium fraxinifolium, was installed on July 12, 1994 at the Fazenda de Ensino, Pesquisa e Extensão (FEPE), at the campus of Ilha Solteira (FEIS / UNESP) in the city Selvíria MS. The design was a randomized complete block, containing 28 progenies, six plants per plot and four replications for the species installed. The height and diameter of the chest height (dch) were measured at 24 years after planting. There was significant genetic variation between the progenies for the characters analyzed. The high survival rate indicates good adaptation of the species in intercropping tests. Estimates of the coefficient of genetic variation showed results of 19.41% and 17.26% for DBH and height, at the individual level, and of 9.7% and 8.63% among progenies. The individual heritabilities ranged from moderate... (Complete abstract click electronic access below) / Mestre

Duas espécies de cetáceos apresentam padrões de distribuição peculiares ao longo da costa brasileira, muito provavelmente em resposta às condições hidrográficas e topográficas que ocorrem entre 20 e 33°S. A primeira espécie, a franciscana ou toninha (Pontoporia blainvillei), é um golfinho de distribuição restrita do Brasil até a Argentina, que ocorre primariamente na plataforma continental interna, raramente ultrapassando os 50 m de profundidade. Já a segunda espécie, o golfinho-pintado-do-Atlântico (Stenella frontalis), é um golfinho de distribuição restrita ao Oceano Atlântico, que ocupa principalmente a plataforma continental. Estas duas espécies apresentam hiatos ao longo da sua distribuição no Brasil que tem consequências na morfologia e estrutura genética das espécies. Através da aplicação de diferentes métodos, o principal objetivo deste estudo foi investigar a influência do ambiente marinho no padrão de distribuição e na estrutura genética destas duas espécies com ênfase na costa brasileira. No primeiro capítulo, investigou-se a relação do ambiente marinho com o padrão de distribuição da franciscana. Para tanto, uma revisão e atualização da distribuição das áreas de manejo da franciscana (FMA), e dos limites dos hiatos, ao longo do Brasil foram realizadas. Análises de nicho ecológico sugerem que os hiatos fazem parte do nicho fundamental da franciscana que seriam, portanto, relativamente adequados para a espécie.No entanto, o estreitamento da plataforma continental parece ser o principal fator que explica a ausência da espécie nos hiatos e, inclusive poderia explicar a diferenciação genética entre algumas FMAs No segundo e terceiro capítulos, a relação entre similaridade genética e distâncias geográficas e ambientais foram investigadas para o golfinho-pintado-do- Atlântico em duas escalas: ao longo de praticamente toda distribuição e em uma escala mais restrita com ênfase no Brasil. Populações geneticamente distintas ao longo de toda distribuição da espécie foram identificadas com base em um marcador mitocondrial, que podem ser resultado Isolamento por Distância e Isolamento por Resistência, relacionados tanto com condições ambientais contemporâneas quanto do passado (Último Glacial Máximo). As análises de estrutura populacional do golfinho-pintado-do-Atlântico no Brasil, investigada mais profundamente com marcadores genômicos, indicam ao menos a existência de três populações (Brasil, Colômbia e Oceânica) suportanto, portanto, a hipótese de uma população isolada no sudeste do Brasil. De forma geral, conclui-se que o ambiente marinho e, principalmente, fatores como extensão da plataforma continental, batimetria e temperatura tem um papel fundamental para explicar o padrão de distribuição destas espécies no Brasil. Além disso, outros processos podem estar envolvidos na estruturação genética do golfinho-pintado-do-Atlântico e também da franciscana como, por exemplo, estrutura social, filopatria e a história evolutiva destas espécies. O maior desafio para conservação da franciscana é seu status de Criticamente Ameaçada no Brasil e, em relação ao golfinho-pintado-do-Atlântico é a deficiência de dados. Uma vez que ambas espécies ocorrem na porção mais desenvolvida do país, os resultados aqui obtidos têm impacto direto na conservação destas espécies, porque trazem informações que podem ser utilizadas em planos futuros de conservação e manejo. / Along Brazilian coastal waters, either franciscana and Atlantic spotted dolphins exhibited distributional gaps, which is most likely resulting from changes in the environmental features between 20 and 33°S. The former species, franciscana (Pontoporia blainvillei), is a river dolphin with restricted distribution from Brazil to Argentina, recorded mainly up to 50 m deep over the inner shelf. The second species, Atlantic spotted dolphin (Stenella frontalis), is a delphinine dolphin distributed across the Atlantic Ocean, being mainly recorded over the continental shelf. The distribution patterns that these species showed in Brazil have a direct influence on the morphology/ecology and genetic struture of both species. Different approaches were applied to address the main goal of this study, which was investigating the influence of marine environment in shaping the distribution pattern, as well as genetic strcuture of franciscana and Atlantic spotted dolphin with emphasis in the Brazilian coastal waters. In the first chapter, I investigated the franciscana distribution in Brazil using an ecological niche modeling approach. In order to do that, I performed a review of records of the species along Brazial and, updated the limits of franciscana management areas (FMAs) and distributional gaps. The results suggested that gaps are within franciscana fundamental niche and, therefore, both gaps would be suitable for franciscana. However, the narrow of continental shelf seems to be the main factor inhibiting the presence of franciscana in these areas. Furthermore, the narrowing of continental shelf play a role to explain the genetic differentiation among FMAs. In the second and third chapters, the relationship between genetic distances and geographic and environmental distances were investigated both in a restrict and a broad scale. I found genetically distinct populations 12 across Atlantic spotted dolphin distribution based on mtDNA, that are probably resulting of Isolation-by-Distance and Isolation-by-Resistance related both with contemporary and past conditions (e.g. Last Glacial Maximum). Furthermore, I investigated population struture using genomic markers (Single Nucleotide Polymorphisms, SNPs) across Western South Atlantic, Caribbean and Eastern Atlantic. The results suggested at least three different populations, and therefore, confirmed previous hypothesis of an isolated population in the southeastern Brazil. Overall, I concluded that marine envinronment, especially the extension of continental shelf, bathymetry and sea surface temperature, are the main factors that explaning the distribution pattern of franciscana and Atlantic spotted dolphin in Brazil. Besides that, other process such as, social structure and phylopatry, as well as biogeographical process might be investigated in further studies. Franciscana is considered “Critically endangered” in Brazil, and Atlantic spotted dolphin has not enough data to determine its conservation status. Since both species are recorded in the most developed region of the country with high anthropic pressure, my results could help in future management and conservation plans for both species in a regional scale.

The Aedes aegypti mosquito is the vector for four infectious diseases of global concern – Yellow Fever, Dengue, Chikungunya, and Zikavirus. Previous attempts to model the expansion of the vector habitat due to global climate change have rarely included characteristics related to the human populations on which this mosquito is dependent. The purpose of this research was to determine whether the inclusion of human population density improves model performance while creating risk maps that can be used to determine where humans are most likely to be exposed to the vector in the future. The resulting model demonstrated that the inclusion of human population density improves the predictive power for A. aegypti and should be considered during model development. Maps produced by the model were also suitable for identifying regions where human populations are most likely to experience increased risk. Finally, two areas at risk of expansion were highlighted as a case study in pairing risk mapping with evidence-based intervention strategies to identify sites that would benefit from mosquito-control efforts. In this case, a low-cost program of insecticide-treated covers for water storage containers would likely work well in both Minas Gerais, Brazil and Northwestern Province, Zambia to mitigate mosquito risk. This research demonstrates that human population characteristic not only improve model fit but also increase the extent to which risk maps are actionable by aiding in targeting interventions.

Submitted by Cláudia Bueno (claudiamoura18@gmail.com) on 2015-10-20T17:21:43Z No. of bitstreams: 2 Dissertação - Túlio Max de Oliveira Guimarães - 2014.pdf: 2190502 bytes, checksum: 95a9c8660ff6a8f4fee3c71a61784e47 (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) / Approved for entry into archive by Luciana Ferreira (lucgeral@gmail.com) on 2015-10-21T10:06:29Z (GMT) No. of bitstreams: 2 Dissertação - Túlio Max de Oliveira Guimarães - 2014.pdf: 2190502 bytes, checksum: 95a9c8660ff6a8f4fee3c71a61784e47 (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) / Made available in DSpace on 2015-10-21T10:06:29Z (GMT). No. of bitstreams: 2 Dissertação - Túlio Max de Oliveira Guimarães - 2014.pdf: 2190502 bytes, checksum: 95a9c8660ff6a8f4fee3c71a61784e47 (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) Previous issue date: 2014-04-23 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / Understand how species are spatially distributed has been exhaustively discussed in ecology over the last decades. Recently, frameworks based on Ecological Niche Models (ENM) have emerged to avoid problems related to the lack of species geographical information, once it identify which environmental suitable conditions of geographic space enable the persistence of species. Recently this approach has become a significant component in Systematic Conservation Planning, helping managers to select better areas to create reserves. Several factors limit the fundamental niche of species and poor geographical information about species distribution may lead to be an underestimation of suitable conditions that one specie occur,, revealing an non-equilibrium with climate. Thus, using good fossil records to construct ecological niche models can be a better way to evaluate and improve ENM predictions and it allows us to estimate other suitable conditions not seen before. Thereby, our aim was to investigate if ENMs built for Mauritia flexuosa, and Tapirus terrestris improve with the addition of fossil information. So, different ENMs were built using, first, current records and, second, using different proportions of fossil data. The results showed that species closer to equilibrium with climate (M. flexuosa) had an improvement in model’s performance with the addition of fossil records, while species with higher non-equilibrium (T. terrestris) decreased the model’s performance. / Entender como as espécies estão espacialmente distribuídas pelo planeta tem sido um assunto exaustivamente discutido em ecologia ao longo das últimas décadas. Recentemente, abordagens baseadas nos Modelos de Nicho Ecológico têm surgido com o intuito de eliminar problemas relacionados à lacuna de informação geográfica sobre as espécies, uma vez que identifica locais no espaço geográfico que apresenta as condições ambientais favoráveis à persistência das mesmas. Vários fatores limitam o nicho fundamental das espécies e informações geográficas enviesadas acerca de sua distribuição podem levar a uma subestimativa das condições adequadas à ocorrência, revelando um desequilíbrio com o clima. Deste modo, a utilização de registros fósseis na construção dos Modelos de Nicho Ecológico pode ser uma maneira de melhorar as predições dos modelos, já que adiciona novas informações ambientais que não haviam sido encontradas atualmente. Deste modo, nosso objetivo foi investigar se os Modelos de Nicho Ecológico construídos para Mauritia flexuosa e Tapirus terrestris apresentaram melhora no poder preditivo pela adição de informação fóssil. Para isso, foram construídos diferentes modelos utilizando dados atuais apenas e modelos utilizando tanto informação atual quanto informação fóssil, em diferentes porcentagens. Através de uma Análise de Variância Fatorial, medimos se a adição de informação fóssil apresentava melhora significativa no poder preditivo dos modelos. Nossos resultados mostram que quando há pouca variação na informação ambiental adicionada (M. flexuosa), os modelos apresentam uma melhora significativa no poder preditivo, ao passo que para aqueles dados com maior variação (T. terrestris) o efeito é inverso. Isso se deve pela variação dos erros de omissão e comissão gerados durante o processo de modelagem.

Coffea arabica is a species with far-reaching impacts on the global economy. Nevertheless, climate-related challenges threaten the coffee industry at its source: its growing regions. The coffee industry is a significant economic driver in Guatemala, but farmers are increasingly reporting losses in crop yield and arable land due to climate-related challenges. Ecological niche modeling (ENM) can be employed to make predictions about the current and future suitability of regions for a species by identifying significant biotic or abiotic indicators. An ENM was used to project suitable land into the future using climate change projection models known as representative concentration pathways (RCPs), for the coffee plant and a number of other species. Due to the potential of shade trees to lessen heat stress on coffee plants, common shade trees for the region were modeled. Additionally, a fungus species responsible for detrimental coffee leaf rust was modeled. Results of these models indicated potential for substantial climate-related habitat losses for the coffee plant in the coming decades. Examination of model predictions allow for greater understanding of the climate-related variables affecting the ecology of the coffee plant, and the potential risks to the industry, in a changing climate. Additionally, ENM models for coffee rust and shade trees can help Guatemalan farmers make informed decisions about farm management.

The genus Castor is represented in Eurasia by Castor fiber, North America by C. canadensis, and has been in North America since the late Miocene. This study aims to assess whether morphology of Miocene-Pliocene C. californicus and extant C. canadensis are distinctly different. Specimens of Castor were compared using geometric morphometrics on cranial material and linear measurements of postcranial material. Species occurrence data were compared with past and future climate data to assess Castor distribution in North America through time. Results show that C. canadensis is highly variable in both cranial and postcranial morphology and C. californicus falls largely within the range of variation seen within the extant species. Past distributions match fossil occurrences of Castor, suggesting confidence in projected models. Morphological and distribution similarities between the two species suggest that they can be treated as ecological analogs, though evaluation of whether they are conspecific will require more data.

Coffea arabica is a species with far-reaching impacts on the global economy. Nevertheless, climate-related challenges threaten the coffee industry at its source: its growing regions. The coffee industry is a significant economic driver in Guatemala, but farmers are increasingly reporting losses in crop yield and arable land due to climate-related challenges. Ecological niche modeling (ENM) can be employed to make predictions about the current and future suitability of regions for a species by identifying significant biotic or abiotic indicators. An ENM was used to project suitable land into the future using climate change projection models known as representative concentration pathways (RCPs), for the coffee plant and a number of other species. Due to the potential of shade trees to lessen heat stress on coffee plants, common shade trees for the region were modeled. Additionally, a fungus species responsible for detrimental coffee leaf rust was modeled. Results of these models indicated potential for substantial climate-related habitat losses for the coffee plant in the coming decades. Examination of model predictions allow for greater understanding of the climate-related variables affecting the ecology of the coffee plant, and the potential risks to the industry, in a changing climate. Additionally, ENM models for coffee rust and shade trees can help Guatemalan farmers make informed decisions about farm management.

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