abstract: A significant portion of stars occur as binary systems, in which two stellar components orbit a common center of mass. As the number of known exoplanet systems continues to grow, some binary systems are now known to harbor planets around one or both stellar components. As a first look into composition of these planetary systems, I investigate the chemical compositions of 4 binary star systems, each of which is known to contain at least one planet. Stars are known to vary significantly in their composition, and their overall metallicity (represented by iron abundance, [Fe/H]) has been shown to correlate with the likelihood of hosting a planetary system. Furthermore, the detailed chemical composition of a system can give insight into the possible properties of the system's known exoplanets. Using high-resolution spectra, I quantify the abundances of up to 28 elements in each stellar component of the binary systems 16 Cyg, 83 Leo, HD 109749, and HD 195019. A direct comparison is made between each star and its binary companion to give a differential composition for each system. For each star, a comparison of elemental abundance vs. condensation temperature is made, which may be a good diagnostic of refractory-rich terrestrial planets in a system. The elemental ratios C/O and Mg/Si, crucial in determining the atmospheric composition and mineralogy of planets, are calculated and discussed for each star. Finally, the compositions and diagnostics of each binary system are discussed in terms of the known planetary and stellar parameters for each system. / Dissertation/Thesis / M.S. Astrophysics 2013

Entender como comunidades são estruturadas a partir de um pool de espécies é uma questão central em Ecologia de Comunidades. Diversas abordagens foram propostas para estabelecer a ligação entre os padrões de estrutura de comunidades e os processos que os geram. As regras de assembleia e a abordagem filogenética em ecologia de comunidades são alguns exemplos. Entretanto, o que estas abordagens não levam em conta é o efeito de processos neutros na estruturação de comunidades. Há um consenso de que tanto nicho como neutralidade afetam a estrutura de comunidades e que se deve avaliar a importância relativa de cada um destes processos. A ideia desta tese foi usar modelos estatísticos para representar como processos neutros e de nicho geram padrões em comunidades. No Capítulo 2 propus uma abordagem baseada em modelos hierárquicos através da qual é possível expressar processos neutros e de nicho. A partir disso, foi possível representar hipóteses em que apenas processos neutros afetam a estrutura da comunidade, apenas processos de nicho ou diferentes combinações entre ambos. Usando seleção de modelos, identifiquei qual a combinação de processos melhor explica as abundâncias observadas das espécies. Com isso, mostrei que as comunidades de samambaias em gradientes altitudinais na Serra do Mar no Paraná, Brasil são estruturadas por uma mistura de filtro ambiental, deriva ecológica e limitação de dispersão. O filtro ambiental define as abundâncias das espécies selecionando as melhores estratégias ecológicas das espécies dependendo da altitude. A variação de abundância entre as espécies que compartilham as mesmas estratégias ecológicas é explicada em parte por deriva ecológica e limitação de dispersão e, em parte, por filtro de habitat independente dos atributos das espécies incorporados no modelo. Com isso, delimitei como processos baseados em nicho e neutralidade afetam a abundância das espécies de samambaias ao longo de gradientes altitudinais. No Capítulo 3 usei um estudo de caso para explorar a ideia central da abordagem filogenética em ecologia de comunidades de que é possível inferir os processos que afetam as comunidades com base em padrões locais de estrutura filogenética. Usei a abordagem de modelos proposta no Capítulo 2 para simular comunidades geradas por processos puramente neutros, puramente de nicho e uma combinação hierárquica entre os dois. Encontrei que comunidades geradas apenas por processos de nicho geram estruturas filogenéticas aleatórias na maioria dos casos. A detecção de estruturas filogenéticas aleatórias foi ainda mais frequente nas comunidades geradas por processos puramente neutros e pela combinação de processos neutros e de nicho, não sendo possível a distinção entre estes dois cenários. Desse modo, o estudo de caso mostrou que estruturas filogenéticas não aleatórias são muito pouco plausíveis e que os processos neutros geram uma forte assinatura nos padrões de estrutura filogenética. Com a abordagem proposta nesta tese foi possível delimitar a influência de processos de nicho e neutralidade em comunidades e entender suas consequências em termos dos padrões por eles gerados. A tradução dos diferentes processos em modelos mistos mostrou-se uma ferramenta poderosa para quantificar padrões e construir explicações de como os processos operam juntos / Understanding how communities are assembled from a species pool is a central question in community ecology. Different approaches to link pattern and processes in community ecology were proposed. Some examples are assembly rules and the community phylogenetic approach. However, one aspect not accounted in those approaches is how neutral processes affect community patterns. There is a consensus that both niche and neutral processes affect community assembly and that the goal should be assess the relative importance of each process. The general idea if this thesis was to use statistical models to represent how niche and neutral generate community patterns. In Chapter 3, I proposed a framework based on hierarchical models to express niche and neutral processes. I used this approach to represent hypothesis in which only niche processes affect community structure, only neutral processes or a hierarchical combination of both explains species abundance. By using model selection, I identifyied which combination of processes better predicts observed abundances on local communities. I showed that fern communities across altitudinal gradients at Serra do Mar in Paraná, Brazil are structured by a mixture of environmental filtering, ecological drift and limited dispersal. Environmental filtering defines species abundance, selecting the best ecological strategies of species depending on altitude. Variation on species abundance sharing the same ecological strategies is explained in part by drift and limited dispersal, and in part by habitat filtering independent of species traits considered in the models. Hence, I refined how niche and neutral processes affect fern abundance on altitudinal gradients. In Chapter 3, I used a case study to explore the idea from community phylogenetics of inferring processes affecting communities based on patterns of phylogenetic structure. I used the modeling framework from Chapter 3 to simulate communities built by niche, neutral and combination of both processes. I found that communities based on niche processes are likely to generate a random phylogenetic structure. The detection of random phylogenetic strucure was even more common on communities built solely by neutral processes and combination of both niche and neutral processes. Therefore, the case study showed that a non random phylogenetic strucure is unlikely and that neutral processes strongly affect the outcome of phylogenetic patterns. Based on the framework proposed on this thesis it is possible to delimit the influence of niche and neutral processes on community assembly and to understand what are the consequences in terms of community patterns. Translating different processes into mixed models can be a powerful tool to quantify patterns and built explanations on how the processes operate together

Human microbial research has become increasingly popular in biomedical areas due to the importance of role of human microbiome in human health. One purpose of studying human microbiome is to detect differentially abundant features from a limited group of subjects across biological conditions. Metagenomic analyses of the human microbial communities are extensively used for biomedical applications due to its reliable and evident comparative discoveries across more than one metagenomes when multiple communities are taken into consideration. Next-generation sequencing technology helps to detect taxonomic compositions of specific features/species contained in human microbial communities. Statistical analysis often starts by generating the Operational Taxonomic Units (OTUs) using taxonomic compositions to classify groups of closely associated human microbiomes. Oftentimes, the counts of features are observed as matched count data with excess zeros. Such data lead some differential abundance analysis methods to apply Zero-Inflated Poisson (ZIP) or Zero-Inflated Negative Binomial (ZINB) regression for modeling the microbial abundance. However, over-dispersion as well as within-subject variation and correlation of matched count data render the standard ZIP and ZINB regression inadequate. To account for the inherent within-subject variation and correlation, independent random effect terms are commonly included in the regressions. Therefore, a robust method that accounts the effect of matched samples and correlated random effects while considering over-dispersion and excess zeros of count data is need for statistical analysis. In this paper, a statistical method, the two-part correlated ZINB model with correlated random effects (cZINB), is proposed for testing the matched samples with repeated measurements.

The hollow curve species abundance distribution describes the pattern of large numbers of rare species and a small number of common species in a community. The species abundance distribution is one of the most ubiquitous patterns in nature and many models have been proposed to explain the mechanisms that generate this pattern. While there have been numerous comparisons of species abundance distribution models, most of these comparisons only use a small subset of available models, focus on a single ecosystem or taxonomic group, and fail to use the most appropriate statistical methods. This makes it difficult to draw general conclusions about which, if any, models provide the best empirical fit to species abundance distributions. I compiled data from the literature to significantly expand the available data for underrepresented taxonomic groups, and combined this with other macroecological datasets to perform comprehensive model comparisons for the species abundance distribution. A multiple model comparison showed that most available models for the species abundance distribution fit the data equivalently well across a diverse array of ecosystems and taxonomic groups. In addition, a targeted comparison of the species abundance distribution predicted by a major ecological theory, the unified neutral theory of biodiversity (neutral theory), against a non-neutral model of species abundance, demonstrates that it is difficult to distinguish between these two classes of theory based on patterns in the species abundance distribution. In concert, these studies call into question the potential for using the species abundance distribution to infer the processes operating in ecological systems.

Understanding the mechanisms that structure biological systems is a primary goal of biology. My research shows that the biological structure is constrained in important ways by general variables such as the number of base pairs in a genome and the number of individuals and species in a community. I used a combination of macroecology, bioinformatics, statistics, mathematics, and advanced computing to pursue my research and published several peer-reviewed scientific manuscripts and open-source software as a result.I was funded through a combination of fellowships and scholarships awarded by the Utah State University School of Graduate Studies, College of Science, and Department of Biology, as well as teaching assistantships awarded through the Department of Biology at Utah State University, and research assistantships funded through a CAREER grant from the U.S. National Science Foundation (DEB-0953694) awarded to my advisor, Dr. Ethan White. With the help of my advisor, I also obtained a computing grant from Amazon Web Services in the amount of $7,500. Altogether, funding for my research and education totaled approximately $123,500. Using over 9000 communities of plants, animals, fungi, and microorganisms, I demonstrated that the forms of empirical species abundance distributions (SADs) are constrained by total abundance and species richness. Using over 300 microbial genomes, I demonstrate that nucleotide aggregation is constrained by genome length and differs between regions of coding and noncoding DNA. General state variables of genomes and ecological communities (i.e. genome length, total abundance and species richness) constrain simple structural properties of each system.

Waterfowl hunting is important historically, culturally, and economically in Mississippi and North America. I evaluated effect of hunting frequency (2 or 4 days/week) on duck abundance, harvest, and hunters’ perceived quality of their experience on Mississippi Wildlife Management Areas (WMAs). Neither relative abundance nor harvest of all ducks, mallard (Anas platyrhynchos), northern shoveler (A. clypeata), or green-winged teal (A. crecca) differed between experimental hunting frequencies. Duck harvest increased with hours spent afield. Hunters’ perceived quality did not differ between hunting frequencies but was greatest when hunters harvested > 4 ducks/ day and increased with harvest of larger sized ducks. I suggest WMAs may be hunted 4 days/week without impacting duck abundance, harvest, or hunt quality. I recommend continued evaluations of hunting frequency on duck abundance, harvest, and hunt quality to sustain science-guided management of waterfowl hunting on Mississippi public lands.

Made available in DSpace on 2015-03-05T16:20:41Z (GMT). No. of bitstreams: 0 Previous issue date: 25 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / O Brasil é visitado anualmente por milhares de aves costeiras que realizam movimentos sazonais da América do Norte para a América do Sul e vice-versa. Destacam-se as que vêm no norte com a aproximação do inverno boreal que chegam à procura de locais de parada e invernada, onde encontram alimentação farta, propiciando-lhes a continuidade do seu ciclo de vida. O presente trabalho tem por objetivo contribuir com o conhecimento a respeito da variação sazonal e influência da paisagem na ocorrência de aves costeiras ao longo do litoral médio na planície costeira do Rio Grande do Sul, Brasil. O trabalho é apresentado através de dois artigos que tratam dos temas propostos, estando formatado em uma versão preliminar de acordo com as normas de submissão da revista científica Journal of Ornithology. O primeiro artigo apresenta dados referentes à ocorrência e a variação sazonal de aves costeiras das famílias Charadriidae e Scolopacidae ao longo de 120 Km de praia durante um período de dois anos evidenciando a importância / The coast of Rio Grande do Sul State, Brazil, includes a remarkable number of habitats used by many Nearctic shorebirds species during the non-breeding season in the austral summer months. During two years we evaluated the abundance of shorebird monthly, along 120 km of the beach in Rio Grande do Sul, southern Brazil. Of the 17 species recorded, the most abundant were the Sanderlings (Calidris alba), White-rumped Sandpiper (Calidris fuscicollis) and Red Knot (Calidris canutus). The highest abundance occurred between October and April, and the lowest abundance occurred between May and September. Of the total species, 14 were migrant shorebirds from north hemisphere, one is a migrant shorebird from south hemisphere and two were resident. Some species were present throughout the year. Nine species were constantly registered, two were sporadic and six were incidental recorded. This study confirms that the beaches of Rio Grande do Sul State, are an important migration stopover and winter site for many shorebir

The invasion of ecosystems by alien species is a growing threat to the delivery of ecosystem services. This study explored the spatial distribution of water hyacinth in the Benoni Lakes and made analysis of its impact on water availability and usability in order to understand the evolution and its propagation rates. The study used satellite imagery for lake level modelling using Remote Sensing and Geographical Information Systems for calculations of area covered by weeds in each lake from 2002 to 2012.The modelling approach illustrates the potential usefulness in projecting invasive plants under climate change and enabled the quantification of long term changes in aquatic weeds. The results showed that aquatic infestations in lakes may be used as powerful predictors of correlations between plant abundance and climate change. The study therefore informs decision makers to identify areas where invasion is likely to occur and increase surveillance for early invaders. / Environmental Sciences / M. Sc. (Environmental Management)

Urban forests play key roles in animal and plant biodiversity and provide important ecosystem services.  Habitat fragmentation and expanding urbanization threaten biodiversity in and around urban areas.  Saproxylic beetles can act as bioindicators of forest health and their diversity may help to explain and define urban-forest edge effects.  I explored the relationship between saproxylic beetle diversity and distance to an urban area along nine transects in the Västra Götaland region of Sweden.  Specifically, the relationships between abundance and species richness and distance from the urban-forest boundary, forest age, forest volume, and tree species ratio was investigated Unbaited flight interception traps were set at intervals of 0, 250, and 500 meters from an urban-forest boundary to measure beetle abundance and richness.  A total of 4182 saproxylic beetles representing 179 species were captured over two months.  Distance from the urban forest boundary showed little overall effect on abundance suggesting urban proximity does not affect saproxylic beetle abundance.  There was an effect on species richness, with saproxylic species richness greater closer to the urban-forest boundary.  Forest volume had a very small positive effect on both abundance and species richness likely due to a limited change in volume along each transect.  An increase in the occurrence of deciduous tree species proved to be an important factor driving saproxylic beetle abundance moving closer to the urban-forest.  Overall, analysis showed inconsistent effects on both abundance and richness as functions of proximity to the urban-forest boundary.  Urban edge effects, forest volume, forest age, and forest tree species make up are all variables that may effect saproxylic abundance and species richness.  Forest managers should consider these variables when making management decisions.

Orientador: Edison Barbieri / Resumo: As praias arenosas e os estuários são ambientes importantes para as aves por serem utilizados como locais de repouso e alimentação, porém ainda há poucas informações sobre a interação das aves com estes ecossistemas. As informações sobre abundância, distribuição e biologia das populações animais são importantes para a preservação dos ambientes estuarinos e das espécies ali presentes. Portanto, este trabalho estudou a assembleia e a dinâmica de populações das aves no Baixio do Arrozal, localizado na Baía de Trapandé, seguindo o pressuposto de que as variações de abundância, dominância e diversidade apresentariam diferenças em relação aos meses e estações do ano. Os dados utilizados foram coletados em censos quinzenais durante o período de abril de 2013 a dezembro de 2016, pelo método do ponto fixo. A partir das amostras obtidas, foram calculadas a frequência de ocorrência, constância abundância, dominância e diversidade. Para o estudo da assembleia foi feito análise de similaridade e teste de correlação com as estações e com os anos de coleta de dados, juntamente com gráfico de barras com erro padrão da abundância total em função da mensalidade e gráfico boxplot deste mesmo índice em função das estações do ano, quanto ao estudo das populações, as variações das abundâncias de cada espécie registrada foram avaliadas através de gráfico boxplot e gráfico de barras com erro padrão em função das estações e da mensalidade. Através da análise de similaridade foram identificados três g... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: The sandy beaches and estuaries are important environments to the birds, because they use these places as resting and foraging areas, but there is not a lot of information about the interaction of birds with these ecosystems. Information about abundance, distribution and biology of animal populations are important for preservation of the estuaries and species. Thus, this work studied the assembly and the dynamic population of birds at the Baixio do Arrozal, in Trapandé Bay, supposing the variations of abundance, dominance and diversity would exhibit differences regarding the months and seasons. The data were collected in fortnightly censuses between April 2013 and December 2016, by the point count method. From the collected samples, we calculated the abundance, constance, dominance and diversity index. For the assembly study were made the similarity analysis and correlation test of dominance, abundance and diversity with seasonality and monthly, together with bar chart with standard error to total abundance in function of monthly and a boxplot chart of abundance in function of seasons. For the population study the variations of abundance were evaluated by boxplot chart and bar chart with standard error in function of months and seasons for each registered specie. The similarity analysis resulted in three different groups, which were determined according to abundance and constance, the group I constituted by Thalasseus acuflavidus, Nannopterum brasilianus e Rynchops niger, the... (Complete abstract click electronic access below) / Mestre