Understanding marine mammal populations and how they are affected by human activity and ocean conditions is vital, especially in tracking population declines and monitoring endangered species. However, tracking marine mammal populations and their distribution is challenging due to difficulties in observation and costs. Using surrounding plankton environmental DNA (eDNA) has the potential to provide an indirect measure of monitoring cetacean abundances based on ecological associations. This project aims to apply statistical methods to assess the relationship of visual abundances of common species of baleen whales with amplicon sequence variants (ASV) of plankton eDNA samples from the NOAA-CalCOFI Ocean Genomics (NCOG) project. Modeling this relationship of eDNA with marine mammal sightings may greatly aid the ability to predict the abundance of whales in the ocean. There are several key challenges associated with the analysis of this NCOG data. Plankton eDNA samples are an example of compositional data, where the proportions of each ASV must sum to one; this provides a challenging constraint for statistical analysis and interpretation. High dimensionality (the number of parameters exceeds the observations) and sparsity (many observed zeros) of the genetic sequencing data also pose challenges in estimating parameters. Finally, the model associations should be adjusted for related factors, including seasonality and oceanographic factors, the latter of which goes beyond this project's scope. This thesis develops and fits models to estimate cetacean abundance from plankton eDNA by leveraging methods of compositional data analysis and high-dimensional regression. This project applies log-ratio data transformations and corresponding log-contrast models to address the compositional aspect of eDNA reads. Regression methods involving high-dimensional data typically rely on dimensionality reduction or regularization. This project implements both reduction and regularization through sparse partial least squares (sPLS) regression. In addition to the data modeling objective of using plankton eDNA to predict baleen whale abundances, this project also identifies ecological correlations between whale abundance and plankton eDNA.

Jan Farkač, Diplomová práce 2018 Abstract Bird species differ in their local densities, which seems to be related to their geographical distribution and species-specific traits. Investigating such a relationship can help us to understand better how the birds inhabit the space. The aims are as follow (i) to take an alternative approach to densities by counting them just in species preferred habitats and (ii) to explain the abundance characteristics such as an absolute density, variation in local densities or occupancy by species-specific traits. The relationship between abundance characteristics (local densities and their coefficient of variation in space) and avian traits such as a habitat specialisation, diet specialisation, PCA of morphological traits, PCA of reproduction traits - as an estimate of slow-fast continuum and a range size were tested using GLM. There are two abundance characteristics significantly related to species specialisation index. I have used the data from the Common Bird Monitoring Program run in the Czech Republic by the Czech Society of Ornithology. Due to the highest amount of records I have selected data from the year 2009 and subsequently species occupying more than 50 transects (out of 129), which resulted in inclusion of 47 species into analyses. This thesis contains...

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

We have used a series of observations of HD119419, performed in 2012 and 2013at the European Southern Observatory 3.6-m telescope in La Silla, Chile. These are high resolutionspectropolarimetric observations with coverage in all four Stokes parameters. We performed a chemical abundance analysis of HD119419, in the absence of any being published previously for this star. We used a LLmodels stellar atmosphere code with effective temperature11500 K and surface gravity log g = 4.0, together with the spectrum synthesis code synmast. Abundances were adjusted until the synthetic spectra matched the mean observed spectra as well as possible, and these abundances were assumed to be representative of the photosphere of HD119419. We found good estimates for some Fe-peak elements and rare-earth elements. The abundance estimates were used to compute least-squares deconvolution Stokes spectra, from which we calculated how the longitudinal magnetic field and net linear polarization varies with rotational phase for HD119419. We calculated an improved rotational period for HD119419 using our longitudinal magnetic field measurements together with previous measurements from the literature, determining it to be 2.60059(1) days. We found that the Stokes QUV are unusually strong for the rare-earth elements in HD119419, considering their weaker Stokes I profiles compared to the Fe-peak elements in particular.

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

A major challenge in agroecosystems is how to manage the systems so that it reduces crop pests and enhances natural pest control. This thesis investigates patterns of crop pests and top-down effects of birds and arthropod predators in relation to land-use composition across spatial scales. In paper (I) I examined the crop distribution and land-use types in relation to the crop raiding patterns in 15 transectsin sites close to and far from forests along with a questionnaire survey at household level. I found severe crop raiding close to forests, but it had no impact on crop composition growing between the two sites. In paper (II) I examined the effect of forest and tree cover, at local and landscape scales, on the abundance of arthropod predators by collecting specimens from 40 home gardens. My result showed higher abundance of arthropod predators when either the home garden or the surroundings had a high tree-cover, compared to when tree-cover at both scales was similarly either high or low. In paper (III) I investigated the effect of excluding birds and arthropod predators on leaf damage on rape seed in 26 home gardens. I found stronger top-down impacts from arthropod predators on crop pests in tree-poor gardens than in tree-rich gardens. There was no effect of birds. In paper (IV) I explored the effect of landscape complexity on bird and arthropod predation using plasticine caterpillars in 36 home gardens across landscapes. The rate of arthropod predation on caterpillars was higher in simple than in complex landscapes. The rate of bird predation did not vary between complex and simple landscapes. In simple landscapes, arthropod predation was higher than that of birds. The overall results suggest that simplified gardens/landscapes still have enough habitat heterogeneity to support arthropod predators for the significant top-down controlling effect on crop pests. However, I did not find clear effect of complexityon the top-down effect of birds. / <p>At the time of the doctoral defence the following papers were unpublished and had a status as follows: Paper 1: Manuscript; Paper 3: Manuscript; Paper 4: Manuscript</p>

Master of Science / Department of Biology / Jesse B. Nippert / The Konza Prairie in northern Kansas, USA contains over 550 vascular plant species; of which, few have been closely studied. These species are adapted to environmental stress as imposed by variable temperature, precipitation, fire, and grazing. Understanding which plant traits relate to drought responses will allow us to both predict drought tolerance and potential future shifts in plant community composition from changes in local climate. Morphological and physiological measurements were taken on 121 species of herbaceous tallgrass prairie plants grown from seed in a growth chamber. Gas exchange measurements including maximum photosynthetic rate, stomatal conductance to water vapor, and intercellular CO[subscript]2 concentration were measured. All plants were exposed to a drought treatment and were monitored daily until stomatal conductance was zero. At this point, critical leaf water potential (Ψ[subscript]crit), an indicator of physiological drought tolerance was assessed. Other measurements include root length, diameter, volume, and mass, leaf area, leaf tissue density, root tissue density, and root to shoot ratio. Traits were compared using pair-wise bivariate analysis and principal component analysis (PCA). A dichotomy was found between dry-adapted plants with thin, dense leaves and roots, high leaf angle, and highly negative Ψ[subscript]crit and hydrophiles which have the opposite profile. A second axis offers more separation based on high photosynthetic rate, high conductance rate, and leaf angle, but fails to provide a distinction between C[subscript]3 and C[subscript]4 species. When tested independently, grasses and forbs both showed drought tolerance strategies similar to the primary analysis. Matching up these axes with long term abundance data suggests that species with drought tolerance traits have increased abundance on Konza, especially in upland habitats. However, traits that relate to drought tolerance mirror relationships with nutrient stress, confounding separation of low water versus low nutrient strategies. My results not only illustrate the utility of morphological and physiological plant traits in classifying drought responses across a range of species, but as functional traits in predicting both drought tolerance in individual species and relative abundance across environmental gradients of water availability.

Master of Arts / Department of Political Science / Emizet N. Kisangani / This study is an effort to shed some light on the causes of civil war. The literature on civil war onset has been framed under three main perspectives: cultural, political and economic approaches. Recent studies, however, tend to narrow the debate and posit explanations for civil war as either greed-motivated or grievance-motivated. This study replicates one of the most prominent econometric models on civil war, the Collier and Hoeffler model (CH), and further validated their economic interpretation of civil war as greed-motivated. Their argument is that greed-led behavior is motivated by an abundance of valuable resources. However, Collier and Hoeffler overlooked one critical element: scarce resources also contribute to discontent and violent protests. This study suggests that the CH model should include resource scarcity to avoid omitting variable bias.

Differences in cropping practices, including tillage, inputs and crop rotations are the driving factors affecting weed dynamics (weed abundance, composition and crop-weed competition), which can ultimately affect crop yields. Several experiments were carried out to assess the impact of long-term organic and conventional cropping systems on weed abundance, weed community composition, crop yield and yield loss using a long-term (18 year) alternative cropping systems study (ACS) at Scott, Saskatchewan, Canada. The ACS study consisted of three input systems, namely high (conventional tillage), reduced (no-till conventional) and organic input systems and three crop rotation diversities (low diversity, diversified annual grains and diversified annual-perennials). A statistical analysis of the 18-year rotation revealed that the organic rotations have four and seven times higher weed density and 32% and 35% lower crop yields than the reduced and the high input systems respectively. Weed community composition was consistently different in organic rotations compared to the two conventional rotations throughout the years, but year to year random variations were more profound. All cropping systems showed an increase in weed density, weed biomass and crop yields over time, probably due to an increase in rainfall over time. Increasing the crop rotation diversity with annual and perennial crops did not reduce weeds, but decreased crop yields in all systems. A two-year micro-plot experiment with four additional weed competition treatments on the ACS study revealed that the wheat yields were lower in the organic rotations even in the absence of weeds, implying that lower crop yields were due to soil fertility related factors. A greenhouse pot experiment from soils obtained from both organic and reduced rotations revealed that wheat yields were still lower in organic compared to the reduced input systems, even after excess mineral N and P were added. Furthermore, no differences in crop yield loss due to weed competition among cropping systems were identified. Overall, this study revealed that eliminating tillage and reducing inputs are possible without long-term changes in weed abundance, weed community composition or affecting crop yields. However, eliminating synthetic inputs as was done in the form of organic crop rotations resulted in increased weed abundance, changed community composition and decreased crop yields.