Plastic and Genetic Determination of Population, Community, and Ecosystem Properties in Freshwater Environments

The hierarchy of biological organization, from molecules to ecosystems, describes the relationships among various biological systems. Of particular interest is assessing how the factors that primarily determine the nature of one hierarchical level also have transcendent qualities that affect the ecology and evolution of higher hierarchical levels. The goal of this dissertation was to use a bottom-up approach to examine the transcendent effects of two factors that strongly determine the nature of their associated level of biological organization. The first, phenotypic plasticity, is a primary factor that determines the phenotype of an individual. The second factor, genetic diversity, largely determines the phenotypic distributions associated with populations. Controlled laboratory experiments on taxa from a freshwater tri-trophic food web were employed to examine the transcendent effects of phenotypic plasticity and genetic diversity on the biological hierarchy because relationships between individuals and populations from different trophic levels are well documented for numerous freshwater species. The results show that phenotypic plasticity can induce changes in population means and variances that promote population persistence and evolvability, and that plasticity provides a mechanistic explanation of community stability in response to changing environments. Similarly, genetic diversity may act as a signal that induces phenotypic plasticity in individuals, modulates community richness and ecosystem properties, and suggests a potential mechanism for the changes in biodiversity. Thus, results from this dissertation show that plasticity and genetic variation can shape the attributes of other biological groups higher in the biological hierarchy, and, in some cases, may also provide a mechanistic explanation for variability observed in higher levels of the biological hierarchy. These results highlight the importance of integrating traditionally disparate biological disciplines and may help to unify biology as a field

Measuring and modeling optical diffraction from subwavelength features

We describe a technique for studying scattering from subwavelength features. A simple scatterometer was developed to measure the scattering from the single-submicrometer, subwavelength features generated with a focused ion beam system. A model that can describe diffraction from subwavelength features with arbitrary profiles is also presented and shown to agree quite well with the experimental measurements. The model is used to demonstrate ways in which the aspect ratios of subwavelength ridges and trenches can be obtained from scattering data and how ridges can be distinguished from trenches over a wide range of aspect ratios. We show that some earlier results of studies on distinguishing pits from particles do not extend to low-aspect-ratio features

An automatic deep learning approach for coronary artery calcium segmentation

Coronary artery calcium (CAC) is a significant marker of atherosclerosis and cardiovascular events. In this work we present a system for the automatic quantification of calcium score in ECG-triggered non-contrast enhanced cardiac computed tomography (CT) images. The proposed system uses a supervised deep learning algorithm, i.e. convolutional neural network (CNN) for the segmentation and classification of candidate lesions as coronary or not, previously extracted in the region of the heart using a cardiac atlas. We trained our network with 45 CT volumes; 18 volumes were used to validate the model and 56 to test it. Individual lesions were detected with a sensitivity of 91.24%, a specificity of 95.37% and a positive predicted value (PPV) of 90.5%; comparing calcium score obtained by the system and calcium score manually evaluated by an expert operator, a Pearson coefficient of 0.983 was obtained. A high agreement (Cohen's k = 0.879) between manual and automatic risk prediction was also observed. These results demonstrated that convolutional neural networks can be effectively applied for the automatic segmentation and classification of coronary calcifications

On the relationship among birds and Trema micrantha in montane forests of Hispaniola

Avian frugivores are of great interest to ecologists because they play an important role in ecosystem functioning, and can serve as important components in habitat restoration. In the Neotropics, observational studies have demonstrated the importance of a variety of fruit trees to numerous bird species, but undoubtedly other tree species exist that are a key resource for birds. I explored the relationship between Trema micrantha (L.) Blume, which produces superabundant fruit nearly continuously, and its disperser assemblage in Hispaniolan pine forest and montane broadleaf forest in the Sierra de Bahoruco, Dominican Republic. In 174 hours of observation at sixteen trees I recorded 513 visits by nineteen species of birds. Birds did not visit Trema in numbers reflecting their relative abundance in each habitat. The most frequent consumer of Trema fruit was the migratory Cape May Warbler, Setophaga tigrina (Gmelin, 1789), but other frequent visitors included the Black-throated Blue Warbler, S. caerulescens (Gmelin, 1789), and the endemic Palmchat, Dulus dominicus (Linnaeus, 1766), and Hispaniolan Highland-Tanager, Xenoligea montana (Chapman, 1917). I recorded 85 aggressive interactions among nine species of birds in Trema trees, with female Cape May Warblers involved in most of these. There was no evidence that Trema was dependent on any one species of bird for dispersal of its seeds, and despite the large proportion of visits by the Cape May Warbler, I found no evidence that any species of bird was dependent upon fruit from Trema. Rather, because male Cape May Warblers dominate females and defend nectar sources in these habitats, I suggest that for female  Cape May Warblers, these scattered Trema trees represent a known, reliable, and accessible source of food which they can defend. Trema trees will benefit these bird species as a food resource, but may also function as a target for many other birds moving across the landscape, thereby facilitating the dispersal of a wider variety of seeds and the restoration of deforested sites

An atlas of Michigan fishes with keys and illustrations for their identification.

http://deepblue.lib.umich.edu/bitstream/2027.42/56435/1/MP192.pd

Spatial stream modeling of Louisiana Waterthrush (\u3ci\u3eParkesia motacilla\u3c/i\u3e) foraging substrate and aquatic prey in a watershed undergoing shale gas development

We demonstrate the use of spatial stream network models (SSNMs) to explore relationships between a semiaquatic bioindicator songbird, Louisiana Waterthrush (Parkesia motacilla), and stream monitoring and benthic macroinvertebrate data in an area undergoing shale gas development. SSNMs allowed us to account for spatial autocorrelation inherent to these environmental data types and stream properties that traditional modeling approaches cannot capture to elucidate factors that affect waterthrush foraging locations. We monitored waterthrush along 58.1 km of 1st- and 2nd-order headwater stream tributaries (n = 14) in northwestern West Virginia over a two year period (2013–2014), sampled benthic macroinvertebrates in waterthrush territories, and collected wetted perimeter stream channel and water chemistry data along a 50 m fixed point stream grid. Spatial models outperformed traditional regression models and made a statistical difference in whether stream covariates of interest were considered relatable to waterthrush foraging. Waterthrush foraging probability index (FPI) was greater in areas where family and genus-level multi-metric indices of biotic stream integrity were higher (i.e. WVSCI and GLIMPSS). Waterthrush were found foraging both among stream flow connected and unconnected sampled sites on relatively further upstream locations where WVSCI and GLIMPSS were predicted to be highest. While there was no significant relationship found between FPI and shale gas land use on a catchment area scale, further information on waterthrush trophic dynamics and bioaccumulation of surface contaminants is needed before establishing the extent to which waterthrush foraging may be affected by shale gas development

Endogenous ROS Levels in C. Elegans Under Exogenous Stress Support Revision of Oxidative Stress Theory of Life-History Tradeoffs

Background: The oxidative stress theory of life-history tradeoffs states that oxidative stress caused by damaging free radicals directly underpins tradeoffs between reproduction and longevity by altering the allocation of energetic resources between these tasks. We test this theory by characterizing the effects of exogenous oxidative insult and its interaction with thermal stress and diet quality on a suite of life-history traits and correlations in Caenorhabditis elegans nematodes. We also quantify demographic aging rates and endogenous reactive oxygen species (ROS) levels in live animals. Results: Our findings indicate a tradeoff between investment in reproduction and antioxidant defense (somatic maintenance) consistent with theoretical predictions, but correlations between standard life-history traits yield little evidence that oxidative stress generates strict tradeoffs. Increasing oxidative insult, however, shows a strong tendency to uncouple positive phenotypic correlations and, in particular, to reduce the correlation between reproduction and lifespan. We also found that mild oxidative insult results in lower levels of endogenous ROS accompanied by hormetic changes in lifespan, demographic aging, and reproduction that disappear in combined-stress treatments–consistent with the oxidative stress theory of aging. Conclusions: Our findings demonstrate that oxidative stress is a direct contributor to life-history trait variation and that traditional tradeoffs are not necessary to invoke oxidative stress as a mediator of relationships between life-history traits, supporting previous calls for revisions to theory

Dynamic nuclear spin polarization in resonant laser spectroscopy of a quantum dot

Resonant optical excitation of lowest-energy excitonic transitions in self-assembled quantum dots lead to nuclear spin polarization that is qualitatively different from the well known optical orientation phenomena. By carrying out a comprehensive set of experiments, we demonstrate that nuclear spin polarization manifests itself in quantum dots subjected to finite external magnetic field as locking of the higher energy Zeeman transition to the driving laser field, as well as the avoidance of the resonance condition for the lower energy Zeeman branch. We interpret our findings on the basis of dynamic nuclear spin polarization originating from non-collinear hyperfine interaction and find an excellent agreement between the experimental results and the theoretical model

Rapid evolution in response to introduced predators I: rates and patterns of morphological and life-history trait divergence

BACKGROUND: Introduced species can have profound effects on native species, communities, and ecosystems, and have caused extinctions or declines in native species globally. We examined the evolutionary response of native zooplankton populations to the introduction of non-native salmonids in alpine lakes in the Sierra Nevada of California, USA. We compared morphological and life-history traits in populations of Daphnia with a known history of introduced salmonids and populations that have no history of salmonid introductions. RESULTS: Our results show that Daphnia populations co-existing with fish have undergone rapid adaptive reductions in body size and in the timing of reproduction. Size-related traits decreased by up to 13 percent in response to introduced fish. Rates of evolutionary change are as high as 4,238 darwins (0.036 haldanes). CONCLUSION: Species introductions into aquatic habitats can dramatically alter the selective environment of native species leading to a rapid evolutionary response. Knowledge of the rates and limits of adaptation is an important component of understanding the long-term effects of alterations in the species composition of communities. We discuss the evolutionary consequences of species introductions and compare the rate of evolution observed in the Sierra Nevada Daphnia to published estimates of evolutionary change in ecological timescales