Located at the interfaces of terrestrial and marine environments, coastal habitats are inherently vulnerable to the effects of global change. Barrier island systems in particular serve not only as protective buffers against storm events, but also as sentinel ecosystems for observation of the impacts of sea level rise, and of increasing storm frequency and intensity. In the mid-Atlantic region, shrub thickets of Morella species compose the dominant forest community. The often monospecific nature of these plant community assemblages is advantageous to ecological studies and cross-scale applications; the relatively low diversity facilitates transitions between scales. My objective was to investigate the distribution and community roles of lianas in mid-Atlantic barrier island forest communities. I quantified environmental variables at two barrier habitats with differing site management histories and corresponding topography, and found that abiotic factors affected distributions of woody species, which subsequently affected vine species distributions. Some association of prevalent vine species with the common woody plants Prunus serotina and Morella cerifera was observed, though neither vines nor woody species demonstrated significant species-specific phytosociological associations. Vines demonstrated a long-lasting effect of arresting or delaying succession, and are potentially responsible for the lack of redevelopment of mature maritime forest at these sites. At Hog Island, Virginia, remotely-sensed data were utilized to determine the three-dimensional structural effects of vine infiltration in woody canopies. Vines were found to reduce canopy height and depth, and increase density, short-term diversity, and light-intercepting biomass. Significant vine infiltration can accelerate senescence of shrub thickets, but often results in persistent tangled masses of vegetation which reduce recruitment of later-successional species. These effects may represent long-term, lasting impacts of vine establishment and expansion in these habitats, affecting community succession towards diverse and stable maritime forest, and significantly altering resource dynamics in these sensitive ecosystems.

The goal of the Encyclopedia of DNA Elements (ENCODE) project has been to characterize all the functional elements of the human genome. These elements include expressed transcripts and genomic regions bound by transcription factors (TFs), occupied by nucleosomes, occupied by nucleosomes with modified histones, or hypersensitive to DNase I cleavage, etc. Chromatin Immunoprecipitation (ChIP-seq) is an experimental technique for detecting TF binding in living cells, and the genomic regions bound by TFs are called ChIP-seq peaks. ENCODE has performed and compiled results from tens of thousands of experiments, including ChIP-seq, DNase, RNA-seq and Hi-C. These efforts have culminated in two web-based resources from our lab—Factorbook and SCREEN—for the exploration of epigenomic data for both human and mouse. Factorbook is a peak-centric resource presenting data such as motif enrichment and histone modification profiles for transcription factor binding sites computed from ENCODE ChIP-seq data. SCREEN provides an encyclopedia of ~2 million regulatory elements, including promoters and enhancers, identified using ENCODE ChIP-seq and DNase data, with an extensive UI for searching and visualization. While we have successfully utilized the thousands of available ENCODE ChIP-seq experiments to build the Encyclopedia and visualizers, we have also struggled with the practical and theoretical inability to assay every possible experiment on every possible biosample under every conceivable biological scenario. We have used machine learning techniques to predict TF binding sites and enhancers location, and demonstrate machine learning is critical to help decipher functional regions of the genome.

The inhibitory effects on Escherichia coli ATPase activity by two venom peptides, lasioglossin II and mastoparan B. Membrane bound F1FO ATP synthase was isolated from E. coli strain pBWU13.4/DK8 and treated with varied concentrations of lasioglossin II and mastoparan B. Lasioglossin II caused very low inhibition of ATPase activity, but the inhibition profile of mastoparan B was suggestive of an interesting biological effect. A relatively shorter total length, a smaller net positive charge, and a reduced amphipathic character of both peptides, as compared to previously tested antimicrobial peptides, may account for the limited degree of inhibition observed in the present study.

The ketogenic diet is commonly used to control epilepsy, especially in cases when medications cannot. The diet typically consists of high fat, low carb, and adequate protein and produces a metabolite called acetoacetate. Seizure activity is characterized by glutamate excitotoxicity and therefore glutamate regulation is a point of research for control of these disorders. Acetoacetate is heavily implicated as the primary molecule responsible for decreasing glutamate in the synapse; it is believed that acetoacetate interferes with the transport of glutamate into the synaptic vesicles. The effects on synaptic transmission at glutamatergic synapses was studied in relation to the ketogenic diet in Drosophila larvae for this thesis. Various measures of synaptic transmission were conducted. Acetoacetate decreased neurotransmission at the synapse. It was also found that acetoacetate has direct effects on the postsynaptic membrane, which indicates a novel role for the metabolite.

Global climate change is projected to impact multiple levels of biodiversity by imposing strong selection pressures on existing populations, triggering shifts in species distributions, and reorganizing entire communities. The Lower Guineo-Congolian region in central Africa, a reservoir for amphibian diversity, is predicted to be severely affected by future climate change through rising temperatures and greater variability in rainfall. Geospatial modelling can be used to assess how environmental variation shapes patterns of biological variation – from the genomic to the community level – and use these associations to predict patterns of biological change across space and time. The overall goal of this dissertation is to examine potential impacts of climate change on amphibian diversity in central Africa. Geospatial modeling is used to: 1) map the distribution of the amphibian fungal pathogen, Batrachochytrium dendrobatidis (Bd) in a biodiversity hotspot in Cameroon under current and future climate; 2) assess phenotypic and adaptive genomic variation in a widespread frog species, Phrynobatrachus auritus, in order to predict areas where populations may best adapt under climate change; 3) determine how amphibian community composition may shift with climate change and which areas may experience greatest loss of functional groups. Findings show that most Bd samples belong to a globally hypervirulent lineage. However, areas of highest predicted environmental suitability for Bd are predicted to shrink under warming temperatures. Within P. auritus, most phenotypic and genomic turnover occurred across known ecological gradients and are heavily influenced by seasonal precipitation. Current amphibian beta diversity is greatest throughout the Cameroonian highlands and forest-savanna ecotones flanking the central Congolian lowland forests. Greatest shifts in community composition under climate change are predicted to occur in coastal Cameroon and its eastern border whereas the greatest predicted loss of functional richness was in central Gabon. Overall, this dissertation shows that areas of elevated environmentally-associated phenotypic, genomic, and community turnover are associated with key ecological gradients. Regions predicted to experience high genomic mismatch, large shifts in community composition, and high loss of functional richness resulting from climate change may warrant conservation attention.

Understanding migratory connectivity is essential for assessing the drivers behind population dynamics and for implementing effective management in migratory species. Genetic markers provide a means to describe migratory connectivity, as well as incorporate population genetic analyses, however genetic markers can be uninformative for species with weak genetic structure. In this study, we evaluate range-wide population genetic structure and migratory connectivity in the prothonotary warbler, Protonotaria citrea, a wetland-dependent neotropical migratory songbird, using high-resolution genetic markers. We reveal regional genetic structure between sampling sites in the Mississippi River Valley and the Atlantic Seaboard with overall weak genetic differentiation among populations (FST = 0.0051). By ranking loci by FST and using subsets of the most differentiated genetic markers (200 – 3000), we identify a maximum assignment accuracy (89.7% to site, 94.3% to region) using 600 single nucleotide polymorphisms. We assign samples from unknown origin nonbreeding sites to a breeding region, illustrating weak migratory connectivity between prothonotary warbler breeding and nonbreeding grounds. Our results highlight the importance of using high-resolution markers in studies of migratory connectivity with species exhibiting weak genetic structure. Using similar techniques, studies may begin to describe population genetic structure that was previously undocumented, allowing us to infer the migratory patterns of an increasing number of species.

The intertidal zone is characterized by persistent, tidally-driven fluctuations in both abiotic (e.g., temperature, [O2], salinity) and biotic (e.g., food availability, predation) conditions, which makes this a very physiologically challenging habitat for resident organisms. The magnitude and degree of variability of these environmental stressors differs between intertidal zones, with the most extreme physiological stress often being experienced by organisms in the high intertidal. Given that many of the fluctuating conditions in this environment are primary drivers of metabolic rate (e.g., temperature, [O2], food availability), we hypothesized that sessile conspecifics residing in different tidal zones would exhibit distinct ‘metabolic phenotypes,’ a term we use to collectively describe the organisms’ baseline metabolic performance and capacity. To investigate this hypothesis, we collected acorn barnacles (Balanus glandula) from low, mid, and high intertidal positions in San Luis Obispo Bay, CA and measured a suite of biochemical (whole-animal citrate synthase (CS) and lactate dehydrogenase (LDH) activity, aerial [lactate]), physiological (O2 consumption rates), morphological (body size), and behavioral (e.g., cirri beat frequency, % time operculum open) indices of metabolism. We found tidal zone-dependent differences in B. glandula metabolism that primarily related to anaerobic capacity, feeding behaviors and body size. Barnacles from the low intertidal tended to have a greater capacity for anaerobic metabolism (i.e., increased LDH activity), feed less when submerged, and be smaller in size compared to conspecifics in the high intertidal. We did not, however, see differences between barnacles from different tidal heights in whole-animal [lactate] following 24h of air exposure, which indicates that the enhanced capacity of low intertidal barnacles for anaerobic metabolism may have evolved to support metabolism during more prolonged episodes of emersion (>>24h) or during events other than emersion (e.g., coastal hypoxia, predation). There were also no significant differences in CS activity or baseline oxygen consumption rates (in air or seawater at 14˚C) across tidal heights, which implies that aerobic metabolic capacity may not be as sensitive to tidal position as anaerobic processes. Understanding how individuals occupying different shore heights differ in their metabolic capacity becomes increasingly interesting in the context of global climate change, given that the intertidal zone is predicted to experience even greater extremes in abiotic stress.

Global climate change is increasing the number of hot days along the California coast as well as increasing the incidence of off-shore upwelling events that lower the pH of intertidal seawater; thus, intertidal organisms are experiencing an increase in more than one stress simultaneously. This study seeks to characterize the global protein response of the eurythermal porcelain crab Petrolisthes cinctipes to changes in thermal, pH, and tidal regime treatments, either combined or individually. The first experiment examined temperature stress alone and sought to determine the effect of chronic temperature acclimation on the acute heat shock response. We compared the proteomic response of cheliped muscle tissue following a month-long acclimation to either (1) constant 10°C, (2) daily fluctuation from 10-20°C, or (3) daily fluctuation from 10-30°C, all followed by either a 30°C acute heat shock or 10°C control. We found that ATP supply via the phosphagen system, changes in glycolytic enzymes, muscle fiber restructuring, respiratory protein fragmentation, and immunity were primarily affected by acclimation and subsequent heat shock. Acclimation to the “extreme” regimes (10°C and 10-30°C) resulted in the greatest proteomic changes, while acclimation to the moderate regime (10-20°C) resulted in a more mild response to heat shock (i.e., fewer adjustments to relative protein abundance). The second experiment sought to determine the proteomic response of gill tissue following a 17 d acclimation to daily changes in pH (ambient pH 8.1 vs low pH 7.6), tidal regime (constant immersion vs 6 h emersion), and temperature (ambient 11°C vs 22-31°C heat shock during emersion). Low pH alone reduced expression of molecular chaperones of the endoplasmic reticulum, lectins, and serine proteases involved in activating the prophenoloxidase cascade. It also increased the abundance of Na+/K+-ATPase, nitrogen metabolism enzymes, and induced changes in tubulin expression, all suggesting an increase in ammonium excretion. Addition of emersion during low pH reduced the abundance of several metabolic proteins including those involved in the proposed ammonium excretion mechanism, suggesting a decrease in metabolic function in part to prevent toxic accumulation of ammonium in the branchial chambers. Combined pH, emersion, and thermal stress increased the abundance of proteins involved in cuticle binding and crosslinking. These results indicate that the responses to pH, tidal cycle, and temperature are highly dependent on one another and that changes in ER protein maturation, ion transport, immunity, and cuticle structure are the primary biochemical systems impacted by these environmental stressors in crustacean gill.

Artificial intelligence has traditionally been approached through centralized architectures and optimization of specific metrics on large datasets. However, the frontiers of fields spanning cognitive science, biology, physics, and computer science suggest that intelligence is better understood as a multi-scale, decentralized, emergent phenomenon. As such, scaling up approaches that mirror the natural world may be one of the next big advances in AI. This thesis presents Coralai, a framework for efficiently simulating the emergence of diverse artificial life ecosystems integrated with modular physics. The key innovations of Coralai include: 1) Hosting diverse Neural Cellular Automata organisms in the same simulation that can interact and evolve; 2) Allowing user-defined physics and weather that organisms adapt to and can utilize to enact environmental changes; 3) Hardware-acceleration using Taichi, PyTorch, and HyperNEAT, enabling interactive evolution of ecosystems with 500k evolved parameters on a grid of 1m+ 16-channel physics-governed cells, all in real-time on a laptop. Initial experiments with Coralai demonstrate the emergence of diverse ecosystems of organisms that employ a variety of strategies to compete for resources in dynamic environments. Key observations include competing mobile and sessile organisms, organisms that exploit environmental niches like dense energy sources, and cyclic dynamics of greedy dominance out-competed by resilience.

The southern Appalachian Mountains have among the highest salamander diversity in the world, largely due to local speciation in the family Plethodontidae. Plethodontid salamanders (i.e., lungless salamanders) are particularly sensitive to habitat climate conditions due to their reliance on cutaneous respiration, and their immediate environmental conditions (microhabitat) likely influence their dispersion and activity more than the large-scale atmospheric conditions. The Northern Gray-cheeked salamander (Plethodon montanus) is restricted to high elevations in the Appalachian Mountains. Our goal was to investigate the relationship between P. montanus and its microhabitat by examining behavioral preference for climatic conditions, characterizing the microclimate with small-scale models, and testing for differences in stress hormones at different elevations. We found that behavioral preference is most restricted by relative humidity, microclimate models predicted far less prevalence at lower elevations than typical coarse-scale models, and stress hormones were elevated at a low elevation plot compared to a high elevation plot.