Biology Theses and Dissertations

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    Sex and the Evolution of a Double Hermaphrodite
    (2023) Ficklin, John Alexander; Haag, Eric S; Biology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    The Kryptolebias marmoratus species complex contains the only known self-fertile hermaphroditic vertebrates. There are three species in this clade and all three live in the mangrove forests across the tropical Americas. All three have individuals with both testis and ovarian tissue in their gonads with two using self-fertility as their main mode of reproduction, and all three have apparent different sex determination and sexual modes. In this dissertation, I explore aspects of sex in these species. K. marmoratus is the androdiecious and self-fertile member of the species complex with sequential hermaphroditism. In this species, the control of sex change from hermaphrodite to male is poorly understood. Individuals that were believed to be genetically identical could be raised in the same environment and change sex at drastically different times or not at all. Small fluctuations and variance in the hormonal profiles of individuals was thought to be a potential cause and while androgen dosing can lead to masculinization of both the gonad and the soma, it was not enough to maintain a permanent transition like what is seen in nature. In K. ocellatus, the obligate outcrosser of the K. marmoratus species complex, it was believed that they were using genetic sex determination to differentiate between males and the females that had hermaphroditic gonads. While we found strong evidence against heteromorphic sex chromosomes, all tests for homomorphic sex chromosomes came back inconclusive due to apparent K. hermaphroditus DNA contaminating the dataset. K. hermaphroditus, the self-fertile hermaphrodite species with exceptionally rare males, appears to be extending its range further and further south and/or hybridizing with K. ocellatus at rates previously underappreciated. The hermaphrodites of the Kryptolebias genus still hold many evolutionary and physiological secrets but can potentially be revolutionary to the understanding of vertebrate sexual development and evolution.
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    Reactivation of plasticity in the adult visual cortex by control of neuronal excitability
    (2023) Borrell, Andrew; Quinlan, elizabeth; Biology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Amblyopia is a highly prevalent form of monocular vision loss that impacts between 1-4% of the worldwide population. Amblyopia is characterized by decreased visual acuity in a single eye and is highly refractory to treatment past a “critical period” of heightened plasticity during early adolescence (>5 years of age). The time course of this critical period is due to the developmental regulation of experience-dependent synaptic plasticity in the primary visual cortex (V1). During early development, visual experience drives activity-dependent changes in NMDA-R subunit composition, refines the convergence of binocular inputs, and promotes the maturation of inhibitory circuits in V1. The transient conditions in V1 that permit the refinement of cortical circuits during the critical period also render V1 vulnerable to the detrimental impacts of amblyopia.The expression of critical period plasticity requires visual experience: dark-rearing delays the onset and closure of the critical period and prevents the experience- dependent change in NMDA-R subunit composition. It is now understood that visual experience in adulthood is also important for the expression of plasticity: sensory deprivation via prolonged dark exposure (DE) rejuvenates the V1 circuit to a juvenile-like state via a homeostatic increase in spontaneous excitatory in V1. Subsequent visual experience during light reintroduction (LRx) enables the expression of critical period plasticity and the functional rewiring of thalamocortical inputs to V1. Here I asked how the homeostatic increase in spontaneous activity induced during DE is regulated by visual experience immediately following LRx (LRxi), and during one day of subsequent day of LRx (LRxs). I demonstrate that the homeostatic increases in spontaneous excitatory neuron activity is maintained during LRxi and is accompanied by increased evoked excitatory neuron activity. These increases in averaged spontaneous and evoked activity returned to baseline by LRxs. Next, I asked whether decreased spontaneous activity following one day of LRx was necessary for the reactivation of critical period plasticity. Using the mouse model of ocular dominance plasticity (ODP) and cell-type specific expression of inhibitory chemogenetic Gi-DREADD receptors in fast spiking Parvalbumin-expressing interneurons, I demonstrated that prolonged disinhibition of spontaneous V1 activity during LRx occludes the reactivation of ODP, but not the reactivation of the plasticity of acuity. These results demonstrate the differing contribution of cortical mechanisms to ocular dominance versus acuity in the regulation of the critical period plasticity, and the necessity of the decrease in average spontaneous activity for the re-expression ODP.
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    (2023) Avalos, Grace; Richardson, Rodney T; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Molecular taxonomic detection is now widespread across the sciences, because of advances in direct PCR, improved marker selection, and increases in sequencing throughput. Facilitated by these advances in sequencing, methodological sensitivity of sample identification has improved substantially. Metagenetic techniques to infer what species are present in a sample by sequencing unknown samples and comparing them to known references has the potential to advance our understanding of biodiversity. Metagenetic analysis of environmental DNA (eDNA) represents a novel, non-lethal method for characterizing floral-associated arthropod communities. Diverse arthropod assemblages interact with flowers, and floral surfaces have been shown to harbor arthropod DNA. We performed metagenetic sequencing on eDNA isolated from flower samples and honey bee-collected pollen samples using multiple markers and compared the frequency and taxonomic breadth of eDNA detections across these genetic markers and substrate types. Understanding which markers and substrates are most effective for eDNA characterization of floral-associated arthropod communities will guide future research and enable low-risk detection of threatened or endangered arthropods.
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    (2023) Wade, Kaitlynn Jean; Wilberg, Michael J; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    The economic and commercial importance of Jonah crabs (Cancer borealis) and Atlantic rock crabs (Cancer irroratus) has increased greatly in the USA. The objectives of my research were to determine spatial distributions, habitat preferences, and potential seasonal movements of both species. Data were obtained from the offshore Northeast Fishery Science Center bottom trawl surveys. Analyses included kernel density estimates, generalized additive models, empirical cumulative distribution functions, and ANOVAs. The spatial distributions of Jonah and Atlantic rock crabs changed over time during the 1970s – 2000s. Compared to Atlantic rock crabs, Jonah crabs preferred slightly warmer temperatures, deeper depths, and muddier sediments. Seasonally, Jonah crabs were found farther offshore in the winter and closer to shore in the fall and spring. Atlantic rock crabs were found closer inshore in the winter and spring and more offshore in the fall. Both species were found to have different seasonal patterns in the Mid-Atlantic Bight
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    (2023) Stahl, Katherine A.; Baldwin, Andrew H; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    In many ditched coastal salt marshes, megapools, or large ponded areas of vegetation dieback,have formed. In combination with sea level rise, this interior marsh loss can decrease wildlife habitat suitability, resilience to storms, and other ecosystem services. However, mechanisms of megapool formation are poorly understood, hampering restoration efforts. Here, we explored differences in environmental characteristics between megapools in different stages of formation (Fully Formed, Partially Formed and Nonformed/Control) and between Elevations within megapools (High, Medium, Low). Using IRIS Films (Indicator of Reduction in Soil), we found that Fully Formed megapools had higher sulfide concentrations than Partially formed, which in turn were greater than Nonformed megapools. We additionally found that lower elevations correlated with higher sulfides, lower plant coverage, lower belowground biomass, lower Carbon Density, and predicted megapool type. We noted that in terms of elevation, vegetative cover, and biomass, Nonformed and Partially formed were more similar as were High and Medium elevations. Whereas in terms of soil characteristics, Fully Formed and Partially formed were more similar as were Medium and Low Elevations. To combat megapools and dieback, we will assess the effectiveness of two restoration techniques, the first of which is assessing the survival and growth of plantings at different spacings, elevations, and megapool formation levels. We found survival and growth was higher in Partially formed megapools than Fully formed, and no impact by spacing or elevation. Our second restoration technique is runnels, or 15” channels that reconnect megapools to ditches, which were installed in January of 2023. The data collected above will act as baseline data, repeated again. These baseline results support a close relationship between pool stages of formation, carbon storage, elevation, vegetation health, biomass production, and sulfide levels (Graphical Abstract).
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    (2023) Alreja, Adit Bipin; Nelson, Daniel C; Biology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    The global rise of antibiotic resistance casts a shadow on treating infectious disease. An alternative to the use of antibiotics is bacteriophage-derived peptidoglycan hydrolases called endolysins. Endolysins, produced at the end of a bacteriophage replication cycle, cause bacterial cell lysis and virion release. When applied exogenously as recombinant proteins, they are also capable of cleaving the Gram-positive bacterial peptidoglycan. Various studies conducted in vitro and in vivo showcase the therapeutic potential of endolysins as the next generation of antimicrobials. Streptococcus pneumoniae is the most common cause of a variety of infections ranging from otitis media to invasive bloodstream infection (bacteremia) and meningitis (brain infection). While pneumococcal vaccination programs have proven to be effective, the high rates of antibiotic resistance reported for S. pneumoniae has led to the CDC classifying it as a “serious” threat. One of the most studied endolysins targeting S. pneumoniae is Cpl-1. This thesis represents an investigation into the molecular basis for dimer formation of the Cpl-1 endolysin which displays antibacterial activity against S. pneumoniae. In addition to disproving a long-accepted mechanism of dimerization of Cpl-1 in the presence of choline, we have conclusively identified the residue involved in the formation of the Cpl-1 dimer. Our findings led to the discovery of a novel C-terminal consensus sequence shared by all pneumococcal endolysins that informs their propensity to form dimers in the presence of choline. Next, through a bioinformatics approach we identified a new endolysin containing this C-terminal consensus sequence, produced it, named it SP-CHAP, and showed that it forms a dimer in the presence of choline, indicative of the widespread dimerization phenomenon associated with pneumococcal endolysins. Of interest, SP-CHAP is the first endolysin with antimicrobial activity against S. pneumoniae that possesses a cysteine, histidine-dependent amidohydrolase/peptidase (CHAP) domain. SP-CHAP was subsequently characterized for its biochemical and antimicrobial properties and benchmarked against Cpl-1. SP-CHAP is active in all physiologically relevant conditions (pH, temperature) against various S. pneumoniae strains and displays no activity towards oral/nasal commensal organisms. This enzyme also displays pneumococcal biofilm eradication ability to a greater extent than Cpl-1, as visualized by confocal microscopy. To further translate the antimicrobial potential of this enzyme, the antimicrobial efficacy of SP-CHAP was validated in a S. pneumoniae mouse nasopharyngeal colonization model. Our results demonstrate the therapeutic potential of SP-CHAP as an attractive endolysin to treat S. pneumoniae infections and warrant further translational development of this enzyme.
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    (2023) Ahn, So Hyun; Glibert, Patricia; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    The toxic mixotrophic dinoflagellate Karenia spp. forms blooms almost annually in the Gulf of Mexico, especially on the West Florida Shelf (WFS). Blooms typically initiate in early fall but can persist from months to years. Daily, Karenia vertically migrates to the surface water during the day, possibly experiencing changes in temperature, light, nitrogen (N), and prey type and availability. Therefore, this dissertation aimed to examine the interplay between Karenia’s photo-autotrophic and phago-mixotrophic metabolism and the short-term fluctuations in environmental conditions to understand how these factors may relate to the conditions under which Karenia spp. are found in the WFS.Title of Dissertation: INTERACTIONS BETWEEN NITROGEN AND TEMPERATURE ON THE METABOLISM OF THE RED-TIDE MIXOTROPHIC DINOFLAGELLATE KARENIA SPP. IN SUPPORT OF PREDICTIVE MODELS: IMPLICATIONS FOR BLOOM DYNAMICS ON THE WEST FLORIDA SHELF So Hyun (Sophia) Ahn, Doctor of Philosophy, 2023 Dissertation directed by: Professor Patricia M. Glibert, Marine Estuarine Environment Sciences A culture of K. mikimotoi balanced photon flux pressure (light availability) with consumption in overall metabolism when pulsed with 15N-NO3-, 15N-NH4+, or 15N-urea over the range of 15-25°C as shown by photosynthetic fluorescence. However, when shifted to 30°C, cells were significantly stressed, but urea-enriched cells showed a smaller decline in fluorescence, implying that urea might induce a photoprotective mechanism by increasing metabolic “pull.” Studies conducted with natural K. brevis winter and summer populations during 2021 showed that thermal history played a critical role. Unusually, summer blooms had higher biomass but were stressed photosynthetically and nutritionally. However, 15N-urea enriched summer cells had higher uptake rates as well as carbon (C) and N cell-1, especially in warmer waters, showing differential thermal responses based on N forms. Mixotrophy grazing measurements showed that K. brevis grazed both the picoplankter Synechococcus as well as the cryptophyte Rhodomonas. Grazing did not selectively target specific qualities of Synechococcus (based on differing N and P of the prey growth media), but ingestion rates were a function of prey-to-grazer ratios (R2=0.76) as well as prey amounts (R2=0.71). NanoSIMS confirmed 15N incorporation from Synechococcus in K. brevis. In natural communities of K. brevis, ingestion rates were also significantly related to prey-to-grazer ratios (p < 0.01) and by temperatures (p < 0.05) to a lesser degree (R2= 0.75) when incubated at ambient (24°C) and ambient temperature ± 5°C (19, 29°C). The grazer effects on the photosynthetic performance of grazer and prey were also examined. Grazing on Synechococcus indirectly reduce the photosynthetic performance of prey, especially at warmer temperatures but had little or no effect on the photosynthesis of K. brevis itself.
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    Application of advanced machine learning strategies for biomedical research
    (2023) Chou, Renee Ti; Cummings, Michael P.; Biology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Biomedical research delves deeply into understanding individual health and disease mechanisms. Recent advancements in technologies have further transformed the field with large-scale data sets, enabling data-driven approaches to identify important patterns and relationships from large data sets. However, these data sets are often noisy and unstructured. Moreover, missing values and high dimensionality further complicate the analysis processes aimed at yielding meaningful results. With examples in ocular diseases and malaria, this dissertation presents novel strategies employing machine learning to tackle some of the challenges in biomedical research. In ocular diseases, sustained ocular drug delivery is critical to retain therapeutic levels and improve patient adherence to dosing schedules. To enhance the sustained delivery system, we engineer peptide sequences as an adapter to impart desired properties to ocular drugs. Specifically, we develop machine learning models separately for three properties–melanin binding, cell-penetration, and non-toxicity. We employ data reduction techniques to reduce the number of features while maintaining the machine learning model performance and apply interpretable machine learning techniques to explain model predictions on the three properties. Experimental validation in rabbits show two-fold increase in drug retention time with the selected peptide candidate. The developed machine learning framework can be further tailored to engineer other properties in molecular sequences with a wide variety of potential in biomedical applications. Malaria is an infectious disease caused by protozoan of the genus Plasmodium and has been a burden in global health. Developing malaria vaccines is challenging due to the diversity in parasite antigen sequences, which may lead to immune escape. To facilitate the vaccine development process, we leverage the wealth of systems data collected from various sources. For facile data management, a database is constructed to store the structured data processed from the results of the bioinformatics tools. Due to the small fraction of Plasmodium proteins labeled as known antigens, and the remaining proteins unknown of being antigens or non-antigens, a positive-unlabeled machine learning method is applied to identify potential vaccine antigen candidates. Beyond malaria, our approach provides a promising framework for identifying and prioritizing vaccine antigen candidates for a broad range of disease pathogens.
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    (1999) Steven, Colin R.; Zohar, Yonathan; Biology; Digital Repository at the University of Maryland; University of Maryland (College Park, MD)
    In the striped bass (Marone saxatilis), and many other commercially important fish species, captivity results in an inability to complete final oocyte maturation (FOM), ovu lation , and spawning. We hypothesize that this effect is mediated by a disruption of the hypothalamo-pituitary-gonadal (HPG) axis at the level of the gonadotropin -releasing hormones (GnRHs). To confirm this hypothesis research was conducted focused on three objectives: First, to complement the battery of assays previously developed for analysis of the GnRH/GtH system in striped bass, an RNAse protection assay was developed to measure specific expression of the three forms of GnRH in striped bass (salmon GnRH, chicken GnRH-If and seabream GnRH). Secondly, effects of GnRH agonist-induced ovulation on the HPG axis of captive striped bass was examined by comparison of several reproductive endocrine parameters between females sampled at four stages of oocyte development. Finally, differences were examined between the reproductive endocrine status of wild and captive female striped bass. We conclude that sbGnRH is the most important form for the preovulatory release of pituitary GtH-II in striped bass. We suggest that captive females synthesize levels of GnRH mRNA that are comparable to their wild counterparts, however fail to release adequate quantities of bioactive GnRH within the pituitary to stimulate completion of FOM. This data may indicate that regulation of sbGnRH in striped bass occurs via post-transcriptional/ translational mechanisms. Furthermore, the presence of salmon GnRH in the pituitaries of captive fema les may be indicative of a possible role for salmon GnRH in the regulation of FOM.
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    Investigating the Utility of Environmental DNA Analysis for the Monitoring and Management of Mid-Atlantic Alosine Fishes
    (2023) Fowler, Chelsea; Plough, Louis V; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Environmental DNA (eDNA) tools can address gaps in fish assessment data while reducing the cost and the impact of sampling on threatened anadromous alosine fishes in Chesapeake Bay. Here, I tested the ability of high-frequency eDNA sampling of river herring to predict fish abundances from sonar-based fish counts on the Choptank River and developed and validated novel species-specific eDNA assays for American and hickory shads. River herring eDNA concentrations from daily eDNA sampling were highly correlated to sonar-based fish counts (Spearman’s Rho = 0.84). This relationship informed a model that could accurately predict fish count from eDNA and relevant covariates (R2 = 0.88). The two new shad assays are highly specific and quantitative, and field testing validated detections in Delaware, Maryland, and North Carolina. This work provides a set of eDNA monitoring tools for the Mid-Atlantic alosines and highlights the capacity for eDNA data to generate quantitative metrics of fish abundance.
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    (2023) Li, Renjian; Li, Ming; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Recent observations in Chesapeake Bay showed that the interaction between lateral circulation and channel-shoal bathymetry generated internal lee waves which subsequently propagated onto shallow shoals and evolved into internal solitary waves, leading to overturning and enhanced turbulent mixing. However, it is unknown under what hydrodynamic conditions the lee waves could be generated and how the nonlinear internal waves evolved. Using an idealized straight channel representative of a coastal plain estuary, we conducted numerical simulations to investigate internal wave generation over a range of river flows and tidal amplitudes. The model results are summarized using the estuarine classification diagram based on the freshwater Froude number Frf and the mixing parameter M. Δh decreases with increasing Frf as stronger stratification suppresses waves, and no internal waves are generated under large Frf. Δh initially increases with increasing M as the lateral flows become stronger with stronger tidal currents, but decreases or saturates to a certain amplitude as M further increases. This regime diagram suggests that internal lee waves can be generated in a wide range of estuarine conditions. To examine the nonlinear evolution of internal waves, a three-dimensional nonhydrostatic model with nested model domains and increasing grid resolution was configured. The lee wave steepens into a shorter elevation wave due to shoaling and soon evolves into a depression with a train of undular waves at its tail as bottom boundary mixing elevates the halocline above the mid-depth. These nonlinear internal waves enhance the turbulent dissipation rate over the deep channel and shallow shoal, suggesting an important energy source for mixing in stratified coastal plain estuaries. In addition, a pH sensor deployed at the middle reach of Chesapeake Bay recorded high-frequency variability in bottom pH driven by along-channel winds. Though wind-driven lateral circulation can advect high pH water downward, the slow air-sea exchange of CO2 limits the lateral ventilation. With DIC and TA budget analysis and comparison with cross-sections at upper- and lower-Bay where strong lateral circulation was confined in the surface layer, we found vertical mixing and replenishment of oceanic water by longitudinal advection could be more important mechanisms to ventilate bottom pH.
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    (2023) Vona, Iacopo; Nardin, William; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Rising sea levels and the increased frequency of extreme events put coastal communities at serious risk. Due to SLR, traditional solutions such as breakwaters (or gray/artificial structures) will become ineffective for wave attenuation and shoreline erosion control. Moreover, gray solutions do not consider the ecological aspects of the coast, and may negatively affect surrounding ecosystems. The “living shoreline” technique includes natural habitat features, such as oysters and/or vegetation into shoreline stabilization, to provide both protection and ecosystem services. Oysters create three-dimensional, complex reef structures that attenuate wave energy and increase sedimentation rates. If coupled with breakwaters, oysters may maintain breakwaters’ efficiency over time as they are expected to grow with SLR. However, guidance for the correct implementation of Natural and Nature Based Features (NNBF) for coastal protection is still unclear, and many authors within the literature have been repeatedly requested more insights. In this thesis, we have therefore studied the coupling between oysters and breakwaters via field, modeling and laboratory experiments, in order to highlight the benevolent aspects of NNBF regarding coastal defense. Field results showed gray breakwaters allowed for shoreline protection (by reducing incoming wave energy) and increased sedimentation rates. However, SLR modeling scenarios showed a gradual reduction of wave attenuation over time, as well as increased sediment export from the coast. When oysters were included in the modeling, on the other hand, wave dampening and sediment retention were preserved through the time. Laboratory experiments showed oyster-reef breakwaters in emergent or near-emergent conditions produced higher drag coefficient compared to gray structures, resulting in greater dissipative features. Higher water levels simulated in our experiments produced less reliable results that will require further investigation. This thesis supports oysters for coastal protection, and emphasizes the positive aspects of NNBF regarding wave attenuation and sediment retention in the face of climate changes and SLR. However, challenges encountered during field studies underlined the importance of environmental and biogeochemical conditions (such as water level, aerial exposure, temperature and seasonality) for oyster reefs’ establishment, growth and survivability. Future restoration plans involving oysters in coastal defense should definitely take these environmental and biogeochemical aspects into account, in order to properly protect the coast in the face of climate changes and SLR, while also providing many other useful ecosystem services for the environment. The coupling between oysters and breakwaters may represent a valuable and effective methodology to protect our coast over a changing climate and a rising sea, where optimal conditions for oysters’ survivability occur and are maintained over time.
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    (2023) Wiltsee, Laura E.; Gray, Matthew W; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Bivalves are prized for the ecosystem services they provide. The removal of particles from the water column through filter feeding and resulting water quality benefits, known as the biofiltration services, of bivalves have been studied for over a century. This has created a wealth of knowledge around the mechanistic drivers of bivalve feeding activity. Recently, Chesapeake Bay ecosystem-wide models have begun incorporating Eastern Oyster (Crassostrea virginica) biofiltration. Acute feeding variability is critically important when estimating oyster biofiltration services at ecosystem scale. Typically, natural seston clearance rate studies last a limited timeframe, with a focus on specific environmental events such as an increase in temperature, drop in salinity, or a tidal cycle.To capture the highly variable filter feeding rate of bivalves, such as the Eastern Oyster, studies have used highly controlled laboratory conditions, with single environmental variable modification. These studies often use indirect methods for estimating clearance rates that commonly lack high-resolution capability. Furthermore, these studies are labor intensive and time consuming, and as a result, few studies have monitored bivalve feeding activities over long periods to understand variation in activity or how these rates may change with seasonal shifts in conditions. These limitations have led to a shortage of knowledge around how clearance rates of oysters vary in response to ambient conditions over both short-term (hourly) and long-term (seasonal) time scales. This study leverages advances in semi-autonomous aquatic observing to track high- resolution, long-term feeding responses of bivalves to subtle variations in environmental conditions. Oyster ex situ clearance rates in the Choptank River (Maryland, USA) were estimated under flow-through conditions, and logged in real-time using fluorometers among replicate oysters over 5-day experiments for 9 months. The measured clearance rates from this system were compared to a mechanistic clearance rate model used by the Chesapeake Bay Program, which is used to estimate the role of oysters in controlling water quality in the Bay. Environmental data were evaluated to build a statistical and random forest model to predict how oyster clearance rates respond to prevailing environmental conditions. This monitoring system and resulting models enable a deeper understanding of feeding variability and how natural seston and environmental variability directly influence oyster physiology.
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    Impact of Plant-Derived Allelochemicals on Harmful Algal Blooms
    (2023) Armstrong, Christen Taylor; Place, Allen; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Harmful algal blooms (HABs) are a global concern in both freshwater and coastal systems; creating dire consequences for public health, water resources, and local economies. Thus, there is a focus among scientists and environmental managers on HAB prediction, prevention, and mitigation. Current chemical mitigation methods include algicides such as copper sulphate, chlorination, and hydrogen peroxide, which can have high financial costs and secondary pollution associated with them. The use of natural allelochemicals produced by plants and bacteria has received considerable attention as an alternative to synthetic algicides, as they can have negligible toxins, be highly selective, and easily degraded in the environment. This dissertation is a coalition of research looking into new sources of plant allelochemicals and whether natural levels of allelochemicals in the water column, can impact phytoplankton communities and the presence of toxin-producing algal species. The first objective focused on the use of the waste product: brewer’s spent grain (BSG), as a new control mechanism to inhibit the growth of toxic algae. BSG extract of doses higher than 250mg/L inhibited the growth of freshwater and marine toxin-producing cyanobacteria and dinoflagellate species (Microcystis aeruginosa and Karenia brevis), while not impacting the diatom and chlorophyte tested (Scenedesmus obliquus and Prorocentrum tricornutum). This same dosage of BSG caused cyanobacteria abundance in lake water to decline by 90% within 4 days and chlorophytes to dominate the community by day 6 during a microcosm study. However, an experiment controlling bacteria levels demonstrated that the decline of K. brevis growth was likely due to the increase in abundance or presence of certain types of bacteria growing with exposure to BSG extract rather than due to chemicals released from the BSG. The second and third objectives shifted focus to the New Jersey Pinelands and whether the chemicals released into the water from terrestrial and marine plants in these waters, like phenolic compounds, impact the phytoplankton community and toxin-producing species. The second objective focused on the spatial and temporal distribution of phycotoxins along two New Jersey estuaries using passive samplers and whether the utility of passive samplers was impacted by the excess phenolic compounds in the water. By utilizing passive samplers in New Jersey, phycotoxins not previously reported in the area were described, such as azaspiracids, goniodomin-A and yessotoxins. However, this objective also showed some of the caveats of passive samplers, especially at sites with high phenolic compounds. The third objective focused on identifying the primary environmental drivers of chlorophyll a concentration and phytoplankton community along the freshwater – marine continuum of two New Jersey Estuaries with varying levels of disturbance. This dissertation explored BSG as a novel control method of HABs, and provided new information for monitoring, managing, and modeling HABs based on phenolic content measured in the water.
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    The Role of Connectivity and Spatial Structure on the Population Dynamics of Marine Fishes
    (2023) Arai, Kohma Herbert; Secor, David H; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Migrations regulate population structure, which can play an important role in conferring stability at aggregate scales via asynchronous responses of population sub-components to perturbation; however, little is known about the importance of spatial structure in population persistence in fishes. My dissertation aims to explore the role of spatial structure on the population dynamics of marine fishes. Two species that exhibit different types of population structure were considered: (i) Atlantic mackerel (Scomber scombrus) in the Northwest Atlantic, comprised of two components that have distinct spawning regions off Canada (northern contingent) and the US (southern contingent); and (ii) striped bass (Morone saxatilis) in the Hudson River (HR), which exhibit early-life partial migration whereby a portion of juveniles remain in their natal freshwater habitats, while others migrate into higher salinity habitats. In Chapter 2, I used otolith stable isotopes (d18O/d13C) to understand contingent mixing of the Northwest Atlantic mackerel over two decades (2000–2019). Prevalent contingent mixing occurred within the US waters, indicating that the northern contingent may provide subsidies to the US mackerel fishery. In Chapter 3, I combined machine learning with otolith d18O isoscapes to predict the geographic origin of the Northwest Atlantic mackerel spanning four decades (1975–2019). Contingent mixing occurred over four decades, including the 1970s when intensive foreign fisheries took place in US waters. Nursery hotspots were detected within spawning regions, but shifted over time. In Chapter 4, for HR juvenile striped bass, I explored the influence of early-life conditions and environmental drivers on partial migration. Otolith chemistry uncovered four dominant early migration modes. Partial migration was associated with larval growth, albeit facultatively controlled by environmental conditions. In Chapter 5, I evaluated how HR striped bass early-stage partial migration influenced recruitment patterns to the adult population over a 3-decade span. As an outcome of partial migration, adults recruited from a variety of nurseries, which exhibited asynchronous dynamics in response to climate variables. Through a comparative analysis of two species that exhibit different types of population structure, I demonstrated how spatial structure can play key roles in the population dynamics of marine fishes, with implications for management and conservation.
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    Climate Change and Vibrio species: Investigation of Environmental Parameters Associated with Occurrence and Transmission
    (2023) Brumfield, Kyle David; Colwell, Rita R.; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Climate change, associated with shifts in the geographical range of biological species, has become increasingly important in emergence and re-emergence of disease. Vibrio spp., native to aquatic ecosystems, are commonly associated with aquatic invertebrates, notably crustaceans and zooplankton. Some species of the genus Vibrio cause infection in humans, of which Vibrio cholerae, the etiological agent of pandemic cholera, is the most documented. Pathogenic non-cholera Vibrio spp., namely Vibrio parahaemolyticus and Vibrio vulnificus, cause gastroenteritis and also septicemia and extra-intestinal infections. They are responsible for a large number of public health emergencies in developed countries, including the United States. As sea temperatures rise and salinity profiles are altered, a pattern of poleward spreading of non-cholera Vibrio spp. has been observed globally, demonstrating significant geographic expansion of these bacterial populations, corroborated by an associated increase in the number of reported vibriosis cases. Since Vibrio spp., including pathogenic vibrios, play an important role in the degradation of polymeric substances, such as chitin, and in biogeochemical processes, they cannot be eradicated. Hence, routine monitoring and an early warning system are needed for public health preparedness. Since the 1960’s, ongoing research has focused on environmental factors linked with occurrence and distribution of clinically relevant Vibrio spp. and their role in disease transmission. We have reported that lack of, or damage to, water, sanitation, and hygiene (WASH) infrastructure, coupled with elevated air temperatures, and followed by above average rainfall promotes exposure of a population to contaminated water, hence increases the risk of an outbreak of cholera. Global predictive intelligence models applicable to diseases caused by non-cholera Vibrio spp. are in development. The research reported here describes results of intensive sampling to detect and characterize Vibrio spp. in the Chesapeake Bay, Maryland, and the Florida Gulf Coast, the latter an area significantly impacted by Hurricane Ian, September 2022, with a spike in confirmed vibriosis cases and deaths during weeks following the storm. Results of this study provide confirmation of environmental predictors for Vibrio spp. and document long-term increase and extended seasonality of Vibrio populations in the Chesapeake Bay. Using satellite remote sensing data, we demonstrate the impact of extreme heat, precipitation, and other key environmental and geophysical factors (e.g., temperature, salinity, and chlorophyll) on prevalence of pathogenic Vibrio spp. in aquatic systems. This study lays the groundwork for a predictive intelligence system for Vibrio spp. and other pathogens under varying climatic scenarios.
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    (2023) Windle, Anna; Silsbe, Greg; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Environmental remote sensing is the science of monitoring physical, chemical, and biological characteristics of the Earth through space and time, and from a distance, by measuring how these environments interact with electromagnetic energy, or more simply through changes in color. This dissertation leverages in situ, satellite, and unoccupied aircraft system (UAS, drones) data to enhance the efficacy of environmental remote sensing in Chesapeake Bay. Satellite data consists of distinct contributions of the surface under observation and the intervening atmosphere. Atmospheric correction (AC) processors seek to isolate the surface signal, and while several variants exist, their accuracy varies widely in optically complex coastal waters. Chapter 2 is a statistical evaluation of four common AC variants applied to data collected by the most recent operational ocean color sensor, the Ocean Land Color Instrument (OLCI) onboard Copernicus Sentinel-3A and -3B satellites. Remote sensing reflectance (Rrs), the product of AC processors from which a suite of water quality metrics is then derived, was obtained from each AC variant and matched in space and time with in situ Rrs data collected in the Chesapeake Bay. AC results varied widely, and the most statistically robust was a neural-net based algorithm (Case 2 Regional Coast Color, C2RCC). The resultant shape and magnitude of Rrs (e.g. color) is governed by the type and concentration of optically active constituents (OACs), namely phytoplankton pigments, chromophoric dissolved organic matter, inorganic sediment, and water itself. In coastal waters where OACs are dynamic and vary independently from each other, deriving accurate water quality metrics remains an open challenge. Chapter 3 applies a spectral clustering classification of OLCI Rrs data (2016-2022) and identifies the fifteen most dominant optical water types (OWTs) of Chesapeake Bay. OWTs were matched in space and time with Chesapeake Bay water quality monitoring data, and a statistical evaluation demonstrates how water quality data are constrained within and across OWTs. In contrast to earth-observing satellites, UAS equipped with optical sensors offer on-demand, highly resolved data. Aquatic UAS applications are in their infancy, and the critical removal of light reflected directly off the skin of water has received little attention in the literature. Chapter 4 proposes four different approaches to remove direct surface reflectance from UAS imagery and evaluates each against in situ Rrs data. The most accurate method is a simple empirical model that exploits measurements in the infrared where water strongly absorbs light; applying this model permits high resolution water quality retrievals with only modest uncertainty. Chapter 5 uses UAS imagery to monitor a wetland restoration site in the Chesapeake Bay across seasons and years. A supervised random forest model is developed with UAS data and used to classify species-specific marsh vegetation with 97-99% accuracy. Vegetation classification maps were compared to as-built planting plans to delineate instances of significant marsh migration. Chapter 6 summarizes how the environmental remote sensing methods used in this dissertation can contribute to a better understanding of coastal research, monitoring, and management by addressing challenges, gaps, and potential solutions at various scales.
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    Knowledge and Processing of Morphosyntactic Variation in African American Language and Mainstream American English
    (2023) Maher, Zachary Kevin; Edwards, Jan; Novick, Jared; Neuroscience and Cognitive Science; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    As people from different social groups come into contact, they must accommodate differences in morphosyntax (e.g., He seem nice vs. He seems nice) in order to successfully represent and comprehend their interlocutor’s speech. Listeners usually have high comprehension across such differences, but little is known about the mechanisms behind morphosyntactic accommodation. In this dissertation, I asked what listeners know about variation in morphosyntax and how they deploy this knowledge in real-time language processing. As a test case, I focused on regularized subject-verb agreement (e.g., He seem nice, They was happy)—which is common in African American Language (AAL), but not in Mainstream American English (MAE)—and compared how listeners adjust their linguistic expectations depending on what language varieties both they and their interlocutors speak. In Experiment 1, I showed that participants who primarily speak MAE 1) recognize that some speakers use regularized subject-verb agreement, 2) evaluate that regularized subject-verb agreement is associated with AAL, and 3) predict that the subject-verb agreement rules of AAL allow for some patterns (They was happy) but not others (*He were happy). This was accomplished using a novel sentence rating task, where participants heard audio examples of a given language variety, then rated written sentences for how likely a speaker of that variety would be to say them. In Experiment 2, I showed that a similar pool of participants did not merely recognize regularized subject-verb agreement; their knowledge of variation lead them to predict that AAL speakers use regularized forms in an acoustically ambiguous context. Participants heard sentences like He sit(s) still, where it is unclear whether the verb includes a verbal -s due to a segmentation ambiguity. They were more likely to transcribe a regularized form (He sit still) when it was spoken by an AAL-speaking voice than when it was spoken by an MAE-speaking voice. Together, these results indicate that listeners have rich mental models of their interlocutors that extend beyond a general awareness of linguistic difference. In Experiment 3, I compared bidialectal speakers of AAL and MAE and monodialectal speakers of MAE. On the rating task from Experiment 1, bidialectal participants showed a greater degree of differentiation between sentences that are grammatical in AAL and sentences that are ungrammatical in AAL, compared to monodialectal participants. However, both groups of participants indicated that ungrammatical sentences are broadly more likely in AAL than MAE, contrary to usage patterns in the world. On the transcription task from Experiment 2, bidialectal participants were overall more likely to transcribe regularized subject-verb agreement, but they differentiated between AAL- and MAE-speaking voices to the same degree as monodialectal participants. Both groups were more likely to use MAE subject-verb agreement (He sits still) than regularized subject-verb agreement (He sit still). These results suggest that bidialectal listeners broadly expect regularized subject-verb agreement to a greater degree than do monodialectal listeners, rather than making stronger predictions about a given speaker. Moreover, while bidialectal listeners have a more granular sense of AAL’s grammatical rules, all listeners still favor MAE, likely reflecting MAE’s dominant status. In Experiment 4, I asked how listeners use their knowledge of variation in subject-verb agreement to guide real-time interpretation of sentences, again comparing bidialectal and monodialectal participants. Participants heard sentences like The duck(s) swim in the pond, where they must rely on the agreement morphology of the verb to determine whether the subject of the sentence is singular or plural, since a segmentation ambiguity makes it unclear whether the noun ends in -s. In MAE, only a plural interpretation is available, while in AAL, a singular interpretation is also available. Participants’ eye-movements were tracked as they looked at and selected images on a screen. Participants were more likely to look at and select a singular image if the sentence was presented in an AAL-speaking voice, compared to an MAE-speaking voice, and bidialectal participants were more likely to look at and select a singular image, compared to monodialectal participants. As with the transcription task in Experiment 3, this suggests that bidialectal participants are broadly more likely to consider the possibility that a speaker uses regularized SVA, compared to monodialectal participants, but their linguistic expectations are not more strongly differentiated based on the grammar of their interlocutor. These results make it clear that listeners have mental models of morphosyntactic variation, which can be characterized along a variety of dimensions, including the syntax, semantics, and indexicality (social meaning) of a given variable. This can serve as a foundation for future inquiry into the details of these models and the real-time switching and control dynamics as listeners adjust to different varieties in their environment.
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    Evolutionary history and consequences of gene flow in bearded manakins
    (2023) Bennett, Kevin Faulkner Philipson; Braun, Michael J; Wilkinson, Gerald S; Biology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Recent advances in DNA sequencing have revolutionized evolutionary biology by allowing for genome-scale studies of non-model organisms. We can now readily connect genotype with phenotype, i.e., identify the genetic basis of particular traits, a key goal in the study of evolution. In addition, genome-scale sequence analysis has shifted our understanding of the frequency and magnitude of gene flow in nature. Once viewed as important only for its role preventing divergence, the common view now is that in many taxa gene flow occurs among many lineages in the early stages of divergence. My dissertation focuses on gene flow in bearded manakins (genus Manacus), which are notable for their intense tandem courtship display, high degree of reproductive skew among males, and bright male plumage. In western Panama, yellow-collared M. vitellinus and white-collared M. candei interbreed in a narrow hybrid zone. Male vitellinus secondary sexual traits, including the yellow collar, have introgressed roughly 50 km west across the hybrid zone into candei populations and then stalled at the east bank of the Río Changuinola, the region’s largest river. Evidence from studies of male-male interaction and female choice implicate positive sexual selection for yellow collars as a driver of introgression. For thirty years since this situation was first described in detail, several key issues have remained unresolved, including why introgression has not continued across the river and what gene or genes are responsible for yellow coloration. In the first chapter, I reviewed the current state of knowledge of the Manacus hybrid zone system and proposed new hypotheses for some of the patterns exhibited by these populations. In the second chapter, I used reduced-representation genome sequencing to investigate whether reduced gene flow across the Río Changuinola alone can explain stalled trait introgression. I found that, although advantageous plumage traits have not introgressed far beyond the river, substantial gene flow is occurring, implicating an additional selective force or forces in preventing trait introgression. In the third chapter, I used whole-genome sequencing of all major Manacus lineages, including unpigmented M. manacus and pigmented M. aurantiacus, to explore the evolution and genetic basis of collar coloration. I identified the carotenoid metabolism gene beta-carotene oxygenase 2 (BCO2) as responsible for collar color differences between vitellinus and candei and uncovered evidence of past introgression introducing aurantiacus BCO2 alleles into vitellinus. I argue that gene flow is likely to be a more common mechanism than previously appreciated for spreading sexual traits among species.
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    The genomics of species divergence in drosophila
    (2023) Carpinteyro Ponce, Javier; Machado, Carlos A; Biology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    How do new species arise and diverge? Has been a fundamental question in evolutionary biology. The process of species divergence can be studied at many different levels of biological organization. However, it is until the recent advancements of genome sequencing technologies that genome-wide signatures of species divergence have started to unveil the complex genomic landscape of speciation. In this dissertation we investigate the landscape of genomic divergence using a classic pair of Drosophila species. We generated four new high quality genome assemblies for Drosophila pseudoobscura and D. persimilis to explore the genomic differences at three different levels. We first characterized the structural variation landscape between D. pseudoobscura and D. persimilis and stablished its association with transposable elements and tested how intrinsic genomic factors, such as recombination, influence the accumulation ofstructural variation associated with transposable elements in both species. With a combination of high-quality genome assemblies and a comprehensive population genomics data set, we also explored how the contribution of recombination rate and introgression promote sequence divergence with the potential of forming species barriers. Moreover, we investigated how gene co-expression networks potentially rewiring between species contribute to the divergence landscape between D. pseudoobscura and D. persimilis. Our work highlights the complex landscape of species divergence occurring at multiple levels of organization. Moreover, the integration of potential species drivers identified at different scales shed lights on the molecular mechanisms involved in speciation.