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Enhancing Bay Scallop Monitoring Using Machine Learning And Semantic Segmentation With Benthic Visual Imagery, Waheed Odubayo

Open Access Master's Theses

Effective monitoring of benthic ecosystems requires scalable approaches capable of simultaneously identifying key species and quantifying habitat composition. In Narragansett Bay Rhode Island, bay scallops, Argopecten irradians, serve as important ecological indicators, yet traditional survey methods remain labor-intensive and spatially limited. This study presents an automated deep learning framework for scallop detection and habitat segmentation using underwater benthic imagery.

The proposed system combines three components: (1) YOLO based object detection for identifying live scallops, (2) U-Net semantic segmentation for quantifying benthic habitat classes (eelgrass and sand/silt), and (3) a geospatial contrastive learning framework (GeoCLR) to leverage spatial continuity in …

Metabarcoding-Biomass Relationships And Internal Standards For Quantitative Dna Metabarcoding, Frances Webber

Open Access Master's Theses

DNA metabarcoding has been widely adopted due to its power in investigating the composition of protistan communities, accurately identifying even small and cryptic taxa. However, the compositional nature of DNA metabarcoding results, and the distortion of natural abundances due to variation of the often-used 18S rRNA gene copy number over several orders of magnitude, renders these results semi-quantitative at best, limiting the application of DNA metabarcoding to ecological study. Here, we constructed mock communities from uni-algal cultures of taxonomically diverse phytoplankton and conducted metabarcoding using multiple primer sets and both DNA and cDNA as PCR templates. For each culture, chlorophyll …

Investigating The Effectiveness Of Best Management Practices In Reducing Fecal Bacteria In Narrow River, Rhode Island, Katherine Thompson

Open Access Master's Theses

Fecal bacterial contamination shapes how communities manage and use estuarine waters, with consequences for ecosystem health and public access. In Rhode Island's Narrow River, elevated concentrations of fecal coliforms and enterococci have restricted shellfishing for decades despite ongoing management efforts. From 2004 to 2018, local organizations implemented Best Management Practices (BMPs) to address water quality challenges, yet their effectiveness remains incompletely understood. This study analyzes three decades of monitoring data using linear regression, generalized additive models, and Before After Control Impact methods to evaluate BMP effectiveness and identify key drivers of contamination. Linear regression revealed spatially variable trends, with bacterial …

Mobile Payment, Financial Behavior And Financial Anxiety: A Multi-Group Structural Equation Modeling Study, Ting An, Jing Jian Xiao, Nilton Porto, Luiz Cruz

Human Development and Family Science Faculty Publications

Purpose: This study aims to examine the association between mobile payment usage and financial anxiety, and explores the mediating role of financial behavior. Moreover, this research also compares the moderating effects of financial education and financial knowledge.

Design/methodology/approach: A sample of 18,584 consumers from the 2021 National Financial Capability Study in the U.S. was analyzed. Structural equation modeling (SEM) was employed to explore indirect associations between mobile payment usage and financial anxiety. Two undesirable financial behaviors, overspending and over-indebtedness were used as mediators between mobile payment and financial anxiety. Moreover, multi-group analyses was conducted for two financial knowledge …

Multi-Year Time Series Reveals Temporally Synchronous Diatom Communities With Annual Frequency Of Recurrence In A Temperate Estuary, Diana N. Fontaine, Tatiana A. Rynearson

Graduate School of Oceanography Faculty Publications

Diatoms are among the most abundant phytoplankton that inhabit coastal ecosystems, forming large blooms that fuel coastal food webs. Although diatoms are often large and morphologically distinct, many are small or morphologically cryptic making it difficult to understand the temporal dynamics of whole diatom communities and the environmental factors that drive them. Here, we investigated diatom diversity and its environmental correlates using 6 yr of monthly surface water samples from the Narragansett Bay Plankton Time Series to investigate the seasonal and annual variability of diatom species occurrence. High-throughput amplicon sequencing of filtered biomass yielded 658 diatom amplicon sequence variants (ASVs), …

Recurring Bleaching Events Disrupt The Spatial Properties Of Coral Reef Benthic Communities Across Scales, Helen V. Ford, Jamison M. Gove, John R. Healey, Andrew J. Davies, Nicholas A.J. Graham, Gareth J. Williams

Graduate School of Oceanography Faculty Publications

Marine heatwaves are causing recurring coral bleaching events on tropical reefs that are driving ecosystem change. Yet, little is known about how bleaching and subsequent coral mortality impacts the spatial properties of tropical seascapes, such as patterns of organism spatial clustering and heterogeneity across scales. Changes in these spatial properties can offer insight into ecosystem recovery potential following disturbance. Here we repeatedly quantified coral reef benthic spatial properties around the circumference of an uninhabited tropical island in the central Pacific over a 9-year period that included a minor and subsequent severe marine heatwave. Benthic communities showed increased biotic homogenisation following …

Exploratory Analyses Of American Lobster Habitat Preferences And Catchability In Ventless Trap Surveys, Annabelle Leahy

Open Access Master's Theses

Numerous factors must be considered in efforts to rebuild sustainable stock levels of the Southern New England (SNE) lobster stock including changing uses of marine space, such as the growth of the offshore wind industry, and stressors such as rising ocean temperatures. These factors may change the species’ habitat use and could further impact the ability of the region to support a healthy lobster population. This work uses data from pre-wind farm construction ventless trap surveys to further characterize the suitable habitat of the SNE lobster stock and to examine the effects of survey design, namely trap position and trap …

Site-Based Assessment Of Oyster Shellfisheries And Associated Bio-Physical Conditions In Ghana And The Gambia, E. O. Chuku, I. Okyere, J. Adotey, S. Abrokwah, E. Effah, R. Adade, D. W. Aheto

Coastal Resources Center Technical Reports

No abstract provided.

Overview Of The Mosaic Expedition: Snow And Sea Ice, Marcel Nicolaus, Donald K. Perovich, Gunnar Spreen, Mats A. Granskog, Luisa Von Albedyll, Michael Angelopoulos, Philipp Anhaus, Stefanie Arndt, H. Jakob Belter, Vladimir Bessonov, Gerit Birnbaum, Jörg Brauchle, Radiance Calmer, Estel Cardellach, Bin Cheng, David Clemens-Sewall, Ruzica Dadic, Ellen Damm, Gijs De Boer, Oguz Demir, Klaus Dethloff, Dmitry V. Divine, Allison A. Fong, Steven Fons, Markus M. Frey, Niels Fuchs, Carolina Gabarró, Sebastian Gerland, Helge F. Goessling, Rolf Gradinger, Jari Haapala, Christian Haas, Jonathan Hamilton, Henna Reetta Hannula, Stefan Hendricks, Andreas Herber

Graduate School of Oceanography Faculty Publications

Year-round observations of the physical snow and ice properties and processes that govern the ice pack evolution and its interaction with the atmosphere and the ocean were conducted during the Multidisciplinary drifting Observatory for the Study of Arctic Climate (MOSAiC) expedition of the research vessel Polarstern in the Arctic Ocean from October 2019 to September 2020. This work was embedded into the interdisciplinary design of the 5 MOSAiC teams, studying the atmosphere, the sea ice, the ocean, the ecosystem, and biogeochemical processes. The overall aim of the snow and sea ice observations during MOSAiC was to characterize the physical properties …

Conceptual And Methodological Advances In Habitat-Selection Modeling: Guidelines For Ecology And Evolution, Joseph M. Northrup, Eric Vander Wal, Maegwin Bonar, John Fieberg, Michel P. Laforge, Martin Leclerc, Christina M. Prokopenko, Brian Gerber

Natural Resources Science Faculty Publications

Habitat selection is a fundamental animal behavior that shapes a wide range of ecological processes, including animal movement, nutrient transfer, trophic dynamics and population distribution. Although habitat selection has been a focus of ecological studies for decades, technological, conceptual and methodological advances over the last 20 yr have led to a surge in studies addressing this process. Despite the substantial literature focused on quantifying the habitat-selection patterns of animals, there is a marked lack of guidance on best analytical practices. The conceptual foundations of the most commonly applied modeling frameworks can be confusing even to those well versed in their …

Barcoding And Its Application For Visualizing Ecological Dynamics, Vitul Agarwal, Colleen B. Mouw

Graduate School of Oceanography Faculty Publications

Time is perceived to be unidirectional and continuous in the philosophy of science. This continuity can play a crucial role in time series analysis as events are generally seen as an outcome of the past, or subject to events that occurred previously in time. In this study, we describe an ordinal approach to perceiving ecological time series – one that relies on pattern formation with both antecedent and future events. Our approach defines a limited set of structural shapes that can occur for past, present, and future time points. Such a library of all possible shapes can then be …

Editorial: Advances In 3d Habitat Mapping Of Marine Ecosystem Ecology And Conservation, Renata Ferrari, Javier X. Leon, Andrew J. Davies, John H.R. Burns, Stuart A. Sandin, Will F. Figueira, Manuel Gonzalez-Rivero

Graduate School of Oceanography Faculty Publications

No abstract provided.

Analyzing Land Cover And Land Use Changes Detection In The Brahmaputra River Basin, Darya Shahidi Masouleh

Open Access Master's Theses

The Brahmaputra River basin (BRB) is one of the largest in Asia, spread over the countries of China, Bhutan, India, and Bangladesh, having a total area of 5,73,000 Sq.km. It is one of the last major free-flowing rivers in the world, and the river and its tributaries provide important social, environmental, cultural, and economic services to more than 60 million people for their livelihood in Bangladesh, northeastern India, Bhutan, and China. The BRB is undergoing rapid environmental changes in recent decades. One of the most important drivers of this change is Land Use, and Land Cover (LULC) changes in this …

Coral Bleaching Response Is Unaltered Following Acclimatization To Reefs With Distinct Environmental Conditions, Katie L. Barott, Ariana S. Huffmyer, Jennifer M. Davidson, Elizabeth A. Lenzb, Shayle B. Matsuda, Joshua R. Hancock, Teegan Innis, Crawford Drury, Hollie M. Putnam, Ruth D. Gates

Biological Sciences Faculty Publications

Urgent action is needed to prevent the demise of coral reefs as the climate crisis leads to an increasingly warmer and more acidic ocean. Propagating climate change-resistant corals to restore degraded reefs is one promising strategy; however, empirical evidence is needed to determine whether stress resistance is affected by transplantation beyond a coral's native reef. Here, we assessed the performance of bleaching-resistant individuals of two coral species following reciprocal transplantation between reefs with distinct pH, salinity, dissolved oxygen, sedimentation, and flow dynamics to determine whether heat stress response is altered following coral exposure to novel physicochemical conditions in situ. Critically, …

Phenotypic Plasticity In Acropora Pulchra Under Varied Environmental Conditions, Dennis A. Conetta

Open Access Master's Theses

The extent to which coral reefs have declined globally has triggered major scientific investment in coral restoration research. However, much of the predictions for reef futures do not include the capacity for coral acclimatization, or phenotypic plasticity, and how this plasticity varies across seasons. In light of this, we outlplanted clonal replicates of distinct genotypes of the reef building coral Acropora pulchra from an existing coral nursery common garden site to three sites on the North Shore of Mo’orea, French Polynesia. After transplantation (October 2019), the outplanted colonies were sampled at all three sites in January and November of 2020, …

A Counter-History Of Rhetorical Ecologies, Madison Jones

Professional and Public Writing Faculty Publications

In this essay, I argue that the ecological turn in rhetorical studies has produced spatiotemporal problems and that these problems are directly tied to the material disciplinary history of ecosystems ecology and its connections to the Anthropocene violence of nuclear colonialism. These spatiotemporal concerns result from rhetoric’s “ecological moment”—a kairotic framework that emphasizes flux but elides material histories. Building from rhetorical scholarship in decolonial historiography and place-based methods, I offer a counterhistory of ecology to demonstrate how our field can better engage with the dynamic narrative pasts that shape contemporary rhetorical ecological inquiry. Through this counterhistory, I provide a method …

Meta-Analysis Of Primary Producer Amino Acid Δ15N Values And Their Influence On Trophic Position Estimation, Matthew D. Ramirez, Alexi C. Besser, Seth D. Newsome, Kelton Mcmahon

Graduate School of Oceanography Faculty Publications

1. Compound-specific stable isotope analysis of individual amino acids (CSIA-AA) has emerged as a transformative approach to estimate consumer trophic positions (TP_CSIA) that are internally indexed to primary producer nitrogen isotope baselines. Central to accurate TP_CSIA estimation is an understanding of beta (β) values—the differences between trophic and source AA δ¹⁵N values in the primary producers at the base of a consumers’ food web. Growing evidence suggests higher taxonomic and tissue-specific β value variability than typically appreciated.
2. This meta-analysis fulfills a pressing need to comprehensively evaluate relevant sources of β value variability and its contribution to …

The Role Of Climate Change In The Decline Of Narragansett Bay Winter Flounder, Joseph A. Langan

Open Access Dissertations

Winter flounder (Pseudopleuronectes americanus) has historically supported productive commercial and recreational fisheries throughout its range in the northwest Atlantic. As a small flatfish that inhabits estuaries, bays, and the coastal zone, this species is vulnerable to shifting environmental conditions in many of the habitats critical to its life cycle. At the southern edge of the species range, the Southern New England/Mid-Atlantic Bight winter flounder stock entered a steep decline during the 1980s following a period of overfishing. Despite repeated reductions in harvest during the proceeding decades, the population has yet to recover. A decreasing trend in recruitment has …

Allopatric And Sympatric Drivers Of Speciation In Alviniconcha Hydrothermal Vent Snails, Corinna Breusing, Shannon B. Johnson, Verena Tunnicliffe, David A. Clague, Robert C. Vrijenhoek, Roxanne A. Beinart

Graduate School of Oceanography Faculty Publications

Despite significant advances in our understanding of speciation in the marine environment, the mechanisms underlying evolutionary diversification in deep-sea habitats remain poorly investigated. Here, we used multigene molecular clocks and population genetic inferences to examine processes that led to the emergence of the six extant lineages of Alviniconcha snails, a key taxon inhabiting deep-sea hydrothermal vents in the Indo-Pacific Ocean. We show that both allopatric divergence through historical vicariance and ecological isolation due to niche segregation contributed to speciation in this genus. The split between the two major Alviniconcha clades (separating A. boucheti and A. marisindica from A. kojimai, …

Energy Stores, Oxidative Balance, And Sleep In Migratory Garden Warblers ( Sylvia Borin) And Whitethroats ( Sylvia Communis) At A Spring Stopover Site, Andrea Ferretti, Scott R. Mcwilliams, Niels C. Rattenborg, Ivan Maggini, Massimiliano Cardinale, Leonida Fusani

Natural Resources Science Faculty Publications

Little is known about how songbirds modulate sleep during migratory periods. Due to the alternation of nocturnal endurance flights and diurnal refueling stopovers, sleep is likely to be a major constraint for many migratory passerine species. Sleep may help to increase the endogenous antioxidant capacity that counteracts free radicals produced during endurance flight and reduces energy expenditure. Here, we investigated the relationship between sleep behavior, food intake, and two markers of physiological condition—the amount of energy reserves and oxidative status—in two migratory songbird species, the garden warbler (Sylvia borin) and the whitethroat (Sylvia communis). In garden warblers, birds with high …

Three-Dimensional Digital Mapping Of Ecosystems: A New Era In Spatial Ecology, Tim D'Urban Jackson, Gareth J. Williams, Guy Walker-Springett, Andrew J. Davies

Biological Sciences Faculty Publications

Ecological processes occur over multiple spatial, temporal and thematic scales in three-dimensional (3D) ecosystems. Characterizing and monitoring change in 3D structure at multiple scales is challenging within the practical constraints of conventional ecological tools. Remote sensing from satellites and crewed aircraft has revolutionized broad-scale spatial ecology, but fine-scale patterns and processes operating at sub-metre resolution have remained understudied over continuous extents. We introduce two high-resolution remote sensing tools for rapid and accurate 3D mapping in ecology—terrestrial laser scanning and structure-from-motion photogrammetry. These technologies are likely to become standard sampling tools for mapping and monitoring 3D ecosystem structure across currently under-sampled …

Sub-Lethal Predatory Shell Damage Does Not Affect Physiology Under High Co2 In The Intertidal Gastropod Tritia Reticulata, Leonardo Querobim Yokoyama, Alexander Turra, Coleen Suckling, Gabriela Torres, Andrew Davies, Ian Mccarthy

Biological Sciences Faculty Publications

Ocean acidification (OA) poses a major threat to marine animals, especially marine shelled invertebrates such as molluscs. Although many organisms are capable of compensating for the effects of OA, this can impose physiological costs and impact performance (e.g. through increased metabolism and decreased growth). Sublethal injuries on shells may provoke changes in energy allocation. Under acidified conditions, organisms would spend less energy on reproduction and somatic growth to repair the damage. Therefore, we analysed the physiological responses of the intertidal gastropod Tritia reticulata during shell regeneration under OA conditions. We simulated a sub-lethal predation event (a notch in the outer …

Mitochondrial Dna Analysis Of Critically Endangered Chinese Pangolins (Manis Pentadactyla) From Nepal, Sandeep Shrestha, Ashish Bashyal, Ashna Dhaka, Thomas J. Mcgreevy Jr., Bill Buffum, Jyoti Joshi, Hemanta Kumari Chaudhary, Sanjay Nath Khanal

Natural Resources Science Faculty Publications

Chinese Pangolins (Manis pentadactyla) are Critically Endangered and one of the most illegally traded mammals globally. We generated first COI sequences from five individuals of this species from Nepal. BLASTn search of our 600bp sequences at GenBank showed pair-wise identity between 99.17% and 100% to M. pentadactyla. There were three haplotypes and a total of five variable sites among five M. pentadactyla sequences. Neighbor-joining tree revealed that all M. pentadactyla from Nepal clustered into same group further splitting into two sub-groups albeit with low bootstrap value, suggesting potential multiple geographic origins. The K2P distance was 0.3% within …

Seasonal Changes In Eastern Hemlock (Tsuga Canadensis) Foliar Chemistry, Ian G. Kinahan, Chad M. Rigsby, Suzanne K. Savage, Nick L. Houseman, Andrew S. Marsella, Anita Oppong, Brenton L. Deboef, Colin M. Orians, Evan L. Preisser

Biological Sciences Faculty Publications

Eastern hemlock (Tsuga canadensis (L.) Carriére; hemlock) is an eastern North American conifer threatened by the invasive hemlock woolly adelgid (Adelges tsugae Annand). Changes in foliar terpenes and phenolics were evaluated in new (current year growth) and mature (1-year old growth) hemlock needles during the growing season and into plant dormancy. From April through September, foliar concentrations of non-volatile soluble phenolics, condensed tannins, lignin, mono- and sesquiterpenes α-pinene, camphene, isobornyl acetate, and diterpene resin were quantified. After September, additional analyses of metabolites that continued to differ significantly in new versus mature foliage were carried out. Total soluble phenolic …

The Frequent Flyer’S Guide To Migration: How Songbird Metabolism And Oxidative Status Respond To Endurance Flight And Diet Quality, Kristen J. Demoranville

Open Access Dissertations

Migratory songbirds are among the best high-performance endurance athletes on the planet and during their annual peregrinations they are particularly vulnerable to oxidative damage because they maintain relatively high metabolic rates at rest, they are able to fly for long durations while operating at 9 times their resting metabolic rate, and they rely on fats to fuel this exercise which increases reactive oxygen species (ROS) formation. The concept of evolutionary economic design of physiological systems considers such phenotypic flexibility in metabolic and antioxidant responses adaptive in that it allows birds to match the capacity of key physiological systems to prevailing …

Modeling Coral Reef Acoustic Propagation Loss, Kayla M. Thilges

Open Access Master's Theses

Quantification of an acoustic metric relating sound propagation on a coral reef to ecological parameters could enhance long-term ecological studies on coral reefs. The acoustic metric constructed in this study is coral reef propagation loss, or the sound intensity reduction with range, in a coral reef environment. Establishment of this benchmark parameterizes the geometric spreading and attenuation factors of the coral reef environment.

Two analyses are conducted in which both passive and active acoustics are used to measure the sound propagation environment across different fringing coral reef sites. In the first analysis, two passive acoustic studies in the literature captured …

Momentum: Research & Innovation For Spring 2019, University Of Rhode Island

Publications (Research and Economic Development)

The Spring 2019 issue of Momentum: Research & Innovation, a periodical focused on research at the University of Rhode Island.

The Importance Of Isotopic Turnover For Understanding Key Aspects Of Animal Ecology And Nutrition, Wales A. Carter, Ulf Bauchinger, Scott R. Mcwilliams

Natural Resources Science Faculty Publications

Stable isotope-based methods have proved to be immensely valuable for ecological studies ranging in focus from animal movements to species interactions and community structure. Nevertheless, the use of these methods is dependent on assumptions about the incorporation and turnover of isotopes within animal tissues, which are oftentimes not explicitly acknowledged and vetted. Thus, the purpose of this review is to provide an overview of the estimation of stable isotope turnover rates in animals, and to highlight the importance of these estimates for ecological studies in terrestrial, freshwater, and marine systems that may use a wide range of stable isotopes. Specifically, …

A Comparison Of The Population Genetic Structure And Diversity Between A Common (Chrysemys P. Picta) And An Endangered (Clemmys Guttata) Freshwater Turtle, Scott W. Buchanan, Jason J. Kolbe, Johanna E. Wegener, Jessica R. Atutubo, Nancy E. Karraker

Biological Sciences Faculty Publications

The northeastern United States has experienced dramatic alteration to its landscape since the time of European settlement. This alteration has had major impacts on the distribution and abundance of wildlife populations, but the legacy of this landscape change remains largely unexplored for most species of freshwater turtles. We used microsatellite markers to characterize and compare the population genetic structure and diversity between an abundant generalist, the eastern painted turtle (Chrysemys p. picta), and the rare, more specialized, spotted turtle (Clemmys guttata) in Rhode Island, USA. We predicted that because spotted turtles have disproportionately experienced the detrimental effects of habitat loss …

The Brown Macroalga Colpomenia Peregrina (Sauvageau, 1927) Reaches Rhode Island, Usa, Lindsay A. Green-Gavrielidis, Niels-Viggo Hobbs, Carol S. Thornber

Natural Resources Science Faculty Publications

Introduced, or nonnative, marine species are a threat to local biodiversity, disrupt marine industries, and can have negative effects on coastal communities. Colpomenia peregrina (Sauvageau, 1927) is one of the most successful brown algal invaders in the world. Originating from the Northwest Pacific, Colpomenia peregrina was first collected in the Northwest Atlantic in Nova Scotia, Canada in the 1960s. Since then populations of C. peregrina have been discovered at 57 sites ranging from Grand Barachois Lagoon, Saint Pierre and Miquelon to South Wellfleet, MA, USA. The spread of Colpomenia peregrina can be attributed to its broad tolerance to environmental conditions, …