Marine Biology Commons^™

Eavesdropping On Animals: Can Bioacoustics Help Save Species?, Zoe Grueskin

Capstones

Around the world, scientists are using sound to study the natural world in a growing field called bioacoustics. Researchers are eavesdropping on frogs and fish, elephants and earthworms, and many hope what they hear can inform and inspire conservation action around the world. From the field’s auspicious beginning with accidentally-recorded whales, to researchers today listening to locations as diverse as the Arctic seafloor and India’s Western Ghats mountain range, this capstone project explores the potential — and limitations — of conservation bioacoustics. Read the story, see photos and listen to audio pieces featuring three bioacousticians and their field recordings here: …

Understanding The Impacts Of Anthropogenic Effects An Habitat Variability Interactions On Maine's Rocky Intertidal Ecosystem, Laura Braun

Electronic Theses and Dissertations

The rocky intertidal ecosystem is an important ecological and cultural aspect of the picturesque Maine coast, playing a vital role in not only Maine’s coastal ecosystem, but also to Maine’s economy. It’s distinct community structure along the sharp elevational gradient and the presence of daily stressors (wave action, heat, and desiccation), make the rocky intertidal ecosystem an important model ecosystem to monitor for effects from anthropogenic impacts. In this thesis, I describe attempts to monitor and understand the impacts of two of these anthropogenic impacts on this system: climate change and industrial harvesting of Ascophyllum nodosum along Maine’s coast. For …

Microplastic Accumulation In The Digestive Tract Of Young-Of-Year Atlantic Sharpnose Sharks (Rhizoprionodon Terraenovae) In The Grand Strand, Sc, Andrew Curtis Sitlinger

Electronic Theses and Dissertations

This study focused on the presence and accumulation of microplastic fibers in the digestive tract and livers of young-of-year Atlantic Sharpnose Sharks (Rhizopriondon terraenovae) from two sampling locations along the Grand Strand of South Carolina. R. terraenovae is a small, mesopredatory elasmobranch found abundantly along northwestern Atlantic Ocean coastlines. Thirty specimens of R. terraenovae were collected from May through August of 2020. Microplastics were found in all specimens. A total of 672 plastic particles were identified over the course of the study, with an average of 22.4 ± 10.5 (SD) plastics per specimen. The majority of the plastics were classified …

Examining The Relationship Between Stomiiform Fish Morphology And Their Ecological Traits, Mikayla L. Twiss

All HCAS Student Capstones, Theses, and Dissertations

Trait-based ecology characterizes individuals’ functional attributes to better understand and predict their interactions with other species and their environments. Utilizing morphological traits to describe functional groups has helped group species with similar ecological niches that are not necessarily taxonomically related. Within the deep-pelagic fishes, the Order Stomiiformes exhibits high morphological and species diversity, and many species undertake diel vertical migration (DVM). While the morphology and behavior of stomiiform fishes have been extensively studied and described through taxonomic assessments, the connection between their form and function regarding their DVM types, morphotypes, and daytime depth distributions is not well known. Here, three …

Integrative Revision Of Five Genera Type Species For Zoanthidea To Bridge The Parataxonomy Gap, Jacob Colbert

All HCAS Student Capstones, Theses, and Dissertations

Cnidarian order Zoanthidea is a relatively understudied group of invertebrates inhabiting a diverse range of marine habitats. Over/During the last two decades, species descriptions within this order have largely been based on a novel molecular parataxonomic system that relies almost exclusively on DNA barcodes to detect and describe new species. DNA barcodes are short, conserved sequences that are readily compared across taxa and used to detect previously described species. The existing taxonomic system, based on anatomical analysis and the identification of evolutionarily informative characters for phylogenetic inference, has been recently replaced by molecular parataxonomy by some scientists/researchers. While molecular sequence …

Caribbean Reef-Building Coral-Symbiodiniaceae Network: Identifying Symbioses Critical For System Stability In A Changing Climate, Shaman Patel

All HCAS Student Capstones, Theses, and Dissertations

Increasing global ocean temperatures and frequency of marine heatwaves pose dire consequences for coral reefs. High temperatures often lead to disruptions in coral symbiosis resulting in coral bleaching, increasing the mortality of corals. However, corals can potentially avoid bleaching peril by associating with thermally tolerant symbionts. Here we provide a tool for understanding symbiosis network stability of Caribbean reef-building corals. We created a network of Caribbean hermatypic corals and their associated Symbiodiniaceae phylotypes. A bleaching model was applied to this network to test for resilience and robustness (R50) to thermal stress. It was also layered with trait data for coral …

Crustacean Assemblage Structure Over The Charlie-Gibbs Fracture Zone Of The Mid-Atlantic Ridge Collected During The 2009 Henry B. Bigelow Expedition, Kathryn Medina

All HCAS Student Capstones, Theses, and Dissertations

The Charlie Gibbs Fracture Zone (CGFZ) consists of two nearly parallel fracture transform faults that intersect the Mid-Atlantic Ridge (MAR) axis. This area has high primary productivity and biomass levels due to the topography and water. A predominant hydrographic feature of the MAR is the Sub-Polar Front (SPF) which runs along the southern edge of the CGFZ and is known as a biogeographical boundary for multiple species. As part of The Census of Marine Life project Patterns and Processes of the Ecosystem of the northern Mid-Atlantic (MAR-ECO), this study analyzed the abundance and distribution patterns of the CGFZ crustacean community …

Atlantic Surfclam (Spisula Solidissima) Population Demographics And Distribution Along The Middle Atlantic Bight, Mauricio González Díaz

OES Theses and Dissertations

The Atlantic surfclam (Spisula solidissima) is a long-lived benthic biomass dominant organism that occurs on the Middle Atlantic Bight (MAB) continental shelf between 10 m and 50 m. Trends in Atlantic surfclam population specific growth and mortality rates were analyzed using four decades of age and length observations obtained from NOAA stock surveys from the 1980s to 2010s in six regions distributed along the MAB. Atlantic surfclam specific growth rates and asymptotic lengths were estimated from the age and length observations using the von Bertalanffy growth model. The analysis showed that the Atlantic surfclam median asymptotic length in …

Internal Vertebral Morphology Of Bony Fishes Matches The Mechanical Demands Of Different Environments, Dana Baxter, Karly E. Cohen, Cassandra M. Donatelli, Eric D. Tytell

Engineering Faculty Articles and Research

Fishes have repeatedly evolved characteristic body shapes depending on how close they live to the substrate. Pelagic fishes live in open water and typically have narrow, streamlined body shapes; benthic and demersal fishes live close to the substrate; and demersal fishes often have deeper bodies. These shape differences are often associated with behavioral differences: pelagic fishes swim nearly constantly, demersal fishes tend to maneuver near the substrate, and benthic fishes often lie in wait on the substrate. We hypothesized that these morphological and behavioral differences would be reflected in the mechanical properties of the body, and specifically in vertebral column …

Impacts Of Algal Morphology And Water Flow On Macroalgal Microplastic Capture, Cheyenne M. Adams

Honors College Theses

Microplastic pollution is a major area of concern in marine environments, especially as microplastics enter the food web. This study used pipe cleaners and two lichen species as algal mimics, and Chaetomorpha sp. and Chondrus crispus as model algal species to test the effects of morphology and biomass on microbead and foam capture. This study also utilized two different water flow methods: vortices and waves. Results suggest that water flow, as well as biomass and morphology, play a role in microplastic capture in macroalgae. For all mimics and algal species, except Cladonia lichens, turfs with increased biomass and length showed …

Variation In Coastal Macroinvertebrate Species Diversity On Intertidal Boulders In Trinidad, California., Louis Antonelli, Alexandra Winkler, Theron Taylor, Natalie Greenleaf

IdeaFest: Interdisciplinary Journal of Creative Works and Research from Cal Poly Humboldt

Coastal environments of Humboldt County provide an optimal habitat for a diversity of macroinvertebrates. This study’s focus is to determine the differences in diversity of coastal macroinvertebrate (CM) species on intertidal boulders. Eleven CM species were visually counted within a one-square-meter quadrat along two height strata of five intertidal boulders. Based upon the Shannon-Wiener diversity index, diversity was measured between the CM species in the lower region (0-1 meter from base of boulder) and the upper region (1-2 meters from base of boulder). The resulting data showed the lower regions of the boulders had a higher average diversity rating, as …

Chemosensory Receptors In Berghia Stephanieae: Bioinformatics And Localization, Kelsi L. Watkins

Masters Theses

Chemosensation is achieved through the binding of chemical signals to chemoreceptor proteins embedded in the membranes of sensory neurons. The molecular identity of these receptors, as well as the downstream processing of chemosensory signals, has been well studied in arthropods and vertebrates. However, very little is known about molluscan chemosensation. The identity of chemoreceptor proteins in the nudibranch mollusc Berghia stephanieae are unknown. Data from other protostome and molluscan studies suggest Berghia may use ionotropic receptors for some forms of chemoreception. This study used a bioinformatics approach to identify potential chemosensory ionotropic receptors in the transcriptome of Berghia. A …

Benthic Community Dynamics And Stony Coral Demographics In Florida In Relation To Acute Disturbances And Chronic Pressures, Nicholas P. Jones

All HCAS Student Capstones, Theses, and Dissertations

The persistence of coral reef communities is threatened by a suite of pressures operating at varying spatial and temporal scales. In general, acute disturbances (short term stochastic events such as marine heatwaves or hurricanes) and chronic pressures, such as ocean warming, have caused the most significant changes to stony coral assemblages (order Scleractinia) and continue to impair recovery potential. Additionally, many coral reefs are subject to local chronic anthropogenic pressures resulting in poor water quality or sedimentation, which further impact stony corals and shape benthic community structure, particularly near urbanized coastlines. For the viability of communities on coral reefs, a …

Relationships Between Mercury And Trophic Level In Nine Coastal Pelagic Fishes Off Southeastern Florida, Emily Akins

All HCAS Student Capstones, Theses, and Dissertations

State and federal agencies have issued consumption advisories for various fish species for many years, including in Florida. Upper-level predatory fish, such as tunas and mackerels, are especially popular with anglers but are susceptible to high levels of mercury through bioaccumulation and biomagnification. This study used two data sets over two time periods, 2010-2012 and 2020-2021, to compare mercury and trophic level relationships in nine coastal pelagic fishes is Southeastern Florida. As these species are popular in recreational fisheries, charter and tournament catches formed the base of the samples that were analyzed for total mercury along with carbon and nitrogen …

Abundance, Site-Fidelity, And Association Patterns Of Coastal Bottlenose Dolphins (Tursiops Truncatus) Off Southeast Florida, Graysen D. Boehning

All HCAS Student Capstones, Theses, and Dissertations

The coastal bottlenose dolphin is well studied throughout its natural range, however, most of the study areas comprised wide, well-protected habitats such as bays and estuaries, and not narrow coastal sandbanks. This study identifies a residential group of coastal bottlenose dolphins utilizing the narrow sandbanks within the Northwestern Atlantic waters off the coast of Palm Beach County, Florida, USA. From 2014-2020, 313 boat surveys were conducted, and 585 individual dolphins were identified using photo-ID. Twenty-four animals were determined to be full-time and 66 animals were determined to be part-time residents. Full-time and part-time residents associated in three social tribes, with …

Validation Of Pilot Protocol: Damage Scoring Of Puget Sound Mollusk Shells, Lauren Doffing

Environmental Science Undergraduate Theses

The Marine Sediment Monitoring Team at the Washington State Department of Ecology observed damage to mollusk shells while studying the benthic communities of Puget Sound. A pilot protocol was written to allow researchers to quantify the damage. Two researchers independently followed the protocol, including reference photos, for a set of samples collected in 2019 from an urban bay, East Possession Sound. Two scores were given to each specimen: highest-level damage and extent of highest-level damage. An additional score was given to bivalve species: rust/stain. The sets of scores were compared to determine if the protocol yielded similar values between the …

Characterizing Endogenous Dicer Products To Unravel Novel Rnai Biogenesis Pathways, Jacob Oche Peter

Dissertations

ABSTRACT

RNA interference (RNAi) is a pervasive gene regulatory mechanism in eukaryotes based on the action of multiple classes of small RNA (sRNA). Exploiting RNAi pathways in non-model systems have great potential for creating potent RNAi technologies. Here, we accessed RNAi-mediated control of gene expression in the two-spotted spider mite, Tetranychus urticae (T. urticae) using engineered dsRNA designed to modulate the host RNAi pathway and increase RNAi efficacy. Analysis of Dicer (Dcr) generated fragments revealed how exogenous RNAs access the host RNAi pathway in this animal, opening avenues for designing RNAi technology for their control. Further, some organisms …

Distribution Patterns Of The Invasive Mussel Arcuatula Senhousia In Mission Bay, San Diego, California: Effects Of Sediment Grain Size And Byssus Thread Production On Predation, Samantha Ahlman

Theses

The ability of bivalves to avoid predation by using defensive behaviors such as burrowing and byssus production may vary depending on the sediment characteristics of a given habitat. The varying sediment characteristics that change with water velocity within estuaries may influence the distribution of bivalves and limit them to areas that optimize their ability to defend against predators. We examined the distribution patterns of the invasive Asian date mussel Arcuatula senhousia relative to the sediment grain size distribution in Mission Bay, an urban estuary located in San Diego, California, USA. Mussels and sediment were collected using an Ekman grab at …

Impacts Of Nitrogen Enrichment On Corals – A Remote Sensing Approach, David E. Carrasco

Master's Projects and Capstones

Anthropogenic activities have resulted in ever-increasing threats to coral reefs globally, wherein the rate of environmental changes have exceeded the historical capacity of corals to adapt. This has threatened the persistence of coral ecosystems and their associated ecosystem services, which billions of people rely on for their livelihoods. The most prevalent stressor is nitrogen enrichment, which while present naturally, is exacerbated by the anthropogenic input of nutrients via the discharge of agricultural and urban waste waters. The focus is to answer the central research question of how nitrogen enrichment impacts corals, and how it interacts with other stressors with particular …

Site Fidelity Of Bottlenose Dolphins (Tursiops Truncatus) Using Elemental Analyses And Photo-Identification, Lauren R. Clance

<strong> Theses and Dissertations </strong>

The objective of this study was to determine if bottlenose dolphins (Tursiops truncatus) in Alabama waters acquire location-specific elemental signatures indicative of site fidelity. I measured trace metal concentrations (Chapter II) and stable isotope ratios (Chapter III) in skin from free-ranging dolphins remotely biopsied in Mobile Bay, the northern Gulf of Mexico (Gulf) and eastern Mississippi Sound (EMSS). Elemental findings were corroborated with photo-identification data. I found that dolphins acquired some location-specific elements indicative of site fidelity, with the greatest differences at geographic extremes, particularly relative to salinity. For trace metals, highest concentrations were found in winter, consistent with higher …

Carrying Capacity Of Cultured Bivalves In Cherrystone Inlet, Va, And The Implications Of Spatial Distribution And Environmental Change, Sophia Chirico

Undergraduate Honors Theses

Aquaculture is a growing industry internationally. In the United States, aquaculture of bivalves occurs throughout the Chesapeake Bay. Cherrystone Inlet, a tidal inlet on the Virginia Eastern Shore, is the location of intensive hard clam culture, and recently oyster aquaculture has become common there as well. Given the intensive culture in Cherrystone and similar systems in the Chesapeake, it is important to understand the carrying capacity of the respective bivalves and how they can be grown together. Carrying capacity is defined here as the largest population of individuals that can be supported that allows individuals to reach a harvestable size …

Accumulation Of Persistent Organic Pollutants In Marine Mammals: A Case Study On Cetaceans, Pinnipeds, And Sirenians, Alydia Moorhead

All HCAS Student Capstones, Theses, and Dissertations

Persistent organic pollutants (POPs) are lipophilic semi-volatile organic chemicals that present a range of challenges to marine biota, specifically marine mammals that often occupy a high trophic position in the food web. POPs have become a global problem since they have been shown to cause immunologic, teratogenic, carcinogenic, neurological, and reproductive complications in living organisms due to their resistance to biodegradation and their lipophilic nature. Marine mammals can accumulate these toxic substances through direct ingestion, trophic transfer, adsorption, and maternal offloading. They are susceptible to both bioaccumulation and biomagnification of POPs. Accumulation of POPs is affected by many variables, including …

Movement Patterns Of The Shovelnose Guitarfish (Pseudobatos Productus) And California Bat Ray (Myliobatis Californica) In The Southern California Bight, Annabel Gong

Theses

While the movement patterns of large elasmobranch species have been studied extensively, those of smaller, mesopredatory species remain understudied. The shovelnose guitarfish (Pseudobatos productus) and the California bat ray (Myliobatis californica) are among the least studied elasmobranchs in the Southern California Bight. This study quantified the broad- and fine-scale movement patterns of these species using passive acoustic telemetry. Twelve guitarfish were surgically implanted with coded acoustic transmitters at a known aggregation site off La Jolla (San Diego County), California, USA and tracked for 849.5 days each, on average. Six bat rays were also implanted here and tracked for …

Development And Validation Of An Edna Protocol For Monitoring Endemic Asian Spiny Frogs In The Himalayan Region Of Pakistan, Muhammad Saeed, Muhammad Rais, Ayesha Akram, Maggie R. Williams, Kenneth F. Kellner, Syed A. Hashsham, Drew R. Davis

School of Earth, Environmental, and Marine Sciences Faculty Publications and Presentations

Wildlife monitoring programs are instrumental for the assessment of species, habitat status, and for the management of factors affecting them. This is particularly important for species found in freshwater ecosystems, such as amphibians, as they have higher estimated extinction rates than terrestrial species. We developed and validated two species-specific environmental DNA (eDNA) protocols and applied them in the field to detect the Hazara Torrent Frog (Allopaa hazarensis) and Murree Hills Frog (Nanorana vicina). Additionally, we compared eDNA surveys with visual encounter surveys and estimated site occupancy. eDNA surveys resulted in higher occurrence probabilities for both A. …

Environment-Driven Shifts In Inter-Individual Variation And Phenotypic Integration Within Subnetworks Of The Mussel Transcriptome And Proteome, Richelle L. Tanner, Lani U. Gleason, W. Wesley Dowd

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

The environment can alter the magnitude of phenotypic variation among individuals, potentially influencing evolutionary trajectories. However, environmental influences on variation are complex and remain understudied. Populations in heterogeneous environments might exhibit more variation, the amount of variation could differ between benign and stressful conditions, and/or variation might manifest in different ways among stages of the gene-to-protein expression cascade or among physiological functions. Here, we explore these three issues by quantifying patterns of inter-individual variation in both transcript and protein expression levels among California mussels, Mytilus californianus Conrad. Mussels were exposed to five ecologically relevant treatments that varied in the mean …

Ocean Quahog (Arctica Islandica) Population Dynamics: Sex-Based Demographics And Regional Comparisons In The Northwest Atlantic, Kathleen M. Hemeon

Dissertations

Arctica islandica (ocean quahog) is the longest-lived bivalve on Earth. Individuals on the deep continental shelf of the Mid-Atlantic (US) can survive for centuries, and when found in the colder, boreal waters of Iceland, ages over 500 years can be reached. The ocean quahog is important in the US, yet very little is known about the resiliency of the ocean quahog stock to fishing activity, and ocean quahog recruitment patterns over time. To quantify and constrain age-reader error prior to age analysis, a triple-method error protocol was developed for A. islandica that included age-reader bias, precision, and error frequency. The …

Habitat Restoration Restores Underwater Soundscapes And Larval Recruitment, Jack Butler, Emily R. Anderson, Mark J. Butler

Biological Sciences Faculty Publications

Habitat degradation alters many ecosystem processes, and the potential for the reestablishment of ecosystem function through restoration is an area of active research. Among marine systems, coastal habitats are particularly vulnerable to anthropogenic degradation and, in response, are the focus of marine ecological restoration. One of the crucial functions of structurally complex coastal habitats (e.g., saltmarshes, seagrass meadows, kelp forests, coral reefs) are as nurseries to coastal and offshore species, many of whose larvae utilize sound to locate suitable nursery habitat. However, the effect of habitat degradation and subsequent restoration on underwater soundscapes and their function as navigational cues for …

Sentience In Decapods: Difficulties To Surmount, Michael L. Woodruff

Animal Sentience

In the target article Crump et al. present 8 criteria to assess whether decapods experience pain. Four of these -- sensory integration, motivational trade-offs, flexible self-protection, and associative learning -- could be used to assess sentience in general. In this commentary I discuss difficulties with using these criteria to provide evidence of sentience in decapods, particularly if this evidence is to change public opinion and policies. These difficulties are lack of evidence, the potential to eventually explain the neurobiological basis of the behaviors chosen as criteria, thereby eliminating any explanatory work for sentience, and the reluctance to bring animals that …

Sentience In Decapods: An Open Question, Mark Briffa

Animal Sentience

Crump et al.’s framework is a powerful tool designed to assist decisions on the ethical treatment of decapod crustaceans. However, the question of whether decapods are sentient (i.e., whether they feel), remains open, perhaps indefinitely. More optimistically, we might design experiments that distinguish among different levels of awareness, sometimes viewed as components of sentience. We should strike a balance between assuming that all organisms are sentient and making unnecessary anatomical assumptions about sentience. Refining current experiments may provide concrete insights about awareness in Decapoda and other taxa.

Phylogenetic And Geographic Relationships Of Cheilostome Bryozoans In The Eastern Pacific, Hannah E. Lee

Cal Poly Humboldt theses and projects

The phylum Bryozoa is an incredibly diverse group of marine invertebrates with a widespread global distribution that is well suited for evolutionary studies but whose phylogenetic relationships are still poorly understood. Although recent studies on bryozoan taxonomies and phylogenies have increased, there is still a lack of assessment of species found at shallow water (<1 m) to intertidal depths. In this study, I aimed to expand the taxonomic sampling and assessment of the phylogenetic diversity of cheilostome bryozoans along the California coastline by utilizing mitochondrial DNA as well as inferring potential correlations between species presence and dispersal range both within and between rocky outer coast and sheltered harbor habitats. Illumina high-throughput sequencing was used to produce mitogenomes for cheilostome bryozoan samples collected off rocks from two rocky intertidal sites and off settlement panels from two harbor sites. Phylogenetic analyses generated evolutionary hypotheses of species relationships alongside geographic mapping of their distribution. This study identified 15 distinct species that represent 10 different families to form the first comprehensive phylogeny for multiple bryozoan families in California across a total range of approximately 973 km of coastline. Three genetically distinct species were found at multiple sites that are separated by a combination of rocky shores and sandy beaches, which indicates that the dispersal range of these species are not limited by geographic barriers along the coast of California. These results provide a future opportunity for further integration of this data with the phylogenies generated in this study to examine more robust evolutionary hypotheses for the phylogenetic and geographic relationships of Californian bryozoan species.