Marine Biology Commons^™

Input, Output And Complete Run Files For The Atlantis Ecosystem Model Deepwater Horizon Oil Spill Simulations Including Fish And Invertebrate Effects, Cameron Ainsworth, Lindsey N. Dornberger

C-IMAGE data

These data include input and output files from the Gulf of Mexico Atlantis model. The simulations are published in Dornberger et al., 2019. The dataset includes every file needed to recreate the simulations: 1) the 18 spatial forcing files needed to recreate the sensitivity analysis; these vary the oil sensitivity threshold K, the fish oil threshold and the invertebrate oil threshold. The file naming scheme indicates parameter values used. 2) the three .prm files needed to recreate the different levels of fishing mortality (F=0.5, 1, 2.0, 10), The F rate indicates an increase in fishing mortality across all fishing sectors …

A Review Of The Global Commercial Cephalopod Fishery, With A Focus On Apparent Expansion, Changing Environments, And Management, Corey Clark

HCNSO Student Capstones

Cephalopods are both important predators and prey in many marine environments and important fishery resources in many countries. The global fishery has expanded almost continuously from landings of 580,000 metric tonnes in 1950 to over 4 m.t. in 2007. Cephalopods are ecological opportunists with highly plastic biological characteristics and varied population dynamics. Nearly all commercially harvested species are short-lived and can reproduce quickly, enabling them to evolve more rapidly under high selection pressure relative to many fish competitors and predators. As a result, they may have the biological means to be successful under conditions of long-term global climate change. This …

Outplanted Acropora Cervicornis Enhances The Fish Assemblages Of Southeast Florida, Ellen Dignon Goldenberg

HCNSO Student Theses and Dissertations

Acropora cervicornis, commonly known as the staghorn coral has historically been a major contributor to reef structural complexity, providing habitat for many functionally important fish species throughout Florida and the Caribbean. Unfortunately, due to disease, bleaching, and local anthropogenic stressors, A. cervicornis populations have suffered drastic declines that have negatively impacted associated reef fish populations. In order to promote recovery, A. cervicornis fragments can be cultivated in nurseries and outplanted back onto reefs. This practice can effectively increase A. cervicornis abundance, but the long-term effects on local fish assemblages, and specifically functionally important grazing fishes, has not been assessed. …

Examining The Effect Of Interstitial Space On Eastern Oysters (Crassostrea Virginica): Applications Of Photogrammetry And Three-Dimensional Modeling, Bailie Lavan

Masters Theses, 2010-2019

Global oyster populations have decreased by as much as 99% in the past century. Oysters are known ecosystem engineers, providing benthic habitat for macrofauna, linking benthic and pelagic food webs, improving water quality, and mitigating shoreline erosion. Restoration efforts are critical in re-establishing native oyster populations. In the Chesapeake Bay, where oyster loss is primarily due to severe over harvest, artificial substrates with geometric shapes are widely used in restoration efforts. However, natural oyster reefs form emergent shapes with a high degree of aggregation and many interstitial spaces (three-dimensional volumetric spaces between oysters within a reef). The lack of interstitial …

Nutrient Concentrations And Effects On Mill Run From Residential, Urban, And Industrial Stormwater Contamination, Melissa Carver

HCNSO Student Theses and Dissertations

Nutrients are introduced into the waters of the Commonwealth of Pennsylvania through various methods, mainly through point and non-point sources. Non-point sources would include agricultural means however, there are often other non-point sources that are often overlooked. Water runoff from stormwater is an important contributor to pollution entering various watersheds. Data was collected at 4 locations (the initial point of reference, residential, urban, and industrial) on Mill Run and 2 locations on Woodcock Creek, through surface water collection methods in dry and wet weather. Nitrate, Nitrite, Total Phosphorus, and Total Nitrogen were among the data collected. Total Phosphorus had an …

Analysis Of "Observer Effect" In Logbook Reporting Accuracy For U.S. Pelagic Longline Fishing Vessels In The Atlantic And Gulf Of Mexico, Thomas J. Morrell

HCNSO Student Theses and Dissertations

Commercial pelagic longline fishers within the U.S. Atlantic, Gulf of Mexico, and Caribbean are required to report all fishing interactions per each gear deployment to NOAA’s Vessel Logbook Program of the Southeast Fisheries Science Center to quantify bycatch, increase conservation efforts, and avoid jeopardizing the existence of vulnerable species listed under the Endangered Species Act (ESA). To provide additional accuracy, the Pelagic Observer Program (POP) of the SEFSC deploys professionally trained observers on longline vessels to produce a statistically reliable subset of longline fisheries data. A comparison of self-reported (“unobserved”) datasets versus observer-collected (“observed”) datasets showed a general consistency for …

Correlation Between Sei Whale Distribution And Chlorophyll-A Concentration In The Western North Atlantic, Dawn Parry

Senior Honors Projects

The sei whale (Balaenoptera borealis) is an endangered baleen whale species whose distribution and migratory movements are poorly understood. Sei whale populations were decimated by commercial whaling in the 19th and 20th centuries. Much of what is currently known about their distributions comes from historical whaling records. Visual sightings, which may be sporadic and limited by weather and access to remote locations, are the primary source of data for recent research. It is thought that sei whale distributions may be influenced by the distribution of their food, which consists of zooplankton (small crustaceans, like shrimp), small fish, and …

Options For Improving Dfad Recovery And Accountability To Minimize Marine Coastal Habitat Damage And Marine Litter, Adam Baske, M. Shiham Adam, David W. Kerstetter

Marine & Environmental Sciences Faculty Proceedings, Presentations, Speeches, Lectures

No abstract provided.

Concentrations Of Polycyclic Aromatic Hydrocarbons (Pahs) In Liver Tissue Of Golden Tilefish Collected Aboard Multiple R/V Weatherbird Ii Cruises In The Gulf Of Mexico From 2012-08-13 To 2017-08-01, Erin Pulster, S. M. Synder, Steven A. Murawski

C-IMAGE data

This dataset contains the concentrations of polycyclic aromatic hydrocarbons (PAHs) in liver tissue of golden tilefish (Lopholatilus chamaeleonticeps) collected aboard multiple R/V Weatherbird II cruises WB1304 (2012-08-13 to 2012-08-25), WB1403 (2013-08-15 to 2013-08-30), WB1502 (2014-08-05 to 2014-08-20), WB1602 (2015-08-15 to 2015-08-30), WB1603 (2015-09-10 to 2015-10-02), WB1701 (2016-08-02 to 2016-09-09), and WB1736 (2017-07-18 to 2017-08-01) in the Gulf of Mexico during the Gulf of Mexico-wide surveys from 2012-2017. PAH was extracted from livers with a modified QuEChERS (Bond Elut, Agilent Technologies, Santa Clara, CA, USA) method optimized specifically for this study species. Extracts were analyzed using Agilent’s 7890B gas chromatograph (GC) …

Assessing The Influence Of Salt Marsh Enhancement On Nekton Communities, Evan Thomas Kwityn

Theses, Dissertations and Culminating Projects

Resiliency projects are being implemented throughout coastal communities with the intention of reducing the loss of salt marsh habitat. Salt marsh enhancement projects may have the benefit of minimizing physical coastal impacts, but enhancement activities are not fully understood as a result of potential impacts on salt marsh ecosystems, particularly nekton or fish and decapod communities. Questions involving salt marsh enhancement remain in regard to negative impacts on nekton communities and hydrologic habitat connectivity. To evaluate the impacts of salt marsh enhancement in reference to nekton community structures, I compared nekton density in restored and non-restored locations on two salt …

Do Indirect Predator Cues Affect Behavior Of The Freshwater Clam Sphaerium Simile?, Jesse Bruce Eichler

Theses, Dissertations and Culminating Projects

Freshwater bivalves provide important ecosystem services, like filtering water and cycling nutrients. Predators affecting the behavior of bivalve prey, therefore, could potentially impact the structure and function of ecological communities. Because little is known about the antipredator responses of sphaeriid clams, I examined the behavior of juvenile and adult freshwater clams, Sphaerium simile, when exposed to two types of indirect predator cues: effluent of a crayfish (Orconectes rusticus) and damaged conspecific clams. Adult clams responded to crayfish effluent by significantly reducing burrowing behavior. Juvenile clams, however, buried indiscriminately regardless of experimental treatment and significantly more often/more quickly than adults. These …

An Analysis Of Citizen Science And Its Effect On Marine Plastic Pollution, Kathryn Munster

Renée Crown University Honors Thesis Projects - All

My Honors thesis is an analysis of pollution data to gain more insight about the growing problem of marine plastic pollution. I retrieved online datasets collected by the Clean Swell trash collection mobile application and then analyzed this data using the Python programming language. After my Python analysis, I used Tableau to create data visualizations. This paper analyzes the effect that citizen science has on plastic pollution. Syracuse University’s recycling and trash figures, provided by Syracuse Haulers, are also analyzed. The purpose of including Syracuse University’s data is to bring a local point of view to this project and possibly …

Comment On Rojas-Bracho And Colleagues (2019): Unsubstantiated Claims Can Lead To Tragic Conservation Outcomes, Karl W. Flessa, Luis Calderon-Aguilera, Carlos E. Cintra-Buenrostro, David L. Dettman, Gregory P. Dietl, David H. Goodwin, David K. Jacobs, Michal Kowalewski, Steven M. Nelson, Kirsten Rowell, Bernard R. Schone, Jansen A. Smith, Francisco Zamora-Arroyo

School of Earth, Environmental, & Marine Sciences Faculty Publications

The vaquita’s decline is a tragic story indeed. However, the lack of action to prevent the extinction of this species is not due to unsubstantiated claims and scientific uncertainty.

Modelling Water Fluxes In Plants: From Tissues To Biosphere, Maurizio Mencuccini, Stefano Manzoni, Bradley O. Christoffersen

School of Earth, Environmental, & Marine Sciences Faculty Publications

Contents Summary 1207 I. Introduction 1207 II. A brief history of modelling plant water fluxes 1208 III. Main components of plant water transport models 1208 IV. Stand-scale water fluxes and coupling to climate and soil 1213 V. Water fluxes in terrestrial biosphere models and feedbacks to community dynamics 1215 VI. Outstanding challenges in modelling water fluxes in the soil-plant-atmosphere continuum 1217 Acknowledgements 1218 References 1218 SUMMARY: Models of plant water fluxes have evolved from studies focussed on understanding the detailed structure and functioning of specific components of the soil-plant-atmosphere (SPA) continuum to architectures often incorporated inside eco-hydrological and terrestrial biosphere …

Bottlenose Dolphin (Tursiops Truncatus) Vocal Responses To Sonar And Spectrally Pink Background Noise, Maria Zapetis

Dissertations

As human populations rise, the level of man-made noise increases globally. Naval sonar and boat traffic are underwater sound sources of particular concern to marine mammal welfare. To better understand the impact of these noise increases on cetaceans, studies can explore animals’ behavioral changes in response to noise. Studies have investigated the ‘dose-response’ relationship between the received sound pressure level of sonar signals and the behavior of cetaceans in the wild, but exposure studies in controlled environments are limited. The studies in this dissertation examined bottlenose dolphin vocal modifications during various experimental noise treatments. Acoustic recordings previously obtained for bottlenose …

Effects Of Elevated Temperature On Gonadal Functions, Cellular Apoptosis, And Oxidative Stress In Atlantic Sea Urchin (Arbacia Punctulata), Jackson B. Johnstone

Theses and Dissertations

Increasing surface sea water temperatures effect on growth, reproduction and development in marine organisms. Sea urchins are excellent indicator species and ideal model organisms to focus on. In this study, I tested the effect of higher temperatures on reproductive functions, heat shock protein (HSP, a chaperone protein produced by cells in response to heat stress) and nitrotyrosine protein (NTP, an indicator of reactive nitrogen species, RNS) expressions, cellular apoptosis, and ceolomic fluid (CF, a body fluid which regulates important physiological processes) conditions in Atlantic sea urchin at three different temperatures. Ten sea urchins were placed in each of six aquariums …

A Snapshot Of The Age, Growth, And Reproductive Status Of Gray Triggerfish (Balistes Capriscus, Gmelin 1789) On Three Artificial Reefs In The Northwest Gulf Of Mexico, Adam M. Lee

Theses and Dissertations

Age, growth, and reproductive status of gray triggerfish (Balistes capriscus) were identified from 2015-2016 on artificial reefs in the northwest Gulf of Mexico. Individuals ranged from 232-432 mm fork length with and a mean fork length of 319 mm. Individuals from age 0.2 to 5.2 yrs were observed with a weight to length relationship of Wg = 1.1 x -104 x FL2.7 (r2 = 0.94, n = 112), where FL = fork length (mm) and Wg = weight (g). A von Bertalanffy growth equation of Lt = 326(1 - e - 0.9 (t + 1.71)) was calculated irrespective …

Ontogeny Of Similarity And Disparity In Length-At-Age Of Coral Reef Fishes In The Family Acanthuridae Between Marine Protected And Fished Areas, Mathias Tjarko Cramer

Theses and Dissertations

Drastic reductions in the harvestable biomass of exploited fish populations on coral reefs and other marine coastal ecosystems have been hypothesized to be a consequence of astronomical and unrelenting fishing pressures, particularly in the coastal small-scale and sustenance fisheries of the world. It has recently been proposed that the causal relationship between fishing pressure and fish biomass is rooted in the negative effects of size-selective fishing mortality, which consequently instigates directional shifts in phenotype (i.e., fishing induced evolution). To mitigate the effects of unsustainable fishing pressures, parcels of traditional fishing grounds have been designated as Marine Protected Areas (MPAs). To …

The Effects Of Salinity On Zootechnical Performance Of Spotted Seatrout (Cynoscion Nebulosus) In Recirculating Aquaculture Systems, Eric Gigli

Master's Theses

The spotted seatrout (Cynoscion nebulosus) is a euryhaline finfish candidate for marine aquaculture in the northern Gulf of Mexico. Aquaculture of this species currently uses salinities of 25 psu or greater making production challenging in areas where high salinity water is not available. This study aimed to document the effects of salinity on zootechnical performance of spotted seatrout embryos, early larvae, and juveniles in recirculating aquaculture systems to assist with the development of protocols for low salinity culture.

Embryos obtained from a volitional spawn at 29 psu were incubated at three salinities (12.5, 18.75, or 25 psu) until …

Evaluating Alternate Management Strategies For Spotted Seatrout (Cynoscion Nebulosus) In The North-Central Gulf Of Mexico, Nathaniel Wallace Jermain

Master's Theses

Spotted Seatrout (Cynoscion nebulosus) receive considerable fishing pressure as the most popular saltwater target species in the north-central Gulf of Mexico. The potential for alternate management strategies, including stock enhancement and reducing discard mortality, to support the sustainability of the stocks and the desires of stakeholders is unknown. The purpose of this study was to provide an objective evaluation of the efficacy of alternate management strategies for Spotted Seatrout in Louisiana, Mississippi, and Alabama. I used a management strategy evaluation (MSE) to measure the performance of 18 alternate management scenarios relative to control scenarios. Scenarios with a high …

Investigating Diel Periodicity In Export Flux In The Gulf Of Mexico Using A Particulate Imaging System, Justin Edward Blancher

Master's Theses

To estimate the diurnal periodicity in the biological pump, a floating array with a marine snow camera system at 150 m depth was used, and particles were imaged at a 40 second interval for a 24 to 30 hour period at five sites in the Gulf of Mexico in June 2017. Each image was processed to identify and size all the particles within the frame, which was then processed to determine diameter, an estimated volume, and settling speed for each particle. Using these parameters, particle mass was estimated using algebraically rearranged calculations for settling speed. Each hour during the deployment …

The Sedimentology Of Cay Sal Bank - An Incipiently Drowned Carbonate Platform, Luis Ramirez

HCNSO Student Theses and Dissertations

Sediment on Cay Sal Bank (CSB) is characterized by its coarse-grain size, poor sorting, predominance of skeletal fragments, and relatively depleted d¹⁸O isotope values. CSB is an incipiently drowned platform in close proximity to the Great Bahama Bank (GBB), a carbonate platform which is not incipiently drowned and characterized by fine-grained, non-skeletal sediment. The GBB has locally well-developed oolitic grainstone facies and coral reef margins, which are both lacking on CSB. Platform-top water depths on the GBB are typically 10 m or less, but CSB depth ranges between 7 and 30 m. CSB is devoid of mud, whereas …

Determining How Risk Effects Predator-Prey Interactions Of Marine Communities In The Nearshore Environment Of South Bimini, The Bahamas, Kendall Brancart

HCNSO Student Theses and Dissertations

Predators often have strong top-down effects on ecosystems and are considered a priority for conservation and management. Predator activity can influence prey distribution, abundance, and foraging behaviors and are likely to influence habitat by impacting ecological and environmental characteristics as well as presence of competitor species. There are knowledge gaps of the functional diversity of fish assemblages, non-consumptive predator effects, and environmental effects on fish assemblages. With this study, effects of top marine predators, such as sharks and great barracuda, on diversity and abundance of prey communities were examined in putative low (north side of South Bimini = lagoon) and …

Assessment Of Heavy Metals In Subsistence-Harvested Alaskan Marine Mammal Body Tissues And Vibrissae, Pilar M. Ferdinando

HCNSO Student Theses and Dissertations

The coastal, indigenous communities around Alaska have subsisted on marine animals for generations, often focusing on large apex predators such as seals, sea lions, and whales. Three species of pinnipeds (harbor seal, Steller sea lion, northern fur seal) and the northern sea otter have all undergone significant population declines since the 1970s, some regions more than others. Archived vibrissae (whiskers) and body tissues from these four species were available from the Bering Sea and throughout the Gulf of Alaska from the 1990s and early 2000s. Tissues from these species are exceedingly difficult to obtain; thus, the archived tissues provided a …

Optimizing Restoration Site Selection Along The Florida Reef Tract For The Coral Species Acropora Cervicornis And Acropora Palmata, Samantha King

HCNSO Student Theses and Dissertations

The decline of Acropora cervicornis and Acropora palmata populations and consequent listing as endangered species has prompted the need for restoration. Since financial resources are limited, optimal sites for restoration should not only be environmentally suitable for outplant survival, but also have a greater capacity to replenish surrounding reefs with larvae. However, in Florida coral larval dispersal patterns and reef connectivity remain poorly studied. Here, we measured long term larval survival and competency of A. cervicornis to calibrate a high resolution (100m) biophysical larval dispersal model of Acropora in the Florida Reef Tract (FRT). This model revealed that there is …

Effects Of Deposited Sediment And Turbidity On Survival And Growth Of Orbicella Faveolata Recruits, Morgan Stephenson

HCNSO Student Theses and Dissertations

Corals are frequently exposed to elevated turbidity and deposited sediment caused from coastal construction, dredging, and/or beach renourishment. This study addresses the effects of turbidity and deposited sediment on the survival and growth of newly settled and 6-week-old Orbicella faveolata recruits and disentangles the effects of turbidity and deposited sediment. We conducted two experiments in which newly settled coral recruits were reared in one of ten different turbidity and deposited sediment treatments for five weeks (0 NTU/ 0 mg cm^-2, 3.4 NTU/ 0 mg cm^-2, 8.2 NTU/ 0 mg cm^-2, 16 NTU/ 0 mg …

The Effects Of Ultraviolet Light Exposure On The Activity Of Catalase In The Coelomocytes Of Sea Urchins Lytechinus Variegatus And Arbacia Punctulata, Kandis Arlinghaus

Undergraduate Theses

Many sea urchins play important ecological roles in their environments, and it is important to study the impacts of environmental stressors on their physiology. Ultraviolet radiation (UVR) exposure has significant negative impacts on marine organisms including an increase in reactive oxygen species (ROS). Oxidative damage by ROS at the cellular level can cause lipid peroxidation, DNA fragmentation, and even cell death that may result in inflammation or disease. To prevent this cellular damage, organisms generate enzymes, such as catalase, that breakdown ROS into harmless substances. Elevated catalase activities under UVB, a range of UVR from 280–315 nm, exposure have been …

Indirect Legacy Effects Of An Extreme Climatic Event On A Marine Megafaunal Community, Robert Nowicki, Michael Heithaus, Jordan Thompson, Derek Burkholder, Kirk Gastrich, Aaron Wirsing

Marine & Environmental Sciences Faculty Articles

While extreme climatic events (ECEs) are predicted to become more frequent, reliably predicting their impacts on consumers remains challenging, particularly for large consumers in marine environments. Many studies that do evaluate ECE effects focus primarily on direct effects, though indirect effects can be equally or more important. Here, we investigate the indirect impacts of the 2011 “Ningaloo Niño” marine heatwave ECE on a diverse megafaunal community in Shark Bay, Western Australia. We use an 18‐year community‐level data set before (1998–2010) and after (2012–2015) the heatwave to assess the effects of seagrass loss on the abundance of seven consumer groups: sharks, …

A Comparison Of Circle And J Hook Performance Within The Grenadian Pelagic Longline Fishery, Anthony G. Burns

HCNSO Student Theses and Dissertations

The development and adaptation of gear technologies to local fisheries has been a management-oriented research strategy commonly used to mitigate the ecological effects of pelagic longline (PLL) gear on bycatch species. Grenada’s PLL fishery primarily targets yellowfin tuna, however while minimal, their bycatch of blue marlin and white marlin exceeds the Total Allowable Catch (TAC) allowed by the International Commission for the Conservation of Atlantic Tunas (ICCAT). A switch to circle hooks may benefit these nontargeted, bycatch species by reducing catch rates and haulback mortality, as well as increasing post-release survival. To determine differences in performance, assessments of 16/0 circle …

The Ellis Island Effect: Invasive Species In The Mid-Atlantic, Paul A.X. Bologna

Sustainability Seminar Series

Global invasions of marine species often follow human migration pathways and primary commerce routes. Exploration, immigration, and commerce to the United States has created hot spots for invasive species to become established. In particular, Ellis Island served as a primary spot for European immigrants over the last century. During the last 3 years, we have documented for the first time four non-native hydrozoans in New Jersey using molecular techniques.

Gonionemusvertens, Moerisiainkermanica, and Bougainvilliatriestinahave origins potentially linked to the Mediterranean indicating a potential group invasion from that region. Aequoreaaustralisis a Pacific hydrozoan whose origin pathway is yet unknown, but has now …