Aquaculture and Fisheries Commons^™

Assessing The Habitat Use, Diet, And Sex Ratios Of Atlantic (Acipenser Oxyrinchus) And Shortnose Sturgeon (Acipenser Brevirostrum) In The Saco River, Me, Caitlyn Little

All Theses And Dissertations

Due to the questionable status of sturgeon populations along the east coast of the United States, there has been considerable research focus on these species in recent years. Previous studies have overlooked the Saco River as an important habitat for sturgeon in the Gulf of Maine. However, the incidental capture of a sturgeon in the Saco River in the fall of 2007 raised questions about the presence of this species and the role that the Saco River might play in the life cycle of these fish. The goals of this thesis were to evaluate the utilization of this habitat by …

State Of The River Report For The Lower St. Johns River Basin, Florida: Water Quality, Fisheries, Aquatic Life, And Contaminants 2013, Environmental Protection Board, City Of Jacksonville, University Of North Florida, Jacksonville University

State of the River Report

No abstract provided.

Multiscale Analysis Of Factors That Affect The Distribution Of Sharks Throughout The Northern Gulf Of Mexico, J. Marcus Drymon, Laure Carassou, Sean P. Powers, Mark Grace, John Dindo, Brian Dzwonkowski

University Faculty and Staff Publications

Identification of the spatial scale at which marine communities are organized is critical to proper management, yet this is particularly difficult to determine for highly migratory species like sharks. We used shark catch data collected during 2006–09 from fishery- independent bottom-longline surveys, as well as biotic and abiotic explanatory data to identify the factors that affect the distribution of coastal sharks at 2 spatial scales in the northern Gulf of Mexico. Centered principal component analyses (PCAs) were used to visualize the patterns that characterize shark distributions at small (Alabama and Mississippi coast) and large (northern Gulf of Mexico) spatial scales. …

How Do Shellfisheries Influence Genetic Connectivity In Metapopulations? A Modeling Study Examining The Role Of Lower Size Limits In Oyster Fisheries, Daphne M. Munroe, Eileen E. Hofmann, Eric N. Powell, John M. Klinck

CCPO Publications

Fisheries can potentially alter evolutionary processes such as genetic connectivity and lead to genotypic changes in stocks. Using an individual-based metapopulation genetics model, we examined the possible influence of oyster (Crassostrea virginica) fisheries on genetic connectivity. We simulated a range of realistic fishing pressures, with and without a minimum size limit (limit = 63.5 mm), over a range of fishing scenarios including single-area and stock-wide fisheries. Movement of a neutral marker gene provided an indicator of gene transfer between populations. Simulations showed that fishing may alter genetic connectivity. Increasing fishing pressure tended to decrease potential for fished populations …

Effect Of Laser Ablation Depth In Otolith Life History Scans, Renée R. Hoover, Cynthia M. Jones

OES Faculty Publications

Life history scans of fish otoliths are bringing new insight into the structure, connectivity, and movement of fish populations. Data obtained from such scans, however, possess in-herent limitations that have not yet been fully addressed or understood. For example, several investigators have noted delays in otolith elemental uptake that do not appear to reflect habitat exposure. We hypothesized that the 3-dimensional structure of otoliths may produce sampling artifacts in the results obtained from laser ablation scans. To test this hypothesis, we sampled sagittal otoliths from juvenile Atlantic croaker Micropogonias undulatus with laser ablation inductively coupled plasma mass spectrometry to obtain …

Gulf-Wide Decreases In The Size Of Large Coastal Sharks Documented By Generations Of Fishermen, Sean P. Powers, F. Joel Frodrie, Steven B. Scyphers, J. Marcus Drymon, Robert L. Shipp, Gregory W. Stunz

University Faculty and Staff Publications

Large sharks are top predators in most coastal and marine ecosystems throughout the world, and evidence of their reduced prominence in marine ecosystems has been a serious concern for fisheries and ecosystem management. Unfortunately, quantitative data to document the extent, timing, and consequences of changes in shark populations are scarce, thwarting examination of long-term (decadal, century) trends, and reconstructions based on incomplete data sets have been the subject of debate. Absence of quantitative descriptors of past ecological conditions is a generic problem facing many fields of science but is particularly troublesome for fisheries scientists who must develop specific targets for …

Similarities Between Line Fishing And Baited Stereo-Video Estimations Of Length-Frequency: Novel Application Of Kernel Density Estimates, Timothy J. Langlois, Benjamin R. Fitzpatrick, David V. Fairclough, Corey B. Wakefield, Sybrand Alexander Hesp, Dianne L. Mclean, Euan S. Harvey, Jessica J. Meeuwig

Fisheries Research Articles

Age structure data is essential for single species stock assessments but length-frequency data can provide complementary information. In south-western Australia, the majority of these data for exploited species are derived from line caught fish. However, baited remote underwater stereo-video systems (stereo-BRUVS) surveys have also been found to provide accurate length measurements. Given that line fishing tends to be biased towards larger fish, we predicted that, stereo-BRUVS would yield length-frequency data with a smaller mean length and skewed towards smaller fish than that collected by fisheries-independent line fishing. To assess the biases and selectivity of stereo-BRUVS and line fishing we compared …

A Genetic Survey Of English Sole Populations In The Salish Sea, Elizabeth S. Gutierrez, Gary A. Winans, Jon Baker, Amanda Cope

STAR Program Research Presentations

This summer I interned at the Northwest Fisheries Science Center in Seattle, WA and participated in NOAA’s Salish Sea Project. The Salish Sea Project’s goal is to identify genetically distinctive groups of species in the Salish Sea that may have unique evolutionary and/or adaptive backgrounds. These findings will allow NOAA to promote and monitor the natural production of species in the Salish Sea, to select representative populations for experimental work regarding pollution, ocean acidification and climate change, to contribute to managing the ecosystem for intra- and inter-species diversity, and to help make informed decisions about adaptive management and marine protected …

Developing Monitoring Methods For Leptasterias Spp. As Sentinel Species In Detecting Local Environmental Changes, Zachary Sturbaum, Kathryn Nuessly, Riley J. Smith, C. Sarah Cohen

STAR Program Research Presentations

Leptasterias spp., a six-rayed sea star, is found in rocky intertidal habitats ranging from Alaska to central California. Leptasterias spp. can be monitored on a broad scale throughout their range by a variety of means using timed counts and random plot censusing in order to detect both large-scale and local-level changes in the environment due to climate change, land-based human activity, or other environmental events. Leptasterias brood their young externally until the embryos grow into fully developed juveniles. These juveniles disperse by crawling away, limiting their dispersal potential. This localized dispersal provides an opportunity to use Leptasterias spp …

Nutritional Content Of Rhinoceros Auklet (Cerorhinca Monocerata) Bill Loads, Dustin Taylor, Ron Heintz

STAR Program Research Presentations

Nutritional Content of Rhinoceros Auklet Bill Loads

Dustin E Taylor

Abstract

An adult Rhinoceros Auklet (Cerorhinca monocerata) can only catch and carry a limited amount of prey to their nestlings after a foraging trip. The auklets therefore must maximize their efficiency by bringing back the most proportionally nutritious prey items to their nestlings. The prey carried back to the nesting sites (known as a ‘bill load’) can contain whole fish, as well as parts, most commonly fish heads. This study is aimed to determine whether returning with just heads to the nestlings was proportionally more nutritious than bringing …

Effects Of Pristane On Growth Of Pink Salmon (Oncorhynchus Gorbuscha), Brielle D. Kemis, Bonita Nelson

STAR Program Research Presentations

Pristane is a naturally occurring hydrocarbon that is generated by copepods in marine ecosystems. Organisms that eat copepods do not readily metabolize pristane, which causes it to accumulate throughout the marine food web. Understanding how pristane affects marine fish is essential because pristane is often used as a bioindicator in lab studies and may be influencing results in those studies. Also, this hydrocarbon may significantly reduce growth of marine fish in the wild. A previous study indicated that pristane is an appetite suppressant and growth retardant in fish. However, the study implemented a feeding regime with unnaturally high levels of …

Likely Effectiveness Of Netting Or Other Capture Programs As A Shark Hazard Mitigation Strategy In Western Australia, Department Of Fisheries

Fisheries Occasional Publications

No abstract provided.

Bait Effects In Sampling Coral Reef Fish Assemblages With Stereo-Bruvs, Stacey R. Dorman, Euan S. Harvey, Stephen J. Newman

Fisheries Research Articles

Baited underwater video techniques are increasingly being utilised for assessing and monitoring demersal fishes because they are: 1) non extractive, 2) can be used to sample across multiple habitats and depths, 3) are cost effective, 4) sample a broader range of species than many other techniques, 5) and with greater statistical power. However, an examination of the literature demonstrates that a range of different bait types are being used. The use of different types of bait can create an additional source of variability in sampling programs. Coral reef fish assemblages at the Houtman Abrolhos Islands, Western Australia, were sampled using …

Estimating The Potential Impacts Of Large Mesopredators On Benthic Resources: Integrative Assessment Of Spotted Eagle Ray Foraging Ecology In Bermuda, Matthew J. Ajemian, Sean P. Powers, Thaddeus J. T. Murdoch

University Faculty and Staff Publications

Declines of large sharks and subsequent release of elasmobranch mesopredators (smaller sharks and rays) may pose problems for marine fisheries management as some mesopredators consume exploitable shellfish species. The spotted eagle ray (Aetobatus narinari) is the most abundant inshore elasmobranch in subtropical Bermuda, but its predatory role remains unexamined despite suspected abundance increases and its hypothesized specialization for mollusks. We utilized a combination of acoustic telemetry, benthic invertebrate sampling, gut content analysis and manipulative experiments to assess the impact of spotted eagle rays on Bermudian shellfish resources. Residency and distribution of adult spotted eagle rays was monitored over …

Fish Assemblage Dynamics And Red Drum Habitat Selection In Bayou St. John And Associated Urban Waterways Located Within The City Of New Orleans, Louisiana, Patrick W. Smith Mr.

LSU New Orleans Theses and Dissertations

Bayou St. John (BSJ) and City Park Lakes and Lagoons (CPLL) are urban waterways in New Orleans, Louisiana. I studied habitat selection of red drum in BSJ, and fish assemblage change in BSJ and CPLL over 40 years. Temperature was found to be the best predictor of red drum habitat selection in Bayou St. John, while salinity and change in depth also were found to be good predictors for certain sites. Potential prey item abundance did not appear to influence habitat selection. Using data from 1971 – 2010, nearshore habitats in CPLL were affected by Hurricane Katrina, but have sense …

An Approach For Use Of Dual Frequency Identification Sonar (Didson) To Quantify Behavioral Aspects Of Piscivory At Ecologically Relevant Time And Space Scales, Victoria E. Price

Master's Theses

Predator-prey interactions of large vagile fishes are difficult to study in the ocean due to limitations in the space and time requirements for observations. Small-scale direct underwater observations by divers (<10m >radius) and large-scale hydroacoustic surveys (10s - 100s km2) are traditional approaches. However, large piscivorous predators identify and attack prey at the scale of meters to tens of meters. Dual- Frequency Identification Sonar, or DIDSON, is a high-resolution acoustic camera operating in the MHz range that provides detailed continuous video-like imaging of objects out to 30 m range. This technology can be used to observe predator-prey interactions at ecologically …

Genetic Variation In Potentially Virulent Vibrio Parahaemolyticus From The Northern Gulf Of Mexico, Nicholas Felix Noriea Iii

Dissertations

Vibrio parahaemolyticus (V_p) is a gram-negative bacterium found naturally in marine and estuarine environments. V_p is found in oysters including those which are later consumed by the public. Sub-populations of potentially virulent Vp contain specific virulence factors and are relevant human pathogens capable of causing gastroenteritis, wound infection, and death. The tdh and trh genes, both encoding hemolysins, have been correlated with the majority of clinical V_p isolates but have not been shown to be the definitive virulence factors.

A total of 146 V_p isolates from the northern Gulf of Mexico were collected and probed …

Effects Of Hypoxia And 4-Tert-Octylphenol On Gene Expression Profiles Of The Sheepshead Minnow (Cyprinodon Variegatus), Arthur Alan Karels

Dissertations

Hypoxia occurs in estuaries of northern Gulf of Mexico and world-wide, with increasing frequency/severity via eutrophication and anthropogenic influences. Hypoxia inducible factors (HIFs) form transcriptional complex and bind DNA at hypoxia responsive elements (HREs) in promoter regions of genes needed for systemic and cellular adaptation of fish to low dissolved oxygen (hypoxia, DO <2.0 mg/ml). Hypoxia-induced activation of HIF-αs can lead to a cascade of downstream activation, such as erythropoietin (EPO). Return to normal DO levels (normoxia), prolyl hydroxylases (PHDs) are activated to degrade HIF-αs back to baseline. Fish are affected by environmental estrogen mimics, like 4-tert-octylphenol (4tOP), binding estrogen receptor alpha (ERα) at estrogen responsive elements (EREs) and activating genes vitellogenin (VTG). Previous research showed overlap or crosstalk between these two mechanistic pathways. Hypoxia triggers unknown factors regulating ERE-mediated ERα signaling pathway, and stressor combinations could increase/decrease hypoxic or endocrine pathway. Research examined molecular/physiological effects of hypoxia (acute and chronic, moderate and severe) and 4tOP (~60μg/L)on adult male and/or female sheepshead minnow (Cyprinodon variegatus). Three genes identified, cloned, and sequenced (HIF-1α, HIF-2α, and PHD3), plus previously identified genes EPO and VTG, were examined in liver/testes exposed to hypoxia and/or 4tOP for cellular/physiological changes. Endpoints examined included mRNA expression from real-time PCR of HIF-1α, HIF-2α, PHD3, EPO, and VTG using cDNA from total RNA extracts, and microarray analyses of genes expressed during the transition from hypoxia back to normoxia. Phylogenetic analyses confirmed isolation of two HIF-α isofoms (HIF-1α and HIF-2α) and the PHD3 isoform. Significant up-regulation of PHD3 occurred within 10 hrs of chronic hypoxia, and persisted when severe (1.5 mg/L) and declined when moderate (~2.5mg/L). Significant up-regulation of HIF-1α and EPO occurred within 30 minutes to 2 hours of onset of acute severe and very severe (~1.08mg/L) hypoxia. Hypoxia acted similar to an estrogen mimic, with huge up-regulation of VTG gene expression in males, and increased VTG levels (additive effect) when hypoxia was combined with 4tOP. Microarray analyses showed 125 genes with significant transcriptional change, with up- or down-regulation from transitions of: (1) hypoxia (72 hrs) to normoxia (74 hrs) and (2) hypoxia+4tOP (72 hrs) to normoxia+4tOP (74 hrs).

Comparison Of Creel Survey Data To Traditional Sampling Techniques In Pit-Lake Fisheries Of Muhlenberg County, Kentucky, Derek L. Rupert

Masters Theses & Specialist Projects

Populations of largemouth bass, Micropterus salmoides, and bluegill, Lepomis macrochirus, were evaluated from five pit-lakes in Muhlenberg County, Kentucky, to determine if accurate proportional stock density (PSD) data can be obtained from a mandatory creel survey. It was hypothesized that the proportion of stock-to-quality (300-400mm) and quality (+400mm) largemouth bass from four years (2007-2010) of creel survey data would be statistically similar to those generated through on-site sampling in 2011. Fish were collected via a combination of gill netting, seining, hook-and-line fishing, and boat-mounted electro-fishing. In two of the pit-lakes, the sampling-generated length frequency data was not significantly …

Big Blue And You: An Interdisciplinary Look At Science And The Ocean, A Students Teaching Students Course, Megan M. Nepshinsky, Alexa Kretsch, Benjamin Negrete

Senior Honors Projects

This class is the second project under the new Honors Program initiative, Students Teaching Students (STS). STS was brought to URI and implemented by Bridget Griffith as part of her Senior Honors Project in 2011. Students apply in their Junior year to design, research, and teach an honors course on a topic about which they are passionate. The STS program allows motivated honors students to have a unique opportunity to lead a class as student professors. This allows students a freedom of creativity on the topic, assignments, and teaching style. Drawing on our own experiences, we were able to create …

Out Of Sight, But Not Out Of Mind: A Look At Nanoparticles In The Marine Environment, Evan Ward, John J. Doyle

Wrack Lines

Nanoparticles exist in many products used by humans, such as sunscreens. medications, cosmetics, paints and electronics. But what is the effect of these tiny particles on the ocean or estuarine environment when the sunscreen washes off? This article looks at that question and at shellfish in particular. Evan Ward and John Doyle are marine scientists at UConn.

Diversity Of The Ohio River Bacterial Communities Using Next-Generation Sequencing Techniques, Emily Michele Anneken

Theses, Dissertations and Capstones

The ability to sequence bacterial genetic material directly from environmental samples has unlocked the field of metagenomics. Next-generation sequencing techniques, such as pyrosequencing, have been instrumental in providing knowledge about bacterial communities. This study focused on identifying the bacterial diversity of the Ohio River via pyrosequencing and compared the diversity of cultivable bacteria versus the entire river community. To ensure the maximum number of cultivable bacteria was obtained, cultures were grown on nonselective media and incubated at river temperature. Bacterial DNA was extracted, sequenced, and classified. The dominant phyla for the Ohio River included Cyanobacteria (38-66% of the total), Actinobacteria …

The Rise And Fall Of Crassostrea Virginica Oyster Reefs: The Role Of Disease And Fishing In Their Demise And A Vignette On Their Management, Eric N. Powell, John M. Klinck, Kathryn Ashton-Alcox, Eileen E. Hofmann, Jason Morson

CCPO Publications

We describe a model designed to simulate the shell carbonate budget of an oyster reef.We identify five parameters descriptive of basic characteristics of the shell carbonate budget of a reef that limit simulation accuracy. Two describe the TAZ (taphonomically-active zone) and the distribution of shell carbonate within it. One is the taphonomic rate in the TAZ. Two determine the volume contribution of shell carbonate and the taphonomic loss rate within the reef framework. For Mid-Atlantic estuaries, model simulations suggest that reef accretion only occurs if oyster abundance is near carrying capacity. Simulations further suggest that reef accretion is infeasible for …

State Of The River Report For The Lower St. Johns River Basin, Florida: Water Quality, Fisheries, Aquatic Life, And Contaminants 2012, Environmental Protection Board, City Of Jacksonville, University Of North Florida, Jacksonville University

State of the River Report

No abstract provided.

Does Large-Scale Ocean Circulation Structure Life History Connectivity In Antarctic Toothfish (Dissostichus Mawsoni)?, Julian Ashford, Michael S. Dinniman, Cassandra Brooks, Allen H. Andrews, Eileen E. Hofmann, Gregor Cailliet, Christopher Jones, Nakul Ramanna

CCPO Publications

A multidisciplinary approach incorporating otolith chemistry, age data, and numerical Lagrangian particle simulations indicated a single, self-recruiting population of Antarctic toothfish (Dissostichus mawsoni) in the Southeast Pacific Basin (SPB) and Ross Sea, with a life history structured by the large-scale circulation. Chemistry deposited prior to capture along otolith edges demonstrated strong environmental heterogeneity, yet the chemistry in otolith nuclei, deposited during early life, showed no differences. Age data showed only adult fish in catches on the Pacific-Antarctic Ridge in the SPB and structuring of life stages consistent with transport pathways from the northern Ross Sea. Lagrangian particle simulations …

Geostatistical Spatiotemporal Modelling With Application To The Western King Prawn Of The Shark Bay Managed Prawn Fishery, Ainslie M. Denham

Theses: Doctorates and Masters

Geostatistical methodology has been employed in the modelling of spatiotemporal data from various scientific fields by viewing the data as realisations of space-time random functions. Traditional geostatistics aims to model the spatial variability of a process so, in order to incorporate a time dimension into a geostatistical model, the fundamental differences between the space and time dimensions must be acknowledged and addressed. The main conceptual viewpoint of geostatistical spatiotemporal modelling identified within the literature views the process as a single random function model utilising a joint space-time covariance function to model the spatiotemporal continuity. Geostatistical space-time modelling has been primarily …

Age Composition And Distribution Of Red Drum (Sciaenops Ocellatus) In Offshore Waters Of The North Central Gulf Of Mexico: An Evaluation Of A Stock Under A Federal Harvest Moratorium, Sean P. Powers, Crystal Hightower, J. Marcus Drymon, Matthew W. Johnson

University Faculty and Staff Publications

Because of a lack of fishery- dependent data, assessment of the recovery of fish stocks that undergo the most aggressive form of management, namely harvest moratoriums, remains a challenge. Large schools of red drum (Sclaenops ocellatus) were common along the northern Gulf of Mexico until the late 1980s when increased fishing effort quickly depleted the stock. After 24 years of harvest moratorium on red drum in federal waters, the stock is in need of reassessment; however, fishery dependent data are not available in federal waters and fishery-independent data are limited. We document the distribution, age composition, growth, and condition of …

High Connectivity In The Deepwater Snapper Pristipomoides Filamentosus (Lutjanidae) Across The Indo-Pacific With Isolation Of The Hawaiian Archipelago, Michelle R. Gaither, Shelley A. Jones, Christopher Kelley, Stephen J. Newman, Laurie Sorenson, Brian W. Bowen

Fisheries Research Articles

In the tropical Indo-Pacific, most phylogeographic studies have focused on the shallow-water taxa that inhabit reefs to approximately 30 m depth. Little is known about the large predatory fishes, primarily snappers (subfamily Etelinae) and groupers (subfamily Epinephelinae) that occur at 100–400 m. These long-lived, slow-growing species support fisheries across the Indo-Pacific, yet no comprehensive genetic surveys within this group have been conducted. Here we contribute the first range-wide survey of a deepwater Indo-Pacific snapper, Pristipomoides filamentosus, with special focus on Hawai'i. We applied mtDNA cytochrome b and 11 microsatellite loci to 26 samples (N = 1,222) collected across …

Environmental Influences On Juvenile Fish Abundances In A River-Dominated Coastal System, Laure Carassou, Brian Dzwonkowski, Frank J. Hernandez, Jr., Sean P. Powers, William M. Graham, Kyeong Park, John Mareska

University Faculty and Staff Publications

We investigated the influence of climatic and environmental factors on variations in juvenile abundances of marine fishes in a river-dominated coastal system of the north-central Gulf of Mexico, where an elevated primary productivity sustains fisheries of high economic importance. Fish were collected monthly with an otter trawl at three stations near Mobile Bay from 1982 to 2007. Fish sizes were used to isolate juvenile stages within the data set, and monthly patterns in juvenile fish abundance and size were then used to identify seasonal peaks for each species. The average numbers of juvenile fish collected during these seasonal peaks in …

Oyster Reefs As Natural Breakwaters Mitigate Shoreline Loss And Facilitate Fisheries, Steven B. Scyphers, Sean P. Powers, Kenneth L. Heck Jr., Dorothy Byron

University Faculty and Staff Publications

Shorelines at the interface of marine, estuarine and terrestrial biomes are among the most degraded and threatened habitats in the coastal zone because of their sensitivity to sea level rise, storms and increased human utilization. Previous efforts to protect shorelines have largely involved constructing bulkheads and seawalls which can detrimentally affect nearshore habitats. Recently, efforts have shifted towards “living shoreline” approaches that include biogenic breakwater reefs. Our study experimentally tested the efficacy of breakwater reefs constructed of oyster shell for protecting eroding coastal shorelines and their effect on nearshore fish and shellfish communities. Along two different stretches of eroding shoreline, …