Animal Sciences Commons^™

Larval Genomics As A Viable, Fisheries-Independent Tool For Investigating Population Structure In Tropical Pacific Tunas, Jacob E. Jaskiel, Hannah E. Aichelman, Giulia Anderson, Louw Claassens, James E. Fifer, Christina M. Hernandez, Alexa K. Huzar, Joel K. Llopiz, Jan W. Witting, Sean P. Mullen, Randi D. Rotjan

Biological Sciences Faculty Publications

Understanding how dispersal, life history, and environmental variability shape genetic connectivity in the open ocean remains a central challenge in evolutionary biology. Highly migratory marine predators like tunas have traditionally been considered genetically homogeneous across ocean basins, yet emerging genomic evidence suggests that cryptic population structure can persist even in species with high gene flow and large effective population sizes. We used 2bRAD sequencing of 348 larval and subadult skipjack (Katsuwonus pelamis), yellowfin (Thunnus albacares), and bigeye tuna (T. obesus) collected from the central Pacific across 7 years of sampling to examine species boundaries, …

Mitochondrial Genome Of The Indo-Pacific Mesophotic Coral Leptoseris Columna (Scleractinia: Agariciidae) Assembled Using Pacbio Long-Read Sequencing, Nomita Rani Adhikary, Daniel J. Barshis, J. Antonio Baeza

Biological Sciences Faculty Publications

Leptoseris columna, a mesophotic coral species belonging to the family Agariciidae, is distributed throughout the Indo-Pacific region. This species is considered as of "Least concern" by the IUCN, yet, faces multiple local and global stressors. To support conservation plans, this study sequenced and characterized the complete mitochondrial genome of L. columna. The complete mitochondrial genome of Leptoseris columna was assembled using PacBio long-reads with a coverage of 459× per bp. The AT-rich mitochondrial genome of Leptoseris columna is 18,546 bp long and comprises 13 protein-coding genes (PCGs), 2 transfer RNA genes (trnM and trnW), and 2 ribosomal RNA …

Automation And Habitat Development For A Space Based Marine Life Environment, Logan Trimmer, Alexander Hang

Harrisburg University Other Works

This project was a cross-collaboration between the Environmental Sciences and Advanced Manufacturing and Robotics programs for the company Monolith Space.

The goal of this project was to design an autonomous system to be able to track qualities of water in an aquaculture system designed to be sent to space.

Nanoparticle Carriers Enhance The Prophylactic Antiviral Effects Of Dsrna In Vitro And Ex Vivo, Shayne Oberhoffner, Stephanie Dewitte-Orr, Starla Richardson, Leah Haile, Dominique Daniels, Erin Cooper, Aizah Ijaz, Janet Velasquez Perez, Mathilde Peruzzi, Bertrand Collet, Paul Craig, Kristof Jenik

Theses and Dissertations (Comprehensive)

Aquaculture now outpaces traditional capture fisheries as the world population and demand for sustainable protein sources increases. Wild and farmed species are increasingly susceptible to pathogen spread as global temperatures rise and stocking densities increase. Despite the devastating losses experienced by aquaculture due to viral infections, there remain few effective prophylactic antiviral therapeutics. Long double-stranded (ds)RNA is a uniquely viral molecule produced by nearly all viruses during their replication cycle, and its detection by salmonids like rainbow trout (Oncorhynchus mykiss) and chinook salmon (Oncorhynchus tshawytsha) leads to the establishment of a defensive antiviral state. Previous in vitro studies demonstrated a …

The Disruption Of Gastrointestinal Hormonal Control Of Digestion In Nile Tilapia By Omeprazole, Rema Abutaha

Theses and Dissertations (Comprehensive)

Stomach acidity is a critical feature of the digestive system, facilitating the breakdown of protein through the activation of the protease pepsin. Gastric acid is secreted by H⁺/K⁺ ATPase, the gastric proton pump. A previous study on Nile tilapia (Oreochromis niloticus) showed that inhibiting the production of stomach acid using the proton pump inhibitor omeprazole (omz), reduced growth that correlated with an acceleration of the rate of gastric emptying. This contrasts with omz exposure studies in mammals in which there is a delay in gastric emptying and no impact on growth. To understand the mechanism …

Retention Time Of Microplastics In The Purple Sea Urchin (Arbacia Punctulata), Alexandra Shore

Honors Theses and Capstones

Marine ecosystems around the world are facing the problem of plastic pollution. Large pieces of plastic eventually degrade into smaller microplastics that are suspended in the water column and sink to the seabed. Sea urchins are exposed to microplastics as they graze on the sea floor and can accidentally consume these pollutants. Sea urchins are ecologically important animals because they physically alter their ecosystem via grazing and are integral part of marine food webs. To better understand how sea urchins interact with microplastics, purple sea urchins were exposed to microfibers and microspheres in a laboratory setting, and the retention time …

6ppd-Quinone In Middle Tennessee Waters: Assessing Ecological Impact, Andrew Davis Todd, Raphael Marquise Chandler, Kerolos Gerges Basalos, Denise Lori Loewinger

Student Scholar Symposium

This poster presents the dangers of a toxic chemical used on car tires that is entering aquatic ecosystems and harming fish populations.

Indigenizing Aquaculture: In Pursuit Of An Integrated Multi-Trophic Aquaculture System For Enhanced Self-Sufficiency In Akaroa Harbour, Aotearoa New Zealand, Cali R. Trainor

Capstone Collection

This study assessed the feasibility of integrating two pre-existing aquaculture activities in Akaroa Harbour, Aotearoa New Zealand into an integrated multi-trophic aquaculture (IMTA) system. The cultivation of giant kelp (Macrocystis pyrifera) presents an opportunity to improve the sustainability of Chinook salmon (Oncorhynchus tshawytscha) farming by introducing alternative food sources for salmon, which can be used to produce fish feed locally, enhancing the self-sufficiency of the community and boosting the holistic efficiency of the system. Macroinvertebrates residing in giant kelp wrack were collected, identified, and quantified to determine if any of the Macrocystis-associated specimens could serve as …

Role Of Recreational Fisher Information In Fisheries Management, Rebecca M. Krogman, Stephen M. Taylor, Aaron J. Adams, Ross E. Boucek, Steven M. Lombardo, Chelsey A. Crandall, Susan F. Steffen, Alejandro Acosta, Eduardo Bone Moron, Sepp Haukebo, Kieran Hyder, Zachary M. Radford, Warren M. Potts

Books & book chapters

Fisheries managers work with the three components of fisheries—biota, environment, and people - to achieve recreational, stewardship, and socioeconomic goals. Although manipulation of biota and the aquatic environment remains popular (e.g. harvest regulation, protecting or enhancing habitats, and guarding water quality), the human dimension of fisheries must also be considered throughout the fisheries management process. Managers can and should engage fishers in a myriad of ways, from identification of problems to guidance on alternatives, and from measurement of change to evaluation of success. In this chapter, we review common fisheries management goals and objectives; detail information needs stemming from those …

Heat Increment Of Feeding In The Common Bottlenose Dolphin (Tursiops Truncatus) Contributes Moderately To Field Metabolic Rate Estimates, Ioulia Koliopoulou, Stacy L. De Ruiter, Jordi Altimiras, Josefin Larsson, Julietta Arenarez, David Rosen, Andreas Fahlman

University Faculty Publications and Creative Works

Digestion elevates metabolism through the heat increment of feeding (HIF) – the energy expended on mechanical and biochemical processes after eating. Quantifying this cost is essential for bioenergetic models that predict energy flow and prey requirements in populations. Using breath-by-breath respirometry, we measured oxygen consumption (V̇ O2 ) in eight common bottlenose dolphins (Tursiops truncatus) before and after feeding standardized meals (1659–2658 kcal of capelin and herring). Metabolic rate rose by ∼37% above resting levels, peaking 60 min after feeding before returning to baseline within 2 h. When scaled across the day, digestion increased daily metabolic needs by ∼8.2% of …

Fisheries Research Report No. 362: Characterising Essential Benthic Habitats And Environmental Drivers Of Fishery Recruitment In The Exmouth Gulf Prawn Managed Fishery, Scott Evans, Nick Konzewitsch, Rachel Marks, Renae Hovey, Gary A. Kendrick, Lynda M. Bellchambers

Fisheries Research Reports

Fisheries management relies on the development and evolution of effective assessment and monitoring techniques that are applicable in a range of fishery contexts (Fletcher et al., 2016; L. M. Robinson et al., 2021). The assessment of fish habitats and environmental drivers that influence recruitment is central to sustainable fisheries management (de Lestang et al., 2010; Galindo-Cortes et al., 2010; Gao & Wang, 2021). Western Australia conducts robust fishery-specific monitoring and assessment programs to ensure the sustainable use of its aquatic resources (Newman et al., 2023). However, few long-term datasets exist that directly monitor critical fish habitats and environmental conditions that …

Fisheries Research Report No. 363 : South-West Freshwater Angling: Estimates Of Participation, Effort And Catch For 2024/25, Claire B. Smallwood, Karina L. Ryan, Eva Lai

Fisheries Research Reports

South-West Freshwater Angling (SWFA) in Western Australia is a licensed fishery primarily targeting the Brown Trout (Salmo trutta) and Rainbow Trout (Oncorhynchus mykiss), which are stocked in selected dams and rivers, as well as the introduced Redfin Perch (Perca fluviatilis) and the native Freshwater Cobbler (Tandanus bostocki). Since 2000/01, annual phone-recall surveys have been undertaken using the SWFA licence database as the sampling frame. This monitoring provides information to understand the fishery and support future management decisions. For the first time, data are reported by basin for different waterbody types (public dams, rivers) as well as for specific key fishing …

Life History And Distribution Of Two Species Of Cownose Ray, Rhinoptera Bonasus And Rhinoptera Brasiliensis, In Mississippi Coastal Waters, Anna Millender

Master's Theses

Historically, the American Cownose Ray (Rhinoptera bonasus) was considered the only rhinopterid residing in the northern Gulf of Mexico (GOM); however, recent studies have confirmed the presence of the Brazilian Cownose Ray (Rhinoptera brasiliensis) throughout this region. The current study investigated the life history and distribution of both species within Mississippi waters, an area that previously represented a data gap for both species. From April 2016 – July 2025, 193 R. bonasus and 94 R. brasiliensis were analyzed to describe the reproductive biology. Reproductive timing, mating, gestation length, and parturition were similar among species. Although more …

Investigating Mariculture-Associated Ecosystem Services Across The Northern Gulf Of Alaska, Josianne Haag

Oceanography

The rapid expansion of mariculture in Alaska can drive physical and chemical alterations to the marine environment by introducing non-native organisms or artificially increasing the biomass of a native species. Currently, the main mariculture products grown in Alaska include the Pacific oyster (Crassostrea gigas), the Pacific blue mussel (Mytilus trosuslus), and three macroalgae species: ribbon kelp (Alaria marginata), sugar kelp (Saccharina latissima), and bull kelp (Nereocystis luetkeana). This dissertation examines how these species can impact their surrounding environment to better inform management practices for this growing industry. This research characterized the resource use of C. gigas and M. trossulus seasonally …

Right Place, Right Time: Intermittent Habitats And Mosaic Structure Drive Juvenile Coho Salmon Growth In A Subarctic Alaska Watershed, Andrew Rothenberger

Fisheries

Pacific salmon (Oncorhynchus spp.) rely on diverse freshwater habitats to complete their lifecycle. Within Alaska’s short summer season, juveniles use a complex mosaic of habitats that vary in quality across space and time, but the patterns of habitat use in large complex watersheds are poorly known and difficult to document. To evaluate how habitat conditions of hydrology types influence juvenile performance, I conducted an in-situ enclosure experiment in the Fox River watershed of Kachemak Bay, Southcentral Alaska, measuring age-0 coho salmon (Oncorhynchus kisutch) growth across four hydrologic types: a glacial and snow-fed natal creek, a groundwater-fed natal creek, a non-natal …

Population Genomics Of Pacific Herring Spawning Aggregations In The Eastern Bering Sea, Sydney A. Almgren

Fisheries

Pacific herring (Clupea pallasii) is a critical forage fish to the marine environment, economy, and culture of Alaska. However, despite the importance of Pacific herring in Alaska and throughout the North Pacific, knowledge gaps exist for foundational genomic characteristics of the species, including genetic population structure and the basis of genetic sex determination. In this thesis, I addressed these knowledge gaps using low coverage, whole genome sequencing. I assessed population structure and genetic diversity across seven sampling sites and found three genetic populations: Unalaska, the farthest south sampling location, Kotzebue, the farthest north, and a third group unassociated with geographic …

Fish-Spec: Fast Identification System For Handheld Spectroscopy And Species Classification, Mitchell Sueker, Nicholas Mackinnon, Gregory Bearman, Amanda Tabb, Diane Kim, Rosalee S. Hellberg, Alireza Akhbardeh, Hamid Reza Marateb, Jianwei Qin, Moon Kim, Fartash Vasefi, Hossein Kashani Zadeh

Food Science Faculty Articles and Research

Accurate fish species identification is critical to prevent mislabeling and fraud in the seafood industry. We present a handheld multi-mode point spectroscopy system that combines fluorescence (365 and 395 nm excitation) and reflectance measurements in the visible to near-infrared (∼350–900 nm) and short-wave infrared (∼900–1700 nm) regions for rapid, non-destructive classification of fish fillets. Tissue spectra were acquired at 25 positions on 68 fillets from 11 species, in both frozen and thawed states. Feature-level fusion across all four modes enabled higher classification accuracy than any single mode alone. A global machine-learning model classified all species with 85 ± 2.8 %, …

Fisheries Research Report No. 360: Best Practice And Policy In Australian Abalone Stock Enhancement, Frdc Project No. 2019/110, Lachlan W. Strain, Anthony M. Hart

Fisheries Research Reports

This report provides the most comprehensive evaluation of abalone stock enhancement in Australia to date. The review demonstrates the significant advancements in abalone stock enhancement and concludes that the knowledge and expertise to undertake large-scale (commercial) abalone stock enhancement is present within Australia. The development of policy/guidelines on marine stock enhancement has occurred across all jurisdictions but is still limited in abalone specific policy that could facilitate commercial enhancement programs effectively. Unfortunately, there is a high degree of variability between jurisdictions in both capacity and policy, which was reflected in the jurisdictional scoring against current “best practice” on marine stock …

Fisheries Research Report No. 357: Recreational Fishing For Marron In South-West Western Australia In 2025 - Estimates Of Participation, Effort And Catch, Claire B. Smallwood, Karina L. Ryan, Eva Lai

Fisheries Research Reports

The smooth marron (Cherax cainii) (‘marron’) is endemic to freshwater dams and rivers of south-west Western Australia. Marron are managed as a single stock within the South-West Recreational Freshwater Resource and are highly vulnerable to over-exploitation due to the biological characteristics of the species (e.g., low fecundity, localised populations) as well as environmental (e.g., habitat loss, reduction in rainfall) and human (e.g., fishing, land clearing) pressures on freshwater ecosystems.

Due to this vulnerability, this species has been the focus of research, monitoring and management since the 1970’s. Since 2000, annual phone-recall (2000 – 2021) and online-recall (2022 – 2025) surveys …

Fisheries Research Report No. 355: Recreational Fishing For Western Rock Lobster In 2024/25: Estimates Of Participation, Effort And Catch, Claire B. Smallwood, Karina L. Ryan, Alissa Tate

Fisheries Research Reports

The Western Rock Lobster (WRL) (Panulirus cygnus) is the most commonly caught Rock Lobster (RL) species in Australia. Catches from the commercial and recreational sectors are required to determine and monitor Total Allowable Commercial Catch (TACC), Total Allowable Recreational Catch (TARC) and the proportion of Allowable Harvest Level (AHL) achieved. The TARC is evaluated annually based on a 5-year average.

Data for the recreational sector are obtained using phone-recall surveys to provide annual estimates of participation, fishing effort and retained catch (by numbers) from recreational fishers who hold a RL licence. Average weight, obtained from boat ramp surveys, are used …

Fisheries Science Update - Western Australian Shark Resource: 2024 Stock Assessment Outcomes, Department Of Primary Industries And Regional Development, Western Australia

Fisheries Science Updates

The Western Australian (WA) shark resource includes more than 100 species of sharks and rays.

Key shark species are sustainably harvested in two commercial shark fisheries that provide fresh, local, affordable seafood to the WA community.

The WA shark resource has been in recovery since the 1990s–2000s when stocks were found to be at risk.

The Department of Primary Industries and Regional Development (DPIRD) tracks stock status by undertaking periodic weight of evidence stock assessments of indicator species.

Gummy, whiskery, dusky whaler, and sandbar sharks, are the indicator species for the WA shark resource, and make up ~80% of the …

Assessing The Effectiveness Of Extension Services On Aquaculture Development In Ashanti Region, Ghana, Bismark Essel

World Maritime University Dissertations

No abstract provided.

Fisheries Research Report No. 354: Recreational Fishing For Abalone In Western Australia In 2024/2025 - Estimates Of Participation, Effort And Catch, Claire B. Smallwood, Karina L. Ryan, Lachlan W. Strain

Fisheries Research Reports

The Western Australian Recreational Abalone Fishery (RAF) operates in shallow coastal waters as a hand collection fishery while wading or diving. Three species of abalone are allowed to be caught. Roe’s abalone (Haliotis roei) are generally collected while wading from the shore in accessible nearshore reef complexes along the West and South Coast Bioregions. Greenlip abalone (H. laevigata) and Brownlip abalone (H. conicopora) are collected while wading (including snorkelling and freediving) and diving (using compressed air) predominantly along the South Coast Bioregion.

Recreational fishing for the three abalone species is licensed and highly regulated, especially in the Western Zone (which …

West Coast Demersal Scalefish Resource Recovery Support Package: 2024-25 Report, Department Of Primary Industries And Regional Development, Western Australia

Fisheries Published Reports

The West Coast Demersal Scalefish Resource (WCDSR) includes over 100 species in inshore (20–250 m deep) and offshore ( > 250 m) demersal habitats of the West Coast Bioregion. These species are caught by charter, commercial and recreational fishers. The WCDSR is in recovery and managed under a 20-year recovery plan (2010–2030). DPIRD tracks recovery progress through scientific stock assessments of indicator species (snapper, WA dhufish, and baldchin groper) every 3 years. The 2021 WCDSR stock assessment showed limited recovery and additional management action was required. In December 2022, the Minister for Fisheries announced commercial and recreational (including charter) sector management …

Comparison Of Pcr-Based Methods For The Detection Of Canned Tuna Species, Chloe P. Castanon, Denise Hernandez, Akshay N. Khetrapal, Rosalee S. Hellberg

Food Science Faculty Articles and Research

Canned tuna is susceptible to mislabeling due to its high consumer demand, complex global supply chains, and range of prices. DNA barcoding of a short fragment of the mitochondrial control region (CR), termed the CR mini-barcode, has been established as an effective method for tuna species identification. However, the high level of DNA degradation in canned tuna products reduces the effectiveness of this method. Therefore, this study aimed to compare CR mini-barcoding to targeted (i.e., real-time or multiplex) PCR-based methods to determine the most effective approach for canned tuna species identification. DNA was extracted in duplicate from 24 canned tuna …

Evaluation Of Dietary Additives On Yellowtail Kingfish (Seriola Lalandi) Gut And Skin Health And Disease Resistance Against Photobacterium Damselae Subsp. Damselae, Md Reaz Chaklader, Lindsey Woolley, Chelsea Woods, Frances Stephens, Richard Smullen, Gavin Partridge

Fisheries Research Articles

The present study evaluated the effectiveness of five dietary additives in improving growth performance, gut and skin health and disease resistance against Photobacterium damselae subsp. damselae (Pdd) in yellowtail kingfish (YTK) (Seriola lalandi). The additives were top-coated onto a commercial diet. The five additives evaluated were brewer’s yeast (BY), a yeast-based mannan oligosaccharide (MOS), a polyphenol product, a monoglyceride product and a combination of MOS and a superoxide dismutase (SOD) product. The monoglyceride and polyphenol products were trialled at both a low and high inclusion level. Diets were fed to YTK in triplicate tanks for 55 days. The …

Fisheries Occasional Publication No. 149 - Economic Contribution Of Wild-Catch Fishing In Western Australia, 2024: Beyond Gross Value Of Production, Dipesh Maharjan, Vilaphonh Xayavong, Ben Fraser, Rebecca Thomas

Fisheries Occasional Publications

The wild-catch fishing industry plays a significant role in Western Australia’s economy, particularly in regional communities. This report summarises the economic contribution of the commercial wild-catch fishing sector in 2024, based on REMPLAN’s input-output (I-O) modelling methodology and DPIRD data and analysis. This report focuses on key economic indicators including total economic output, gross value added (GVA), and employment (FTEs).

Key findings:

• Total Economic Output of the wild-catch fishing industry is $1.22 billion (total value of goods and services produced, including intermediate inputs)
• Gross Value Added (GVA) of the wild-catch fishing industry is $487 million (value of profit, wages, salaries …

Fisheries Science Update - South Coast Demersal Scalefish Resource - September 2025, Department Of Primary Industries And Regional Development, Western Australia

Fisheries Science Updates

The Department of Primary Industries and Regional Development (DPIRD) monitors the status of Western Australia’s demersal scalefish resources by undertaking regular stock assessments on indicator species.

This summary provides key outcomes of the 2024 assessment of the South Coast Demersal Scalefish Resource (Fisheries Research Report No. 339).

Fisheries Science Update - Kimberley Demersal Scalefish Resource - September 2025, Department Of Primary Industries And Regional Development, Western Australia

Fisheries Science Updates

The Department of Primary Industries and Regional Development (DPIRD) monitors the status of Western Australia’s demersal scalefish resources by undertaking regular stock assessments on indicator species.

This summary provides key outcomes of the 2025 assessment of the Kimberley Demersal Scalefish Resource (Resource Assessment Report No. 4).

Resource Assessment Report No. 05: West Coast Deep Sea Crustacean Resource 2024 Assessment, Emma-Jade Tuffley, Simon De Lestang

Resource Assessment Reports

The West Coast Deep Sea Crustacean resource consists of crystal crab (snow) (Chaceon albus), champagne crab (spiny) (Hypothalassia acerba) and giant crab (Pseudocarcinus gigas). The resource is mainly accessed by the commercial West Coast Deep Sea Crustacean Managed Fishery (WCDSCMF), which primarily targets crystal crabs. The West Coast Rock Lobster Managed Fishery (WCRLMF) also retains a small amount of champagne crabs as byproduct of deep-water rock lobster fishing. The WCDSCMF is a pot-based fishery using baited pots operated in a long-line formation in shelf edge waters ( > 150 m in depth) off the West …