Marine Biology Commons^™

A Genomic Investigation Of Divergence Between Tuna Species, Pavel V. Dimens

Dissertations

Effective management and conservation of marine pelagic fishes is heavily dependent on a robust understanding of their population structure, their evolutionary history, and the delineation of appropriate management units. The Yellowfin tuna (Thunnus albacares) and the Blackfin tuna (Thunnus atlanticus) are two exploited epipelagic marine species with overlapping ranges in the tropical and sub-tropical Atlantic Ocean. This work analyzed genome-wide genetic variation of both species in the Atlantic basin to investigate the occurrence of population subdivision and adaptive variation. A de novo assembly of the Blackfin tuna genome was generated using Illumina paired-end sequencing data and …

Effects Of Shoreline Development And Freshwater Discharge On Nekton Assemblage And Trophic Structure In A Northern Gulf Of Mexico Estuary, Glenn Schumacher

Master's Theses

Coastal salt marshes support a diversity of nekton and facilitate critical ecosystem functions but are threatened by shoreline development and climate change. Therefore, coastal ecosystem managers have begun incentivizing the use of living shorelines (LS), erosion control structures incorporating native plantings, to mitigate ecological consequences of marsh loss. However, post-restoration climate changes may shift habitat templates and negate positive effects of ecosystem restoration. I evaluated the ecology nekton along LS, natural marshes, hardened shorelines and greyed shorelines within Biloxi Bay, Mississippi, during a high freshwater discharge (HFD) period by comparing nekton assemblage (using species richness, Shannon-Wiener diversity, and relative abundance), …

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 …

Induced Spawning Of Captive Tripletail Lobotes Surinamensis, Nicholas Adams

Master's Theses

The Tripletail, Lobotes surinamensis, is an emerging candidate species for U.S. marine aquaculture. This work aimed to address two bottlenecks for hatchery production of the species by developing a hormonal induction protocol to obtain fertile spawns from captive brooders and a method for sex identification of candidate brooders.

Single pairs selected among a captive-held broodstock conditioned under a natural photothermal cycle were induced with one of five treatments (n = 5 or 6 replicates per treatment). Control (no hormone) and hCG (1,100 IU.kg^-1 for females, 550 IU.kg^-1 for males) pairs did not spawn. Pairs treated with GnRHa …

Using Deep Learning And Uav Imagery To Detect Elkhorn Coral In St. Croix’S East End Marine Park, Samuel Wyatt

Master's Theses

Elkhorn coral, or Acropora palmata, is an important reef building species that promotes species abundance and other ecological services to the communities in the US Virgin Islands. We captured high resolution imagery of a reef in St. Croix’s East End Marine Park using a Wingtra One UAV. We then used deep learning techniques to detect individual coral colonies. We compared two deep learning models, FasterRCNN and MaskRCNN, and found that the models achieved accuracy shores up to 0.78. These scores improved when examining only larger corals in shallow waters. The model was able to both detect Elkhorn coral and …

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 …

Kinorhynch Diversity In The Southern Gulf Of Mexico And A Description Of Dracoderes Chaac Sp. Nov., Stephen C. Landers, Kellan Hoffman, Nuria Sanchez, Martin Sorensen

Gulf and Caribbean Research

Sediment collections from the southern Gulf of Mexico between the Texas—Mexico border and the Yucatán Peninsula have resulted in many new kinorhynch species distribution records and the finding and taxonomic description of a new species, Dracoderes chaac sp. nov. This study focused on the non—echinoderid members of the Phylum Kinorhyncha, many of which are rare or restricted to only a few locations. A total of 136 specimens were identified from 24 sediment stations, distributed among the following species: Antygomonas gwenae, Campyloderes vanhoeffeni, Centroderes readae, Condyloderes flosfimbriatus, Co. rohalorum, Cristaphyes panamensis, Dracoderes chaac sp. nov., …

Temporal And Spatial Occurrence Of Karenia Brevis Blooms In The Northcentral Gulf Of Mexico, Jonathan Jackson, Yee Lau, Paul Mickle, Just Cebrian

Gulf and Caribbean Research

No abstract provided.

Life History Of Swordfish, Xiphias Gladius, Caught In The Northern Gulf Of Mexico, Anna K. Millender, Jeremy M. Higgs, Nancy J. Brown-Peterson, Michael J. Andres, James S. Franks

Gulf and Caribbean Research

The current study examined 93 Swordfish, Xiphias gladius, (64 females, 27 males, 2 unknown) ranging in size from 77.6–246.3 cm lower jaw fork length (LJFL) from the northern Gulf of Mexico (GOM). Samples were collected between March and August in 2005–2007, 2017–2019 and 2021. Age estimates of 51 Swordfish resulted in a maximum observed age of 11 years (205.0 cm LJFL) and 7 years (190.4 cm LJFL) for females and males, respectively. Observed and back—calculated length—at—age data were fitted to 4 growth models (2— and 3— parameter von Bertalanffy, Gompertz, and logistic). The 2—parameter von Bertalanffy was the model …

Stony Coral Tissue Loss Disease And Other Diseases Affect Adults And Recruits Of Major Reef Builders At Different Spatial Scales In The Dominican Republic, Aldo Croquer, Someira Zambrano, Samuel King, Aurelio Reyes, Rita I. Sellares Blasco, Andreina Valdez Trinidad, Maria Villalpando, Yira Rodriguez-Jerez, Estefany Vargas, Camilo Cortes-Useche, Macarena Blanco, Johanna Calle-Triviño, Rebecca García-Camps, Ana C. Hernández-Orquet, Ruben Torres, Iker Irazabal, Laura Díaz, Yassmin Evangelista, Emy Miyazawa

Gulf and Caribbean Research

Monitoring programs can help understand coral disease dynamics. Here, we present results from a national program in the Dominican Republic (DR) aimed at evaluating coral diseases 3 times a year following a nested spatial design. Prevalence of coral diseases in DR varied from sites to regions, suggesting that disease dynamics can be driven by local processes and/or across larger spatial scales. Three diseases were common: Dark Spot (DSD), Yellow Band (YBD) and Stony Coral Tissue Loss Disease (SCTLD). DSD and YBD were more prevalent across the western coast (north and south), whereas SCTLD was restricted for the study period to …

Phylogenetic Origins And Age-Based Proportions Of Malacho (Elops Smithi) Relative To Ladyfish (Elops Saurus): Species On The Move In The Western Gulf Of Mexico, Damon Williford, Nicolette S. Beeken, Joel Anderson, Polly Hajovsky, Roberta Weixelman

Gulf and Caribbean Research

Two species of ladyfish occur in the Gulf of Mexico (GOM), Elops saurus and Elops smithi, that are morphologically indistinguishable except for vertebral counts but can also be identified by mitochondrial DNA haplotypes. Here we expand on previous work, most of which has occurred in Florida, and examine the demography, phylogenetics, geographic distribution, and age—structure of ladyfishes in Texas estuaries. Fishery—independent gill net data demonstrated that ladyfishes increase in abundance from north to south along the Texas coast. The abundance of ladyfishes also increased in Texas waters from 1982–2021, which coincides with recent trends of warmer winters. Genetic data …

Distribution, Maturity, Age And Growth Of Gray Snapper (Lutjanus Griseus) In The Northwestern Gulf Of Mexico, Joel Anderson, Dusty Mcdonald, Ethan Getz, Roberta Weixelman, Faye Grubbs, Jason Ferguson

Gulf and Caribbean Research

Recent population expansion of Gray Snapper, Lutjanus griseus, in the northern Gulf of Mexico is driving increasing catch in the recreational fishery in Texas. We assessed long—term trends in distribution and abundance of Gray Snapper in Texas using fishery—dependent and fishery—independent data collected by the Texas Parks and Wildlife Department in the years 1980 — 2019. Boosted regression trees (BRT) were used to evaluate factors (water quality, season, depth, bay and inlet distance) driving Gray Snapper presence in fishery—independent samples of juveniles (seines) and subadults (gill nets) found in estuaries. Estuarine Gray Snapper were subsequently sampled from gill nets, …

Implications Of Community-Based Management Of Marine Reserves In The Philippines For Reef Fish Communities And Biodiversity, Sara E. Marriott, Courtney Cox, Rizaller C. Amolo, Dean Apistar, Roquelito H. Mancao, Kim De Mutsert

Faculty Publications

Overfishing and destructive fishing practices are major threats to marine biodiversity in the Philippines, where over 1.9 million small-scale fishers are supported by these biodiverse marine communities. Nearly 50% of all marine fish capture in the Philippines is from artisanal fisheries, with much of it not reported or under-reported. Marine reserves, where fishing is prohibited have been created in many local government units to help restore and preserve this biodiversity. The success of these marine reserves is still under serious debate with effective management still representing a significant challenge. The lack of a governance system to centrally managed marine reserves …

Sperm Repository For A Breeding Program Of The Eastern Oyster Crassostrea Virginica: Sample Collection, Processing, Cryopreservation, And Data Management Plan, Huiping Yang, Yuanzi Huo, Jayme C. Yee, Scott Rikard, William C. Walton, Eric A. Saillant

Faculty Publications

The Eastern oyster Crassostrea virginica (Family Ostreidae) is one of the most important fishery and aquaculture species in the U.S. and is a keystone species for coastal reefs. A breeding program was initiated in 2019 to support the fast-growing aquaculture industry culturing this species in the Gulf of Mexico. Oysters from 17 wild populations in embayment along the U.S. Gulf of Mexico coast from southwest Florida to the Matagorda Bay, Texas were used as broodstock for the program to maximize genetic diversity in the base population. A sperm repository of the broodstock was established to support the breeding project. The …

Editorial: Unraveling Mechanisms Underlying Annual Plankton Blooms In The North Atlantic And Their Implications For Biogenic Aerosol Properties And Cloud Formation, Michael Behrenfeld, Sarah D. Brooks, Peter Gaube, Kristina D.A. Mojica

Faculty Publications

No abstract provided.

Polycyclic Aromatic Hydrocarbons And The Microbiomes Of Two Benthic Species, Samantha Ells

Master's Theses

The presence of oil has been shown to affect the microbiomes of the water column, sediments, and organisms, both by altering the diversity and the composition of those microbial communities. If the microbiome is altered it may no longer provide benefits to its host organism, impacting its ability to survive. Thus, it is important to understand the effects of large-scale contamination events including the Deepwater Horizon oil spill. This study set out to examine the effects of oil exposure on the microbiome of two benthic species, southern flounder (Paralichthys lethostigma) and eastern oysters (Crassostrea virginica) to further understand the effects …

Population Parameter Estimation And Stable Isotope Analysis Of Gulf Sturgeon (Acipenser Oxyrinchus Desotoi) In The Pascagoula River, Alfonso Cohuo

Master's Theses

Gulf Sturgeon (GS), Acipenser oxyrinchus desotoi, are a threatened, anadromous fish species in the northern Gulf of Mexico. Their range is from the Pearl River, LA, in the west to the Suwannee River, FL, in the east with a longitudinal divide at Mobile Bay, AL, creating a western population unit (WPU) and an eastern population unit (EPU). Sturgeon belonging to the WPU exhibit lower abundances, higher mortality rates, and are overall less studied than their EPU counterparts. Notable data gaps for the WPU includes the absence of recent population parameter estimations and confirmed feeding habitat. My thesis aims to …

Spatial And Seasonal Patterns Of Above- And Belowground Vegetation Biomass And Potential Drivers In The Pascagoula River Delta, Ms, Evan Grimes

Master's Theses

Coastal wetlands provide a valuable wealth of services to the greater coastal ecosystem and human communities. However, threats such as sea level rise and conservation projects, such as freshwater diversions, have the potential to alter coastal wetlands in different ways. In this thesis, I describe the effects of inundation and nitrogen on vegetation productivity using a field-sampling approach and an in situ controlled mesocosm experiment, called a marsh organ. The West Channel of the Pascagoula River contained significantly higher belowground biomass than the East Channel, which is more anthropogenically modified. Vertical distribution of belowground biomass did not strongly vary between …

Environmental Dna (Edna) Surveys For The Smalltooth Sawfish, Pristis Pectinata, In The Chandeleur Islands, Louisiana, Emma M. Humphreys

Honors Theses

The Critically Endangered smalltooth sawfish, Pristis pectinata, was historically found throughout tropical and subtropical coastal waters of the Atlantic Ocean. As a result of mortalities in fisheries and habitat degradation, they became largely restricted to southwest Florida in the U.S. and the Bahamas by the 1980s. However, recent public encounter reports of sawfish in the Florida panhandle, Mississippi, and Louisiana suggest this species is occasionally present in northern Gulf of Mexico waters. Targeted species surveys are needed to improve our understanding of the occurrence and status of this species in these waters. This research used environmental DNA (eDNA) methods …

Patterns Of Habitat Use And Trophic Structure In Turtle Grass (Thalassia Testudinum)-Dominated Systems Across The Northern Gulf Of Mexico, Christian Hayes

Dissertations

Seagrass structural complexity is a primary driver of nekton recruitment and faunal community structure. Few studies, however, have quantified the role of seagrass complexity on habitat use and trophic structures over large spatial scales. A large-scale simultaneous survey was conducted to assess relationships of multiple seagrass morphological complexity metrics to nekton habitat use, trophic dynamics, and blue crab (Callinectes sapidus) growth and mortality across the Northern Gulf of Mexico. Seagrass morphological and nekton community characteristics depended on site and season, and regional variation in seagrass morphology was an important driver of juvenile nekton abundance, species richness, beta diversity, …

Trophic Ecology Of Mesopelagic Fish Larvae And Juveniles In The Northern Gulf Of Mexico, Emily Gipson

Master's Theses

The deep-pelagic environment encompasses ocean waters below 200 m depth, and comprises 90% of the volume of the Gulf of Mexico. Deep-pelagic fishes are important prey for many oceanic consumers, but relatively little is known about their early life history, including larval fish trophic ecology. An understanding of the role deep-pelagic fish larvae have in oceanic food webs is important in the development of ecosystem models that examine the connectivity (via vertical migrations) between the deep-pelagic and epipelagic environments with respect to trophic interactions, nutrient cycling, and carbon sequestration. In this study, archived plankton samples collected during 2010 and 2011 …

Assessing The Occurrence Of Trichechus Manatus Latirostris In Mobile Bay, Alabama Using Edna, Elora Pierce

Honors Theses

In the past several decades Florida manatees (Trichechus manatus latirostris) have begun to expand their summer range into the northern Gulf of Mexico. Because this is a recent occurrence, not much is known about their habitat use and distribution in this region. Citizen-sourced sighting data suggests that Florida manatees frequent subembayments of Mobile Bay, Alabama, reaching a sighting peak in August. To assess the occurrence of manatees in this area environmental DNA surveys were used from winter (February 19-20) and summer (August 21-22) of 2018. At each of the 21 sites ranging from the mouth of Mobile Bay, …

Updated Status Of Bayou Darter, A Narrowly Ranged Endemic In A Geomorphically Active Watershed, Joshua Hubbell, Loren Stearman, Jacob Schaefer

Faculty Publications

Comparison of historical and current data are critical in establishing population trends for imperiled taxa. In this paper we revisit the status of the Bayou darter Nothonotus rubrum, an endemic fish restricted to the Bayou Pierre river system, Mississippi, USA. The Bayou Pierre has experienced substantial geomorphic change in the past century, leading to questions about persistence of this imperiled species. We employed historical field notes and museum records to identify collection localities, and we resampled 32 of these localities using methodologies comparable to the original samples. We further sampled an additional 10 sites with similar methodologies to fill …

Seasonal Occurrence, Horizontal Movements, And Habitat Use Patterns Of Whale Sharks (Rhincodon Typus) In The Gulf Of Mexico, Eric R. Hoffmayer, Jennifer A. Mckinney, James S. Franks, Jill M. Hendon, William B. Driggers, Brett J. Falterman, Benjamin Galuardi, Michael E. Byrne

Faculty Publications

In the northern Gulf of Mexico (GOM), whale sharks (Rhincodon typus) form large aggregations at continental shelf-edge banks during summer; however, knowledge of movements once they leave aggregation sites is limited. Here we report on the seasonal occurrence of whale sharks in the northern GOM based on over 800 whale shark sightings from 1989 to 2016, as well as the movements of 42 whale sharks tagged with satellite-linked and popup satellite archival transmitting tags from 2008 to 2015. Sightings data were most numerous during summer and fall often with aggregations of individuals reported along the continental shelf break. Most sharks …

Patterns Of Dispersion, Movement And Feeding Of The Sea Urchin Lytechinus Variegatus, And The Potential Implications For Grazing Impact On Live Seagrass, Adrianna Parson, Joseph M. Dirnberger, Troy Mutchler

Gulf and Caribbean Research

The sea urchin Lytechinus variegatus is a known grazer of both living and dead tissue of turtlegrass, Thalassia testudinum, occasionally denuding large areas of seagrass. Field studies have attempted to assess effects of herbivory on seagrass by enclosing urchins at various densities. However, it is unclear how unrestricted urchins affect seagrass at lower densities more typically observed in the field. This study describes movement, feeding, and distribution of L. variegatus within beds of T. testudinum in St. Joseph Bay, Florida (USA) to quantify this urchin’s impact as a seagrass grazer. Urchins were absent from portions of seagrass beds closest to …

A Sea Turtle Population Assessment For Florida's Big Bend, Northeastern Gulf Of Mexico, Ryan M. Chabot, Ryan C. Welsh, Cody R. Mott, Jeffrey R. Guertin, Brian M. Shamblin, Blair E. Witherington

Gulf and Caribbean Research

Coastal waters of Florida’s Big Bend, Gulf of Mexico (GOM) once supported one of the largest sea turtle fisheries in the United States. To fill an information gap in this region on abundance and distribution of sea turtles, we used vessel—based distance sampling and active capture methods to characterize current foraging aggregations near the St. Martins Marsh Aquatic Preserve. Over 10 sampling periods between 2012—2018, we completed 513 km of transects and recorded 819 turtles among 4 species—green turtle (Chelonia mydas, n = 624), Kemp’s ridley (Lepidochelys kempii, n = 147), loggerhead (Caretta caretta, …

Elevating Dissolved Oxygen—Reflections On Developing And Using Long-Term Data, Nancy N. Rabalais

Gulf and Caribbean Research

This prospectus took me about as long to generate as my 36—year record of working on the issue of northern Gulf of Mexico (nGOM) oxygen deficiency, or so I felt. There was so much to cover, but I focused on the issue of hypoxia on the Louisiana continental shelf from the early 1980s to present and my participation in the research and outreach. Not that I was ignoring other aspects of my academic research career (e.g., stone crab populations and their differences in physiology and larval development along the nGOM coast; settlement of crab megalopae, especially blue crabs, on artificial …

Oldest Indo-Pacific Lionfish (Pterois Volitans/P. Miles) Recorded From The Northwestern Gulf Of Mexico, Raven D. Blakeway, Alexander Q. Fogg, Glenn A. Jones

Gulf and Caribbean Research

Indo-Pacific lionfish (Pterois volitans/miles) were first detected off the coast of Florida in the 1980s, with aquaria release being the most likely mechanism for introduction. Since then, lionfish have proliferated through the Western Atlantic Ocean, Caribbean Sea, and Gulf of Mexico (GOM). Here, we report the oldest lionfish aged on record in the Western Atlantic, removed from Flower Garden Banks National Marine Sanctuary (FGBNMS) in the GOM. In August 2018, a research expedition removed 745 lionfish from FGBNMS, of which a subset were retained for age and growth estimation. The oldest lionfish was a 10 y old male, …

Review: Formation And Metabolic Function Of Coral Rubble Biofilms In The Reef Ecosystem, Andres Sanchez-Quinto, Luisa I. Falcon

Gulf and Caribbean Research

When coral dies, their calcareous skeletons constitute coral rubble in conjunction with the cementing activity of coralline algae and bacteria, creating a secondary reef structure which takes from years to decades to form. Healthy coral reefs differ from coral—rubble dominated reefs in microbial taxonomic composition and metabolic functional roles. The metabolisms of healthy reefs are dominated by autotrophic pathways, where carbon and nitrogen fixation dominate, while the metabolism of rubble—dominated reefs predominate in degradation of organic matter. Nitrogen fixation is 3 orders of magnitude lower in rubble—dominated reefs than in healthy reefs. Coral—rubble harbors a vast diversity of microbes that …

Assessment Of Genetic Diversity In Largetooth Sawfish, Pristis Pristis, Populations Over The 20th Century, Ann Fearing

Master's Theses

The Critically Endangered Largetooth Sawfish, Pristis pristis, experienced global declines in range and abundance over the past century and Australia is now their last stronghold. This research aimed to understand whether these declines have been accompanied by a reduction in levels of genetic diversity. Using P. pristis tissue samples sourced from natural history specimens, three fragments (616-bp, 386-bp, 141-bp) in the mitochondrial DNA (mtDNA) control region were PCR-amplified. At each fragment, significant genetic structure was found in P. pristis overall (Φ_ST=0.946, N=9; 0.813, N=54; 0.771, N=99). The Indo-West Pacific and Atlantic/Eastern Pacific each harbor genetically distinct lineages of …