Project Leader: Justin McDonald, Lab Technician/M.S. Student

Project Details

Figure 1. An adult Greater Amberjack caught in the Alabama Artificial Reef Zone. Background: The Greater Amberjack (Seriola dumerili) is a widely distributed pelagic, epibenthic, member of the Carangidae family found in warm temperate waters. These fish are the largest carangid in the Gulf of Mexico and are known for having high endurance and fighting capability making them highly desirable to recreational fisherman. In Alabama, the recreational catch of Greater Amberjack has dominated landings (historically through present) with a peak catch near 2.5 million pounds in 2003. Greater Amberjack were declared “overfished” in a 2006 stock assessment and have retained that designation through the latest stock assessment in 2016. The goal of this study is to examine the age composition, as well as reproductive seasonality, of Greater Amberjack throughout the Alabama Artificial Reef Zone (AARZ). This data will provide better estimates for the health of the stock off the Alabama coast and provide additional data to increase the precision of models used in future stock assessments.

Project Leader:Mark A. Albins, Ph.D., Research Associate

Project Details

Background:

Artificial reefs are often used to increase fishing opportunities, particularly in areas like the Northern Gulf of Mexico, where natural reef habitat is limited. Yet, the ecological and fisheries benefits of such reefs remain a topic of debate. Reefs could serve to attract animals away from nearby habitats, aggregating them in known locations and thereby making them easier to catch. Reefs could also increase habitat availability and/or food resources resulting in increased production. The Alabama Department of Conservation and Natural Resources Marine Resource Division has recently deployed a large number of new artificial reefs in the inshore and offshore waters of Alabama. These reefs have been added to an extensive existing network of artificial reefs to enhance nearshore fishing opportunities and increase the amount of high-quality habitat available for important fisheries species such as Red Snapper.

Project Leader:Trey Spearman, Project Manager

Project Details

Figure 1. An example of a side-scan image mosaic created from a square nautical mile survey off the coast of Alabama.

Background:

The benthic habitat assessment program of the Fisheries Ecology Lab developed from a need to assess marine benthic habitats in an accurate and efficient manner. Using bathymetric and side-scan sonar, benthic habitats ranging from oyster reefs, seagrass beds, and artificial and natural reef structures have been mapped in the nearshore and offshore coastal areas of Alabama since 2007. These data are used in support of a wide variety of research projects of the University of South Alabama’s Department of Marine Sciences and the Dauphin Island Sea Lab.

Project lead: Jackie Wilson, Research Technician

Background: For generations, the dynamic estuarine systems of Mobile Bay and Mississippi Sound have provided ecologically and economically important resources, upon which the livelihoods and cultural heritage of Alabama’s coastal communities rely. Often referred to as the nursery of the Gulf of Mexico’s fertile crescent, where freshwater influx from the Alabama river delta combined with rich, saline Gulf water, create an ideal habitat for juvenile species of all phyla. Among these, oysters (Crassostrea virginica), blue crab (Callinectes sapidus), and speckled trout or spotted seatrout (Cynoscion nebulosus) are fundamental to coastal socioeconomics, providing crucial ecosystem services including shoreline protection, commercial and recreational fisheries, working waterways for local jobs and public access, cultural experiences, and picturesque vistas sought by visitors from across the globe. Today, populations of these species are under threat or near collapse as a result of anthropogenic activities negatively impacting the environmental conditions of Gulf estuaries.

Project Leader:Edward Kim, Master’s Student

Project Details

Background:

Gray Snapper (Lutjanus griseus) constitute a significant recreational fishery and minor commercial fishery throughout the Gulf of Mexico, and a recent assessment in 2018 determined that the overall stock has been undergoing prolonged overfishing. Spatiotemporal gaps in our understanding of these fish that could better inform management still exist, particularly within the northcentral Gulf of Mexico. The absence of regional baseline data, combined with projections of population growth due to climatic warming, highlights the need for supplementary monitoring efforts. This study will investigate the abundance and distribution of Gray Snapper in the Alabama Artificial Reef Zone through the analysis of remotely operated vehicle footage from 2011 to 2019. This study will also examine the age, growth, and reproduction of Gray Snapper through predominantly fishery-dependent sampling in the coastal and offshore waters of Alabama and Mississippi. The findings from these studies will introduce new data for incorporation in future assessments, provide guidance for management decisions, and promote informed support of the fishery.

Project Leader:Dylan Kiene, Ph.D. Student

Project Details

Background:

The Coastal Alabama Acoustic Monitoring Program (CAAMP) is a long-standing monitoring program that has previously tracked the movement of several estuarine species including Red Drum (Sciaenops ocellatus) and Spotted Sea Trout (Cynoscion nebulosus). In 2019 CAAMP was redesigned to study Southern Flounder (Paralichthys lethostigma). Southern Flounder exhibit sexual dimorphism - a distinct difference in the size, appearance, and life history between sexes. Male Southern Flounder typically don’t get very large (<12in) and spend most of their lives offshore, while the females grow larger and mature in the estuarine waters of the Mobile Bay area. When female Southern Flounder reach maturity they migrate offshore during the late fall/winter to spawn.

Project Leader:aia Muñoz - Abril

Project Details

Background:

The second most fished member of Scombridae in the world is yellowfin tuna, Thunnus albacares. It is a top predator that lives in tropical and subtropical waters and some of the only teleosts that have developed physiological thermoregulation mechanisms to keep their muscles hotter than the surrounding water. Due to the characteristics of the species and other factors such as the fishery, it has been reported that populations of yellowfin tuna from different oceans have fragmented, which constitutes a threat to the species and its habitat, as it makes them more sensitive to extinction. Removing top predators from the marine ecosystem can cause trophic cascades and reorganization.

Project Leader:Trey Spearman, Research Assistant

Project Details

Effects of large-scale habitat modification on demersal fish and mobile invertebrates within Alabama’s Artificial Reef Zone

Figure 1: Trawl deployment (top) and catch brought on deck (bottom). Background: South of Mobile Bay, Alabama, the Alabama Artificial Reef Zone (AARZ) covers almost 2700 km2 of the continental shelf. This area has become a hotspot for recreational and commercial fishing due to artificial reef placement. With a growing need for both ecosystem-based fisheries management and fishery-independent data to support it, more information is needed on the demersal community residing within the AARZ. Quantitatively examining the demersal community across this reef zone will provide data to benefit current and future ecosystem-based modeling and management.

Project Leader: Sean P. Powers, Ph.D.

Project Details

Dataset DOI:

Localized depletion of marine and estuarine populations often results from large-scale natural and anthropogenic disturbances (e.g., hurricanes, oil spills) as well as overharvest of fisheries resources. Understanding how such localized depletions may affect populations at larger regional scales requires knowledge of connectivity among local populations within the larger regional landscape or metapopulation. Efforts to restore populations following such decreases requires similar knowledge. During the 2010 Deepwater Horizon oil spill, dramatic declines of oysters occurred within subtidal areas in estuaries west and east of the Mississippi River. We examined trajectories of particles, which were parameterized to mimic oyster larvae, using the ADvanced CIRCulation (ADCIRC) model to evaluate potential connectivity within and among embayments from Western Louisiana to Alabama. Patterns of larval settlement, which we defined as the intersection of a larval particle with known or expected oyster habitat at any point 13 to 21 days post-release, reflected much greater local contributions, with 50-90% of settled particles originating within the same subdivision of embayments. Exchange among subdivision was much less (0-40%) and settlement originating from outside the embayment of release was trivial under most scenarios (0-14%). Connectivity between adjacent basins was greatest for larvae released in the southern portions of the embayment, whereas connectivity among non-adjacent basins was not predicted under the scenarios modeled. Because most local populations are relatively isolated on ecological timescales, areas suffering from extensive local depletion are likely to require extensive time to recover due to the lack of larval subsidy from the overall regional population. Restoration would require building stepping-stone populations or reefs within and among basin to restore a high degree of connectivity.

Project Leader:Dylan Kiene, Ph.D. Student

Project Details

Background:

Vast expanses of intertidal sand/mudflats serve as critical links in the food web of nearshore communities along the southcentral Alaska coastline. One of the largest expanses of intertidal sand/mud flats occurs in the Copper River Delta and southeastern Prince William Sound (Orca Inlet). The rich abundance of benthic invertebrates residing in the sediment provides a significant prey resource for numerous species of fish, crabs, birds, and marine mammals. At seven stations located throughout Orca Inlet and the Western Copper River Delta, monthly otter trawl surveys were performed from April through October of 2002 – 2006. A diverse fish assemblage dominated by flatfish, sculpins, snake prickleback, and Crangon shrimp is present on the Copper River Delta. Several of the demersal fish species and one crab species that occur within the Copper River Delta are of significant value to recreational and commercial fisheries. Pacific Halibut, Lingcod, English Sole, Starry Flounder, and Dungeness crab appear to use the extensive network of sloughs and tidal mudflats as nursery habitats. To more accurately forecast future conditions and to ensure sustainable management, scientists and managers require sound scientific information to distinguish between natural and human-induced variability.

Project Lead: Dylan Kiene, Ph.D. Student

Background: Vast expanses of intertidal sand/mudflats serve as critical links in the food web of nearshore communities along the southcentral Alaska coastline. One of the largest expanses of intertidal sand/mud flats occurs in the Copper River Delta and southeastern Prince William Sound (Orca Inlet). The rich abundance of benthic invertebrates residing in the sediment provides a significant prey resource for numerous species of fish, crabs, birds, and marine mammals. At seven stations located throughout Orca Inlet and the Western Copper River Delta, monthly otter trawl surveys were performed from April through October of 2002 – 2006. A diverse fish assemblage dominated by flatfish, sculpins, snake prickleback, and Crangon shrimp is present on the Copper River Delta. Several of the demersal fish species and one crab species that occur within the Copper River Delta are of significant value to recreational and commercial fisheries. Pacific Halibut, Lingcod, English Sole, Starry Flounder, and Dungeness crab appear to use the extensive network of sloughs and tidal mudflats as nursery habitats. To more accurately forecast future conditions and to ensure sustainable management, scientists and managers require sound scientific information to distinguish between natural and human-induced variability.

Project Leader: Reid Nelson, Ph.D. Student

Project Details

Retrospective tracking of fish movement and habitat use

Background:

The otolith, or fish ear bone, is a stone like structure in the head of a fish mainly composed of calcium carbonate (CaCO3) (Figure1). It is a fish sensory structure that aids in orientation and detection of vibrations. It grows continuously throughout the life of a fish laying down annual rings that can be used to age a fish similar to tree aging. As a fish grows new material is deposited into the CaCO3 otolith matrix, and trace elements from the surrounding environment are incorporated into the otolith. Unlike bone or tissue, which can be reabsorbed and reworked through metabolic processes in the fish, otoliths are metabolically inert, meaning that once trace elements are incorporated into the otolith they remain locked in the otolith structure throughout the life of a fish. Given this, retrospective tracking of fish movements, especially across salinity gradients is possible and determination of what age a fish experienced certain habitats is also possible. Estuarine obligate species use a variety of different water bodies with varying salinities throughout their lives and using laser ablation otolith microchemistry these age-dependent patterns of estuary use can be reconstructed. Knowing what habitats fish use and making sure these habitats remain viable and available is essential to the success of a fishery.

Project Leader:Sean Powers, Ph.D., Principal Investigator

Project Details

Background:

Ecosystem-based fishery management has evolved from an abstract concept to a broadly accepted tenet for effective conservation and management of marine resources. Despite this, fishery managers are increasingly tasked with gathering more fisheries-independent data to fulfill current, single species management objectives. Given finite resources, these two objectives are often in competition. The goals of the FI project are to provide a unique fisheries-independent survey design that fully addresses both ecosystem and single species management objectives in the northern Gulf of Mexico.

Project Leader:Sean Powers, Ph.D. and Crystal Hightower, Lab Manager

Project Details

Background:

Red Snapper is one of the most economically important fisheries in the Gulf of Mexico. The species is currently overfished and extensive efforts have been put towards developing models to estimate stocks and develop management plans. Even though we have seen an increase in population as a result of these management plans, the spawning potential is lower than the rebuilding target. Further research is needed to accurately assess the population.

Project Leader:Sean P. Powers, Ph.D., Principal Investigator

Project Details

Greater amberjack (Seriola dumerili) discard mortality in the Gulf of Mexico recreational hook-and-line fishery and the efficacy of descender devices in discard mortality reduction

Project lead:

Sean P. Powers, Ph.D., Principal Investigator Post-doctoral researcher: Kelly S. Boyle Collaborator: Erin Bohaboy, University of Florida

Background:

Greater amberjack are considered overfished in the Gulf of Mexico and recreational fishing results in a high rate of regulatory discard because of closed periods and length restrictions (SEDAR 2014). This species is targeted mainly by the recreational fishery (SEDAR 2014) and estimates of survival following discard are necessary for stock assessment. Most efforts to estimate discard mortality are based on initial observations of survival when fish are released. A recent study (Jackson et al. 2018) indicates the promising potential of acoustic telemetry to examine longer-term survival and behavior of released fish.

Project Leader: Justin McDonald, Lab Technician

Project Details

High Dollar Red Snapper Tagging Program

Background

Red Snapper is an economically significant fish in the Gulf of Mexico. However the species is currently overfished and extensive efforts have been put towards developing models to estimate stocks and develop management plans. Recreational fishing mortality is a significant component of these models and can be difficult to estimate. To increase the accuracy of these estimates, a high dollar red snapper tagging program was put into place.

Project Leader:Pearce Cooper

Project Details

Sheepshead, Archosargus probatocephalus: population connectivity and estuarine residency as inferred from population genomics and otolith chemistry

Background and summary of approach:

The study of population connectivity and subdivision is vital to the proper management and conservation of species and furthers the study of evolutionary biology and ecology. Sheepshead, Archosargus probatocephalus, are a euryhaline sparid fish that are ecologically, commercially, and recreationally important in the southeastern United States 1. Population genetic data (microsatellite genotypes) indicate genetic divergence in sheepshead across the tip of the Florida Peninsula and both morphologic and population genetic data indicate divergence across Apalachee/Apalachicola Bay in the Florida Panhandle 2. Divergence across Apalachee/Apalachicola Bay is not proximal to any known hydrographic barriers and may be maintained by divergent selection between the divergent environments/ecosystems of the fresher, turbid, and more productive north central Gulf of Mexico coastal waters and the salty, clear waters of the west coast of the Florida Peninsula. In collaboration with the Marine Genomics Laboratory at Texas A and M University Corpus Christi, we aim to re-examine sheepshead population structure using reduced representation genomics and more extensive geographic sampling to increase the resolution of neutral population structure (Figure 1) and make inferences on patterns of selection by partitioning out putatively selected loci using multiple methods of genomic outlier detection.

Project Leader: Merritt McCall, Masters Student

Project Details

Background

Oyster reefs are a vital component of nearshore, estuarine ecosystems. The ecosystem services provided by these reefs are highly valuable to humans and marine species alike: they protect shorelines from erosion, filter surrounding water, provide an incomparable nursery habitat for a wide range of juvenile fishes and mobile crustaceans, and create structure and shelter for their respective prey species. Efforts to restore essential oyster reef habitat along the US Atlantic and Gulf Coasts have been extensive, with 259 reef restorations documented in the northern Gulf of Mexico alone.