Date of Award
Fall 12-20-2024
Level of Access Assigned by Author
Open-Access Dissertation
Degree Name
Doctor of Philosophy (PhD)
Department
Ecology and Environmental Sciences
Advisor
Heather Leslie
Second Committee Member
Nichole Price
Third Committee Member
Damian C. Brady
Additional Committee Members
Shannon Meseck
Roger Mann
Abstract
The sea scallop (Placopecten magellanicus) fishery is the largest and most valuable wild scallop fishery in the world. Offshore, it is among the most lucrative federal fisheries in the U.S. and supports a highly profitable near-shore fishery in Maine. The sustainability of wild capture fisheries for sea scallops are uncertain and aquaculture efforts are developing in response. Areas where both wild and aquacultured populations of the same species co-occur offer a unique opportunity to explore interactions among these populations and to develop new and innovative ways to monitor and, potentially, manage them. This dissertation investigates the patterns and underlying dynamics of variation in the reproductive ecology of wild and cultured shellfish populations and provides quantitative measures in support of the application of environmental DNA (eDNA) tools to detecting life history events of sea scallops. Environmental DNA (eDNA) provides a potential solution to the challenges of monitoring, detecting, and quantifying commercially important species with complex life histories. It has the potential to be used for adult stock assessments, larval transport models, and to estimate recruitment potential, provided patterns in eDNA occurrence and their significance are well understood. To determine the capacity for eDNA to be applied in natural systems, groundtruthing of these tools in laboratory settings is needed. eDNA approaches - like metabarcoding and quantitative polymerase chain reaction (qPCR) assays - may help disentangle the complex ecology of sea scallops and other marine invertebrates by providing a direct approach for species identification and enumeration of gametes and larvae in the water column. These relationships have not been validated for sea scallop eggs or larvae and have not been tested in the field over wild scallop beds or on scallop aquaculture farms. We also do not know how sampling at different depths and points in time influences one’s ability to distinguish eDNA from adults vs. gametes and larvae. As scallop aquaculture continues to expand alongside the existing wild scallop fishery in Maine, there is a need to understand the consequences of farming scallops at a large scale and explore and develop novel methods for monitoring and potentially managing commercially important shellfish populations like sea scallops. Chapter 1 provides an overview of the existing biological, ecological, and management landscapes for sea scallops in New England and, specifically, along the coast of Maine, and highlights current knowledge, information gaps, challenges, and applications of eDNA methods. In Chapter 2, we compared the morphometrics of farmed and wild scallops at three locations in Penobscot Bay, Maine, to determine spawning synchronicity in farmed and wild scallops and if they allocate energy differently to their reproduction and growth. Our main objectives were to (1) identify the progression and onset of spawning events, (2) compare reproductive investment, (3) compare morphometrics (gonad, meat, total viscera, and shell masses), and (4) explore differences in energy allocation between farmed and wild scallops. The spawning timing and magnitude are highly variable in both wild and cultured populations of sea scallops, but generally occur at similar time periods in each year. Overall, farmed scallops in this study invested more energy in soft tissues (gonads, viscera, meat) whereas wild scallops invested more energy in shell across all size classes. Larger meat yields from farmed scallops offer a significant potential return on investment for scallop growers, while their larger gonads suggest an increased potential for reproductive output with ecological ramifications for both aquaculture and wild harvest industries. These results shed light on the complex interplay between aquaculture and the natural environment, highlighting the need to further investigate the ecological consequences of cultivation on sea scallop populations and develop new and innovative ways to do so. In Chapter 3, considering these knowledge gaps, we aim to (1) quantify relationships between scallop larval density and DNA copy number, (2) quantify eDNA shedding and degradation rates of scallops, and (3) relate these rates to the biomass of non-spawning scallops in mesocosms. Through lab-based larval collections and dilution series, we established a significant linear relationship between scallop larval density and gene copy values, identifying an average value of 3.41 x 107 gene copies per larvae. Using mesocosm-based controlled lab experiments, we determined that gene copy quantities generally increased with increasing adult scallop biomass through time. Together, the results of these experiments support interpretation of eDNA signals generated by larval and adult scallops and inform sampling practices that use eDNA to monitor biological processes, particularly in the context of ecosystem-based fisheries management of sea scallops. In Chapter 4, using scallop aquaculture farms and wild scallop beds as research sites, we used gene copy number, determined through qPCR primers, GSIs, and plankton tows to evaluate the capacity of eDNA tools to detect life history events of sea scallops and the spatial and temporal variability in these signals. The objectives of this work are to (1) determine the ability of eDNA tools to successfully detect sea scallop DNA in the field, (2) evaluate spatial (across depth and across sites) and temporal (across spawning seasons) differences in sea scallop eDNA distribution, and (3) evaluate the use of eDNA methods to detect biological processes, such as sea scallop spawning and larval presence. The available scallop qPCR probe and primers successfully detected scallop eDNA on scallop aquaculture farms and above a wild wellcharacterized, deeper scallop bed. There was temporal (across weeks) and spatial (across sites and depths) variation in these signals on farms and above wild beds. With one exception, associations between larval density and gene copy were not found at farms in any sampling year. Scallop eDNA was detected at all depths, but not during all sampling events, above the well characterized wild scallop bed. Scallop eDNA was detected at all depths - sometimes at high concentrations - at a site lacking scallops, suggesting that transport of eDNA and quantifying stochasticity in ‘background’ signals is an important consideration in future studies. Scallop eDNA signal increased at wild population sites and across depths after maximum GSI were observed and during the time of assumed peak larval presence from 30-45 days after spawning. In Chapter 5, I review the outcomes of this work and provide direction and recommendations for future research, highlighting a need to evaluate the ecological interactions between wild and farmed sea scallop industries. I suggest evaluating interactions through the lens of the connections between environmental variability and life histories of scallops as a necessary step in planning for the future of this resource and the potential fitness impacts in wild and farmed populations. Lastly, I express an urgent need for continued ground truthing of eDNA tools, a move toward standardization of methods, and an evaluation of the relevance of laboratory-based experiments to field-based applications and monitoring.
Recommended Citation
Jekielek, Phoebe, "Integrating Life History and Environmental DNA (eDNA) Data to Enhance Detection of Sea Scallop (Placopecten magellanicus) Populations" (2024). Electronic Theses and Dissertations. 4115.
https://digitalcommons.library.umaine.edu/etd/4115
