RESEARCH

Research Interests

Oyster cages at the Virginia Institute of Marine Science

My research is on conservation genetics of marine fish and invertebrates with an applied focus on aquaculture and sustainable fishing. In the U.S., more seafood is being imported than exported, amounting to a seafood trade deficit that stands at $20 billion. Further, marine ecosystems are some of the most rapidly changing environments, creating a moving target for responsive conservation and sustainable use. My ultimate scientific goals address these challenges to improve ecosystem resilience, aquaculture yield, and inform sustainable fishing. To do this, I use genomics to identify population structure, assess genetic diversity, detect loci related to disease mitigation, and reveal genetic signatures of environmental adaptation over space and time in commercially valuable and threatened marine species.

Ongoing Research

1. Population structure of the eastern oyster

The eastern oyster is an iconic example of a declining yet human-managed species. In marine systems, human activities such as aquaculture and commercial translocation have facilitated gene flow between historically isolated populations. While these types of interventions can be beneficial for immediate commercial outcomes, they also present concerns about the evolutionary consequences of human-induced gene flow.

My research on the population structure of the eastern oyster details the extent of human-induced introgression and its beneficial, neutral, and detrimental effects to wild ecosystems. This insight will inform management of the U.S. wild eastern oyster fishery, valued at >$200 million/year.

Eastern oysters spawned for genetics research

2. Quantifying oyster shell bioerosion with x-ray techniques

X-ray images of eastern oyster shells with polydora tunnels

In collaboration with the Coastal Disease Ecology Lab at the Smithsonian Environmental Research Center

The mud blister worm (Polydora sp.) is a prolific bioeroding worm which infects the eastern oyster across its entire native range (Texas - Nova Scotia). Mud blister worms excavate holes and burrows in the oyster shell, creating weak “blister” points. This negatively impacts shell health and causes odors and imperfections that reduce the value of infected oysters on the half shell market.

My research uses x-ray imaging to detect the extent of shell erosion in oyster shells from across the range. I will use x-ray data and genetics to understand the links between bioeroder infection, shell blistering, and genes related to shell building and repair. Access to x-ray imaging was generously provided by the Smithsonian National Zoo and Conservation Biology Institute for this project.

3. Genomic mitigation of parasite infection

Wild eastern oyster populations have been dramatically reduced to 1% of historic abundance, in part due to parasitic infection. Mortality from parasites also constrains aquaculture production and creates substantial monetary losses for aquaculture farmers annually.

My research uses population-level genomics data and innovative parasite detection methods to identify if specific regions of the genome or general heterozygosity mitigates parasitic infection in the eastern oyster. I am identifying loci of functional immune significance which are significantly associated with mitigation of parasite load. These loci can then be targeted for selective breeding in aquaculture, or for conservation in wild populations which contain adaptive loci in high prevalence.

Eastern oyster shells from Florida, Texas and South Carolina with mud worm blisters

4. Temporal marine genomics with historic DNA

In collaboration with the Shellfish Pathology Laboratory at the Virginia Institute of Marine Science

Populations typically experience small fluctuations in genetic change over time, but when extreme events occur, they can produce substantial population-level changes within short timescales. In aquaculture, stressful environmental events such as parasite epizootics can cause severe loss. Further, the effect of these intense parasite outbreaks on nearby wild populations is not well understood.

My research aims to reveal temporal genomic evolution response of the eastern oyster to an intense epizootic event (1999-2002) in the Chesapeake Bay. This host-parasite system with preserved tissues from before and after the epizootic provides an ideal model for studying how species adapt to disease intensification from rapid climatic change over short timescales.

(a) Temporal oyster samples preserved in FFPE blocks, (b) epizootic trend in weighted parasite prevalence, and (c) parasite spores, credit: Carnegie et al 2021.

Completed Research

Shark & swordfish market substitutions

Eppley, M.G., Coote, T. DNA barcoding reveals mislabeling of endangered sharks sold as swordfish in New England fish markets. Conserv Genet 26, 381–390 (2025). https://doi.org/10.1007/s10592-025-01675-5

Mako shark meat in a New England market that was collected for the study.

Substitution of seafood products is a pressing issue for both conservation efforts and consumer rights. Substitution occurs when a product is mislabeled, accidentally or purposefully, to sell under an inaccurate name. Accidental substitution (misidentification) occurs when unidentifiable cut or frozen filets are passed through the supply chain and shipped domestically or internationally. Purposeful substitution occurs in favor of selling cheaper or more widely available species in the place of expensive or high-demand species.

My research evaluated substitutions in marketed seafood in southern New England. I used DNA barcoding on a fragment of the mitochondrial cytochrome oxidase I (COI) subunit to determine species-level identification of collected tissue samples. I found evidence of endangered sharks (I. oxyrinchus - shortfin mako shark) being sold as swordfish.

In conclusion from this research, I recommend prioritizing local catch by reducing internationally-imported seafood in markets, establishing seafood import monitoring programs and making data publicly-available, routinely and randomly testing a diversity of taxa across the supply chain for seafood fraud, and preventing endangered shark products from entering the market through catch, landing, and retention bans.