RESEARCH

Research Interests

I am broadly interested in understanding how organisms genetically adapt over space and time to abiotic and biotic environments.

Examining blisters caused by parasitic worms on an eastern oyster shell

In my PhD research, I aim to (1) delineate range-wide population structure of the eastern oyster, (2) identify genomic regions in the eastern oyster involved with adaptation to parasitic infection, and (3) highlight the utility of preserved museum DNA for temporally-informed marine disease genomics research.

Longer term, I have a keen interest in continuing genomics research with contemporary and historic DNA specimens to better understand disease and parasite effects on host evolution over time. My ultimate goal is to promote scientific understanding and informed conservation of species threatened by climate change and disease (particularly in marine environments) with spatial and temporal 'omics approaches.

Population structure of the eastern oyster

How do abiotic stressors and geography shape the neutral and adaptive genetic diversity at the population level across the seascape?

Local adaptation in marine systems has historically been assumed to be infrequent, resulting in weak population-level genetic differentiation (Sanford & Kelly 2011). However, marine coastline habitats are characterized by strong environmental gradients and complex mosaics that can create spatially differentiated selection on species with wide distributions (Riginos et al. 2016).

My research will integrate range-wide genomic data and seascape environmental data (temperature, salinity) to understand how environmental factors are shaping genetic differentiation between wild eastern oyster populations.

Collection sites for seascape study

Genomic response(s) to disease

Does targeted selection at specific immune-related loci or general genetic diversity (heterozygosity) determine response to disease in eastern oysters, and are these genomic mechanisms population-specific or generalizable range-wide?

Eastern oyster shells from Florida, Texas and South Carolina with outlined occurrences of parasitic mud worm blister tunnels.

Landscape and seascape genomics studies focus on identifying candidate genes or loci under selection to abiotic environments, but they often do not include selection by spatial variation of biotic factors such as disease (Kozakiewicz et al. 2018; Fraik et al. 2020). Disease, however, can impose strong forces of selection on the host, making it a key part of the selective landscape (Johnson et al. 2015).

My research will use genomic tools and analyses to identify if specific regions of the genome or general heterozygosity may be involved in adaptation of a response to disease in the eastern oyster.
Prior research on disease resistance in eastern oysters has been primarily conducted with experimental techniques and selective breeding approaches to isolate lines of individuals that survive disease exposure (Potts et al. 2021).

However, survival via genomic response to disease may result from either targeted adaptation at specific loci, or from general genome-wide (multi-locus) heterozygosity (Hansson & Westerberg 2002; Blanchong et al. 2016; Portanier et al. 2019; Budischak et al. 2023). In the instance of targeted adaptation at specific loci, selection acts directly on particular immune-related loci, allowing an individual to resist or tolerate infection (Hansson & Westerberg 2002; Acevedo-Whitehouse et al. 2005; Råberg et al. 2007). If and how general genetic diversity could be advantageous in boosting an individual's disease response via resistance or tolerance is unknown (Budischak et al. 2023), but it is hypothesized that heterozygote advantage may play a role. My research may potentially identify loci of functional significance associated with adaptation to disease in the eastern oyster. These loci could then be targeted for genomic interventions such as selective breeding efforts or used to maintain reservoirs of genetic diversity by conserving wild populations with genomic disease response loci.

Temporal Marine Disease Genomics with hDNA

Populations typically experience small fluctuations in genetic change over time. However, environmental selection events can produce substantial population genetic changes within short timescales (Habel et al. 2014, Campbell-Staton et al. 2017, Card et al. 2018, Coleman et al. 2020, Coleman and Wernberg 2020). These environmental selection events can reduce population-level genetic diversity, affect heterozygosity, or change the temporal consistency of allele frequencies (Luikart et al. 1998, Shama et al. 2011). One method to investigate population-level genetic change over timescales is with historic DNA (hDNA), which can reveal genomic evolution to selection events or environmental change (Holmes et al. 2016, Dehasque et al. 2020, Snead and Clark 2022). While studies using hDNA have increased with advances in modern sequencing technology, only 4% of published temporal genomics studies explore how organisms have adapted to disease over time (Clark et al. 2023). This research has focused on understanding the geospatial patterns of disease emergence and spread (Dunnum et al. 2017, Card et al. 2021), but even less attention has been spent studying the effect of disease on the host, particularly during periods of increased disease virulence or prevalence called epizootics.

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

The potential utility of museum collections for studying diseases effects on hosts over temporal scales has not yet been fully realized (Card et al. 2021). My research aims to reveal temporal genomic evolution response in 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.

Shark & Swordfish Market Substitutions

Eppley, M., Coote, T. (In review). DNA identification of endangered shark meat substituted for swordfish in New England markets. Target Journal: Conservation Genetics. Preprint: www.researchsquare.com/article/rs-4547946/v1

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

Eppley, M. (2020). A Study of Shark and Swordfish Meat Substitutions in New England Markets. Senior Theses. 1431. https://digitalcommons.bard.edu/sr-theses/1431/

The substitution of seafood products is a principal issue for both conservation efforts and consumer rights. Substitution of seafood products occurs when a product is mislabeled, accidentally or purposefully, to sell a product under an inaccurate name. Mislabeling occurs throughout the boat-to-market supply chain process, and is fueled by misidentification and profit ventures (e.g. selling lesser-value species under the name of high-value species). Accidental substitution via misidentification easily occurs when unidentifiable cut or frozen filets are passed through the hands of third party distributors to be 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 (Cline 2012).

New England’s southern region of Massachusetts, Connecticut, and Rhode Island has a historic reliance on fisheries and seafood consumption. The appetite for seafood in southern New England includes top-predators such as the Shortfin Mako shark (Isurus oxyrinchus), Common Thresher shark (Alopias vulpinus), and Swordfish (Xiphias gladius). My research aimed to evaluate the percentage of substitutions in shark and Swordfish meat, which share remarkable visual similarities, collected from markets and grocery stores in southern New England. DNA barcoding was applied to a fragment of the mitochondrial cytochrome oxidase I (COI) subunit to determine species-level identification of collected tissue samples.

With global declines in shark populations, assessments of CITES Appendix II and highly consumed species are critical for conservation efforts. As such, the mislabeling of shark and Swordfish meat poses a challenge to managing healthy stocks of Mako, an IUCN Red List Endangered species, and Thresher, an IUCN Red List Vulnerable species.