My research asks how organisms interact with their physical environment, and how those interactions shape where species live, how well they grow, and whether they survive. I combine field monitoring, laboratory experiments, and modeling to build mechanistic frameworks that predict the performance of species with ecological, economic, or conservation value, drawing on functional genomics, ecophysiology, and biomechanics to trace how environmental stressors act on individuals, populations, and fisheries.
I am a believer in interdisciplinary science. My graduate training was in ecophysiology and biomechanics; postdoctoral work in biomedicine and functional genomics added tools such as RNA-seq, bisulfite sequencing, and genome editing that I now apply to ecological and management questions. Projects are listed with their funding, collaborators, and links to open code and lab notebook entries. For papers, see Publications; for repositories, see Code & Data.
Jump to: Coastal shellfish fisheries · Oyster climate resilience · Mussel attachment · Salmon behavior genomics · Earlier work · Funding
Coastal shellfish fisheries
Washington Department of Fish and Wildlife, 2023-present
As lead of WDFW’s Coastal Shellfish Unit, I direct research and monitoring on how climate change affects commercial shellfish fisheries worth more than $120M a year, and I designed monitoring programs for eight recreational fisheries. The unit works with federal, state, and tribal partners and advisory groups to build harvest and management plans aimed at long-term sustainability and climate resilience.
Climate-driven recruitment of Pacific razor clams
How ocean conditions drive year-to-year recruitment in the razor clam (Siliqua patula) populations that support one of Washington’s most popular recreational fisheries.
Coastal Dungeness crab in a changing ocean
Estimating recreational crab harvest at Westport and Grays Harbor with Bayesian state-space models that fill gaps between sampled days and carry uncertainty through to the final estimate, and monitoring Dungeness crab larvae with light traps on the outer coast.
Burrowing shrimp and on-bottom bivalve aquaculture
Assessing burrowing shrimp as a threat to on-bottom bivalve aquaculture, presented to the Integrated Pest Management Working Group (2024).
Oyster climate resilience
University of Washington School of Aquatic and Fishery Sciences and NOAA Northwest Fisheries Science Center, 2020-2023
Triploidy and marine heatwaves in Pacific oysters
Many farmed Pacific oysters are triploid: an extra chromosome set makes them functionally sterile, so energy that would go to reproduction goes to growth instead. Using hatchery experiments that simulated marine heatwaves and low-tide desiccation, we found that triploid oysters had dysregulated stress responses and higher mortality than diploids, which helps explain the “triploid mortality” events growers in Washington and elsewhere have reported in hot summers. The work was done with industry (Taylor Shellfish) and tribal (Jamestown S’Klallam Tribe) partners. The results were published in Global Change Biology (2023), with an invited commentary in the same journal, and covered by Hakai Magazine, Popular Science, and The Atlantic. A companion whole-genome bisulfite sequencing study examines how DNA methylation differs between diploid and triploid oysters after thermal stress (manuscript in preparation).
heatwave data & code hatchery tank build Tag-seq analysis WGBS analysis
Hatchery conditioning for climate-resilient oyster seed
Poor summer survival limits U.S. oyster production. Working with Taylor Shellfish, Nisbet Oyster Co., Pacific Hybreed, and the Jamestown S’Klallam Tribe, we tested broodstock and early-life conditioning (heat and mechanical stress priming, and immune priming with poly(I:C)) as a way to use transgenerational and developmental plasticity to make seed more resilient, without the cost or loss of genetic diversity that comes with selective breeding.
Ribosomal DNA copy number as a predictor of phenotype
Ribosomal DNA drives ribosome production and is tied to growth, development, and metabolism, yet its copy number is rarely studied in shellfish. We used whole-genome sequencing of diploid and triploid oyster families to measure rDNA and mitochondrial copy-number variation as candidate genomic predictors of stress tolerance and growth.
Mussel attachment under ocean change
Genomic markers for resilient mussel attachment
Mussels hold onto farm lines with byssal threads, protein fibers whose strength drops under acidification, warming, and hypoxia. We exposed Mytilus trossulus to these stressors, measured thread strength, and sequenced foot and gill gene expression to find genetic markers that could guide broodstock selection for strong attachment in future oceans.
The ecomechanics of mussel attachment (Ph.D. research)
Mussels are ecosystem engineers, and in suspended raft aquaculture how well they hold on predicts farm yield. Working with academic (UC Santa Barbara), state (Washington Department of Natural Resources), and industry (Penn Cove Shellfish) partners, my dissertation showed that ocean acidification weakens the adhesive plaque (Nature Climate Change, 2013) while warming weakens the thread itself (Conservation Physiology, 2019), that hypoxia interrupts the DOPA cross-linking that cures the adhesive (J. R. Soc. Interface, 2018), that seawater conditions after secretion change adhesive strength (Biofouling, 2018), and that pH and oxygen fluctuate at small scales inside mussel aggregations, with consequences for raft aquaculture (J. Shellfish Res., 2019).
Salmon behavior genomics
Gene expression and territoriality in sockeye salmon
Tag-seq of brain, liver, and gonad tissue from territorial and social sockeye salmon, used to identify differentially expressed genes and co-expression networks associated with behavior (manuscript in preparation). The analysis has since been rebuilt as a fully reproducible Quarto project.
Earlier work
- Biomedical engineering and stem cell biology (2018-2020). At the Mayo Clinic and Children’s Hospital of Philadelphia I developed injectable, mussel-inspired adhesive hydrogels for bone tissue engineering, contributed to work on conductive and 3D-printed scaffolds, studied human endoderm development in pluripotent stem cells, and reviewed genome-editing approaches for modeling beta-cell disease. See biomedical publications.
- Functional morphology. Undergraduate and early graduate work on the mechanics of fiddler crab claws (BMC Evol. Biol., 2013) and drift-particle capture by sea urchin spines (JEMBE, 2014).
Funding
- 2022-2024Improved climate resilience in oysters through optimization of hatchery-based environmental conditioning practicesUSDA NIFA Special Research Grants for Aquaculture Research Program (SRGARP) · $325,611 · co-PI (PI: S.B. Roberts)
- 2022-2023Identifying genomic architecture features that contribute to critical phenotypes in shellfishUSDA NRSP-8 National Animal Genome Research Program · $10,000 · co-authored proposal (PI: S.B. Roberts)
- 2021-2022Development of genomic markers for environmental resilience in musselsPacific States Marine Fisheries Commission (PSMFC) · $124,980 · co-PI (PI: E. Carrington)
- 2020-2025Leveraging transformative 'omics technologies to alleviate barriers to American shellfish productionNOAA National Oceanographic Partnership Program (NOPP) · $233,135 · co-authored proposal (PI: S.B. Roberts)
- 2015-2017Mussel adhesion in a high CO2 world: uncovering the molecular basis of weak attachment (#65-7259)University of Washington Royalty Research Fund · $37,029 · co-authored proposal (PI: E. Carrington)
Fellowships and awards are listed in the CV.