Yuan Liu, Ph.D., PMP, eDNA Service Manager
Turning Invisible Genetic Traces into Knowledge for Ocean Stewardship
Yuan Liu, Ph.D., leads the eDNA Service at GMGI. eDNA is a transformative technology that captures traces of genetic material organisms leave behind and analyzes them for sensitive, non-extractive detection of species across habitats and seasons. This methodology aspires to reveal the hidden diversity of ocean life and inform real-world marine science and management.
Through the GMGI eDNA Service, Dr. Liu and her team hope to make these cutting-edge technologies accessible and impactful for researchers, industry, conservation groups, and government agencies. Through the Service’s consultation, training, and applied research, Dr. Liu’s team works to advance ocean stewardship and support data-driven decisions in a rapidly changing world.
Research Focus
GMGI’s eDNA Service focuses on advancing and applying eDNA technologies to understand marine biodiversity and support ecosystem-based decision-making. eDNA provides a sensitive, non-extractive approach for detecting species presence, community composition, and ecological change. Under Dr. Liu’s direction, the service combines operational expertise leveraging GMGI’s research strengths and extensive experience in eDNA research to ensure that all workflows and analysis methods are grounded in rigorously validated science and optimized for real-world applications.
A key priority of the program is scaling eDNA for practical use by creating an efficient, agile, and high-quality workflow that incorporates new cutting-edge methodologies and translates genomic outputs into ecological indicators that are useful for researchers, managers, and industry partners. In this way, the service is a bridge between technical innovation and actionable environmental monitoring.
Another major focus is to evaluate how marine communities respond to natural and human-driven change. Dr. Liu’s earlier work at the NOAA Northeast Fisheries Science Center applied eDNA technologies across the U.S. continental shelf to assess finfish communities, characterize habitats, and examine how offshore wind development may influence fish assemblages. Additional projects explored epibiotic communities in aquaculture settings and the ecological role of aquaculture structures as habitat for wild fish. These studies demonstrate the versatility of eDNA as both a monitoring tool and an approach for addressing broader ecological questions.
A defining ambition of the GMGI eDNA Service is to cultivate a dynamic, two-way exchange of knowledge between its applied service work and GMGI’s research teams. This integrated approach ensures that service workflows reflect the most current and reliable scientific advancements, while insights from applied projects inform ongoing research and methodological development. Through scalable workflows, robust QA/QC procedures, and accessible reporting tools, the service advances GMGI’s mission in translational environmental genomics and expands the use of eDNA in environmental monitoring and decision-making.
Together, these efforts position the eDNA Service at the intersection of molecular ecology, fisheries science, and applied environmental genomics, extending what is possible for ocean observation in a rapidly changing world.
Featured Projects
Dr. Liu’s Previous eDNA Projects, Prior to GMGI
Aquaculture Structures as Fish Habitat
This project evaluates how oyster aquaculture cages contribute to marine habitat complexity and finfish biodiversity. Using a combination of eDNA metabarcoding, video surveys, and structural assessments, we examine how fish communities use these aquaculture features. Findings demonstrate that aquaculture gear can provide habitat comparable to natural structures, informing sustainable aquaculture practices.
Related publications: Mercaldo-Allen et al. 2023; Mercaldo-Allen et al. 2021; Liu et al. 2019, Frontiers in Marine Science.
eDNA Applications for Fisheries Surveys
This project develops and validates eDNA methods for characterizing finfish communities across coastal and shelf ecosystems. Collaborating with NOAA NEFSC, we apply metabarcoding approaches to assess habitat use, community shifts, and seasonal dynamics. These data support ecosystem-based fisheries management and complement traditional survey methods.
Related work: eDNA program at NOAA Northeast Fisheries Science Center. Read blog post here.
Epibiotic Communities on Cultivated Kelp
We study the epibiotic organisms that colonize sugar kelp grown in Southern New England, exploring patterns of biodiversity and ecological interactions. By integrating molecular and morphological analyses, this work reveals how aquaculture substrates shape biofouling communities. The results help inform best practices for kelp farming and environmental monitoring.
Related publication: Liu et al. 2022, Algal Research.
Featured Collaborators
John Logan, Ph.D., Massachusetts Division of Marine Fisheries
Heather Kinney, The Nature Conservancy
Annie Murphy, Ph.D., Inspire
Rich Balouskus, State of Rhode Island, Department of Environmental Managemen
Environmental DNA program, NEFSC, NOAA
Renee Mercaldo-Allen, Aquaculture Systems and Ecology Branch, NEFSC, NOAA
Peter Auster, Ph.D., University of Connecticut / Mystic Aquarium
Featured Publications From Past eDNA Work
See Dr. Liu’s full list of publications here.
Mercaldo-Allen R., Auster P. J., Clark P., Dixon M. S., Estela E., Liu Y., et al. (2023). Oyster aquaculture cages provide fish habitat similar to natural structure with minimal differences based on farm location. Front. Mar. Sci. 10. doi: 10.3389/fmars.2023.1058709
Liu Y., Wikfors G. H., Clark P., Pitchford S., Krisak M., Dixon M. S., et al. (2022). A deep dive into the epibiotic communities on aquacultured sugar kelp Saccharina latissima in Southern New England. Algal Res. 63, 102654. doi: 10.1016/j.algal.2022.102654
Mercaldo-Allen R., Clark P., Liu Y., Phillips G., Redman D., Auster P. J., et al. (2021). Exploring video and eDNA metabarcoding methods to assess oyster aquaculture cages as fish habitat. Aqua Environ. Interacts 13, 277–294. doi: 10.3354/aei00408
Liu, Y., Wikfors, G. H., Rose, J. M., McBride, R. S., Milke, L. M., and Mercaldo-Allen, R. (2019). Application of Environmental DNA Metabarcoding to Spatiotemporal Finfish Community Assessment in a Temperate Embayment. Front. Mar. Sci. 6:674. doi: 10.3389/fmars.2019.00674
King A, Jenkins B, Wallace J, Liu Y, Wikfors G, Milke L, Meseck S (2015) Effects of CO2 on growth rate, C:N:P, and fatty acid composition of seven marine phytoplankton species. Mar Ecol Prog Ser 537:59–69
Funding Sources
Massachusetts Department of Agricultural Resources
Massachusetts Life Sciences Center
Massachusetts Technology Collaborative
eDNA Service Gallery
