Ann Holmes

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PhD Student
Graduate Group in Ecology

University of California, Davis
Department of Animal Science
2403 Meyer Hall
One Shields Avenue
Davis, CA 95616


BA (honors), Biology, Cornell University

MS (expected), Biology, San Francisco State University/Romberg Tiburon Center

Research Interests

Conservation genetics, molecular ecology, fish, crustaceans, aquatic food webs, marine ecology.

Research Projects

I am optimizing a method that uses DNA to detect endangered Delta Smelt in the San Francisco Estuary. Rare fish like Delta Smelt can be hard to monitor using traditional methods such as trawl sampling. However, fish can be detected using just a sample of water (environmental DNA or eDNA). Like forensic methods that sample DNA at a crime scene, we use a high-sensitivity assay to detect the presence of Delta Smelt without directly sampling the fish.

eDNA detection may enable more targeted, less invasive, and less expensive monitoring of fish compared with traditional trawl sampling. Better detection of Delta Smelt could help inform conservation and water management strategies in California. In order for eDNA sampling to be used for monitoring, the methods must be validated. We are in the process of a series of experiments and field collections to validate and optimize eDNA detection of Delta Smelt.

I use genetic methods such as quantitative PCR (qPCR) and high-throughput sequencing (HTS) that have broad application in conservation and management of aquatic species and ecosystems. My MS research (Kimmerer Lab, San Francisco State/Romberg Tiburon Center) used HTS to study plankton food web interactions in the Cache Slough Complex of the San Francisco Estuary.

Upcoming presentations:

Interagency Ecological Program Annual Workshop (March 6-8, 2018), poster to be submitted

Recent presentions:

Ecological Society of America (August 6-11, 2017), late-breaking poster session

Water Quality Health Indicator and Data Science Symposium, Cal EPA Surface Water Ambient Monitoring Program (June 29-30, 2017), invited presentation and poster

Interagency Ecological Program Annual Workshop (March 3, 2017), invited presentation

Bay Delta Science Conference (November 15, 2016), presentation and poster