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 Dec 2016), Biology, San Francisco State University

Research Interests

Conservation genetics; molecular ecology; fish; crustaceans; aquatic food webs

Research Projects

Endangered species can be hard to locate in the wild. Aquatic species such as fish can be detected using DNA left behind in water (environmental DNA or eDNA). eDNA sampling may enable more targeted, less invasive, and less expensive monitoring of fish compared with traditional trawl sampling. I am developing a method that uses eDNA to detect Delta Smelt, a critically endangered species. Delta Smelt are endemic to the San Francisco Bay-Delta, a crucial water supply for California. Certain features of the dynamic estuarine environment (e.g. high turbidity, variable flows) make eDNA detection of fish challenging. However, highly sensitive detection of Delta Smelt could greatly inform conservation and water management strategies in California.

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 San Francisco Estuary.

Recent presentions:

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

Interagency Ecological Program (IEP) workshop (March 3, 2017), invited presentation

Upcoming presentations:

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

Ecological Society of America (August 6-11, 2017)