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

Curriculum Vitae


BA, honors, Biology (Ecology & Evolution), Cornell University

MS, Biology (Ecology, Evolution & Conservation), San Francisco State University

Research Interests

Conservation genetics, environmental DNA (eDNA), molecular ecology, fish, crustaceans, plankton, aquatic food webs, marine ecology, bats.

Research Projects

Fish are often surveyed by trawl, but data shows that trawls are not very good at catching a representative sample of fish communities. Some fish are able to avoid the trawl. Others may be hard sample because they are very rare. And surveying fish in different habitats (like shallow water) or life stages (such as larvae) requires different gear which is costly and time-consuming.

A relatively new method called environmental DNA (eDNA) sampling detects fish species with just a sample of water. Similar to forensic methods that sample trace amounts of DNA at a crime scene, we use a high-sensitivity DNA assay to detect the presence of rare species without directly sampling them. I am using an eDNA approach to detect endangered Delta Smelt in the San Francisco Estuary. In addition to better detection of Delta Smelt, eDNA poses a minimal risk of harm to fish and the environment. It may also be less expensive. However, eDNA detection in the San Francisco Estuary is particularly challenging because estuaries are very dynamic ecosystems.

To help develop eDNA as reliable approach for fish monitoring, my research seeks to improve eDNA methods and data interpretation in estuaries. With validation, eDNA detection of Delta Smelt could help inform conservation and management strategies in California. We are conducting experiments and field collections to validate and optimize eDNA detection of Delta Smelt.

The genetic methods I use such as quantitative PCR (qPCR) and high-throughput sequencing (HTS) 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 webs in the Cache Slough Complex of the San Francisco Estuary. I was recently funded by the Yolo Basin Foundation to study bat diets in our region using genetics. Stay tuned for more on this project in 2019!

Connect with me on twitter @planktonherder

Recent presentions:

“Experimental work informs Delta Smelt environmental DNA (eDNA) protocol development” at Bay Delta Science Conference (September 10-12, 2018), Best Student Presentation Award

“Environmental DNA (eDNA) Protocol Development for Rare Fish in Turbid Estuaries” at American Fisheries Society annual meeting (August 19-23, 2018), oral presentation

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

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



Kimmerer, W., Ignoffo, T. R., Bemowski, B., Modéran, J., Holmes, A., & Bergamaschi, B. (2018). Zooplankton Dynamics in the Cache Slough Complex of the Upper San Francisco EstuarySan Francisco Estuary and Watershed Science, 16(3).