Ann Holmes

Ecogeomorphology in Baja

Position Title
PhD Candidate

Graduate Group in Ecology
Department of Animal Science

2131 Meyer Hall #9

Connect with me on twitter @planktonherder


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

The genetic methods I use have broad application in conservation and management of species and ecosystems. 

Environmental DNA analysis of Delta Smelt

Environmental DNA (eDNA) is an exciting new sampling method that detects species with just a sample of water. Similar to forensic science, we use a high-sensitivity assay to detect DNA without collecting species or disturbing the environment. Very few studies have applied eDNA sampling in estuaries, which are ecologically important habitats. Estuaries are particularly challenging environments for eDNA sampling because of high water flow and back-and-forth tidal action. My research uses eDNA to detect Delta Smelt (Hypomesus transpacificus), an endangered species found only in the San Francisco Estuary. Through a series of experiments and field collections, this research improves methods and data interpretation of eDNA detection in estuaries. With validation, eDNA could help inform conservation and management strategies of Delta Smelt and other endangered species. This research is funded by the California Department of Fish and Wildlife and the California Department of Water Resources.

Non-invasive analysis of bat diets in the Yolo Bypass using DNA

In the Sacramento Valley and throughout their range, Mexican free-tailed bats (Tadarida brasiliensis) may be providing valuable ecosystem services by consuming agricultural pests. However, traditional analysis of bat diets (guano dissection) doesn't detect prey species very well. Diet analysis using DNA identifies more prey species with better resolution. This study will use DNA metabarcoding (Illumina high-throughput genetic sequencing) to describe feeding patterns of Mexican free-tailed bats in the Yolo Bypass Wildlife Area between Davis and Sacramento. The results of this study will provide a detailed understanding of local bat ecosystem services and new insights into seasonal feeding patterns during the critical pupping season. This research will also help develop reliable and specific DNA methods for bats in the Yolo County region to help increase representation of bats in local conservation plans. This project will start in the Spring of 2019 and is funded by the Yolo Basin Foundation.

Biodiversity assessment of Suisun Marsh, the largest tidal wetland in the San Francisco Estuary

This study will use eDNA to monitor fish and invertebrate communities in Suisun Marsh, the largest tidal wetland in the San Francisco Estuary and the US west coast. Traditional monitoring surveys (trawling and seining) are currently used to evaluate conservation, restoration, and management actions in the marsh, including operation of the Suisun Marsh Salinity Control Gate. However, these surveys may be under-sampling diverse communities of fish and invertebrates. eDNA shows promise as a more sensitive method for assessing biodiversity. Particular groups of interest in Suisun Marsh include native and invasive fishes, invasive clams, and crustaceans such as amphipods that are food for fish. eDNA can also be used to detect new and potentially harmful invasive species that are present in low densities. A better understanding of species distributions in space and time could help guide future restoration to support native species. While eDNA sampling has been used in a range of aquatic habitats, eDNA has not yet been used to characterize fish and macroinvertebrate communities in the San Francisco EstuaryThis research will start in the Summer of 2019 and is funded by the Garden Club of America.

Recent Presentions

"How low can you go? Limits of detection and quantification for Delta Smelt environmental DNA." Poster presentation at the Interagency Ecological Program annual workshop, Folsom, CA (March 5-7, 2019).

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

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

Poster at the Interagency Ecological Program annual workshop, Folsom, CA (March 6-8, 2018).

Poster at the Ecological Society of America annual meeting, Portland, OR (August 6-11, 2017).

Invited oral presentation and poster at the Water Quality Health Indicator and Data Science Symposium, Cal EPA Surface Water Ambient Monitoring Program, Sacramento, CA (June 29-30, 2017).

Invited presentation at the Interagency Ecological Program Annual Workshop, Folsom, CA (March 3, 2017).

Oral presentation and poster at the Bay Delta Science Conference, Sacramento, CA (November 15, 2016).


Holmes, A, and Finger, AJ. 2019. Environmental DNA analysis of Delta Smelt. Technical report for the California Department of Fish and Wildlife, prepared by the Genomic Variation Laboratory, University of California-Davis, Davis, CA.

Kimmerer, W, Ignoffo, TR, 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).