Ann Holmes

Ann in Baja

Position Title
PhD Candidate

Graduate Group in Ecology
Department of Animal Science

2131 Meyer Hall #9


BA, Biology with honors, Cornell University

MS, Biology, San Francisco State University


I'm a fourth year PhD Candidate in Ecology. My research combines field biology, aquatic ecology, conservation genetics, analytical chemistry, and bioinformatics. I study fish, plankton, and bats using trace DNA in the environment. Much of my work involves developing environmental DNA (eDNA) methods in estuaries and interpreting results for potential applications in the real world (e.g. conservation and management). I've also applied molecular methods to study predation by copepods (a type of plankton) and am currently doing the same for insect-eating bats. My research uses quantitative PCR (qPCR) and high-throughput genetic sequencing.


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

Methods: quantitative PCR (qPCR), high-throughput sequencing, metabarcoding.


Environmental DNA analysis of Delta Smelt

Collecting eDNA samples in the San Francisco Estuary
Here I am collecting eDNA samples in the San Francisco Estuary.

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 (qPCR) to detect DNA in a small sample of water without collecting organisms 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. I've used eDNA to detect Delta Smelt (Hypomesus transpacificus), an endangered species found only in the San Francisco Estuary. The purpose of my experiments and field collections is to improve methods and data interpretation of eDNA detection of rare species 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

Undergraduate students sample bat guano for DNA analysis.
Undergraduate students (L-R) Khyana Yearwood, Victor Martinez, Shayan Kaveh, and Serra Perry sample bat guano (trap in foreground) for DNA analysis (Summer 2019).

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 uses 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. Undergraduates Shayan Kaveh, Serra Perry, and Khyana Yearwood are currently working on this project which is funded by the Yolo Basin Foundation. You can read about Shayan's experience as an undergraduate research assistant here

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

Field technicians count and measure fish species on the Suisun Marsh Survey.
Field technicians count and measure fish on the Suisun Marsh Survey in the San Francisco Estuary. The results of eDNA sampling will be compared to fish counts such as this one.

This study uses eDNA to monitor fish and invertebrate communities in Suisun Marsh, the largest tidal wetland in the San Francisco Estuary and the US west coast. Monthly 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 EstuaryUndergraduates Shayan Kaveh, Serra Perry, and Khyana Yearwood are currently assisting with this project which is funded by the Garden Club of America Award in Coastal Wetlands Studies and Prop 1 funding through the California Department Fish and Wildlife.

Collaborations with other labs at UC Davis

In collaboration with PhD candidate Gina Tarbill (Sollmann Lab), we are using DNA metabarcoding to study the impacts of high intensity fires on pollinator networks in the Sierra Nevada.

In collaboration with Dr. Andrew Rypel, we are using eDNA to describe fish distributions in Lower Putah Creek in Davis and Winters, CA.

Recent Presentions

"eDNA in Estuaries: Enclosure experiment shows capabilities and limitations of eDNA detection of delta smelt." eDNA Symposium: How to Achieve a True Consensus for Best Environmental DNA Practices, Davis, CA (Jan 29, 2020).

"Knowing your limits: Tide, distance, and site influence eDNA detection of caged fish in a tidal estuary." Poster presentation at the 3rd Annual eDNA Government Technical Exchange Workshop, St. Petersburg, FL (Nov 18-20, 2019).

"A study of Mexican free-tailed bat diets in the Yolo Bypass using DNA." Public Talk at Yolo Basin Foundation Flyway Nights, Davis, CA (Nov 7, 2019).

"Knowing Your limits: Environmental DNA Detection In a Tidal Estuary Using Caged Fish." Poster presentation at American Fisheries Society-The Wildlife Society Joint Annual Meeting, Reno, CA (Sept 30-Oct 3, 2019).

"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


Holmes, A and Kimmerer, WJ. Genetic detection of phytoplankton in estuarine copepods. In review.

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.


Williamson, M., Bellido, F, Broad, A., Gaffney, S., Hernandez, D., Holmes, A., Lo, V., Moore-O’leary, K., Pekny, J., Powelson, K., Preckler-Quisquater, S., Statham, M., Weiner, J. & Schwartz, M. 2019. Kern and Pixley Wildlife Refuge Climate and Water Threat Assessment. Report submitted to US Fish and Wildlife Service, University of California-Davis, Davis, CA.

Kimmerer, WJ, 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).

More about me...


Scuba diving at the Great Barrier Reef, Australia.
Scuba diving at the Great Barrier Reef, Australia.
Kayaking in Baja.
Kayaking in the Gulf of California, Baja, Mexico with the UC Davis Ecogeomorphology Field Course.

I've been a certified Scuba diver for over 20 years and have completed 100 dives. I completed my Research Diver certification at UC Davis Bodega Marine Lab in 2016 . I've worked at and done research in the scientific collections of three natural history museums. I used to be a competitive rower and currently enjoy daily runs with my dog Pearl.