- Graduate Group in Ecology
- Department of Animal Science
BA, Biology with honors, Cornell University
MS, Biology, San Francisco State University
I'm a PhD Candidate in Ecology using DNA to study aquatic organisms, food webs, and biodiversity. My current study organisms are fish, crustaceans, and bats.
I support undergraduates in research through mentoring and compensated opportunities on my projects.
Please consider donating to our crowdfunding campaign supporting a research project applying eDNA in Northern California Marine Protected Areas: https://experiment.com/projects/adapting-genetic-technology-for-marine-conservation
Topics of interest: Conservation genetics, marine ecology, marine protected areas, estuaries, molecular ecology, environmental DNA (eDNA), metabarcoding, qPCR, fish, crustaceans, plankton, bats, trophic interactions.
Environmental DNA analysis of Delta Smelt
Environmental DNA (eDNA) is trace DNA shed by organisms in water that allows for indirect species detection. eDNA detection is less invasive than other common methods used in monitoring such as trawls and electrofishing. In this project, we use a high-sensitivity assay (real time PCR or qPCR) targeting Delta Smelt (Hypomesus transpacificus), an endangered fish found only in the San Francisco Estuary. Few studies have used eDNA sampling in estuaries; environmental conditions such as high turbidity and dynamic water movement present challenges for sample collection and detection using eDNA. We used experiments and field studies to optimize eDNA sampling methods and data interpretation. This research is funded by and carried out in collaboration with the California Department of Fish and Wildlife and the California Department of Water Resources.
Biodiversity of Suisun Marsh, San Francisco Estuary using eDNA metabarcoding
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) evaluate conservation, restoration, and management actions in the marsh, including operation of the Suisun Marsh Salinity Control Gate. Particular groups of interest in Suisun Marsh include native and invasive fishes, invasive clams, and crustaceans such as amphipods that are food for fish. We are developing eDNA as a complement to conventional monitoring. eDNA can potentially detect species that avoid nets or that occur in very low densities (e.g. endangered species or newly invasive species). A better understanding of species distributions in space and time could help guide future restoration to support native species. eDNA has not yet been used to characterize fish and macroinvertebrate communities in the San Francisco Estuary.
Undergraduates Shayan Kaveh, Victor Martinez, Serra Perry, and Khyana Yearwood provided valuable assistance with field sampling and laboratory work. This project is funded by the Garden Club of America Award in Coastal Wetlands Studies to me, and Prop 1 funding through the California Department Fish and Wildlife to Dr. Andrea Schreier. Serra Perry received a 2020 Provost's Undergraduate Fellowship (PUF) for her honors thesis research developing metabarcoding methods for San Francisco Estuary fish and invertebrates using mock communities.
Non-invasive analysis of bat diets in the Yolo Bypass using DNA
In this study, we are using DNA to characterize the diets of Mexican free-tailed bats (Tadarida brasiliensis) that provide valuable ecosystem services by consuming agricultural pests in the Sacramento Valley. DNA can identify more prey species with better resolution compared with microscopic studies of guano. 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 also helps 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, Victor Martinez, Serra Perry, and Khyana Yearwood provided valuable assistance with field sampling and laboratory work. This project is funded by the Yolo Basin Foundation, UC Davis Jastro Research Fellowship, and a Seed Grant from the UC Davis Genome Center. Khyana received a 2021 Provost's Undergraduate Fellowship (PUF) to study bat endoparasites using metabarcoding. Shayan Kaveh (UC Davis '20) describes his experience as an undergraduate research assistant on this project from 2019-2020 here.
Collaborations with other labs at UC Davis
In August 2021 we completed our second year of eDNA sampling in Marine Protected Areas (MPAs) off the coast of central California. Our eDNA samples are paired with hook and line in surveys conducted by the California Collaborative Fisheries Research Program (CCFRP). Samples will be sequenced using a universal fish barcode and a rockfish (Sebastes spp.) barcode. This research is in collaboration with Ecology graduate student Helen Killeen (Morgan Lab, Bodega Marine Laboratory) and Population Biology graduate student Keira Monuki (Sanford Lab, Bodega Marine Laboratory). Undergraduates Khyana Yearwood and Serra Perry provided valuable assistance with sample collection. Undergraduates Juan de la Torre, Tien Ly, and Cristina Gonzalez are providing valuable assistance with data management using SQL and bioinformatic analysis. This study is funded by the California-Nevada Chapter of the American Fisheries Society, Western Division of the American Fisheries Society, and a seed grant from the UC Davis Genome Center.
In collaboration with Dr. Andrew Rypel, Dennis Cocherell and Mackenzie Miner (Department of Wildlife, Fish and Conservation Biology), we are comparing eDNA detection to fish detected using traditional sampling (traps and electroshocking) in Putah Creek in Davis and Winters, CA. Undergraduates Khyana Yearwood and Serra Perry provided valuable assistance with sample collection. Undergraduates Tien Ly and Cristina Gonzalez are providing valuable assistance with bioinformatic analysis. This study is funded by Solano County Water Agency.
In collaboration with Ecology graduate student Gina Tarbill (Sollmann Lab, Department of Wildlife, Fish and Conservation Biology), we are using DNA metabarcoding to characterize pollinator networks in regions of the Sierra Nevada mountains that have experienced high intensity fires. Undergraduate Viviane-Lee Reed is providing valuable assistance with data analysis. This research is partially funded by the Davis Botanical Society.
Nagarajan, R, Bedwell, M, Holmes, A, Sanches, T, Acuna, S, Baerwald, M, Barnes, Blankenship, S, Connon, R., M. Deiner, K, Gille, D, Goldberg, C, Hunter, M, Liukart, G, Meyer, R, Watts, A, and Schreier, A. 2022. Environmental DNA Methods for Ecological Monitoring and Biodiversity Assessment in Estuaries. Estuaries and Coasts, In press. https://doi.org/10.1007/s12237-022-01080-y
Holmes, A and Kimmerer, W. 2022. Phytoplankton prey of an abundant estuarine copepod identified in situ using DNA metabarcoding. Journal of Plankton Research, 44(2): 316-322. https://doi.org/10.1093/plankt/fbac002
Toczydlowski, R, Liggins, L, Gaither, M, Anderson, T, Barton, R, Berg, J, Beskid, S, Davis , B, Delgado, A, Farrell, E, Ghoojaei, M, Himmelsbach, N, Holmes, A, Queeno, S, Trinh, T, Weyand, C, Bradburd, G, Riginos, C, Toonen, R, and Crandall, E. 2021. Poor data stewardship will hinder global genetic diversity surveillance. PNAS, 118(34): e2107934118. https://doi.org/10.1073/pnas.2107934118
Kimmerer, W, Ignoffo, T, Bemowski, B, Modéran, J, Holmes, A, and Bergamaschi, B. 2018. Zooplankton Dynamics in the Cache Slough Complex of the Upper San Francisco Estuary. San Francisco Estuary and Watershed Science, 16(3). https://escholarship.org/uc/item/63k1z819
Holmes, A, Baerwald, M, Rodzen, J, Schreier, B, Mahardja, B, and Finger, A. In prep. Turbidity influences detection of a rare fish using environmental DNA.
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.
"What do bats eat? Genetic analysis of bat guano." Public Talk at Yolo Basin Foundation Flyway Nights, Davis, CA (Nov 5, 2020).
"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).
"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
More about me
I currently serve as president of the UC Davis Chapter of the Society for Conservation Biology. I've been SCUBA diving for over 20 years and became a Research Diver in 2016. I worked in the scientific collections of Philadelphia's Academy of Natural Sciences (Drexel) and the Museum of Comparative Zoology (Harvard), and was an undergraduate researcher at the California Academy of Sciences through the NSF's Research Experience for Undergraduates (REU) program. I was a Division I athlete and team captain on the Cornell rowing team and competed nationally and internationally in rowing for over a decade. I currently enjoy running and road biking.