Graduate Group in Ecology
Department of Animal Science
BA, Biology with honors, Cornell University
MS, Biology, San Francisco State University
The genetic methods I use have broad application in detection, conservation and management of species in vital ecosystems. I work with very low concentration DNA samples that require careful handling and data interpretation to prevent false positive detections and decrease false negative detections.
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
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
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 work on this project which is funded by the Yolo Basin Foundation.
Biodiversity assessment of Suisun Marsh, the largest tidal wetland in the San Francisco Estuary
This study will 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 Estuary. Undergraduates Shayan Kaveh, Serra Perry, and Khyana Yearwood work on 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.
"eDNA in Estuaries: Enclosure experiment shows capabilities and limitations of environmental DNA detection of a rare fish." Graduate Student Symposium in Ecology, Davis, CA (Feb 7, 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).
"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
“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).
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 Estuary. San Francisco Estuary and Watershed Science, 16(3).