Education

BA, Biology, Cornell University

MS, Biology, San Francisco State University

PhD, Ecology, UC Davis

Interests

My publications and CV are linked at the bottom of this page. I recently accepted a position as a Research Scientist in the Omics Group at the Northern Gulf Institute/Mississippi State University and NOAA Atlantic Oceanographic and Meteorological Laboratory in Miami, Florida.

I study biodiversity, conservation, ecology, and trophic relationships of freshwater, estuarine, marine and wetland-associated species using genetic tools. My goal is to help make conservation genetic data more accessible for sustainable resource management and inclusive development. I’m especially excited the intersection of eDNA, population genetics, and phylogenetics. The taxonomic scope of my work is broad and currently includes fish, bats, and arthropods. 

I mentored UC Davis undergraduates through compensated research opportunities, training in eDNA methods and bioinformatics, student-driven projects, and conference presentations. Undergraduate research conducted by Serra Perry '21 and Khyana Yearwood '22 (now Junior Specialists in this lab) and Cristina Gonzalez '23 (now a Lab Tech in the Prober Lab at Caltech), is described below. Former undergraduate researcher Shayan Kaveh '20, now a Science Communicator at Sustainable Conservation (San Francisco, CA), describes his experience studying fish communities and bat diets with me here. ​​​​​

Topics of interest: conservation genetics, DNA metabarcoding, ecosystem services, endangered species, environmental DNA (eDNA), estuaries, evolution, marine ecology, Marine Protected Areas (MPAs), mentorship, museum and natural history collections, open access data and data sharing, phylogenetics, qPCR, trophic interactions, wetlands.

Graduate research projects

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 typically more sensitive and less invasive than conventional sampling methods. This project targets delta smelt (Hypomesus transpacificus), a critically endangered fish endemic to the San Francisco Estuary. High turbidity, high and variable flow, and tidal action in the upper estuary present challenges for eDNA detection. We are using experimental work and enclosure studies to gain a better understanding of how eDNA interacts with the environment. This work helps delineate the capabilities and limitations of eDNA of rare species in dynamic environments. This project 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 is developing eDNA methods for monitoring fish and invertebrates in the San Francisco Estuary. My contribution to this project focuses on Suisun Marsh, the largest tidal wetland in the San Francisco Estuary and the US west coast. I conducted eDNA sampling paired with the Suisun Marsh Fish Survey, a monthly trawl and seine survey that helps evaluate conservation, restoration, and management actions in the marsh. We are developing and optimizing a multi-locus eDNA metabarcoding approach, including creating reference sequence databases for resident fish, mollusks, and crustaceans and potential invasive species. This project is funded by CA Prop 1 funding through the California Department Fish and Wildlife to Dr. Andrea Schreier and Dr. Ravi Nagarajan, as well as the Garden Club of America Award in Coastal Wetlands Studies to me.

Undergraduates Shayan Kaveh, Victor Martinez, Serra Perry, and Khyana Yearwood provided valuable assistance with field sampling and laboratory work. 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

The largest bat colony in California is just minutes from UC Davis: each summer about 250,000 Mexican free-tailed bats (Tadarida brasiliensis) roost and raise their pups in the Yolo Basin Wildlife Area. The bats are thought to provide valuable ecosystem services by consuming agricultural pests in the Central Valley, but the diet of these bats has not been studied in over 25 years. In this study we apply DNA metabarcoding to gain new insights into the feeding patterns of bats during the critical pupping season. This research  helps develop reliable and specific DNA methods that demonstrate the value of bats and help increase their representation in local conservation plans.

This project is funded by through the Yolo Basin Foundation Graduate Student Fellowship, as well as a UC Davis Jastro Research Fellowship and a Seed Grant from the UC Davis Genome Center. Undergraduates Shayan Kaveh, Victor Martinez, Serra Perry, and Khyana Yearwood provided valuable assistance with field sampling and laboratory work. Khyana received a 2021 Provost's Undergraduate Fellowship (PUF) to study bat endoparasites using metabarcoding.

Collaborations with other labs at UC Davis

We are developing eDNA methods to characterize biodiversity in Northern California Marine Protected Areas (MPAs). We collected eDNA samples are paired with hook and line in surveys conducted by the California Collaborative Fisheries Research Program (CCFRP) and in Point Reyes National Seashore. Samples are sequenced using a universal fish barcode and a rockfish (Sebastes spp.) barcode. This research is in collaboration with Dr. Helen Killeen (graduate of the Morgan Lab, Bodega Marine Laboratory; now a postdoc at the Farallon Institute) and Population Biology graduate student Keira Monuki (Sanford Lab, Bodega Marine Laboratory). Undergraduates Khyana Yearwood, Serra Perry, Juan de la Torre, Tien Ly, and Cristina Gonzalez providing valuable assistance with field sampling, data management, and bioinformatic analysis. This study is funded by the California-Nevada Chapter of the American Fisheries Society, Western Division of the American Fisheries Society, a seed grant from the UC Davis Genome Center, the Neubacher Marine Science Fund (National Park Service), and through generous community support of our Experiment.com crowdfunding campaign and the Experiment Foundation.

In collaboration with Dr. Andrew Rypel, Dennis Cocherell and Mackenzie Miner (Department of Wildlife, Fish & Conservation Biology), we are using eDNA detection to characterize fish communities in Putah Creek, a regulated stream used as a model system for stream restoration. eDNA results are compared with traditional sampling (traps and electroshocking) to assess how the technology can best complement existing monitoring efforts. Undergraduates Khyana Yearwood, Serra Perry, Tien Ly and Cristina Gonzalez provided valuable assistance with sample collection and bioinformatic analysis. This study was funded by a Solano County Water Agency grant to Dr. Rypel and graduate scholarships awarded to me by the Diablo Valley Flyfishing Club, California Fly Fishers Unlimited, Marin Rod & Gun Club, and Fly Fishers of Davis.

In collaboration with Dr. Gina Tarbill (graduate of the 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. Undergraduates Shayan Kaveh, Victor Martinez, Serra Perry, Khyana Yearwood and Viviane-Lee Reed assisted with laboratory work and data analysis. This research is partially funded by the Davis Botanical Society.

Undergraduate research projects mentored

Cristina Gonzalez (BS, Genetics and Genomics, 2023) conducted an independent research project to assess the capabilities and limitations of eDNA metabarcoding for species-specific identification of nearshore fishes in Northern California. This project is especially concerned with rockfish (Sebastes spp.) and other fishes common in California's Marine Protected Areas. Her work is focused on optimizing the eDNA bioinformatics pipeline for high-throughput sequencing data and curating reference sequences. She gained proficiency in molecular ecology laboratory techniques and bioinformatic methods. Cristina presented a poster on her research at the UC Davis Undergraduate Research Conference. This work is conducted in collaboration with Dr. Christina Pasparakis (Bodega Marine Lab), Dr. Helen Killeen (Farallon Institute), and Population Biology PhD candidate Keira Monuki. 

Khyana Yearwood (BS, Biochemistry and Molecular Biology, 2022) designed a project using DNA metabarcoding to characterize gastrointestinal endoparasite communities in local bats. This research builds on the bat diet study described above and has allowed Khyana to explore her interest in disease ecology. She presented posters at the 2022 North American Congress for Conservation Biology (Reno, NV) and at the joint 2022 International Bat Research Conference/North American Symposium on Bat Research (Austin, TX). Khyana won a UC Davis Provost's Undergraduate Fellowship and a North American Society for Bat Research Award to fund her research. Khyana has made valuable contributions to several eDNA projects over more than 3 years and now works as a lab technician in the Genomic Variation Laboratory.

Serra Perry's (BS, Environmental Science and Management, 2021) Honors Thesis Is Environmental DNA Quantitative for Species Monitoring in the San Francisco Estuary? evaluated eDNA methods for conservation and management in the San Francisco Estuary. Her research contributed to a multi-year, multi-institution collaborative project funded by the California Department of Fish and Wildlife and Proposition 1. She presented her findings to the Department of Animal Science and in a poster at the 2022 North American Congress for Conservation Biology (virtual) and won a UC Davis Provost's Undergraduate Fellowship to fund her research. Serra made valuable contributions to several eDNA projects over 2.5 years. After graduation Serra worked in a molecular lab at UC Berkeley and conducted field surveys for the California Department of Fish and Wildlife; she now works as a lab technician in the Genomic Variation Laboratory.

Publications

Holmes, AE, Baerwald, MR, Rodzen, J, Schreier, BM, Mahardja, B, and Finger, AJ. 2024. Evaluating environmental DNA detection of a rare fish in turbid water using field and experimental approaches. PeerJ, 11, e16453. https://doi.org/10.7717/peerj.16453 (Special issue: Advancing the Environmental DNA and RNA Toolkit for Aquatic Ecosystem Monitoring and Management)

Crandall, ED, Toczydlowski, RH, Liggins, L, Holmes, AE, Ghoojaei, M, Gaither, MR, Wham, BE, Pritt, AL, Noble, C, Anderson, TJ, Barton, RL, Berg, JT, Beskid, SG, Delgado, A, Farrell, E, Himmelsbach, N, Queeno, SR, Trinh, T, Weyand, C, Bentley, A, Deck, J, Riginos, C, Bradburd, GS, and Toonen, RJ. 2023. Importance of timely metadata curation to the global surveillance of genetic diversity. Conservation Biology, e14061. https://doi.org/10.1111/cobi.14061

Nagarajan, R, Bedwell, M, Holmes, AE, Sanches, T, Acuña, S, Baerwald, M, Barnes, Blankenship, S, Connon, R., M. Deiner, K, Gille, D, Goldberg, C, Hunter, M, Jerde, C, Luikart, G, Meyer, R, Watts, A, and Schreier, A. 2022. Environmental DNA Methods for Ecological Monitoring and Biodiversity Assessment in Estuaries. Estuaries and Coasts, 45: 2254–2273. 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

DATASETS and REPORTS

Nagarajan, R, Holmes, A, and Schreier, A. 2023. Reference sequence databases for eDNA metabarcoding of San Francisco Estuary fishes and invertebrates [Dataset]. Dryad. https://doi.org/10.5061/dryad.0p2ngf25z

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.

Selected Presentations

Influence of flow regime on freshwater fish assemblage characterized using environmental DNA sampling (Talk), International Congress for Conservation Biology (ICCB), Kigali, Rwanda, July 23-27, 2023

Delineating ecosystem services provided by free-tailed bats in rice fields using non-invasive genetic sampling (Poster), International Congress for Conservation Biology (ICCB), Kigali, Rwanda, July 23-27, 2023

Non-invasive Diet Analysis of Bats in a Productive Agricultural Region Using DNA Metabarcoding. Oral presentation at joint meeting of International Bat Research Conference and North American Symposium for Bat Research, Austin, TX, August 7-12, 2022 and North American Congress for Conservation Biology, Reno, NV, July 17-21, 2022

Comparison of environmental DNA and traditional sampling for fish monitoring in Lower Putah Creek. Poster presentation at American Fisheries Society California Nevada Chapter meeting, Folsom, CA, May 24-27, 2022

Use of environmental DNA for fish monitoring in dynamic habitats: Capabilities and limitations of detection. Oral presentation at International Congress for Conservation Biology, virtual, Dec 13-17, 2021

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. Oral presentation 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