Ann E. Holmes

Ann Holmes smiles at the Camera with a blue hat and a white beaker in hand with blue ocean and gren island in the backgroun

Research Highlights

Research Interests

Conservation genetics, biodiversity, community ecology, trophic ecology, and evolutionary biology.

Environmental DNA (eDNA) fieldwork and laboratory methods, bioinformatics, statistics, phylogenetic methods, data sharing, metadata management, and reference sequence databases.

Ann E. Holmes Ph.D.

Research Scientist I

754.300.8089

Ann.Holmes@noaa.gov

Ann Holmes

4301 Rickenbacker Causeway
Miami, Florida 33149

About

Dr. Ann Holmes is a molecular ecologist and conservation geneticist in the Molecular & Computational Biodiversity (MCB) Group in NOAA ‘Omics at the Northern Gulf Institute and AOML. She is studying the use of environmental DNA (eDNA) metabarcoding (i.e., derived using high-throughput sequencing) occurrence data and metadata for detection of Aquatic Invasive Species (AIS). This work forms a springboard for a community consensus process developing minimum requirements and best practices enabling the addition of species occurrences derived from eDNA metabarcoding to the United States Geological Survey (USGS) open access Nonindigenous Aquatic Species (NAS) Database (https://nas.er.usgs.gov/). These processes and products facilitate more equitable access to high-quality genetic biodiversity datasets (“big data”) to better understand and conserve imperiled and at-risk species and ecosystems.
Ann received her PhD in Ecology from the University of California, Davis. Her graduate work operationalized molecular ecology approaches to address research questions relevant to biodiversity, conservation, and natural resource management. She studied spatiotemporal dynamics, trophic ecology, endangered species, and invasive species in aquatic, estuarine, coastal, and wetland habitats. Prior to graduate school, Ann worked in museum collections and competed nationally and internationally in rowing. Ann also holds a BA in Biology from Cornell University and an MS in Biology from San Francisco State University.

Current Work & CV

Current Work

Research Scientist I, Northern Gulf Institute, Mississippi State University
NOAA Affiliate, Ocean Chemistry and Ecosystems Division

Download Full CV

Education

2023, PhD, Ecology (Ecological Genetics & Genomics), University of California, Davis, CA

2018, MS, Biology (Ecology, Evolution & Conservation Biology), San Francisco State University, San Francisco, CA

2001, BA cum laude, Biology (Ecology & Evolution), Cornell University, Ithaca, NY

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. The 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, Liukart, G, Meyer, R, Watts, A, and Schreier, A. 2022. Environmental DNA Methods for Ecological Monitoring and Biodiversity Assessment in Estuaries. Estuaries and Coasts, 44, 2254-2273. https://doi.org/10.1007/s12237-022-01080-y

    Holmes, AE 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, AE, 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

    Awards

    Best Student Poster, American Fisheries Society California-Nevada Chapter Annual Meeting, Long Beach, CA (2023)

    Chancellor’s Award for Excellence in Mentoring Undergraduate Research, University of California, Davis (2021)

    Best Student Presentation, Bay Delta Science Conference, Sacramento, CA (2018)

    Best Graduate Biology Poster, San Francisco State University Poster Showcase, San Francisco, CA (2016)

    Fellowships & Scholarships

    Neubacher Fund for Marine Science at Point Reyes National Seashore (2023)

    Diablo Valley Flyfishing Club Wisecarver Memorial Scholarship (2022)

    California Fly Fishers Unlimited Bob Bittner Scholarship (2022)

    Marin Rod & Gun Club Scholarship (2022)

    Fly Fishers of Davis Scholarship (2022)

    Experiment Foundation Ocean Solutions Grant (2022)

    Sullivan Environmental Sciences Scholarship (2019)

    The Garden Club of America Award in Coastal Wetlands Studies (2019)

    Henry A. Jastro Research Fellowship, University of California, Davis (2018-2020)

    Yolo Basin Foundation Graduate Student Fellowship (2018-2020)

    Graduate Group in Ecology Fellowship, University of California, Davis (2016-2019)