Ann Holmes

RESEARCH

Below are the main themes of my research; links for papers are added as they are published. You’re welcome to contact me with any questions!

Biodiversity & Ecological Interactions

PLANKTON FOOD WEBS

Here I used eDNA metabarcoding to evaluate feeding patterns of Pseudodiaptomus forbesi, a key food source for fish in the upper San Francisco Estuary.
Photo of field sampling courtesy of Toni Ignoffo.

📄 Holmes & Kimmerer 2022

📄 Kimmerer et al. 2018

ENDANGERED SPECIES

The study evaluated targeted eDNA detection methods for critically endangered delta smelt (Hypomesus transpacificus) under turbid conditions in the San Francisco Estuary.
Image via flicker © 2007 by U.S. Fish & Wildlife Service (License: CC BY 2.0)

📄 Holmes et al. 2024

COMMUNITY ECOLOGY

This work used eDNA metabarcoding to study fish communities in a restored creek. Pictured here are tule perch (Hysterocarpus traskii), a California native species and the only freshwater surfperch (Embiotocidae).
Photo: A. Holmes

Manuscript in preparation.

Applied Ecology & Conservation

ECOSYSTEM SERVICES

Diet analysis of Mexican free-tailed bats using DNA metabarcoding reveals ecosystem services and food web dynamics. Pictured: A non-releasable ambassador bat with NorCal Bats. Photo: S. Kaveh

📣 Highlighted in How Yolo County bats help sustainable farming methods

MARINE PROTECTED AREAS

Rockfish (Sebastes sp.) are a key group in our study of Marine Protected Areas. Some of this work was paired with California Collaborative Fisheries Research Program community angling surveys. Pictured: The California Coast Exhibit at the California Academy of Sciences. Photo: A Holmes

🐟 Project spotlight by the Pt. Reyes National Seashore Association

ESTUARY MONITORING

Ongoing work to support eDNA biomonitoring in Suisun Marsh, the largest wetland on the US West Coast, conducted in parallel with the Suisun Marsh Fish Study. Photo: A. Holmes

🗂️ Custom regional reference sequence databases

Open Science & Decision Support

FAIR DATA PRINCIPLES

Two papers originated from the GEOME Datathon, a collaborative project to improve accessibility and reusability of biodiversity genomic data. Led by Dr. Eric Crandall of the Diversity of the Indo-Pacific Network (DIPnet), Summer 2020

📄 Crandall et al. 2023

📄 Toczydlowski et al. 2021

INVASIVE SPECIES

An invasive colonial tunicate (Family Styelidae) at a marina in Bodega Bay, California. Photo: A. Holmes

Manuscript in preparation.

eDNA FOR MANAGEMENT

Fisheries monitoring in the San Francisco Estuary. Photo: A. Holmes

This paper originated from discussions at the symposium How to Achieve a True Consensus for Best Environmental DNA Practices held at UC Davis in January, 2020:

📄 Nagarajan, Bedwell, Holmes et al. 2022

This paper originated from a working group of the US Marine Biodiversity Observation Network (MBON):

📄 Watts et al. 2026