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

Food web research conducted on a small boat in the upper San Francisco Estuary, 2015. A vacuum manifold allows for parallel filtering of eDNA samples in the field. Photo: T. Ignoffo

📄 Holmes & Kimmerer 2022

📄 Kimmerer et al. 2018

ENDANGERED SPECIES

Critically endangered delta smelt (Hypomesus transpacificus). Adults measure just 5-6 cm and are difficult to sample using trawls.
Image via flicker © 2007 by U.S. Fish & Wildlife Service (License: CC BY 2.0)

📄 Holmes et al. 2024

COMMUNITY ECOLOGY

Native tule perch (Hysterocarpus traskii), pictured here, are part of the fish community in a restored stream. Some natural history fun facts: they’re the only freshwater surfperch (Embiotocidae) and, like other surfperches, they give birth to live young (viviparity). Photo: A. Holmes

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

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

eDNA FOR MANAGEMENT

How to Achieve a True Consensus for Best Environmental DNA Practices laid the groundwork for this synthesis of the challenges and applications of eDNA in estuaries. Pictured: fisheries monitoring in the San Francisco Estuary. Photo: A. Holmes

📄 Nagarajan, Bedwell, Holmes et al. 2022