Fish Ecology | Archaeology | Geochemistry

I am an Assistant Project Scientist at UC Santa Cruz in the Institute of Marine Sciences and National Marine Fisheries Service, Southwest Fisheries Science Center.

At the core of my research is the development and application of novel geochemical tracers and quantitative statistical methods to answer fundamental questions in fish ecology. My current focus is on reconstructing the life history of modern and historic Chinook Salmon populations in California and contrasting their responses to long-term climatic and landscape scale changes.

I collaborate with research groups at UC Santa Cruz (IMS, NOAA), UC Davis (WFCB, CWS, EPS), and ANU (RSES). In addition I work directly with many state and federal agencies to translate our scientific findings into management actions.


Research Projects

Over the last 5 years, I have studied several endangered and threatened fish in California, including Chinook Salmon, Delta and Longfin Smelt, and White Sturgeon. For these projects I applied a combination of microstructure and geochemical analyses (trace elements, strontium, oxygen, sulfur isotopes) to otoliths and other fish hard parts (scales, spines, fin rays) to better understand fish life histories, movement patterns, habitat use, and environmental exposure. Read more about these projects here

The effects of climate change on the life history of spring-run Chinook Salmon through time

Climate change is transforming California and is threatening already vulnerable salmon populations. This project will use archival tissues (otolith ear stones) from modern and historical spring-run Chinook Salmon to understand how shifts in migration timing and habitat use allowed salmon to cope with highly variable environmental conditions. We will learn how salmon responded to the recent drought and flood periods (2012-2020 CE), the California Gold Rush Period (~1835-1870 CE), the Little Ice Age (~1560-1780 CE), and the Megadrought Period (~1200-1410 CE). This effort will provide the insights needed for developing climate-adapted conservation actions to support salmon into the future.

Funding Source: Delta Stewardship Council and Bureau of Reclamation

Spring-run Chinook Salmon aggregating during their upstream spawning migration in Butte Creek. Picture by Carson Jeffres.

The core research team (from left to right): Carson Jeffres, George Whitman, Malte Willmes, Flora Cordoleani, Jeff Rosenthal, Jelmer Eerkens, and Rachel Johnson. Missing here are Eric Palkovacs and Pedro Valencia Landa.
Historic collections of Chinook Salmon otoliths and vertebrae. Photo courtesy of the UC Davis Peter D. Schulz Osteoichthyology Collection.

Data and Tools

IRHUM Database

The IRHUM (Isotopic Reconstruction of Human Migration) database is a web platform to access, explore and map strontium isotope data.

IsoFishR

Data reduction and analysis tool for laser-ablation strontium isotope data in R. Available on GitHub and PLOSONE.

OGFLtools

R package written by Christian Denney with utility functions used in the OGFishlab at UC Davis. Available on GitHub.

SFEcol

R package that uses images of the San Francisco Estuary and its wildlife to create color palettes. Available on GitHub.


Delta Science Fellowship 2017-2019

In search of refuge: Investigating the thermal life history of Delta Smelt through in-situ oxygen isotope ratio analysis of otoliths

The Delta Smelt (Hypomesus transpacificus) is a small pelagic fish and rapidly approaching extinction. It is endemic to the Sacramento-San Joaquin Bay-Delta which is an important link in California’s water supply. This estuary is managed for human use as well as for several species of threatened and endangered fish and the Delta Smelt is at the center of conflict between human and environmental uses of the limited water resources.

Here we used strontium (87Sr/86Sr) and oxygen (δ18O) isotope tracers from archived Delta Smelt otoliths to reconstruct life history and thermal resilience at fine temporal scales. 87Sr/86Sr ratios from otoliths can be used to reconstruct salinity habitats, while δ18O reflects the water temperature a fish has experienced.

The combination of these two isotopic tracers will allow us to investigate the relationship between Delta Smelt abundance, freshwater outflow and water temperature. Understanding this relationship can give new insights into resilience and habitat utilization of Delta Smelt in the face of warming water temperatures during prolonged drought periods and long-term climate change.