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Salmon Life History Research in California’s Central Valley

Our team uses microchemical analyses to quantify salmon life history diversity across freshwater, estuarine, and marine ecosystems to improve conservation, management, and recovery.

A program of the Southwest Fisheries Science Center’s Fisheries Ecology Division.

The Salmon Life History Team uses life history theory to understand how traits and phenotypes linked to life history diversity function to support locally adapted and resilient salmon populations. We focus on understanding how changes in the environment—habitat modification, flow regimes, changing ocean conditions—function to promote or truncate different components of life history diversity within and among populations. We integrate isotopic analyses in archival tissues with fish surveys, environmental monitoring data, field experiments, and quantitative models to evaluate ways in which changes in the environment shape salmon life histories relevant to their conservation, management, and recovery.

In order to detect changes in life history traits and behaviors, life history strategies must first be identified. We primarily use isotopes in archival tissues (otoliths and eye lenses) to study variation in migration size and timing, age at maturation, habitat use, contaminant exposure, diet, growth, and connectivity in Central Valley fish populations. We have developed maps of isotope gradients across freshwater landscapes recorded in salmon tissues that help identify critical habitats for survival, growth, and reproductive success of endangered and threatened salmon and those targeted by fisheries.

Our team focuses on principles of translational ecology to bridge the gap between scientists, the public, and decision makers. We strive to promote management-relevant science conducted by Fisheries Ecology Division researchers to ensure science is at the table where decisions are being made on Central Valley salmon and water resources. In this capacity, we provide science support the West Coast Region’s Central Valley Office. Our team is made up of academic partners at the University of California Davis’ Center for Watershed Sciences where we mentor staff, postdoctoral researchers, graduate and undergraduate students and promote core values in diversity, equity and inclusion in fisheries science. We operate a modern isotope preparation and otolith imaging laboratory and work closely with UC Davis’ Stable Isotope Facility and Interdisciplinary Center for Inductively-Coupled Plasma Mass Spectrometry.

Our Research

Tracking Critical Habitats with Isotope Diaries in Fish

A salmon’s otoliths—tiny bones in the head that help a fish maintain balance—contain a diary of its movements and a timeline of changes in diet. We use the chemistry recorded in daily bands (similar to tree growth rings) to track organisms that are too small to tag as they move among rivers, floodplains, estuaries, and the ocean over their lifetime. Strontium isotopes (87Sr/86Sr) in otoliths and carbon (δ13C), nitrogen (δ15N), and sulfur (δ34S) isotopes in salmon eye lenses provide natural markers to reconstruct time-resolved habitats critical to salmon growth, survival, and reproductive success. These markers allow us to develop isotopically distinct habitat maps that can be used to quantify year-to-year changes in the relative importance of different salmon rearing habitats.

Learn more about our salmon habitat research

Using Ancient Salmon Bones to Reveal Key Drivers for Recovering Modern Populations

Chinook salmon populations in California are in decline due to the combined effects of habitat degradation, water diversions, and shifting climate regimes. Effective salmon conservation and management relies on understanding their life history diversity and ability to adapt to environmental change. Monitoring efforts and geochemical tools have provided crucial insights into modern salmon population dynamics and behavior in California, but these data were collected only after significant population declines and extirpation from a large fraction of their historic habitat.

We are addressing this critical data gap by reconstructing key life history metrics (age, growth, habitat use, migration timings, genotype) in adult salmon otoliths preserved over a 6000-year time series in archeological sites on the Feather River. This will allow us to derive drivers of salmon resilience that allowed salmon to persist through mega droughts and landscape evolution, data that can inform future management and conservation actions in a changing climate.

Life History Diversity in Natural and Regulated Rivers

Environmental variability across the landscape creates a mosaic of diverse habitats resulting in physical and behavioral differences in outmigrating salmon. We use juvenile salmon monitoring data and otolith strontium isotopes to track the expression and survival of different life history strategies in relation to dam operations, droughts and wet years, and water temperature.

Learn more about our salmon life history diversity research

Tracking Contaminant Exposure and Sources of Nutritional Supplements and Deficiencies

Having tools to track shifts and quality of diet over the lifetime of individuals helps us understand how fish condition and diet influence growth, survival, and ultimately reproductive success. Our team documents nutritional histories of migratory fish in the San Francisco Bay watershed using microchemical analysis of otoliths and eye lenses. Examples of our work include:

  • Using a novel combination of x-ray fluorescence microscopy and depositional chronology in otoliths to reveal for the first time provenance, life stage, and duration of toxic selenium (Se) diet exposure over the lifetime of an organism
    Learn more about our contaminant exposure research
  • Demonstrating that eye lenses, a protein-rich depositional tissue that becomes inert after forming, represent a single tissue in fish whose individual layers can be used to reconstruct diet chronology through changes in ẟ13C, ẟ34S, ẟ15N over time
    Learn more about our fish eyes and food web research
  • Measuring thiamine (vitamin B1) in salmon eggs to monitor nutritional status and thresholds that may lead to reproductive failure for salmon. This work is conducted by an interdisciplinary team of scientists working to understand the causes, impacts, and hatchery mitigation options to support healthy salmon populations. We are working with anglers and fishing industry partners to monitor the nutritional status of Chinook salmon caught in the Central California coastal fishery.
    Learn more about our thiamine deficiency research

Our Team

Team Leader: Rachel Johnson

Co-PI: Carson Jeffres

  • Malte Willmes
  • George Whitman
  • Eric Holmes
  • Miranda Bell-Tilcock
  • Abigail Ward
  • Alexandra Chu
  • Ally Li
  • Matthew Salvador
  • Kimberly Evans
  • Francheska Torres
  • Matthew Emard
  • Nicholas Wright
  • Miranda Lowe-Webb