Background

Otoliths are hard structures located in the brain cavity of fish. These structures are formed by a 

buildup of calcium carbonate within a gelatinous matrix that produces light and dark bands similar 

to the growth rings in trees. The width of the bands corresponds to environmental factors such as 

temperature and food availability. As juvenile salmon encounter different environments in their 

migration to sea, they produce growth increments of varying widths and visible “checks” 

corresponding to times of stress or change. The resulting pattern of band variations and check marks 

leave a record of fish growth and residence time in each habitat type. This information helps Puget 

Sound restoration by determining the importance of different habitats for the optimal health and 

management of different salmon populations. The USGS Western Fisheries Research Center (WFRC) 

provides otolith research findings directly to resource managers who put this information to work. 

Otolith Research for Puget Sound 

Otolith Applications

Annual Growth

Otoliths have long been recognized as a way to 

determine the age of fish. Differences in summer 

and winter growth appear visually on the otolith as 

light and dark bands called annuli. Additionally, 

freshwater and ocean growth can be distinguished. 

For example, a 5-year old fish might have 2 

freshwater and 3 ocean annuli visible, indicating 

the general life history pattern of the individual 

fish. Individual based growth rates can be 

determined, since otolith size is related to fish size. 

Microstructure: Where did the fish grow up?

Daily growth increments are used to infer growth 

patterns and residency time in different habitats 

(FW-freshwater, D-delta, and B-bay). This type of 

analysis is also useful in determining the age of 

very young fish (in days) and whether a fish is wild 

or from a hatchery. 

Fish Identification

Otoliths can be marked with an otolith “tag” by 

manipulating temperatures to create a unique 

pattern on the otolith or by bathing the fish in a 

chemical that leaves a fluorescing band on the 

otolith. This is useful in identifying individuals 

from a certain research treatment or hatchery 

group.

U.S. Department of the Interior USGS FS 2007-3042 

U.S. Geological Survey May 30, 2007 
Microchemistry Reveals Details of Habitat Use

Quantities of certain elements (strontium and 

calcium have been used so far) can be measured 

from core to edge of the otolith. The results 

correspond to the migration history of the fish, 

since different environments have different 

amounts of these elements which get incorporated 

into the otolith. This can be used independently or 

in conjunction with the analysis of daily growth to 

indicate saltwater entry on the otolith. Since the 

elemental composition of water from various river 

systems differs, this technique can be used to 

discriminate among stocks or determine lake or 

river of origin. This technique can be applied in 

verifying the anadromy (salt water migration) of 

individual fish by looking for a marine signal. It 

can even be used to identify the maternal life 

history type (i.e. freshwater (kokanee) v. 

anadromous (sockeye) based on the signal in the 

otolith nucleus. 

Future Needs

An important USGS focus is to support restoration 

of Chinook salmon populations in Puget Sound by 

determining the importance of estuaries as nursery 

habitat for juvenile fish. This information helps 

managers and stakeholders choose restoration 

projects to achieve the most efficient use of limited 

funds. This knowledge would be developed by 

documenting variations in estuary habitat use by 

Chinook salmon populations in Puget Sound and 

elsewhere. Restoration depends on knowing length 

of residence and growth of juvenile salmon in 

various estuaries, and most importantly, how these 

fish contribute to the adult populations returning to 

spawn. Other research may focus on life history 

and growth of Puget Sound forage fish, bull trout, 

and baseline research on Elwha River salmon 

before and after removal of dams. Otolith analysis 

by USGS would be the primary tool, supported 

with field sampling by various Tribal, federal, and 

state partners and USGS. 

Community Conservation in Action: 

USGS Partners

• Skagit River-Skagit River System 

Cooperative, Seattle City Light 

• Snohomish River-NOAA Fisheries, Tulalip 

Tribe 

• Nisqually River-U.S. Fish and Wildlife 

Service, Nisqually Indian Tribe, NW Indian 

Fisheries Commission, Ducks Unlimited 

• Elwha River- USGS (Water Resources 

Division, Biological Resources Division, 

Geologic Division, Coastal Division), Lower 

Klallam Elwha Tribe 

• Cedar River-Seattle Public Utilities, 

Washington Trout, WA Dept. of Fish and 

Wildlife 

• Snake River-U.S. Fish and Wildlife Service, 

Idaho Fish and Game, USGS, UC Berkeley 

• Deschutes River-U.S. Fish and Wildlife 

Service, Confederated Tribes of the Warm 

Springs Reservation 

• Fisheries and Oceans, Canada-Pacific 

Biological Station 

For additional information, please contact: 

Lyman Thorsteinson, Center Director 

U.S. Geological Survey 

Western Fisheries Research Center 

6505 NE 65th Street 

Seattle, WA 98115 

Phone: (206) 526-6282 

FAX (206) 526-6654 

http://wfrc.usgs.gov