Life History of Pacific Northwest Fishes through Age and Growth Structures

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The focus of our research is the ecological analysis of Pacific Northwest fishes through age and growth structures such as: scales, fin rays and otoliths (small calcium carbonate deposits beneath the brain used in hearing and balance that grow in proportion to the overall growth of the fish). These structures are utilized as research tools for understanding life histories and habitat importance related to both species and habitat preservation as well as restoration. Various research techniques are continually being applied, either alone or in combination, to answer questions of concern. The techniques include, but are not limited to: aging from otoliths, analyzing otolith microstructure patterns for growth, residence and thermal marks, identifying migration patterns, maternal signals and stock of origin from otolith microchemistry (through incorporation of elements from surrounding habitat), aging and growth from scales, and utilizing fin rays as a non-lethal substitute for otoliths.

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Nisqually River Delta

Image of Nisqually River Delta. (Courtesy: Sayre Hodgson, Nisqually Indian Tribe)

Puget Sound Fall Chinook Estuarine Utilization

Puget Sound Chinook salmon are just one of many species whose populations have declined to precariously low levels (ESA threatened status) coinciding with widespread loss of estuarine and nearshore habitats throughout Puget Sound. Juvenile fall Chinook salmon utilize several habitats during their migration to the open ocean.  One important habitat is the estuary, particularly tidal deltas, which provide a migratory corridor, protection from predators, and opportunity to forage, grow and adapt to seawater.  In response to the loss of vital habitat, monitoring and restoration efforts within the tidal delta and nearshore habitats of large river deltas are becoming common throughout Puget Sound.  A baseline of information that includes characterization of life history types, estuary residence times, growth rates, and habitat use is needed for evaluating the potential response of natural and hatchery origin Fall Chinook salmon to restoration efforts, therefore helping to evaluate restoration success and guide complementary monitoring efforts.

The Western Fisheries Research Center (WFRC) and its partners are using otoliths to examine the life history of Fall Chinook salmon within several large river deltas of Puget Sound (Skagit, Snohomish, Nisqually rivers).  Chinook residence times and growth rates in various habitats, and the overall importance of estuarine utilization to juveniles as well as the returning adult population are the focus of the research.

Processed otolith from a juvenile Chinook salmon

A processed otolith from a juvenile Chinook salmon depicting microstructure marking of daily increments with an image analysis program. Credit: Karl Stenberg, USGS - Western Fisheries Research Center. (Public domain.)


Eric Beamer - Skagit River System Cooperative (Tribal)

Chris Ellings and Sayre Hodgson - The Nisqually Indian Tribe

Correigh Greene and Josh Chamberlain - NOAA Fisheries

Isa Woo and Melanie Davis - USGS, Western Ecological Research Center

Seattle City Light

U.S. Fish and Wildlife Service

Environmental Protection Agency

Ducks Unlimited


Related Publications/Reports:

Beamer, E.M., J.C. Sartori, and K.A. Larsen. 2000. Skagit Chinook life history study progress report number 3. Prepared for: Non-Flow Coordination Committee (NCC) under the Chinook Research Program in the Non-Flow Mitigation part of the Skagit Fisheries Settlement Agreement. Federal Energy Regulatory Commission Project Number 553. 19 p.

Beamer, E.M. and K. Larsen. 2004. The importance of Skagit delta habitat on the growth of the wild ocean-type Chinook in Skagit Bay: Implications for delta restoration. Internal Skagit River System Cooperative report. 6 p.

Beamer, E., A. McBride, C. Greene, R. Henderson, G. Hood, K. Wolf, K. Larsen, C. Rice, and K. Fresh. 2005. Delta and nearshore restoration for the recovery of wild Skagit River Chinook salmon: Linking estuary restoration to wild Chinook salmon populations. Supplemental document to Beamer, E., R. Bernard, B. Hayman, B. Hebner, S. Hinton, G. Hood, C. Kraemer, A. McBride, J. Musslewhite, D. Smith, L. Wasserman, and K. Wyman. Skagit Chinook Recovery Plan, Appendix D. 327 p.

Lind-Null, A., K.Larsen, and R. Reisenbichler. 2008.  Characterization of estuary use by Nisqually Hatchery Chinook based on otolith analysis. U.S. Geological Survey Open-File Report 2008-1102, 12 p.

Lind-Null, A., K. Larsen, and R. Reisenbichler. 2008.  Pre-Restoration habitat use by Chinook salmon in the Nisqually Estuary using otolith analysis. U.S. Geological Survey Open-File Report 2008-1021, 14 p.

Lind-Null, A., and K. Larsen.  2009.  Pre-restoration habitat use by Chinook Salmon in the Nisqually Estuary using otolith analysis—An additional year: U.S. Geological Survey Open-File Report 2009-1106, 18 p.

Larsen, K., J. Duda, K. Stenberg, M. Beirne, M. McHenry, K. Fresh, and R. Reisenbichler. 2010. Using otolith analysis to establish habitat use patterns of migratory juvenile Chinook salmon in the Elwha River. Pages 75-79 in Extended Abstracts from the Coastal Habitats in Puget Sound (CHIPS) 2006 Workshop, Port Townsend, Washington, November 14-16, 2006. Edited by G. Gelfenbaum, T.L. Fuentes, J.J. Duda, E.E. Grossman, and R.K. Takesue. U.S. Geological Survey Open-File Report 2009-1218, 136 p.

Lind-Null, A., and K. Larsen. 2010. Otolith analysis of pre-restoration habitat use by Chinook salmon in the delta-flats and nearshore regions of the Nisqually River estuary. U.S. Geological Survey Open-File Report 2010-1238, 28 p.

Duda, J.J., M.M. Beirne, K. Larsen, D. Barry, K. Stenberg, and M.L. McHenry. 2011. Chapter 7: Aquatic ecology of the Elwha River Estuary Prior to Dam Removal.  Pages 175-224 in Coastal habitats of the Elwha River, Washington—biological and physical patterns and processes prior to dam removal. U.S. Geological Survey Scientific Investigations Report 2011–5120, 264 p.

Lind-Null, A., and K. Larsen.  2011.  Validation of a freshwater otolith microstructure pattern for Nisqually Chinook salmon (Oncorhynchus tshawytscha). Nisqually Indian Tribe, Department of natural Resources, Salmon Recovery Program, Technical Report No. 2011-1.

Davis, M.J., C.S. Ellings, I. Woo, S. Hodgson, K. Larsen, and G. Nakai. 2018. Gauging resource exploitation by juvenile Chinook salmon (Oncorhynchus tshawytscha) in restoring estuarine habitat. Restor. Ecol. 26(5): 976-986. DOI: 10.1111/rec.12643.


Non-Native West Coast American Shad Life History


American shad

American shad (Alosa sapidissima), Credit: USGS. (Public domain.)

American shad, an anadromous species native to the East Coast of the United States, was transported to California in 1871.  Over the years, they have expanded their range south to Mexico and north to Alaska. Since American shad have become well-established and numerous in many systems, it is important to understand their potential impacts and interactions with threatened fish species, such as salmon. Understanding these interactions may become more important as environmental conditions change.  There have been a few shad investigations in their introduced range but much of our knowledge of shad biology and ecology is from East Coast populations.  Baseline life history information is crucial to understanding the extent to which this non-native species can impact native fishes. 

The WFRC and its partners are using otoliths and scales as tools to increase our knowledge of shad life history throughout its entire West Coast range.  Most recently, the research is focused on the use of otolith microchemistry to help explain habitat usage and migration (i.e., Do some shad, as juveniles, move back and forth between fresh and estuarine or marine waters? Do some shad exhibit extended freshwater rearing in their first year?), and more accurately describe life history characteristics of the adult population as a whole. This would include microchemical patterns from otoliths to corroborate repeat spawning patterns initially identified through scale analysis.

Otoliths American Shad

Otoliths from a 5-year old American shad captured in the Umpqua River, OR. Credit: Lisa Wetzel, USGS - Western Fisheries Research Center. (Public domain.)

Strontium to calcium ratios (Sr/Ca) of American shad otoliths

Variation in American shad life history patterns illustrated through strontium to calcium ratios (Sr/Ca) of American shad otoliths from Columbia River, WA midsize fish (a-c), Columbia River, WA estuary fish (d-f), and Vancouver Island, British Columbia marine residents (g-i). Solid black lines indicate annuli; dashed black lines indicate the otolith edge. Higher Sr/Ca indicates marine (above 0.0010). Credit: Lisa A Wetzel, USGS - Western Fisheries Research Center. (Public domain.)


USGS - WFRC, Columbia River Research Laboratory

Chris Zimmerman - USGS, Alaska Science Center

University of Washington - School of Aquatic and Fisheries Sciences

University of Michigan - Cooperative Institute for Limnology and Ecosystems Research

NOAA - Great Lakes Environmental Research Laboratory (AISP)

Bonneville Power Administration


Related Publications/Reports:

Parsley, M.J., S.T. Sauter, L.A. Wetzel. 2011.  Impact of American shad in the Columbia River. Final Report Performance Period: May 1, 2007 – January 15, 2011. Prepared for U.S. Department of Energy, Bonneville Power Administration, Portland, OR. Contract Nos. 00036371, 0004154, 00045991, Project No. 2007-275-00. 121 p.


Validation of a Non-Lethal Approach to Life History Examination


Juvenile bull trout

Juvenile bull trout. Credit: Bart Gamett, U.S. Forest Service. (Public domain.)

Many freshwater and anadromous fish species, including bull trout, display diverse life history patterns, are highly migratory, and use multiple habitats throughout their life history. Connectivity among these different habitats is critical for providing access to spawning, rearing, foraging, overwintering, and migratory habitats. However, to protect connectivity, we must first know what habitats are used and when they are used. Migratory and life history patterns of salmonids, including bull trout and other listed fishes, is predominately evaluated using tagging techniques. Unfortunately, these methods only provide information for specific life stages, are not practical for young fish, suffer from low recapture rates, are temporally limited due to tagging constraints and are expensive for fish like bull trout with large-scale migratory behaviors or that use diverse habitats.

Sectioned rainbow trout fin ray

Sectioned rainbow trout fin ray showing the laser scar from microchemical analysis. Credit: Lisa Wetzel, USGS - Western Fisheries Research Center. (Public domain.)

Fortunately, life history information can be obtained through alternative means. Examination of fish otoliths, both visually and chemically, can be used for obtaining life history information about fish including age, growth and habitat usage. Specifically, microchemical analysis of otoliths can provide information on migratory behavior, individual life history patterns, maternal life history patterns, and large-scale habitat use in basins with significant variation in water chemistry. Microchemistry studies have typically relied on analysis of otoliths from incidental mortalities or lethal sampling, but there is interest in moving toward non-lethal methods, especially for threatened and endangered species such as bull trout. Fin rays can potentially be used as an alternative to otoliths for answering the same questions but in a non-lethal way. Some initial microchemistry research obtained similar results between otoliths and rays. However, questions remain as to the extent to which microchemical analysis of non-lethally removed fin rays can be used to obtain the same information normally obtained through lethal sampling of otoliths.

Using rainbow trout and steelhead as proxies for the endangered bull trout, WFRC and its partners are examining otoliths and rays to provide a clearer understanding of how fin rays develop relative to otoliths, and to determine the utility of rays regarding the existence of chemical signals associated with maternal effects.

Graph of microchemical results showing a spike in strontium

Graph of microchemical results showing a spike in strontium (blue circles; generally higher in saltwater than freshwater) near either edge of the above fin ray; this was part of a laboratory experiment mimicking saltwater exposure for comparing the tracking ability of migration history between otoliths and fin rays. Credit: Tamas Ugrai, University of Washington. (Courtesy: Tamas Ugrai)


Roger Peters - U.S. Fish and Wildlife Service