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Open-File Report 2010–1238

Final Report Presented to the Nisqually Indian Tribe

Version 1.1, May 2011

Otolith Analysis of Pre-Restoration Habitat Use by Chinook Salmon in the Delta-Flats and Nearshore Regions of the Nisqually River Estuary

By Angie Lind-Null and Kim Larsen


The Nisqually Fall Chinook population is one of 27 salmon stocks in the Puget Sound (Washington) evolutionarily significant unit listed as threatened under the federal Endangered Species Act (ESA). Extensive restoration of the Nisqually River delta ecosystem is currently taking place to assist in recovery of the stock as juvenile Fall Chinook salmon are dependent on the estuary. A pre-restoration baseline that includes the characterization of life history strategies, estuary residence times, growth rates, and habitat use is needed to evaluate the potential response of hatchery and natural origin Chinook salmon to restoration efforts and to determine restoration success. Otolith analysis was selected as a tool to examine Chinook salmon life history, growth, and residence in the Nisqually River estuary. Previously funded work on samples collected in 2004 (marked and unmarked) and 2005 (unmarked only) partially established a juvenile baseline on growth rates and length of residence associated with various habitats (freshwater, forested riverine tidal, emergent forested transition, estuarine emergent marsh, delta-flats and nearshore). However, residence times and growth rates for the delta-flats (DF) and nearshore (NS) habitats have been minimally documented due to small sample sizes. The purpose of the current study is to incorporate otolith microstructural analysis using otoliths from fish collected within the DF and NS habitats during sampling years 2004–08 to increase sample size and further evaluate between-year variation in otolith microstructure. Our results from this analysis indicated the delta-flats check (DFCK) on unmarked and marked Chinook samples in 2005–08 varied slightly in appearance from that seen on samples previously analyzed only from 2004. A fry migrant life history was observed on otoliths of unmarked Chinook collected in 2005, 2007, and 2008. Generally, freshwater mean increment width of unmarked fish, on average, was smaller compared to marked Chinook followed by tidal delta and DF/NS portions respectively. The average complete tidal delta and DF/NS growth rates for unmarked Chinook were consistently lower than for marked Chinook during all years; however, sample sizes were small during some years. The complete tidal delta and DF/NS growth rates were highest during 2008 compared to all other sampling years for both unmarked and marked Chinook. Unmarked Chinook, on average, spent longer in the tidal delta compared to marked Chinook. Our results from this report suggest that otolith microstructural analysis can be a valuable tool in establishing baseline information on the utilization of Nisqually River estuary habitats by juvenile Chinook salmon prior to the newly funded restoration efforts.

Revised May 26, 2011

First posted September 28, 2010

For additional information contact:
Director, Western Fisheries Research Center
U.S. Geological Survey,
6505 NE 65th Street
Seattle, Washington 98115

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Suggested citation:

Lind-Null, Angie, and Larsen, Kim, 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.









References Cited

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