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Fishery Bulletin 1 10(4) 
Chinook salmon were released from hatcheries after our 
study period, we considered only releases occurring at 
least 10 days before our final cruise of the spring: either 
June 19 (2007, 2008) or June 14 (2009, 2010). This cutoff 
is conservative (i.e., may underestimate %H) because 
recovery of subyearling Chinook with CWTs (n=127) in 
our study took an average of 32 days (range: 2-104 days) 
from time of release at hatcheries. 
Extensive fish-tagging programs active throughout 
the Columbia River basin also provided information 
about the geographic origins of many individuals col- 
lected in the purse seine. In particular, nearly 30 mil- 
lion juvenile salmon (largely of hatchery origin) are 
tagged with CWTs (Regional Mark Information System 
[RMIS], database available at http://www.rmpc.org, 
accessed June 2011) and 2.5 million hatchery and wild 
salmon are tagged with PIT tags each year (PIT Tag 
Information System [PTAGIS], database available at 
http://www.ptagis.org, accessed June 2011). Both tag 
types provide information about release location and 
timing; we used this information to estimate the geo- 
graphic origins of the salmon we collected. 
For fish containing either CWT or PIT tags, we ex- 
tracted the tags, “read” the tag code visually (CWTs) 
or electronically (PIT tags), and determined the release 
location from the appropriate online database. To sim- 
plify our analysis, release locations were grouped into 5 
geographic regions (Fig. 1): below Bonneville Dam (rkm 
235, excluding the Willamette River); mid-Columbia 
River (between Bonneville Dam and the mouth of the 
Snake River [rkm 522]); upper Columbia River (acces- 
sible waters above the confluence with the Snake River); 
Snake River (all accessible waters of the Snake River); 
and Willamette River. We could not determine release 
locations from the few tags (29 CWTs and 2 PIT) that 
either had no release information (i.e., agency codes or 
blank tags) or were not in the databases; some CWTs 
were lost before they could be read. 
Environmental data 
To gain insight into the environmentally driven dynam- 
ics of the estuarine fish assemblage, we recorded both 
local and regional environmental data for each purse 
seine set. These 2 environmental data types were 
expected to reflect different types of variability: local 
data would vary at very short time scales (minutes to 
hours) within the estuary, and regional data would rep- 
resent longer term variability (days to weeks) at larger 
spatial scales. Our local data consisted of tidal stage and 
height information for each set and in situ conductiv- 
ity, temperature, and depth (CTD) profiles made from 
the surface to the bottom measured before every set of 
the net. For purposes of this analysis, we used in situ 
temperature and salinity measurements at the surface 
(depth of 1 m) and near-bottoin (depth of 7 m) to char- 
acterize the local water column. Because of equipment 
problems, CTD casts were not conducted during 2 of 
our cruises in 2007 (7-1 and 7-6) and 2 cruises in 2008 
(8-1 and 8-7; for dates of these cruises, see Table 1). For 
these 4 cruises, we substituted modeled temperature 
and salinity data provided by the Center for Coastal 
Margin Observation and Prediction (Batista 5 ); compari- 
sons between modeled data and in situ temperature and 
salinity measurements indicated that they were highly 
correlated (coefficient of correlation [r]>0.82). 
We estimated tidal stage (time relative to low tide) 
for each set on the basis of low tide predicted for Ham- 
mond, Oregon, (NOAA station 9439011; http://tidesand- 
currents.noaa.gov), which is within 500 m of our Trestle 
Bay sampling station. We also used this station to pre- 
dict low tide at the North Channel site because pre- 
dicted timing of tidal inundation was similar. We used 
observed (versus predicted) tidal heights recorded at 
Astoria, Oregon (NOAA station 9439040) because tidal 
heights were not available for the Hammond station. 
We used regional environmental data that character- 
ized both riverine and marine conditions because es- 
tuarine fishes likely were influenced by both freshwa- 
ter and marine environments. Regional riverine data 
consisted of daily river flow records from Quincy, Or- 
egon (rkm 87; U.S. Geological Survey [USGS] surface 
water station 14246900; http://www.usgs.gov, accessed 
August 2011) and daily temperature measurements 
at the Dalles Dam (rkm 304; USGS surface water 
station 14105700), both averaged over the days of the 
cruise. These stations were the nearest to the estuary 
among the stations where respective data types were 
collected. 
Marine environmental data reflected conditions both 
near the mouth of the Columbia River and across the 
North Pacific Ocean. Local marine data included daily 
sea-surface temperatures (SST) measured at Stonewall 
Bank (NOAA Data Buoy 46050; 44°38.3'N, 124°32.0'W; 
http://www.ndbc.noaa.gov, accessed April 2012), daily 
Bakun upwelling index (UI) for 45°N, 125°W (http:// 
www.pfeg.noaa.gov/products/PFEL/modeled/indices/ 
upwelling, accessed April 2012), and daily sea-level 
height (SLH) estimated for Astoria (http://ilikai.soest. 
hawaii.edu/uhslc/htmld, accessed April 2012). We used 
2 indices describing the dominant modes of variability 
across the North Pacific Ocean at monthly intervals: 
the Pacific Decadal Oscillation (PDO) index (Mantua 
et ah, 1997; http://www.jisao.washington.edu/pdo) and 
the North Pacific Gyre Oscillation (NPGO) index (Di 
Lorenzo et al., 2008; http://www.o3d.org/npgo). We es- 
timated pairwise Spearman correlation coefficients be- 
tween environmental variables to determine how they 
were related to each other (Sokal and Rohlf, 1995). 
Analytical approach 
All analyses were designed to explore how juvenile 
salmon and the estuarine fish assemblage varied at 
temporal scales ranging from days to years. Because of 
our focus on juvenile salmon, our analyses of salmon, 
5 Batista, A. 2012. Unpubl. data. Center for Coastal Margin 
Observation and Prediction, Oregon Health and Science 
Univ., Portland, OR 97239. 
