2 
Fishery Bulletin 1 15(1) 
We collected data on the run composition of adult 
steelhead as they migrated past Lower Granite Dam 
(LGD) on the Snake River, 695 km from the ocean. 
Adults returning from the Pacific Ocean to spawn in 
tributaries of the Snake River must ascend fish ladders 
at 8 dams during their migration; Lower Granite Dam 
is the final dam they encounter before dispersing to 
spawn. An observation window on the LGD fish ladder 
(the primary sampling “gear”) allows the enumeration 
of fish by species as they migrate upstream. A trap- 
ping facility (a diversion gate in the fish ladder with 
chutes leading to a holding tank) located above the ob- 
servation window (the secondary sampling gear) allows 
the interception of fish and the collection of biological 
data (Harmon, 2003). Counting and sampling returning 
adult steelhead at the dam provide the data for calcu- 
lating run composition (Schrader et al.^). Surprisingly, 
the primary literature is sparse on the statistical prop- 
erties of estimates derived with current methods and 
applied to run composition. 
In our study, we examined the properties of estima- 
tors of fish composition and confidence intervals (CIs) 
derived from weightings of counts of fish at the obser- 
vation window, data on origin (wild versus hatchery) 
obtained from the samples taken at the trapping facili- 
ty, and compositional data (sex, age, and genetically de- 
fined stock) collected from wild fish subsampled at the 
trapping facility. We considered counts at the observa- 
tional window to provide a census of fish passing the 
dam. Initially, we assumed trapping rates (proportion 
of time the trap was open) could be precisely controlled 
to obtain a constant proportion of the fish throughout 
the run and, therefore, that data could be pooled across 
time to estimate abundance. However, logistical issues 
that affected trapping rates through time led us to in- 
vestigate temporally stratified estimators. Individual 
CIs (for each group considered independently) and 
joint CIs (for all groups within a variable of interest 
considered simultaneously) were derived 1) by using 
closed-form asymptotically normal equations or 2) a 
2-step bootstrap sampling method, by origin (hatchery 
or wild) of the fish, by using compositional data collect- 
ed from wild fish. Using simulations, we compared the 
options for developing accurate estimates of abundance 
and CIs with good coverage; we then applied the pre- 
ferred method from the simulations to empirical data 
to develop guidance for sampling and interpreting fish- 
eries data on fish composition. 
Materials and methods 
We used data to describe the abundance and compo- 
sition of wild adult steelhead migrating past LGD to 
1 Schrader, W. C., M. P. Corsi, P. Kennedy, M. W. Ackerman, M. 
R. Campbell, K. K. Wright, and T. Copeland. 2013. Wild 
adult steelhead and Chinook salmon abundance and com- 
position at Lower Granite Dam, spawn year 2011. 2011 
annual report. Idaho Dep. Fish Game, IDFG Rep. 13-15, 89 
p. [Available at website.] 
spawn in the Snake River during spring 2011. Spawn- 
ing year (SY) 2011 is defined as the year when adult 
steelhead migrate past LGD between 1 July 2010 and 
30 June 2011. Although all steelhead in the Snake 
River basin spawn in the spring, the majority migrate 
past LGD during the previous fall, and a smaller por- 
tion migrates during the spring just before spawning. 
Later in this section, we describe the data set and es- 
timation procedures and the simulations developed to 
test the bias of the estimators and the coverage of the 
associated CIs. A complete description of the collec- 
tion methods and data used in this study is given by 
Schrader et al.^ 
Data collection 
Primary sampling stage (counts from the observation win- 
dow) Adult steelhead were counted as they passed a 
viewing window located in the LGD fish ladder, which 
they must ascend to migrate upriver. Counts of fish 
observed from the window were conducted during a 
majority of the year and occurred daily at 0400-2000 
Pacific Time. Counts from videos were used in lieu of 
counts from the window in November, December, and 
March and occurred at 0600-1600. Most fish pass the 
window during the 10-16 h of daylight when counts 
are made. The ladder is drained and closed in January 
and February, and, as a result, adult steelhead can- 
not migrate upriver during those months. Count data 
were downloaded from the U.S. Army Corps of Engi- 
neers website (website). The steelhead count consists of 
all fish >30 cm in fork length identified as O. mykiss. 
Daily counts were aggregated on a weekly basis. We 
further combined weeks into longer time periods (up to 
2 months) if few fish (<75 individuals) were passing the 
window during a week — a level observed typically early 
and late in the migration season. 
Secondary sampling stage (trapping rates) Trapping 
rates were determined by a committee of co-managers 
balancing sampling requirements for multiple projects 
with fish handling concerns. The trap is operational 
24 h/day and the trapping rate determines how long 
a trap gate remains open 4 times/h, such that a daily 
systematic sample (by time) is taken from the fish as- 
cending the fish ladder. Thus, the trapping rate (pro- 
portion of an hour that the trap gate is open) approxi- 
mates the desired proportion of the population to be 
sampled. Trapping rates are typically 10-20%; for the 
majority of the SY2011 run, it was set at 10%. 
Trapped fish were anesthetized and examined to 
determine whether they were of hatchery or wild or- 
igin. In the Snake River basin, most hatchery-origin 
steelhead have a clipped adipose fin; however, some 
are released with an intact adipose fin to supplement 
natural populations. Therefore, undipped steelhead 
were examined for the presence of dorsal or ventral 
fin erosion, which often occurs in hatchery-reared fish 
(Latremouille, 2003). Undipped hatchery fish may also 
be identified by the presence of a coded wire tag, by 
