Download Habitat Use by Juvenile Salmonids in the Smith River Estuary

Transactions of the American Fisheries Society 134:1147–1158, 2005
q Copyright by the American Fisheries Society 2005
DOI: 10.1577/T04-092.1
[Article]
Habitat Use by Juvenile Salmonids in the Smith River
Estuary, California
REBECCA M. QUIÑONES*1
AND
TIMOTHY J. MULLIGAN
Department of Fisheries Biology, Humboldt State University,
Arcata, California 95521, USA
Abstract.—Estuaries are highly productive areas that serve as important nursery habitat for many
species of fish. Estuaries provide juvenile salmonids Oncorhynchus spp. with foraging habitats,
refuge from predators, and areas in which smoltification and orientation for return migrations can
occur. Our primary goal was to describe how juvenile salmonids use the Smith River estuary in
northern California, a system that is largely devoid of instream cover and the slough habitat it
once contained. The presence of juvenile salmonids was quantified through direct observation
(snorkel surveys) and calculations of relative densities in the midchannel and stream margin habitats
of the estuary. We completed a total of 755 dives between May 1999 and November 2000. We
found that significant differences existed between the relative densities of juvenile Chinook salmon
O. tshawytscha and trout (coastal cutthroat trout O. clarkii clarkii and steelhead O. mykiss) observed
in habitats with and without cover along stream margins. Stepwise logistic analysis was used to
correlate the presence or absence of Chinook salmon and trout to stream reach, habitat type, flow
(m3/s), salinity (‰), temperature (8C), and depth (m). In general, juvenile salmonids appeared to
preferentially use habitats with overhanging riparian vegetation. However, Chinook salmon presence was most correlated with areas of low salinity (,5‰), while trout presence was most influenced by habitat type. Trout were present most often in stream margin habitats, regardless of other
physical factors. Our study demonstrates that riparian vegetation may be an essential component
of juvenile salmonid rearing habitat in estuaries with little instream cover.
In the Pacific Northwest, studies have shown
that estuaries provide juvenile salmonids with
rearing areas that can play an important role in
determining successful oceanic existence and survival (Healey 1982; Levy and Northcote 1982;
Wissmar and Simenstad 1988; Magnusson and Hilborn 2003). Estuaries can provide juvenile salmonids with foraging habitats, refuge from predators, and areas in which smoltification and orientation for return migrations can occur (Simenstad et al. 1982; Iwata and Komatsu 1984; Moser
et al. 1991). Estuarine entrance and residency vary
among species and can fluctuate according to climate, flow regime, and tidal cycle and to the size
and condition of individuals at the time of emergence (Healey 1982; Kjelson et al. 1982; Simenstad et al. 1982). Once juvenile salmonids reach
the estuary, high mortality rates can decrease the
seasonal abundance of juveniles rearing in unsuitable habitats. Healey (1991) attributed estuarine mortality to high predation rates or to a lack
* Corresponding author: [email protected]
1 Present address: Klamath National Forest, Supervisor’s Office, 1312 Fairlane Road, Yreka, California
96097, USA.
Received June 1, 2004; accepted April 11, 2005
Published online August 10, 2005
of suitable rearing areas in the Nitinat River and
Nanaimo River estuaries, Vancouver Island, Canada. He found that less than 30% of downstream
migrant coho salmon Oncorhynchus kisutch could
be accounted for in the estuary. Juvenile salmonid
survival has been shown to increase when structural cover is available in the presence of predators
such as adult coastal cutthroat trout O. clarkii clarkii (Gregory and Levings 1996). Although the
presence of structural cover did not change encounter rates between predator and prey, Gregory
and Levings (1996) determined that escape was
facilitated when vegetation was present. Therefore, the presence of cover may enhance juvenile
salmonid survival during estuarine rearing.
In the Smith River, California, declines in populations of Chinook salmon O. tshawytscha and
steelhead O. mykiss have been attributed to habitat
degradation and overexploitation (Moyle et al.
1989). Based upon historical maps (Monroe et al.
1975) and aerial photographs, we estimated a 40%
reduction in the surface area of the Smith River
estuary between 1856 and 1966. During this time
period, diking and drainage drastically reduced the
amount of rearing habitat available to juvenile salmonids. Smith River populations have decreased
to the point that spring-run Chinook salmon and
summer-race steelhead are considered to be at
1147
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QUIÑONES AND MULLIGAN
‘‘high risk of extinction’’ and fall-run Chinook and
sea-run cutthroat trout are considered to be at
‘‘moderate risk of extinction’’ (Nehlsen et al.
1991).
We sought to understand how juvenile salmonids use the Smith River estuary, a system largely
devoid of the tidal slough habitat it once contained.
We further wanted to describe (1) the habitats used
by juvenile salmonids, (2) whether differences in
habitat use existed between species, and (3) the
role that overhanging riparian vegetation plays in
the system. Although juvenile salmonids have
been observed in estuarine habitats dominated by
riparian vegetation, these habitats have not been
studied extensively. Levings et al. (1991) suggested that an integrated study was necessary to
compare sedge Carex spp. marshes and riparian
vegetation in terms of the quality of habitat they
provide to rearing juvenile salmonids. They stated
that habitats dominated by riparian vegetation offer fewer foraging opportunities and provide less
refugia from predators than do sedge marshes.
Studies in the Pacific Northwest have suggested
that tidal sloughs and marshes are valuable estuarine rearing habitats for juvenile salmonids (Healey 1982; Simenstad et al. 1982; McCabe et al.
1986). However, riparian vegetation can provide
juvenile salmonids with protection from solar radiation and predation and is a source of terrestrial
and detrital food items. Thus, riparian vegetation
may play an important role in providing rearing
habitat to juvenile salmonids in estuaries where
habitat alteration has resulted in the loss of slough
habitat.
For years, researchers have used direct observation to characterize habitats used by juvenile
salmonids (Northcote and Wilkie 1963; Everest
and Chapman 1972; Hankin and Reeves 1988). As
well as being cost effective, direct observation can
more accurately describe the habitat use by the
target species than can other methods, such as
beach seining, trapping, and poisoning (Northcote
and Wilkie 1963; Goldstein 1978; Hillman et al.
1992). However, the validity of direct observation
methods for quantifying the abundance of fish in
the observed habitats has been questioned. Burnham and Anderson (1984) suggested that the bias
of transect counts could be improved through the
collection of distance data and the subsequent calculation of a detectability function. However, transects with small widths (5 m or less) can ensure
high visibility and almost uniform detectability
within the sampling units, allowing for an unbiased estimator of density (Burnham et al. 1985).
For this reason, we chose to conduct strip transect
snorkel surveys of units with small widths to estimate the relative densities of juvenile salmonids
in Smith River estuarine habitats.
Study Area
The Smith River drains approximately 278 km2
in northern California and southern Oregon
(McCain et al. 1995). It extends 20 km inland and
flows into the Pacific Ocean 5.6 km south of the
California–Oregon border. The Smith River drainage is one of the most pristine systems remaining
in California and continues to support strong runs
of Chinook salmon, coho salmon, steelhead, and
cutthroat trout. The freshwater component of the
system is managed as both a federal and state wild
and scenic river and as part of the National Recreational Area and California State Park systems;
these management designations help the freshwater component to retain a natural state. The estuarine portion of the system, however, has been
heavily impacted by drainage and diking.
Field sampling took place in the upstream-most
5 km of the 6.5-km Smith River estuary, from the
mouth of Rowdy Creek downstream to the mouth
of Islas Slough (Figure 1). The study area was
segmented into three consecutive river reaches:
upper, middle, and lower. Reaches were defined
according to specific characteristics (Table 1). The
upper reach had low bottom salinity, gravel substrate, and older (;15 years old) riparian vegetation. The middle reach had intermediate bottom
salinity, cobble substrate, and young (,10 years
old) riparian vegetation. The lower reach had high
bottom salinity, sand substrate, and marsh vegetation. The west bank of the lower reach had patches of riparian vegetation that were scoured away
by winter flows in 1999. Because the lower reach
and the portion of the estuary downstream of Islas
Slough shared similar habitat characteristics (cover, salinity, substrate, morphology, and tidal influence), we subsampled this habitat by limiting our
sampling to areas upstream of Islas Slough. Reaches were further divided into stream margin and
midchannel habitats. Stream margin habitat extended from the riverbank to the extent of overhanging riparian vegetation, 5 m perpendicular
from shore. The remaining habitat not classified
as stream margin was identified as midchannel
habitat.
With winter flows exceeding 26,000 m3/s, the
Smith River estuary retains few instream cover
components. Through field verification, we estimated that less than 10% of the reaches we sam-
1149
SALMONID HABITAT USE IN THE SMITH RIVER
itat, the habitat had to provide cover in a minimum
of 50% of its surface area. The amount of riparian
vegetation acting as cover was estimated by visually projecting the habitat boundaries upwards
and noting the percentage of the habitat that was
covered by overhanging vegetation. The percentage of surface area covered by overhanging vegetation was reevaluated throughout the sampling
periods. No-cover habitats, on average, provided
cover in less than 5% of their surface area. Thus,
a total of three habitats (cover, no cover, midchannel) in three reaches (upper, middle, lower)
were sampled in the estuary. Cover habitat in the
lower reach was associated with the patches of
riparian vegetation present in 1999. Cover habitat
was not present in the lower reach in 2000.
Methods
FIGURE 1.—Map of reaches sampled for juvenile salmonids in the Smith River estuary, Del Norte County,
California, during 1999 and 2000. The latitude and longitude of the river mouth are 418939670N and
1248209260W.
pled contained typical forms of in-channel cover,
such as large woody debris, undercut banks, and
large boulders. Instead, ‘‘cover’’ consisted almost
exclusively of overhanging riparian vegetation.
Because our focus was to quantify the role that
riparian vegetation played in providing habitats
actively used by juvenile salmonids, the stream
margin habitats were stratified into those that offered cover (cover habitat) and those that did not
(no-cover habitat). To be classified as cover hab-
Direct observation.—Aerial photographs (1998)
and geographical information systems (GIS) software were used to determine the surface area (km2)
of each reach and habitat. After estimating the total
surface area of the three habitat types, we randomly placed sampling units of known widths and
lengths within each type. The GIS software was
also used to determine the length of midchannel
units. The width of midchannel units and the
length and width of stream margin units were measured in the field each time a unit was sampled.
The units were systematically sampled by snorkel
surveys from May to October of 1999 and 2000
(Table 2). The study months were identified by
preliminary snorkel surveys (1998) as encompassing the period when juvenile Chinook salmon
migrate through the estuary and when juvenile
trout are also present. Divers were trained in species identification for several weeks before surveys
started. We completed a total of 755 dives during
the 2-year study. Preliminary studies also found
that juvenile salmonids spend more time in upper
TABLE 1.—Mean (range) temperature, salinity, dissolved oxygen (DO), and depth, and dominant substrate and vegetation of the upper, middle, and lower reaches of the Smith River estuary, California, during May to October 1999
and 2000.
Reach
Variable
Upper
Middle
Lower
Temperature (8C)
Salinity (‰)
DO (mg/L)
Depth (m)
Substrate
Vegetation
18.7 (15.5–23.0)
0.1 (0–0.2)
7.5 (1.6–11.3)
1.09 (0.3–2.5)
Gravel (2–62 mm)
Red alder Alnus rubra
Sitka willow Salix sitchensis
(;15 years old)
19.1 (17.1–21.3)
0.2 (0–5.3)
6.6 (0.1–10.2)
0.52 (0.15–1.1)
Cobble (62–150 mm)
Red alder
Sitka willow
(,10 years old)
18.1 (15.6–20.2)
3.2 (0–26.4)
6.5 (1.9–16.2)
0.49 (0.1–1.6)
Sand (,2 mm)
American bulrush Scirpus americanus
Spike rush Eleocharis macrostachya
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QUIÑONES AND MULLIGAN
TABLE 2.—Total number of possible dive units, total surface area of all possible units, number of dive units sampled,
and surface area of units sampled in upper, middle, and lower reaches of the Smith River estuary, California, during
May to October 1999 and 2000. See Methods for definitions of variables.
Possible dive units
Year
Reach and habitat type
1999
Upper, cover
Upper, no cover
Upper, midchannel
Upper, total
Middle, cover
Middle, no cover
Middle, midchannel
Middle, total
Lower, cover
Lower, no cover
Lower, midchannel
Lower, total
Upper, cover
Upper, no cover
Upper, midchannel
Upper, total
Middle, cover
Middle, no cover
Middle, midchannel
Middle, total
Lower, no cover
Lower, midchannel
Lower, total
2000
Number
52
46
401
6.5
55.8
260
6.5
186.7
895
75
23
401
5.5
57
260
109.5
710.5
and middle reaches than in lower parts of the estuary. Therefore, approximately twice as much effort was spent in the snorkel surveys in upper and
middle reaches than in the lower reach. Sample
size calculations used for stratified sampling with
equal probability were used to determine the sampling intensity within each habitat and reach
(Cochran 1977). Direct observation surveys were
not conducted in Tillas or Islas sloughs (Figure 1)
because of poor visibility conditions. Fish species
composition in Islas Slough was determined
through the use of Alaska-style fyke nets during
concurrent surveys (Quiñones 2003).
To enhance detection of juvenile salmonids and
increase visibility, snorkel surveys were conducted
during slack to ebbing tides from 1000 to 1600
hours, thereby decreasing the influence of turbid
salt water. Visibility during the surveys was further
enhanced by defining the widths of the sampling
units: 5 m for units along the stream margin and
3 m for midchannel units, well below the distance
required for the identification of juvenile salmonids under normal visibility conditions within the
estuary. Measurements taken in 1998 determined
that visibility in the estuary often exceeded 10 m.
Visibility was defined as the distance (m) to which
a diver could positively identify a juvenile salmonid plastic model, approximately 70 mm in size,
Surface area
(km2)
6.50
5.75
203.59
215.84
0.81
6.99
136.91
144.71
0.81
23.33
787.20
811.35
9.38
2.88
204.49
216.74
0.63
7.11
136.97
144.71
24.08
787.26
811.35
Dive units sampled
Number
10
6
10
6
9
8
6
8
11
8
2
8
5
9
8
8
8
Surface area
(km2)
1.25
0.75
0.0051
2.0051
0.75
1.125
0.0042
1.8792
0.75
1.00
0.0075
1.7575
1.00
0.25
0.0041
1.2541
0.625
1.125
0.0042
1.7542
1.00
0.0054
1.0054
placed at a depth of 2–3 m. Narrow unit widths
ensured that detectability remained uniformly high
during the surveys, removing the need for divers
to note ancillary information such as distance and
angle of observation. In this case, fish counted
within the units were equivalent to counts made
in long, narrow quadrants (Burnham and Anderson
1984). Divers surveying the stream margin first
laid out a floating line (25 m long and 5 m away
from shore) to define the area to be sampled. We
were able to maintain unit widths because diking
in the estuary has resulted in approximately
straight stream banks. After a 20-min wait, two
divers began the survey at the downstream end of
the unit and swam towards a third diver stationed
at the upstream end. Divers counted and identified
all fish present in the units. The two species of
trout (steelhead and coastal cutthroat trout), however, were counted as one group due to difficulty
in visually distinguishing between the two species
during snorkel surveys. Swimming across the
channel to sample midchannel units proved to be
problematic because of the flow regime and width
of the estuary, which were often greater than 50
m3/s and 600 m, respectively. We therefore modified procedures used in coral reefs (Thresher and
Gunn 1986) to survey the midchannel areas. Our
procedure used one diver that counted and iden-
SALMONID HABITAT USE IN THE SMITH RIVER
1151
tified all fish present in the unit while being towed
at approximately 1 knot by a 3.7-m skiff across
the channel between fixed beginning and ending
points. Midchannel units were as long as the river
was wide minus 5 m at either end so that midchannel units would not overlap with stream margin units. Preliminary studies had shown that rather than being dispersed by the motions of the boat
and diver, juvenile salmonids tended to be attracted
to the diver as a potential source of cover. Consequently, this behavior could lead to an overestimation of the relative abundance of juvenile salmonids in the midchannel.
Classical sampling theory formulas were used
to calculate estimated fish density and the associated variance for each stratum, allowing for comparisons to be made (Seber 1982; Burnham and
Anderson 1984; Burnham et al. 1985). Strata were
defined as unique habitat and reach combinations.
Estimated totals (Ŷij) and estimated variances of
estimated totals (V̂[Ŷij]) for particular species were
calculated for each habitat i and reach j by use of
the following equations:
where Xij is the total surface area (m2) in habitat
i within reach j. These equations allowed us to
standardize the number of fish present in each habitat by the proportion of area surveyed as well as
by the number of surveys in each habitat, resulting
in relative densities that could be directly compared. To compare relative densities of fish between habitats, species, or reaches, we calculated
95% confidence intervals (95% CI; level of significance 5 0.05) for differences in density. If the
95% CIs excluded zero, we concluded that there
was a significant difference in density. For individual species, differences of interest included (1)
between reaches with the same habitat type i and
(2) between habitat types within the same reach j.
We also compared how different fish species use
the same habitat in the same reach. For each cald ), we calculated a correculated difference (DIF
sponding variance estimate by means of
Ŷij 5 Nij·ȳij,
ˆ ij1 2 D
ˆ ij2
d 5D
DIF
where Nij is the total number of units possible in
each stratum,
Oy
k51
,
ni j
ˆ ˆ ij) 5 N2ij·V(ȳ
ˆ ij),
V(Y
where
s i2j
N i j 2 n i j s i2j
,
Ni j
ni j
1
2
O (y 2 ȳ ) .
5
ij
ij
and
2
ni j 2 1
Mean density (fish per unit area), D̂ij, and the
corresponding variance were calculated as
D̂ i j 5
Ŷ i j
Xi j
and 95% CIs were constructed as
i jk
yijk is the number of fish (Chinook salmon or trout)
observed in a particular stratum (k 5 1, . . . , nij)
within a particular reach, and nij is the number of
units sampled in habitat i (cover, no cover, midchannel) and reach j (upper, middle, lower). The variance of the estimated totals can be estimated by
V̂(ȳ i j ) 5
where
ˆ d
d 6 2 Î V(DIF).
DIF
n ij
ȳ i j 5
ˆ d 5 V(D
ˆ ˆ ij1) 1 V(D
ˆ ˆ ij2),
V(DIF)
and
ˆ ˆ i j ) 5 1 V(Y
ˆ ˆ i j ),
V(D
X 2i j
Because we made no adjustment for multiple
comparisons, it is possible that 2–3 of the 43 comparisons we made were incorrect (Quiñones 2003).
Therefore, our use of multiple comparisons was
meant to describe general patterns in the data and
not to make predictive determinations (Ott 1993).
Physical parameters.—Surface and bottom measurements of salinity (‰), dissolved oxygen (mg/
L), and temperature (8C) were recorded with a YSI
Model 85 field meter after every other dive. Average depths (m) for all units were measured with
a marked depth line during the 2000 field season.
Daily flow (m3/s) measurements for the Smith River at the Jedediah Smith Redwoods State Park station were collected from the California Data Exchange Center (CDEC; http://cdec.water.ca.gov/).
We used stepwise logistic regression (Afifi and
Clark 1996) to correlate Chinook salmon and trout
presence–absence individually with year (1999,
2000), reach (upper, middle, lower), habitat type
(cover, no cover, midchannel), flow, salinity, temperature, and depth collected in 2000. Using this
method, we calculated the probability of Chinook
salmon and trout presence as influenced by different combinations of the physical parameters. A
1152
QUIÑONES AND MULLIGAN
level of significance of 0.05 was used to determine
which physical parameters significantly influenced
the presence–absence of each group. Another stepwise logistic regression was conducted based on
the minimum, intermediate, and maximum values
for each variable to determine what conditions
were most likely to influence the presence of juvenile Chinook salmon and trout.
Size comparison.—A 30-m 3 2-m beach seine
was used to collect Chinook salmon, steelhead,
and coastal cutthroat trout throughout the sampling
season in all reaches. The fork length of captured
salmonids was measured to the nearest millimeter.
Beach seining also allowed for verification of species identification and provided anecdotal species
composition information.
Results
Direct Observation
We observed total of 25,541 juvenile salmonids
in the 755 snorkel surveys completed in 1999 and
2000. The relative density (fish/m2) of juvenile
Chinook salmon ranged from 0.004 to 6.832 in
1999 (Figure 2) and from 0.006 to 4.397 in 2000
(Figure 3). The relative density of juvenile trout
ranged from 0.001 to 0.346 (Figure 2) in 1999 and
from 0.001 to 0.724 in 2000 (Figure 3). Regardless
of the reach, both Chinook salmon and trout exhibited the highest densities in cover habitats and
progressively diminishing densities in no-cover
and midchannel habitats. An exception to this
trend for Chinook salmon was noted in 2000 in
the upper reach, where the midchannel habitat had
a higher density than did the no-cover habitat (Figure 3) but the difference in densities was not significant. For trout, one exception was found during
1999 in the lower reach, where no-cover and midchannel habitats had equal densities (Figure 2).
In 1999, the Chinook salmon relative densities
in the upper and lower reaches were significantly
higher in the cover habitat (upper: 6.832; lower:
2.431) than in either the no-cover (0.859; 0.044)
or midchannel (0.035; 0.004) habitats (Figure 2).
No significant differences were found between
Chinook salmon densities in the no-cover and midchannel habitats of these reaches. In contrast, trout
relative density in the upper reach was not significantly different between the cover (0.346) and nocover (0.188) habitats but was significantly higher
in the no-cover habitat than in the midchannel
(0.001) (Figure 2). In the middle reach, Chinook
salmon and trout densities were significantly different among all habitats, resulting in relatively
high densities in the cover habitat (Chinook salmon: 5.336; trout: 0.343), moderate densities in the
no-cover habitat (Chinook salmon: 0.133; trout:
0.058), and low densities in the midchannel habitat
(Chinook salmon: 0.028; trout: 0.002) (Figure 2).
The relative density of trout in the lower reach was
significantly higher in cover habitat (0.084) than
in no-cover habitat (0.001) and was the same in
the no-cover and midchannel habitats (0.001) (Figure 2).
In the upper and middle reaches during 2000,
Chinook salmon and trout relative densities were
significantly higher in cover habitat (Chinook
salmon, upper: 4.397; trout, upper: 0.724; Chinook
salmon, middle: 3.954; trout, middle: 0.637) than
in the other two habitat types (Figure 3). Relative
densities in the upper and middle reaches were
moderate in no-cover habitat (Chinook salmon,
upper: 0.036; trout, upper: 0.096; Chinook salmon,
middle: 0.04; trout, middle: 0.101) (Figure 3). Upper- and middle-reach Chinook salmon and trout
densities were significantly lower in midchannel
habitat (Chinook salmon, upper: 0.07; trout, upper:
0.001; Chinook salmon, middle: 0.025; trout, middle: 0.004) than in cover and no-cover habitats
(Figure 3). Because the lower reach was devoid of
cover habitat in 2000, fish densities in the remaining two habitat types were compared. In the
lower reach during 2000, no significant differences
were found for Chinook salmon and trout densities
in no-cover (Chinook salmon: 0.21; trout: 0.12)
and midchannel (Chinook salmon: 0.006; trout:
0.002) habitats (Figure 3).
Relative densities were also compared between
Chinook salmon and trout within the same habitat
and reach. Significant differences were found between Chinook salmon and trout densities in the
cover habitats of all reaches during 1999 and 2000
(Figures 2, 3). In contrast, no significant differences were found between Chinook salmon and
trout densities in the no-cover and midchannel
habitats in either year. Confidence interval calculations and comparisons of relative density by
species, habitat, and reach are documented in Quiñones (2003).
Physical Parameters
Temperatures ranged from 15.58C to 238C during both sampling periods in all reaches (Table 1).
Average temperatures differed among reaches by
18C or less (18.1–19.18C). Although all reaches
had bottom salinities that were different than surface salinities (0‰), salinity ranges differed
among reaches (Table 1). Salinities were lowest in
SALMONID HABITAT USE IN THE SMITH RIVER
1153
FIGURE 2.—Relative densities (62 SEs) of juvenile Chinook salmon and trout (coastal cutthroat trout and steelhead
combined) observed in cover, no-cover, and midchannel habitats of the upper, middle, and lower reaches, Smith
River estuary, California, during May to October of 1999. Note that the y-axis scales are different for each graph.
Relative densities are standardized observed densities (number of fish/unit).
the upper reach (0–0.2‰), intermediate in the middle reach (0–5.3‰), and highest in the lower reach
(0–26.4‰). Dissolved oxygen varied greatly within and among reaches (0.1–16.2 mg/L) (Table 1).
However, average dissolved oxygen measurements
among reaches differed by 1 mg/L or less. Water
depth was deepest in the upper reach (0.3–2.5 m),
intermediate in the lower reach (0.1–1.6 m), and
shallowest in the middle reach (0.15–1.1 m) (Table
1). Average depths were greatest in the upper reach
(1.09 m) and similar between the middle (0.52 m)
and lower (0.49 m) reaches. Flows during the sample
periods ranged from 6.71 to 60.37 m3/s in 1999 and
from 7.28 to 52.47 m3/s in 2000 (CDEC; http://
cdec.water.ca.gov/). Flows peaked during the first 2
weeks of sampling and decreased throughout the
sampling period in both years.
Based on a level of significance of 0.05, stepwise logistic regression showed that Chinook
salmon presence–absence was significantly influenced by year (P , 0.000001), cover habitat (P 5
0.00021), and salinity (P 5 0.03469). In contrast,
trout presence–absence was significantly influenced by the midchannel habitat (P 5 0.00022),
1154
QUIÑONES AND MULLIGAN
flow (P 5 0.01034), lower reach (P 5 0.02483),
and cover habitat (P 5 0.04286). Thus, the probability of estimating Chinook salmon presence–
absence from year, salinity, and cover habitat can
be calculated by
1/[1 1 exp(2.80120.153 · salinity
21.744 · cover habitat22.197 · year)],
where the presence or absence of cover habitat is
coded as 1 or 0, respectively, as are the years 1999
and 2000. Similarly, the probability of estimating
trout presence–absence with midchannel habitat,
flow, lower reach, and cover habitat variables can
be calculated by
1/[1 1 exp(24.677 1 5.682 · flow
1 1.619 · lower reach 1 3.273 · midchannel habitat
2 0.73 · cover habitat)],
where the absence and presence of the lower reach,
midchannel habitat, and cover habitat are coded as
0 (absence) or 1 (presence).
A second stepwise logistic regression that included only those parameters significantly influencing presence–absence found that salinity (P 5
0.00201) was the single most influential variable
in determining the presence of Chinook salmon,
regardless of the year or presence of cover habitat.
This model correctly classified the presence of
Chinook salmon 86.33% of the time. When we ran
the model with a range of salinities, we determined
that Chinook salmon were most likely to be present
in areas where salinity was 5‰ or less. In contrast,
trout presence was most influenced by the absence
of the midchannel habitat (P , 0.000001). Consequently, trout were most likely to be present in
margin habitats (cover, no cover), regardless of the
reach or flow conditions. This model correctly
classified the presence of trout 88.60% of the time.
Size Comparison
In 1999 and 2000, juvenile Chinook salmon captured in the estuary were consistently larger than
trout (Table 3). Throughout the field season, the
mean length of Chinook salmon ranged from 71
to 117 mm, while the mean length of trout ranged
from 50 to 98 mm. Of the 253 individuals collected
via beach seining and measured, 189 were Chinook
salmon and 64 were trout. Coastal cutthroat trout
made up approximately 10% of the juvenile trout
collected; steelhead made up the remaining 90%.
Discussion
Juvenile Chinook salmon and trout in the Smith
River estuary appeared to use habitats in different
ways, as reflected by their relative densities. While
both groups were most abundant in cover habitats,
juvenile Chinook salmon preferred cover habitat
over no-cover and midchannel habitats to an equal
degree. Of the physical parameters we measured,
salinity exerted the greatest influence on Chinook
salmon presence. Juvenile trout apparently preferred cover habitats the most, no-cover habitats
moderately, and midchannel habitats the least.
This general pattern suggests either that cover is
more important to rearing Chinook salmon than to
trout or that trout prefer to associate with stream
margin habitats whether vegetated or not. However, trout may be displaced from preferred habitats by salmon when salmon are larger or are present at higher densities (Everest and Chapman
1972; Young 2004). Everest and Chapman (1972)
concluded that fish of similar size, regardless of
species, will use the same physical space. However, niche overlap was minimized when individuals reflected natural size variability (i.e., when
Chinook salmon are larger that trout). Of the factors that Everest and Chapman (1972) analyzed,
depth appeared to have the strongest influence on
the distribution of juvenile Chinook salmon and
steelhead. Chinook salmon abundance was positively correlated with depth, whereas steelhead
abundance was negatively correlated with depth,
indicating that the larger fish (juvenile Chinook
salmon) preferred the deeper habitats away from
the stream margin while the smaller fish (juvenile
steelhead) preferred shallower habitats along the
stream margin. However, depth was not found to
significantly influence Chinook salmon or trout
habitat selection in the Smith River estuary. Perhaps the juvenile salmonids studied by Everest and
Chapman (1972) exhibited territoriality common
in the freshwater life history stage, while those in
the Smith River estuary conformed to schooling
behavior in preparation for an oceanic existence.
Our analysis indicates that juvenile Chinook salmon and trout compete for cover habitat. Regression
of physical parameters from the Smith River estuary found that the presence of cover significantly
influenced the presence of both groups of fish, suggesting that cover habitat was preferred by both.
Because relative densities were higher for Chinook
salmon than for trout in all habitats and reaches
(except the no-cover habitat in 2000), Chinook
salmon may have displaced trout from cover hab-
1155
SALMONID HABITAT USE IN THE SMITH RIVER
FIGURE 3.—Relative densities (62 SEs) of juvenile Chinook salmon and trout (coastal cutthroat trout and steelhead
combined) observed in cover, no-cover, and midchannel habitats of the upper, middle, and lower reaches, Smith
River estuary, California, during May to October of 2000. Note that the y-axis scales are different for each graph.
Relative densities are standardized observed densities (number of fish/unit).
TABLE 3.—Fork lengths (range and mean; mm) of juvenile Chinook salmon and trout (cutthroat trout and steelhead
combined) collected during three sampling periods from the Smith River estuary, California, during May to October
1999 and 2000.
Chinook salmon
Trout
Sampling period
N
Range
Mean
N
Range
Mean
Spring (May–Jun)
Summer (Jul–Aug)
Fall (Sep–Oct)
57
73
59
49–88
65–116
83–145
71
82
117
9
40
15
32–72
54–105
72–123
50
76
98
1156
QUIÑONES AND MULLIGAN
itat by their sheer abundance. Furthermore, Chinook salmon captured in the estuary were larger
than trout by an average of 20%, possibly resulting
in strong, asymmetric interspecific competition, as
was witnessed by Young (2004). Consequently,
cover in the Smith River estuary may be limiting
to juvenile trout rearing.
Other parameters that have been shown to influence juvenile salmonid habitat selection include
food abundance, predation risk, temperature, and
velocity (Grand and Dill 1997; Giannico and Healey 1999; Bradford and Higgins 2001; Welsh et al.
2001; Beecher et al. 2002). Grand and Dill (1997)
and Giannico and Healey (1999) found that juvenile coho salmon adapted their use of cover in
response to a combination of factors, including
food availability, predation risk, density of competitors, ontogenetic phase, and distance between
patches of cover. In general, juvenile coho salmon
preferred sites that offered both accessible refuge
from predation (cover) and open foraging areas.
In the Smith River estuary, 90% of the accessible
cover is located in the upper and middle reaches,
where Chinook salmon and trout relative densities
were the highest. A concurrent study (Quiñones
2003) found that juvenile salmonids rearing in the
Smith River estuary were predominately feeding
on aquatic insects that were only found in the upper and middle reaches, supporting the idea that
juvenile salmonids were actively choosing habitats
that minimized the risk of predation and provided
foraging opportunities. Conversely, temperature
and flow (our surrogate for velocity) did not appear
to significantly influence Chinook salmon and
trout presence–absence in the estuary. However,
temperatures exhibited closely matched ranges and
averages among habitats and reaches, and flow was
measured at the system (Smith River) scale so that
among-habitat or among-reach differences were
not detectable.
In our study, all reaches were designated as estuarine habitats by the presence of a halocline, as
reflected by higher salinity at the bottom than at
the surface. However, the classification system described by Cowardin et al. (1979) classified the
upper reach as a riverine system because salinity
never increased above 5‰. Due to its location in
the upstream portion of the estuary, the upper
reach may be described best as an ecotone, a zone
of transition between freshwater and brackish water (Miller and Sadro 2003). Miller and Sadro
(2003) found that coho salmon in the Winchester
Creek estuary, Oregon, disproportionately used the
upper estuarine reaches rather than the lower
reaches. They concluded that this finding highlighted the importance of the stream–estuary transition zone as rearing habitat. Similarly, Healey
(1982) found that Chinook salmon fry did not occupy high-salinity areas in the Nitinat River system. The ecotone may also be important to juvenile
salmonids rearing in the Smith River, as relative
densities were highest in the upper reach. However, Chinook salmon fry in some estuaries demonstrate extended periods of residency in saline
waters. Myers and Horton (1982) reported a 1month delay between captures of juvenile Chinook
salmon in the upper and lower parts of the estuary
in Yaquina Bay, Oregon; once in the lower estuary,
the juvenile Chinook salmon continued to grow
for several months. In Yaquina Bay, fry may have
increased their fitness by taking advantage of the
foraging opportunities found in areas of the estuary that possessed higher salinities. In contrast,
the fitness of Smith River salmonids may have
been reduced because they did not take advantage
of foraging opportunities in the lower part of the
estuary, as reflected in the low relative densities
in the lower reach. The behavior of juvenile salmonids in the Smith River estuary possibly demonstrated a trade-off between foraging opportunities and predator avoidance (Magnhagen 1988).
One habitat component that enhances predator
avoidance is structural cover (Gregory and Levings 1996). Thus, riparian vegetation in the Smith
River estuary may provide juvenile salmonids with
cover from predation.
Intertidal marshes have been identified as the
most valuable habitat for juvenile salmonids rearing in estuaries (Healey 1982; Simenstad et al.
1982; McCabe et al. 1986). We sought to understand how juvenile salmonids used the Smith River
estuary, a system largely devoid of tidal sloughs
and their associated intertidal marshes. Relative
densities of Chinook salmon and trout were highest in the upper reach, moderate in the middle
reach, and lowest in the lower reach of the estuary.
We suggest that juvenile salmonids resided in the
upper and middle reaches of the Smith River estuary, while they used the lower reach only as a
migratory corridor to the sea. Kjelson et al. (1982)
reported that Chinook salmon smolts used the
brackish-water bays of the Sacramento–San Joaquin estuary as migratory corridors. After comparing their results to other studies, Kjelson et al.
(1982) concluded that Chinook salmon in more
northerly estuaries were more likely to selectively
rear in brackish water (salinity . 20‰). Chinook
salmon in the Smith River estuary exhibited hab-
SALMONID HABITAT USE IN THE SMITH RIVER
itat use similar to that of Chinook salmon in the
Sacramento–San Joaquin estuary, as they were significantly more abundant in portions of the estuary
with low salinities (,5‰). Juvenile salmonids in
our study were probably migrating at night, similar
to subyearling Chinook salmon in the Sixes River,
Oregon (Reimers 1973), because juvenile salmonids were seldom seen in the lower reach. Migrating at night would have offered refuge from
some predators in the lower portions of the Smith
River estuary, where little cover is available. It
should be noted that the lower reach of the Smith
River estuary offered less than 10% of its surface
area as cover.
The importance of riparian vegetation as cover
may be further accentuated in the Smith River estuary because of the virtual lack of tidal channels
and instream structures, which have been shown
to provide refuge from predation in other systems.
Cover might be of the utmost importance in the
Smith River estuary because its high water clarity
would also make fish more vulnerable to predation
(Gregory 1993). To enhance juvenile salmonid
production, the protection and reestablishment of
riparian vegetation must be an essential part of
integrated watershed management, particularly in
estuaries with little instream cover and few tidal
channels, such as the Smith River estuary.
Acknowledgments
We thank D. Hankin and W. Bigg for their statistical advice and the California Sea Grant for
providing the funding for this project (RC/155).
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