Geomorphic habitat type, drift cell, forage fish, and juvenile salmon

Journal of Environmental Science and Engineering A 1 (2012) 688-703 Formerly part of Journal of Environmental Science and Engineering, ISSN 1934-8932

Geomorphic Habitat Type, Drift Cell, Forage Fish and

Juvenile Salmon: Are They Linked?

J. Anne Shaffer1, Patrick Crain2, Todd Kassler3, Dan Penttila4 and Dwight Barry5

1. Coastal Watershed Institute, Port Angeles, Washington 98362, USA

2. Olympic National Park, Port Angeles, Washington 98362, USA

3. Washington Department of Fish and Wildlife, Molecular Genetics Laboratory, Olympia Washington 98501, USA

4. Salish Sea Biological Incorporated, Anacortes, Washington 98221, USA

5. Huxley College of the Environment-Peninsulas, Western Washington University, Port Angeles, Washington 98362, USA

Received: December 16, 2011 / Accepted: January 10, 2012 / Published: May 20, 2012. Abstract: The role of geomorphic habitat type, drift cell scale, and geographic scale in defining fish use of nearshore habitats is poorly known, particularly for Pacific salmon and their prey. In this study, key areas of nearshore habitat in central and western Strait of Juan de Fuca were categorized by geomorphic habitat type and assessed for fish use within a degraded (Elwha) and intact comparative drift cells over a one year period. Juvenile Chinook and coho salmon were also sampled for genetic analysis to define regional dispersal patterns. Key findings are: (1) Ecological function of the area’s nearshore is complex, with very strong seasonal variation in fish use both within and across GMHT (geomorphic habitat type); (2) GMHT link to nearshore function for fish use differs depending on the fish species and time of year. Surf smelt and sand lance were the most abundant. And they were seasonally used embayed, spit, and bluff shorelines more than lower rivers. Juvenile Chinook, coho, and chum salmon occurred in much lower density than forage fish species, and used lower rivers more than other GMHTs; (3) When GMHTs were combined and analyzed at the drift cell scale, the degraded drift cell had different ecological patterns than the intact drift cell; (4) Cross regional juvenile fish use of nearshore is an important component of habitat use: juvenile Chinook and coho from as far away as the Columbia River Oregon and Klamath River California utilize central Strait of Juan de Fuca shorelines. Forage fish species may do so as well. Drift cell and cross regional scales are therefore most important for accurately defining nearshore ecological function, management, and restoration actions.

Key words: Nearshore, geomorphic habitat type, fish use, Elwha, Chinook.

1. Introduction

The geomorphology of the marine nearshore

reflects basic habitat hydrologic regime, and

determines the type and quality of aquatic and riparian

habitat that in turn dictate habitat function for a

variety of marine species. Geomorphology may thus

serve as an assessment tool for management practices

including ecosystem-based management and the

design of marine reserve networks [1].

Geomorphic classification systems for aquatic

Corresponding author: J. Anne Shaffer, marine ecologist,

main research field: marine ecology. E-mail: [email protected].

habitats have been developed to define ecological

function in riverine and Pacific Northwest nearshore

marine ecosystems [1-5]. Information is now

emerging on the role geomorphology plays in the

ecological and species-specific function within

nearshore systems, and how to integrate

geomorphology into nearshore restoration

management for salmon [6, 7]. Salmon use of

nearshore habitats is the focus of restoration actions

across the Pacific Northwest. Unfortunately salmon

use of the nearshore is complex, and therefore not

thoroughly understood [7]. As a result, effective

salmon restoration is often done based on single

DAVID PUBLISHING

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Geomorphic Habitat Type, Drift Cell, Forage Fish and Juvenile Salmon: Are They Linked?

689

species and its habitat considerations. Specific

ecological linkages between ecosystem scale

nearshore habitat function, geomorphic habitats, and

restoration actions are of increasing interest to

scientists and practitioners for defining restoration

actions and priorities.

The nearshore of inland marine waters of the

Pacific Northwest is an important migratory corridor

for many Puget Sound salmon populations, including

federally ESA listed stocks of Columbia River and

Puget Sound Chinook (Oncorhynchus tshawytscha),

Strait of Juan de Fuca/Hood Canal Summer Chum (O.

keta), steelhead (O. mykiss), sea-run cutthroat

(O .clarki), and bull trout (Salvelinus confluentus), as

well as the forage fish (surf smelt, Hypomesus

pretiosus, sand lance, Ammodytes hexapterus, and

herring, Clupea harengus) on which they depend [8].

Fish use can therefore serve as an indicator of habitat

function.

The nearshore habitat of the Strait of Juan de Fuca

is delineated by the physical features of tidal influence

and light limitation, which is generally defined as the

area that extends from treeline to -30 meters (90 feet)

below MLLW (Mean Lower Low Water) [7, 8].

The nearshore of inland marine waters of the

Pacific Northwest, including the Strait of Juan de

Fuca, has been classified utilizing geomorphic

habitat classifications [4, 9] and includes shorelines

that are significantly degraded due to disruption to

habitat forming processes from in-river damming and

lower river and shoreline armoring and alterations [8,

10]. The Strait of Juan de Fuca presents a microcosm

of both impacted and intact shorelines, and includes

drift cells that have completely intact sediment

processes, as well an entire drift cell that is

significantly degraded due to shoreline alteration and

in-river dams. The Elwha River dams are now being

removed (dam removal began in September 2011).

This restoration will partially restore nearshore

sediment processes [8, 11]. The restoration project is

one of the largest restoration projects in the nation.

Efforts are underway to better understand Pacific

Northwest nearshore systems and in particular the

relationship between habitat form and function to

support shoreline and nearshore management. If

possible, scientists and managers would like to model

habitat function by type [12]. Understanding the

linkages between physical habitat forming processes

and habitat function is necessary for successful long

term species and ecosystem management and cross

regional restoration. This study addreses the fish use

(defined as fish presence and density) of the nearshore,

and the role geomorphic habitat type and ecological

degradation play in nearshore fish use. The work also

explores the scale at which this habitat function for

fish is relevant for Pacific Northwest marine

ecosystem management.

2. Methods and Materials

Nearshore habitats within the Strait of Juan de Fuca

(Fig. 1) were categorized into the following

geomorphic landform habitat types: lower rivers (both

main and side channels of river and associated estuary

within tidal influence), embayments, spits, and bluff

shorelines. Sampling sites within each habitat type

were identified, and sampled using standard beach

seining techniques [13]. To define the role disrupted

habitat forming processes play in habitat function, the

sites were identified as being within either an intact

(comparative) or degraded (Elwha) drift cell.

2.1 Beach Seines

For all seines a 30 or 24 m net with 0.635 cm mesh

wing and 0.30 cm mesh bag was deployed by boat in

2-3 meters of water and then pulled onto the shore,

and all fish in the net were identified to lowest species,

and 20 of each species were measured to nearest

millimeter. Sampling was conducted weekly if

possible from March to October to capture salmonid

outmigration, and then monthly until the following

March. To define the role disrupted habitat forming

processes plays in habitat function, the sites were


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identified as being within either an intact or degraded

(Elwha) drift cell. Data were summarized to monthly

densities and lengths by species, and ecological

indices of species richness and species diversity were

calculated by site and week. The seining data from the

Elwha west estuary/lower river were provided for

geomorphic analysis with permission by authors [14].

Seining data were then analyzed to address the

following questions:

Are ecological indices (species richness and

diversity) different between geomorphic habitat types

(GMHT), or between degraded and intact drift cells?

Are densities of Chinook, chum, and coho

salmon, and post larval juvenile and adult surf smelt

and sand lance related to GMHT, and/or to degraded

or intact drift cells?

Are there any statistical interactions between drift

cell and GMHT?

Species densities (fish/m3) and species diversity

(Shannon’s H′) were log transformed [log(x+1)]

before analysis. Species richness was analyzed

without transformation. GEE (generalized estimating

equations) with an autoregressive correlation structure

were used to analyze species richness and individual

species density for both the degraded and intact drift

cells and between geomorphic habitat types. Month,

GMHT, and the interaction term Month × GMHT

were used as predictor variables. To account for

disparity between the numbers of seines between

habitat types, ANOVAs using type-III sums of

squares were used to analyze diversity (H′). Month,

GMHT, and the Month × GMHT interaction term

were used as predictor variables in the ANOVA. In all

cases, Bonferroni error corrections were used on the

pair-wise analyses to correct for errors arriving from

multiple hypothesis testing. All statistical analyses on

these data were performed using R 2, version 7.2 [15],

GEE were performed using geepack [16, 17] and the

ANOVAs were performed using the car package 1.2-9

[18].

Fig. 1 The Strait of Juan de Fuca study area. Map provided by Terry Johnson, Washington Department of Fish and Wildlife.

Geomorphic Habitat Type, Drift Cell, Forage Fish and Juvenile Salmon: Are They Linked? 691

2.2 Genetic Analyses

To assess the distance of juvenile fish in the

nearshore which are traveling, a total of 58 of the

juvenile Chinook salmon and nine juvenile coho

captured were also sampled for genetic analysis that

provided probability of stock origin. Genetic tissue

samples of juvenile Chinook salmon were collected

from a sub-set of the total number of Chinook salmon

captured at nearshore sampling seining stations

discussed above.

Tissue samples were collected from up to 10 fish

per day from each sample location. Due to the

combined issues of extra handling stress, a small field

crew, limited funding, and the large geographic area

of the project, the number of tissue samples was

limited to approximately 10% of fish collected. For

these fish, genetic samples were collected by clipping

a small quantity of tissue from the dorsal fin. No more

than 30 percent of the fin was clipped. Each clipping

was placed in individual vials with lab grade ethyl

alcohol, and the vial labeled with unique identification

number. Record of fish size, sample number, date, and

location were made.

In the lab, genomic DNA was extracted for all

samples by digesting a small piece of fin tissue using

silica membrane based kits obtained from

Macherey-Nagel (Bethlehem, PA, USA) following the

manufacturers recommendations. Thirteen

microsatellite loci combined into five multiplexes

were screened for this study. Descriptions of the loci

and PCR (polymerase chain reaction) conditions are

given in Table 1.

PCR reactions were conducted with a thermal

profile as follows: an initial denaturation step of 2 min

at 94 °C, 40 cycles of denaturation at 94 °C for 15 s,

30 s at the appropriate temperature for each multiplex,

and 1 min at 72 °C, plus a final extension at 72 °C for

10 min and final holding step at 10 °C. Genotypes

were visualized using an ABI-3730 DNA Analyzer

(Applied Biosystems, Foster City, CA, USA) with

internal size standards (GS500LIZ 3730) and

GENEMAPPER 3.7 software. Standardization of

genetic data to GAPS allele standards was conducted

following published protocol [19]. Table 1 Percent of total fish and percent of the dominant species for each site by geomorphic habitat type, March 2007-2008. D = degraded (Elwha) drift cell.

Site

Total seines (% of total)

Total fish

% of all fish for site/GM

HT

Chinook O.

tshawytscha

Coho O.kisutch

ChumO. keta

Surf Smelt (adult = > 120 mm)

H. pretiosus

Surf Smelt(juv =

50-120 mm)H. pretiosus

Surf Smelt (pl = <50

mm) H.

pretiosus

Herring(juv = 50-120 mm)

Clupea harengus

Northern Anchovy

E. mordax

Sand lance A

hexapterus

3-Spine stickleback

G. aculeatus

Cottids

Shiner perch

C. aggregata

Cutthroat

Embayments 131 (29)

40 1 1 1 16 28 1 6 8 5 0 7 0 0

Freshwater Bay (D) 28 12,259 6 4 0 1 14 6 9 56 1 7 0 0 1 0

Crescent Bay 41 11,563 6 2 2 2 42 14 0 4 0 21 1 3 1 0

Pysht Shoreline 30 31,720 17 0 0 0 11 79 0 2 0 0 0 3 0 0

W. Twins Shoreline

32 19,810 10 0 0 0 10 17 4 19 30 0 0 20 0 0

Spits 21 (5) 4 3 0 5 5 37 8 31 0 10 0 0 0 0

Ediz Hook (D) 9 3,101 2 6 0 3 5 20 1 51 0 12 0 0 0 0

Dungeness Spit 12 5,049 3 0 0 6 4 54 14 11 0 8 0 0 0 0

Bluffs 29 (6) 16 0 0 0 1 3 45 1 0 0 0 0 0 0

Elwha Bluffs (D) 13 5,518 3 10 1 9 1 43 15 20 0 1 0 0 0 0

Dungeness Bluffs 16 24,960 13 0 0 0 1 6 90 2 0 0 0 0 0 0

Lower river & Estuary

276 (60)

40 2 1 1 0 1 0 0 0 0 23 42 25 1

Elwha (D) 52 16,258 9 12 2 1 0 0 0 0 0 0 70 10 0 0

Pysht 80 25,139 13 0 1 1 0 7 0 0 0 0 50 108 26 0

Salt Creek 118 32,678 17 0 3 5 0 0 0 0 0 0 17 49 122 0

Twins 26 1,477 1 0 0 1 0 0 0 0 0 0 0 86 0 6

Total 459 189,532 100


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The origin of the Chinook and coho salmon smolts

collected in the Strait of Juan de Fuca was explored by

assigning them with a program written that uses a

partial Bayesian procedure based on Rannala and

Mountain probabilities [20], and the EM

(expectation-maximization) algorithm to calculate the

stock-source probabilities (posterior probabilities) for

each smolt and is effectively identical to methods

employed by the program ONCOR. A more detailed

description of the methods used by this program is in

Ref. [21]. GAPS v2.1+ baseline was used to define the

allele frequencies for baseline stocks.

3. Results

3.1 Beach Seines

A total of 459 seines were sampled over the 13

month study period. A total of 185 of these were from

embayed (131 seines), spit (25 seines), and bluff (29

seines) sites. The remaining 274 seines were taken

from lower river sites. Challenging sampling

conditions of swell and fog, combined with limited

agency resources, resulted in the majority of sampling

occurring along sites that could be accessed by shore.

Comparable numbers of fish were taken from

embayed shorelines and lower river sites despite

difference in sampling effort. For all fish caught from

all sites, 65% were captured during spring and

summer sampling; 35% for fall and winter (Table 1).

Species richness and diversity varied seasonally by

site, GMHTs, drift cell, and date (Figs. 2-4). Both

were higher during spring and summer months across

all sites, with the exception of diversity in degraded

embayed shoreline areas, which, while consistently

lower than the intact shoreline sites, was also high

during winter months. Species diversity was highest

along embayed shorelines and lower rivers, and

lowest along feeder bluffs and spits. Ecological

indices were significantly different between

geomorphic habitat types. Differences in species

diversity were significantly different across

months.

These two indices were also significantly different

between degraded and intact drift cell. Species

richness was significantly different between the

degraded and intact drift cells (Fig. 2), due primarily

to the significantly lower species richness of the

degraded embayed shoreline. Spit and bluff habitats

within the degraded drift cell also had consistently

lower species richness than the intact drift cell, but

differences were not statistically significant. For all

habitats combined, species diversity was also

significantly lower in the degraded drift cell than the

intact drift cell (Fig. 4).

Densities of all fish varied dramatically with season,

GMHT

Bluffs Embayments Lower River Spit

Drift Cell Drift Cell Drift Cell Drift Cell

Comparative Degraded Comparative Degraded Comparative Degraded Comparative Degraded

1

2

3

4

5

6

7

8

9

10

Sp

eci

es

Ric

hn

ess

Fig. 2 Mean species richness by geomorphic habitat type and drift cell. Error bars represent the 95% confidence interval.


693

Fig. 3 Species diversity (H’) by month, GMHT, and drift cell. Lines are spline smoothers of the data points.

Fig. 4 Mean species diversity (H’) by drift cell. Error bars represent the 95% confidence interval.

GMHT, and drift cell (Fig. 5). Densities of total fish,

and a number of individual species including Chinook,

coho, surf smelt, and sand lance showed significant

seasonal variation and high variability with

geomorphic habitat type; however, only the forage

fish species (surf smelt and sand lance) densities were

significantly different between GMHTs, with highest

numbers along embayments, spits, and bluffs.

Chinook and coho densities were significant different

between GMHTs, while chum were not statistically

different across GMHTs. Densities of Chinook, chum,

and coho salmon were significantly different under the

GMHT × month interaction term. The GMHT ×

month interaction did not show statistically significant

differences between densities of individual forage fish

species.


694

(a)

(b)

Geomorphic Habitat Type, Drift Cell, Forage Fish, and Juvenile Salmon: Are They Linked?

695

(c)

(d)

Fig. 5 (a) Juvenile salmon and post larval, juvenile, and adult forage fish; (b) surf smelt; (c) herring densities; (d) sand lance

densities ( 4 2

fishm

) for combined geomorphic habitats of comparative and degraded (Elwha) drift cells.


696

When GMHT sites were compared, there were no

consistent trends in differences in densities of

individual fish species between degraded and intact

drift cells, with only a half dozen or so species,

although the habitat comparisons at the drift cell scale

were statistically different. ANOVA results for

individual species densities between drift cells

revealed that only chum salmon and total, post larval,

and juvenile surf smelt densities were significantly

different between degraded and intact drift cells, with

lower densities of all in the degraded drift cell (Fig.

5 a-5d). More specifically, the density of surf smelt

and chum salmon were significantly lower along

degraded spits and bluffs than intact bluffs and

shorelines, and there were significantly fewer juvenile

surf smelt along degraded embayed shoreline

compared to intact bluffs and spits. There were also

fewer surf smelt along degraded bluffs compared to

the intact embayed shoreline, and significantly fewer

post larval surf smelt along the degraded spit

compared to intact drift cell spit. Adult surf smelt

densities were also significantly different by month

between degraded and intact drift cell spits.

3.2 Genetic Analysis

The three largest posterior probabilities for

assignments to a population for each of the 58

individual Chinook salmon juveniles sampled for

genetic material are presented in Tables 2 and 3. The

highest posterior probabilities for individual

assignment to a specific population were low in some

cases. Confidence in assignments can be improved by

Table 2 The top three stock origin assignments of 58 Chinook salmon smolts to GAPS baseline populations. Areas collected: CB = Crescent Bay; P = Pysht; FB = Freshwater Bay.

Individual #1 Assignment #1 Posterior probability

#2 Assignment #2 Posterior probability


07IX0011/CB Dungeness R. 0.7888 Elwha_H 0.1176 Elwha_W 0.0936

07IX0012/CB Elwha_H 0.9449 Elwha_W 0.0549 Dungeness R. 0.0002

07IX0013/CB Elwha_W 0.4499 Dungeness R. 0.4274 Elwha_H 0.1228

07IX0014/CB Abernathy_NFH_Fa 0.6709 Lewis_R_LSu 0.2605 Spring_Cr_H 0.0508



07IX0018/FB Dungeness R. 0.9980 Elwha_H 0.0019 Elwha_W 0.0001

07IX0019/FB Hanford Reach Fall 0.5235 Methow Summer_H 0.4717 Snake Fall 0.0045

07IX0020/FB L_Yakima_R_Fa 0.6813 Methow Summer_H 0.1870 Hanford Reach Fall 0.1201

07IX0021/FB Lewis_R_LSu 0.9915 Hanford Reach Fall 0.0071 Abernathy_Cr_Fa 0.0010

07IX0028/CB Methow Summer_H 0.8834 L_Yakima_R_Fa 0.0672 Hanford Reach Fall 0.0447

07IX0029/CB Green_R_Fa 0.9908 Abernathy_Cr_Fa 0.0086 Spring_Cr_H 0.0006

07IX0030/CB Abernathy_Cr_Fa 0.8531 Abernathy_NFH_Fa 0.1433 Hanford Reach Fall 0.0027

07IX0031/CB Abernathy_NFH_Fa 0.5344 Spring_Cr_H 0.4654 Green_R_Fa 0.0002

07IX0032/CB Abernathy_Cr_Fa 0.9205 Methow Summer_H 0.0705 L_Yakima_R_Fa 0.0085

07IX0033/CB Yakima_R_bright_Fa 0.9992 L_Yakima_R_Fa 0.0007 Methow Summer_H 0.0000

07IX0034/CB Abernathy_NFH_Fa 0.8515 Abernathy_Cr_Fa 0.1480 Spring_Cr_H 0.0004

07IX0035/CB Abernathy_Cr_Fa 0.8054 Spring_Cr_H 0.1871 Abernathy_NFH_Fa 0.0047

07IX0036/CB Elwha_W 0.8619 Elwha_H 0.1204 Dungeness R. 0.0174

07IX0037/CB Elwha_W 0.5358 Elwha_H 0.4642 Methow Summer_H 0.0000



07IX0074/CB Spring_Cr_H 0.5569 Abernathy_NFH_Fa 0.4372 Green_R_Fa 0.0038

07IX0075/P Spring_Cr_H 0.6965 Abernathy_NFH_Fa 0.2764 Abernathy_Cr_Fa 0.0249

07IX0077/P Elwha_H 0.5918 Elwha_W 0.4082 Dungeness R. 0.0000

07IX0078/P Abernathy_Cr_Fa 0.9961 Spring_Cr_H 0.0025 Lewis_R_LSu 0.0011


697

(Table 2 continued)

Individual #1 Assignment #1 Posterior probability



07IX0079/P Methow Summer_H 0.9897 Hanford Reach Fall 0.0056 Snake Fall 0.0023

07IX0081/P Spring_Cr_H 0.5831 Abernathy_Cr_Fa 0.3273 Abernathy_NFH_Fa 0.0763

07IX0082/P Hoko_H_Fa 1.0000 Willapa Fall 0.0000 Hanford Reach Fall 0.0000


07IX0084/CB Elwha_H 0.4129 Elwha_W 0.2882 Puyallup 0.2719




07IX0106/CB L_Yakima_R_Fa 0.9897 Hanford Reach Fall 0.0069 Marion_Drain_Fa 0.0026


07IX0108/CB L_Yakima_R_Fa 0.6820 Hanford Reach Fall 0.1639 Methow Summer_H 0.1523

07IX0109/CB Elwha_H 0.4475 Dungeness R. 0.3623 Elwha_W 0.1901

07IX0110/CB Hanford Reach Fall 0.9590 L_Yakima_R_Fa 0.0204 Methow Summer_H 0.0201




07IX0116/CB Abernathy_NFH_Fa 0.4135 Abernathy_Cr_Fa 0.4036 Spring_Cr_H 0.1823

07IX0117/CB Hanford Reach Fall 0.7784 Marion_Drain_Fa 0.2007 Snake Fall 0.0203

07IX0118/CB Klamath River fall 0.9859 Abernathy_Cr_Fa 0.0083 Yakima_R_bright_Fa 0.0024

07IX0119/CB Snake Fall 0.8112 Marion_Drain_Fa 0.1067 Hanford Reach Fall 0.0794

07IX0121/CB Methow Summer_H 0.7051 L_Yakima_R_Fa 0.2493 Hanford Reach Fall 0.0300

07IX0122/CB Methow Summer_H 0.6110 Hanford Reach Fall 0.2800 Yakima_R_bright_Fa 0.0750

07IX0123/CB Spring_Cr_H 0.7858 Abernathy_Cr_Fa 0.2125 Abernathy_NFH_Fa 0.0016


07IX0125/CB Hoko_H_Fa 0.9999 Elwha_H 0.0001 Dungeness R. 0.0000



07IX0129/CB Klamath River fall 0.9999 Abernathy_Cr_Fa 0.0001 Willapa Fall 0.0000

07IX0130/CB Yakima_R_bright_Fa 0.7903 Hanford Reach Fall 0.1034 Snake Fall 0.0703

07IX0131/CB Marion_Drain_Fa 0.5897 Methow Summer_H 0.2549 L_Yakima_R_Fa 0.0912

07IX0132/CB Willapa Fall 0.9984 Hanford Reach Fall 0.0014 Lewis_R_LSu 0.0001

07IX0133/CB Willapa Fall 0.9954 Abernathy_Cr_Fa 0.0045 Spring_Cr_H 0.0001

Table 3 Stock of origin composition of 58 Chinook collected and analyzed over sampling period.

Collection date (week) Elwha-Dungeness* (%) Columbia River* (%) Klamath River * (%) Washington coast (%) 06/22/07 100 0 0 0 07/05/07 50 50 0 0 07/12/07 100 0 0 0 07/16/07 83 17 0 0 08/02/07 0 100 0 0 08/14/07 63 38 0 0 08/28/07 0 86 14 0 09/12/07 44 22 11 22 Overall average 47 45 4 4 * indicates federally listed stock.


698

combining the posterior probabilities of baseline

populations that are geographically or genetically

similar into aggregates or reporting groups. Thus, a

total of four reporting groups were defined by

combining several populations with similar

geographic origin: Elwha/Dungeness, Columbia River

late run, WA Coast, and Klamath River (Table 3). The

Elwha/Dungeness Reporting Group accounted for

46.0% of the assignments, Columbia River late run

44.4%, Washington Coast 6.4% and Klamath River

3.2% (Table 3).

Size of Chinook analyzed for genetic composition

ranged between 72-146 mm fork length. Over the life

of the study the Chinook size ranged between

approximately 85-144 mm fork length. Coho analyzed

for genetic composition ranged from 94-161 mm fork

length, with an average of 130 mm (Tables 4 and 5).

Within these reporting groups, the paper identified

at least 14 discrete populations of Chinook salmon:

three from Puget Sound, two from the Washington

Coast, one from the Klamath River, and ten from the

Columbia River (Table 3). For coho, four discrete

populations were identified, which combined

Columbia River and Strait of Juan de Fuca stocks

(33% each), Hood Canal (22%) and Washington

Coast (11%) (Tables 4 and 5). Genetic analysis of

juvenile Chinook and coho salmon collected over

successive months from Crescent Bay indicate that

Columbia River and Elwha stocks use the central

Strait nearshore consistently, and throughout the

outmigration season (Table 4).

4. Discussion

Working in the nearshore environment is

challenging due to remote sampling locations and

severe and variable environmental conditions [8, 22],

this resulted in a disparate number of samples from

the different geomorphic habitat types, a low sample

size for genetic analysis, and problematic replication

issues for the drift cell comparison analysis. Each of

these likely contribute to the extremely high

variability observed, and should be considered when

interpreting results. With that caveat in mind, this

work illustrates that fish use of the nearshore, as

defined by fish density and ecological indices, is

extremely complex, driven primarily by season,

species, and life history and less by geomorphic

habitat type. Surf smelt and sand lance, which do not

have an anadromous life history, spawn on and

migrate along the connected shorelines of

embayments, spits, and bluffs, and use lower rivers

less frequently. Thus they were found in high numbers

along spit, bluff, and embayed geomorphic habitat

types throughout the spring, summer, and fall months

and in far fewer numbers along lower river sites. Surf

smelt densities also reflect relative habitat quality at a

Table 4 Stock of origin for 9 coho collected during sampling period.

Hood canal Columbia river Wa Coast SJdF

22% 33% 11% 33%

Table 5 The top three stock origin assignments of 9 coho salmon smolts to GAPS baseline populations.

Fish ID Collection date Size (fork) mm Site collected Best estimate Probability 2nd best estimate Probability

90382-005 23-May-07 114 Crescent Beach Columbia_R 0.896 Juan_de_Fuca 0.104

90382-006 23-May-07 113 Crescent Beach Juan_de_Fuca 0.920 Columbia_R 0.069

90382-007 23-May-07 138 Crescent Beach Columbia_R 0.922 Juan_de_Fuca 0.074

90382-008 23-May-07 161 Crescent Beach Juan_de_Fuca 0.830 Columbia_R 0.154

90382-009 23-May-07 128 Crescent Beach S_Washington_Coast 0.997

90382-010 23-May-07 150 Crescent Beach Juan_de_Fuca 1.000

90382-022 24-Jul-07 94 Freshwater Bay Columbia_R 0.991

90382-073 8-Jul-07 149 Crescent Beach Hood_Canal 0.970 Juan_de_Fuca 0.021

90382-113 14-Aug-07 127 Crescent Beach Hood_Canal 0.985 Juan_de_Fuca 0.015


699

drift cell scale. In contrast, andaromous outmigrating

juvenile salmon depend on lower rivers as they

transition from riverine to marine habitats, and have

discrete outmigration times [23-27]. So it is not

surprising that, in this study, juvenile salmon were

found in higher proportional numbers in lower rivers

than along shorelines, and in higher proportion along

shorelines within the drift cell associated with

outmigration.

Other than smelt, individual species abundance

overall were not consistently good indicators of the

ecological function of a drift cell. While surf smelt

densities appeared to reflect drift cell state, salmon

densities did not. Surf smelt have very specific

spawning substrate requirements (1-7 mm grain size)

[23, 27]. The higher densities of surf smelt in the

intact drift cell shorelines may be related to increased

proportion of available potential surf smelt spawning

habitat previously documented there [23]. Comparing

fish densities to proportion of substrate suitable for

spawning indicates that there is more appropriate

habitat in the spit, bluff, and embayment shorelines

for that species [23] (Fig. 6).

Overall, basic ecological indices of species

diversity and richness showed a greater relationship to

habitat quality at the drift cell scale. The Elwha drift

Fig. 6 Relative surf smelt and sand lance density (circles) by sediment class (sides of triangle) and ghmt (fill color of the circle).


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cell, which is a degraded habitat in terms of sediment

processes and form [23], also had lower species

diversity and richness than areas with intact processes.

Assessing geomorphic and drift cell results for salmon

reveals that while function is lower overall in the

degraded drift cell, it still supports some of the highest

density of juvenile salmon. This high abundance of

federally listed salmon is undoubtedly in large part

due to significant hatchery practices in the Elwha

River [14]. Collectively these results suggest that, for

Pacific Northwest systems, species life history and

seasonal component of habitat use of nearshore

habitats dictates function—not geomorphic habitat

type. Understanding the fish use at both the nearshore

geomorphic habitat type and drift cell scales is

therefore important for accurately defining relative

habitat function and related management priorities.

The drift cell scale is the most appropriate scale to

define priorities for preservation and restoration

actions to restore nearshore ecosystem processes and

ecological function. Smaller geomorphic scale

projects that focus on species-specific restoration and

protection actions and smaller sites without linkages

to larger drift cell scale ecosystem habitat function

should be considered a lower priority. Put in the

contect of this study, the Elwha drift cell, which has

degraded habitat forming processes and functioning at

a lower ecological level, would be appropriate for

restoration. If restoring for surf smelt spawning and

migration, restoration work should focus on

embayments, spits, and bluffs. If the restoration focus

is on salmonid species, work on hatchery practices,

and the restoration of ecosystem processes of the

severely degraded lower river/estuary is the highest

priority. The Dungeness drift cell is most appropriate

for protection of the existing processes that define it,

on a relative scale, as a higher ecologically

functioning drift cell.

Our results further illustrate the regional and cross

regional fish use of the nearshore, and highlight the

little understood and rarely considered cross-regional

importance of restoration decisions, with both

Chinook and coho salmon from as far away as

Columbia River and Kalamath systems found to be

utilizing Strait of Juan de Fuca shorelines during their

initial summer at sea. This use seems to continue

throughout the summer, and likely represents

successive groups of fish migrating through the area,

as the size of fish encountered during our seining

efforts did not increase over time. Our sample size is

too small to clearly understand cross-regional drift cell

use, but these preliminary results are compelling.

Understanding the complexities of this long distance

shoreline migration by juvenile salmon, and possibly

forage fish, is therefore a recommended priority for

further study.

The documentation of Columbia and Klamath

Chinook salmon stocks in the central and western

Strait, including the Elwha nearshore—which is the

site of an internationally significant fisheries

restoration via the removal of two dams [8, 11]—is

equally important and illustrates the regional

importance of habitat management and restoration

actions. These data suggest that restoration actions,

including the Elwha dam removal project, may have

cross-regional benefit, including for ESA listed stocks

from across the northwest.

Finally, the documentation of Columbia River and

Klamath River Chinook salmon stocks in the central

and western Strait also illuminates the importance of

the north coastal system for federally listed ESA

Chinook salmon stocks. While adult and blackmouth

Columbia River Chinook salmon are intercepted

regularly from Alaskan to Californian waters,

documenting Columbia River and Klamath age 0+

fish in the central Strait of Juan de Fuca in early July

suggests a rapid long distance migration to the north

along coastal Washington, and supports data published

by others [24] showing that these fish must have

migrated along the nearshore of coastal Washington to

reach the Strait of Juan de Fuca. The Washington coast

consists of open coastline and a series of small and


701

relatively isolated estuaries between the Columbia

River and the Strait of Juan de Fuca. Given the

dependence of juvenile Chinook salmon on estuarine

habitat and the documented use of these habitats by

other federally listed fish species [25, 26] it is logical

to conclude that these fish depend on these small

estuaries during their northern migration. Details of

the relative function of these small isolated estuaries

on the outer coast for young of the year migrating

salmon have not been well defined, but are an

important next step for both management and

assessment actions. Work in Puget Sound has revealed

high importance of small isolated non-natal estuaries

for ESA Chinook salmon stocks [6, 7, 28], further

justifying additional assessment to define how these

habitats work in other regions of the Northwest.

Similar work should also focus on forage fish, which

depend on many of the same nearshore habitats and

play an equally critical role in marine ecosystem

function [27].

5. Conclusion

Nearshore habitat function for fish is complex, and

defined by season, species, and life history. This study

shows that geomorphic habitat type is important for

some types of fish use, but is not a sole indicator for

habitat function, and in fact, overall ecological

function is better defined at the drift cell rather than

geomorphic habitat type scale. Further, nearshore

habitats are functionally important for critical ESA

species from across many regions of the Pacific

Northwest. Protecdtion, restoration, and habitat

management actions should be therefore scaled,

designed, and implemented with a cross-regional,

multi species, and ecological habitat awareness.

Additional study at a larger scale that includes

additional intact and impaired drift cells is

recommended to assess and provide additional

resolution to our findings.

Acknowledgments

This nearshore assessment project was sponsored

by the North Olympic Peninsula Lead Entity and

funded by the Salmon Recovery Funding Board

(SRFB/RCO). Cheryl Baumann is the NOPLE

coordinator; Tara Galuska is the RCO project manager.

Grant partners include Lower Elwha Klallam Tribe,

Peninsula College, USGSW, WWU, and the Elwha

Nearshore Consortium. The Clallam MRC (Marine

Resources Committee) and Clallam County senior

biologist Cathy Lear, as well as Peninsula College

Senior Vice President Bill Eaton provided important

funding and support for college student interns,

including Jesse Charles, Chris DeSisto, Bryan Hara,

Erica Hirsh, Keelan Hooper, Mario Laungayan, Romy

Laungayan, Shea McDonald, Tiffany Nabors, Ross

McDorman, Sean Oden, Rebecca Paradis, Jacob Ray,

Melanie Roed, Justin Rondeau, Trista Simmons, Ben

Warren, Karen Wilkie, Eric Wood, and Steve Wyall.

Mr. Jack Ganzhorn provided additional supervision of

Peninsula College Fisheries program students. This

material is based upon work supported in part by the

National Science Foundation under REU Grant No.

0452328 awarded jointly to Peninsula College and

Western Washington University. Any opinions,

findings and conclusions, or recommendations

expressed in this material are those of the authors and

do not necessarily reflect the views of the National

Science Foundation. Jenna Schilke and Tyler Ritchie,

formerly with WDFW, supervised much of the field

work and conducted statistical analyses. Dave Parks,

and DNR provided sediment data and scientific

guidance. Chuck and Neva Novak and Ben and Irene

Palzer, Malcolm Dudley, Chuck Janda, Pam Lowry,

Joe Murray and Norm Shaff, and Merrill & Ring

provided access to private property beaches. Pam

Sangunetti (USACoE) and Kevin Ryan (USFWS) and

refuge volunteers provided invaluable partnership and

field support. Charlie and Kendra Parks, Port Angeles

High School, and Andy Stevenson, provided both

field support and good will. Anna Kagley and Kurt

Fresh (NOAA) provided a loaner net for seining,

seining data sheet format, and genetic sampling data


702

sheets and vials. Kurt Fresh and two anonymous

reviewers provided helpful manuscript review. The

Lower Elwha Klallam Tribe, as a formal federal

co-manager, continues to provide the will, culture, and

expertise that has resulted in a national scale

restoration project within the Elwha ecosystem. Thank

you to all.

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Geomorphic habitat type, drift cell, forage fish, and juvenile salmon

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