Relationships Among Juvenile Anadromous Salmonids, Their Freshwater
Habitat, and Landscape Characteristics Over Multiple Years and Spatial
Scales in the Elk River, Oregon
Kelly Marie Burnett
PhD Dissertation
11 July 2001
Fisheries Science
Oregon State University, Corvallis, Oregon
AN ABSTRACT OF THE DISSERTATION OF
Kelly Marie Burnett for the degree of Doctor of Philosophy in Fisheries Science presented on July 11,
2001. Title: Relationships Among Juvenile Anadromous Salmonids, Their Freshwater Habitat, and Landscape
Characteristics Over Multiple Years and Spatial Scales in the Elk River, Oregon.
Abstract approved: ___________________________________________________
Gordon H. Reeves
Research on the distribution of juvenile salmonids in streams has been dominated by studies examining
small areas over short periods. However, information relevant to freshwater influences on population persistence is likely to derive from longer-term, multi-scale studies. Relationships were examined among juvenile
anadromous salmonids, their freshwater habitat, and landscape characteristics throughout the Elk River,
Oregon over 7 years at multiple spatial scales. Ocean-type chinook salmon (Oncorhynchus tshawytscha), coho
salmon (O. kisutch), coastal cutthroat trout (O. clarki) and winter-run steelhead (O. mykiss) comprised the salmonid assemblage. Habitat selection was quantified at stream system, valley segment, and channel unit scales
by selection ratios estimated with bootstrapping methods. Unconstrained valleys in tributaries and pools in
the mainstem were typically selected by each species except steelhead, which often avoided these. Valley segment types generally did not differ for characteristics routinely assessed in stream surveys. Thus, fish probably
perceived other biotic or abiotic differences among valley segment types. Evidence suggested competition may
have influenced selection by coho and chinook salmon. Discriminant analysis indicated that level of use by
juvenile chinook salmon appeared related to valley segment type and spatial position. Unconstrained valleys,
nearby valley segments, and valley segments with larger, deeper pools, containing more wood were most highly
used by chinook salmon. Mean volume and maximum depth of pools were each directly related to catchment
area, which explained more variation than landscape characteristics summarized at any of five spatial scales.
At each scale except the most spatially extensive, wood density in valley segments was negatively related to
the percent area in resistant rock types and positively related to the percent area in mature to old forests.
The most variation was explained with these landscape variables summarized at an intermediate spatial
scale (i.e., sub-catchment). Although spatial scales appeared similar in processes affecting wood density,
finer scales omitted key source areas for wood delivery, and coarser scales included source areas less tightly
coupled to wood dynamics in surveyed channels. If only 1 or 2 years of data or one spatial scale had
been examined, as commonly occurs, conclusions may have differed substantially from those in this study.
Copyright by Kelly Marie Burnett
July 11, 2001
All rights reserved
Relationships Among Juvenile Anadromous Salmonids,
Their Freshwater Habitat, and Landscape Characteristics
Over Multiple Years and Spatial Scales in the Elk River, Oregon
by
Kelly Marie Burnett
A DISSERTATION
submitted to
Oregon State University
in partial fulfillment of
the requirements for the
degree of
Doctor of Philosophy
Completed July 11, 2001
Commencement June 2002
Doctor of Philosophy dissertation of Kelly Marie Burnett presented on
July 11, 2001
APPROVED:
___________________________________________________________________
Major Professor, representing Fisheries Science
___________________________________________________________________
Head of Department of Fisheries and Wildlife
___________________________________________________________________
Dean of Graduate School
I understand that my dissertation will become part of the permanent collection of Oregon State University libraries.
My signature below authorizes release of my dissertation to any reader upon request.
___________________________________________________________________
Kelly Marie Burnett
ACKNOWLEDGMENTS
I thank Gordie Reeves, my major professor, for sharing freely of his knowledge, encouragement, time, and
perspective. I am also indebted to the members of my graduate committee, Bob Gresswell, Norm Johnson, Flo Leibowitz, Bill Liss, and Fred Swanson for their support, advice, and willingness to serve. I especially want to convey
my gratitude to Norm Johnson for re-awakening then fostering my interest in policy and to Bob Gresswell for his
unofficial guidance initially and for serving officially when I most needed it. My lucky draw brought Flo Leibowitz
to the committee as grad rep, and I appreciate her summary of my work, “It takes a watershed to raise a smolt.”
Thanks are offered to my honorary committee member and chief statistical consultant, George Weaver.
I am also thankful to my other statistical advisors Pat Cunningham, Lisa Ganio, Manuela Huso, Julia
Jones, Chris Moyer, and Cindy Rugger and to Wallace Erickson for advise on bootstrapping methods.
In addition to Gordie Reeves, I thank Fred Everest, Jim Sedell, DeDe Olsen, and Bruce Hansen for recognizing
the value of a long-term study and keeping Elk River alive for the past 15 years even when there was little funding to
do so. Numerous people were responsible for collecting the years of data that I examined. For their time in field,
I am appreciative of David Anderson, Alex Atkins, Kristen Bremm, Lisa Brown, Barb Campbell, Lance Campbell,
Mark Chambers, Glen Chen, Jane Chen, Kelly Christiansen, Kevin Cooper, Charley Dewberry, Pat Dickenson,
Lorretta Ellenburg, Kris Fausti, Ken Fliszar, Karen Garbriel, Mark Garner, Kitty Griswold, Jon Grunbaum, Dave
Hankin, Bruce Hansen, Lisa Heigh, Deb Hildebrand, Carl Jahn, Nick Leone, Brad Lovett, Tad Lueck, Joe Lumianski,
Aaron McKee, Cory McKeone, Deian Moore, Chris Moyer, Ian Osborne, Dave Price, Cathy Quinn, Miranda Raugh,
Gordon Reeves, Todd Reeves, Kirsten Schumaker, Jake Smith, Mark Smith, Burke Strobel, Cindy Studebaker, Gary
Susac, Craig Tinus, Eric Veach, Chuck Wheeler, Greg Wiebe, Aleah Yung, and Jon Ziedler. It was a pleasure to
have experienced such an amazingly, beautiful place as Elk River with this talented and devoted group of people.
I consider the friendships of my fellow graduate students, Kitty Griswold and Chris Zimmerman,
to be among the most rewarding outcomes of this endeavor and am fortunate to have had access to
their editorial gifts. A picture is worth a thousand words, so I thank Kelly Christiansen and Kathryn
Ronnenberg for turning my words into well designed graphics. I also thank Kelly Christiansen for his
GIS and database skills. I am appreciative of Tori Stratton for her numerous hours in the library and
overall assistance with literature and of Tami Lowry for a keen eye and willingness to edit references.
I am blessed with colleagues, friends, and family that have supported me throughout. Charles Warren opened his
door to me almost 20 years ago setting me on this journey and has been my mentor and expanding my perspectives
ever since. Jim Sedell and Gordie Reeves have taken many chances on me that have provided enormous opportunities for my professional growth. I hope not too many of these were wasted and some of their bets on me paid
off. My respect and gratitude for them both is boundless. My thanks to Sharon Clarke seem inconsequential compared to her technical expertise, friendship and strength. I am eternally grateful to my parents, Zelma and Bill
Burnett, for their love, sustenance, and expectation that I do my best. Finally, to my husband, Sean McGinty, I
could not have done this without your daily encouragement and hard work. Although the situation was not easy,
you handled it with grace, enabling me to do what had to be done. Enough appreciation can never be expressed.
CONTRIBUTION OF AUTHORS
Dr. Gordon H. Reeves was an advisor and editor on all manuscripts included in this work. Dr. Robert
E. Gresswell was an advisor and editor on all manuscripts. Sharon E. Clarke was a GIS analyst and an
editor for Chapters 2, 3, and 4. Kelly R. Christiansen was a GIS analyst and an editor for Chapter 4.
CONTENTS
CHAPTER 1. INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1
CHAPTER 2. CHARACTERIZING HABITAT FOR AND SELECTION BY JUVENILE
ANADROMOUS SALMONIDS AT MULTIPLE SPATIAL SCALES OVER MULTIPLE
YEARS (1988-1994) IN THE ELK RIVER, OREGON . . . . . . . . . . . . . . . . . . . . . . .
5
Abstract . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
5
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
6
Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
7
Study area and salmonid community . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Valley segments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Channel unit features and juvenile salmonid densities . . . . . . . . . . . . . . . . . . . . . . . .
Stream discharge and water temperature. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Selection by juvenile salmonids. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Statistical analysis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
7
7
7
9
9
10
Results. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
11
Habitat characterization. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Stream system scale. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Valley segment scale. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Habitat selection. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Stream system scale. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Valley segment scale . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Channel unit scale. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Interannual variation in selection. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
11
11
11
12
12
16
16
16
Discussion. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
16
Habitat characterization. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Habitat selection. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Stream system scale. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Valley segment scale. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Channel unit scale. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Management implications. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
16
20
20
20
21
22
Conclusions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
22
References. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
22
Appendices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
25
CONTENTS
CHAPTER 3. VALLEY SEGMENT USE BY JUVENILE OCEAN-TYPE CHINOOK
SALMON (Oncorhynchus tshawytscha) IN TRIBUTARIES OF THE ELK RIVER,
OREGON (1988-1994) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
29
Abstract. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
29
Introduction. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
30
Methods. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
30
Study area. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Valley segments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Channel unit features and juvenile chinook salmon densities . . . . . . . . . . . . . . . . . . .
30
31
32
Statistical Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
33
Developing the grouping variable . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Developing canonical functions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Among-year differences in channel unit features comprising canonical functions . . . . . . . . .
Applying models to classify new observations . . . . . . . . . . . . . . . . . . . . . . . . . . .
34
35
36
36
Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
36
Valley segment use by juvenile ocean-type chinook salmon . . . . . . . . . . . . . . . . . . . .
Among-year differences in channel unit features comprising canonical functions . . . . . . . . .
Applying models to classify new observations . . . . . . . . . . . . . . . . . . . . . . . . . . .
36
38
38
Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
41
Valley segment use by juvenile ocean-type chinook salmon . . . . . . . . . . . . . . . . . . . . .
Relevance of multiple years of study . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Management implications. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
41
42
43
Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
44
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
44
Appendix . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
47
CHAPTER 4. COMPARING RIPARIAN AND CATCHMENT-WIDE INFLUENCES OF
LANDSCAPE CHARACTERISTICS ON CHANNEL UNIT FEATURES IN TRIBUTARIES
OF THE ELK RIVER, OREGON . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
50
Abstract . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
50
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
50
CONTENTS
Study Area . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
51
Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
52
Digital stream layer and valley segment identification. . . . . . . . . . . . . . . . . . . . . . . .
Landscape characterization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Analytical units . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Digital coverages of landscape characteristics . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Differences among spatial scales in landscape characteristics . . . . . . . . . . . . . . . . . . . .
Regression of channel unit features with catchment area and landscape characteristics . . . . . . .
Channel unit features . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Developing regression models . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
52
53
53
53
54
54
54
55
Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
56
Landscape characterization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Regression of channel unit features with catchment area and landscape characteristics . . . . . . .
56
58
Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
59
Landscape characterization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Regression of channel unit features with catchment area and landscape characteristics . . . . . . .
59
60
Summary and Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
61
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
61
CHAPTER 5. SUMMARY AND CONCLUSIONS . . . . . . . . . . . . . . . . . . . . . . .
64
BIBLIOGRAPHY . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
66
FIGURES
2.1. Location and map of the Elk River, Oregon with valley segments identified for
anadromous fish-bearing sections of the mainstem and its tributaries . . . . . . . . . . . . . . .
7
2.2.
8
Spatial scales examined in the Elk River, Oregon. . . . . . . . . . . . . . . . . . . . . . .
2.3.
Selection ratios of juvenile salmonids for the mainstem and tributaries in Elk River,
Oregon (1988-1994) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
12
2.4.
Selection ratios of juvenile salmonids for unconstrained valleys, alluviated canyons,
and constrained canyons in Elk River, Oregon (1988-1994) . . . . . . . . . . . . . . . . . . . .
17
2.5.
Selection ratios of juvenile salmonids for pools, fastwater habitats, and side channels
in Elk River, Oregon (1988-1994) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
18
FIGURES
3.1.
Location and map of the Elk River, Oregon with valley segments identified for
anadromous fish-bearing sections of its tributaries . . . . . . . . . . . . . . . . . . . . . . . . . .
31
3.2.
Example to calculate the influence of each valley segment type (It) in Red Cedar
Creek on the influenced valley segment Red Cedar Creek 1 . . . . . . . . . . . . . . . . . . . . .
33
3.3.
Mean and 95% confidence intervals for canonical scores when valley segments were
classified into juvenile chinook salmon use groups for tributaries of the Elk River, Oregon . . . . .
37
3.4.
Box and whisker plots of chance-adjusted correct classification rates (i.e., Cohen’s
kappa values) when valley segments from tributaries of the Elk River, Oregon were
classified as new observations by canonical functions developed with data from 1988, 1989,
1991, and 1994 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
39
4.1. Location and map of the Elk River, Oregon with valley segments identified for
anadromous fish-bearing sections of its tributaries surveyed in 1988 . . . . . . . . . . . . . . . .
52
4.2.
Analytical units used to summarize landscape characteristics at five spatial scales
illustrated for the valley segment North Fork Elk River 2. . . . . . . . . . . . . . . . . . . . . .
54
4.3.
Distribution of landscape characteristics among analytical units at each of the five
spatial scales in tributaries of the Elk River, Oregon . . . . . . . . . . . . . . . . . . . . . . . .
58
4.4.
Results of linear regressions for stream distance between each pair of valley
segments and the absolute difference between residuals from among-scale regressions of channel
unit features with landscape characteristics for tributaries of the Elk River, Oregon . . . . . . . .
59
4.5.
Results of linear regression between the percent area in forests of medium to very large
diameter trees and road density at the sub-network scale for tributaries of the Elk River, Oregon . .
59
TABLES
2.1.
Characteristics of mainstem and tributary valley segments in the Elk River, Oregon . . . .
9
2.2.
Estimated total relative density (standard error) of juvenile salmonids in the Elk River,
Oregon (1988-1994) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
10
2.3.
Estimated total relative density (standard error) of juvenile salmonids in the mainstem
and tributaries of the Elk River, Oregon (1988-1994) . . . . . . . . . . . . . . . . . . . . . . .
10
2.4.
Estimated stream discharge and water temperature in the Elk River, Oregon (1988-1994) .
11
2.5.
Percent of habitat area sampled for fish (pi) at the stream system, valley segment and
channel unit scales in the Elk River, Oregon (1988-1994) . . . . . . . . . . . . . . . . . . . . .
11
TABLES
2.6.
Results of comparing means for channel unit features within and among years at the
stream system scale in the Elk River, Oregon (1988-1994) . . . . . . . . . . . . . . . . . . . . .
13
2.7.
Results of comparing means for channel unit features within and among years at the
valley segment scale in the mainstem of the Elk River, Oregon (1988-1994) . . . . . . . . . . . .
14
2.8.
Results of comparing means for channel unit features within and among years at the
valley segment scale in the tributaries of the Elk River, Oregon (1988-1994) . . . . . . . . . . . .
15
2.9.
Results from regressions to explain interannual variation in selection ratios for habitat
types selected by juvenile salmonids at three spatial scales in Elk River, Oregon . . . . . . . . . .
19
3.1.
32
Characteristics of tributary valley segments in the Elk River, Oregon . . . . . . . . . . . .
3.2.
Number of valley segments in the High and Low groups for observed use by juvenile
chinook salmon in tributaries of the Elk River, Oregon (1988-1994) . . . . . . . . . . . . . . .
34
3.3.
Group, High (H) or Low (L) observed use by juvenile chinook salmon, into which
each valley segment was designated annually (1988-1994) for tributaries of the Elk River, Oregon .
34
3.4.
Seven-year mean (standard deviation) of channel unit features for tributary valley
segments in the Elk River, Oregon (1988-1994) . . . . . . . . . . . . . . . . . . . . . . . . . .
35
3.5.
Results of discriminant analysis to distinguish between valley segments that were highly
used by juvenile chinook salmon and those that were not in tributaries of the Elk River, Oregon
(1988-1994) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
37
3.6.
Results from direct and jackknifed classification of valley segments from tributaries of
the Elk River, Oregon . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
38
3.7.
Annual mean (standard error) of selected channel unit features in tributaries of the Elk
River, Oregon . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
38
3.8.
Results when valley segments from tributaries of them Elk River, Oregon were classified
as new observations by canonical functions developed with data from 1988, 1989, 1991, and 1994.
39
3.9.
Identity of valley segments misclassified by canonical functions for tributaries of the Elk
River, Oregon (1988-1994) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
40
4.1.
Characteristics of tributary valley segments in the Elk River, Oregon (1988) . . . . . . . .
53
4.2.
Description of landscape characteristics for the Elk River, Oregon . . . . . . . . . . . . .
55
4.3.
Results from linear regression to explain among-valley segment variation in channel unit
features in tributaries of the Elk River, Oregon . . . . . . . . . . . . . . . . . . . . . . . . . . .
56
APPENDICES
A.2.1. Percent of total estimated area at the stream system, valley segment, and channel unit
scales in the Elk River, Oregon (1988-1994) . . . . . . . . . . . . . . . . . . . . . . . . . . . .
25
A.2.2. Estimated total relative density (standard error) of juvenile salmonids in valley segment
types for the mainstem of the Elk River, Oregon (1988-1994) . . . . . . . . . . . . . . . . . . .
26
A.2.3. Estimated total relative density (standard error) ofjuvenile salmonids in valley segment
types for the tributaries of the Elk River, Oregon (1988-1994) . . . . . . . . . . . . . . . . . . .
26
A.2.4. Estimated total relative density (number/100m2) of juvenile salmonids in valley
segments of the Elk River, OR (1988-1994) . . . . . . . . . . . . . . . . . . . . . . . . . . . .
27
A.3.1. Annual estimates of channel unit features for tributary valley segments in the Elk River,
OR (1988-1994) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
47