Review
of
the
Status
of
Chinook
Salmon
(
Oncorhynchus
tshawytscha)
from
Washington,
Oregon,
California,
and
Idaho
under
the
U.
S.
Endangered
Species
Act
Prepared
by
the
West
Coast
Chinook
Salmon
Biological
Review
Team
17
Dec
1997
The
Biological
Review
Team
(
BRT)
for
chinook
salmon
included,
from
NMFS
Northwest
Fisheries
Science
Center:
Peggy
Busby,
Dr.
Stewart
Grant,
Dr.
Robert
Iwamoto,
Dr.
Robert
Kope,
Dr.
Conrad
Mahnken,
Gene
Matthews,
Dr.
James
Myers,
Philip
Roni,
Dr.
Michael
Schiewe,
David
Teel,
Dr.
Thomas
Wainwright,
F.
William
Waknitz,
Dr.
Robin
Waples,
and
Dr.
John
Williams;
NMFS
Southwest
Region:
Gregory
Bryant
and
Craig
Wingert;
NMFS
Southwest
Region
(
Tiburon
Laboratory):
Dr.
Steve
Lindley,
and
Dr.
Peter
Adams;
NMFS
Alaska
Fisheries
Science
Center
(
Auke
Bay
Laboratory):
Alex
Wertheimer;
and
from
the
USGS
National
Biological
Service:
Dr.
Reginald
Reisenbichler.
iii
CONTENTS
List
of
Figures
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ix
List
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xiii
Executive
Summary
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xv
Acknowledgments
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xxvii
Introduction
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1
The
"
Species"
Question
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3
Background
of
Chinook
Salmon
under
the
ESA
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4
Summary
of
Information
Presented
by
the
Petitioners
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5
Distinct
Population
Segments
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5
Population
Abundance
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6
Causes
of
Decline
for
Chinook
Salmon
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7
Information
Relating
to
the
Species
Question
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9
General
Biology
of
Chinook
Salmon
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9
Ecological
Features
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12
Geological
Events
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12
Ecoregions
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13
Coastal
Range
(#
1)
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13
Puget
Lowland
(#
2)
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18
Willamette
Valley
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3)
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18
Cascades
(#
4)
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22
Sierra
Nevada
(#
5)
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22
Southern
and
Central
California
Plains
and
Hills
(#
6)
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23
Central
California
Valley
(#
7)
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23
Eastern
Cascades
Slopes
and
Foothills
(#
9)
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23
Columbia
Basin
(#
10)
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24
Blue
Mountains
(#
11)
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24
Snake
River
Basin/
High
Desert
(#
12)
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25
Northern
Rockies
(#
15)
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25
Marine
Habitat
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26
Chinook
Salmon
Life
History
and
Ecology
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27
Juvenile
Life
History
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27
Ocean
Distribution
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30
Size
and
Age
at
Maturation
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32
Run
Timing
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34
Straying
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35
Fecundity
and
Egg
Size
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37
Other
Life­
History
Traits
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39
Regional
Variation
in
Life­
History
Traits
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39
iv
Puget
Sound
to
the
Strait
of
Juan
de
Fuca
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40
Washington
and
Oregon
coasts
(
Hoko
River
to
Cape
Blanco)
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55
California
and
southern
Oregon
coast
(
south
of
Cape
Blanco)
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56
California
Central
Valley
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58
Columbia
River
ocean
type
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63
Lower
Columbia
River
(
to
the
Cascade
Crest)
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63
Upper
Willamette
River
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66
Columbia
River
(
east
of
the
Cascade
Crest)
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69
Columbia
River
Stream
Type
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74
Genetic
Information
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78
Background
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78
Statistical
Methods
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78
Previous
Genetic
Studies
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80
Alaska
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.
80
Pacific
Northwest
overview
.
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81
Yukon
and
British
Columbia
.
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83
Washington
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85
Columbia
River
Basin
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86
California
and
Oregon
.
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.
89
Levels
of
Genetic
Differentiation
among
Populations
.
.
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92
New
Studies
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.
94
Regional
patterns
of
genetic
variability
.
.
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.
94
British
Columbia,
Washington,
Oregon,
and
California
.
.
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.
.
103
Columbia
and
Snake
Rivers
.
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.
107
Summary
.
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.
109
Discussion
and
Conclusions
on
ESU
Determinations
.
.
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.
111
Evolutionary
Significance
of
Life­
History
Forms
.
.
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111
Major
Chinook
Salmon
Groups
.
.
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113
California
Central
Valley
.
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.
.
113
Coastal
basins
and
Puget
Sound
.
.
.
.
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.
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113
Columbia
River
.
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114
ESU
Descriptions
.
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.
.
115
1)
Sacramento
River
Winter­
Run
ESU
.
.
.
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.
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.
115
2)
Central
Valley
Spring­
Run
ESU
.
.
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.
118
3)
Central
Valley
Fall­
Run
ESU
.
.
.
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.
119
4)
Southern
Oregon
and
California
Coastal
ESU
.
.
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.
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.
.
119
5)
Upper
Klamath
and
Trinity
Rivers
ESU
.
.
.
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.
120
6)
Oregon
Coast
ESU
.
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.
121
7)
Washington
Coast
ESU
.
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.
121
8)
Puget
Sound
ESU
.
.
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.
122
9)
Lower
Columbia
River
ESU
.
.
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.
122
10)
Upper
Willamette
River
ESU
.
.
.
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.
123
11)
Mid­
Columbia
River
Spring­
Run
ESU
.
.
.
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.
124
12)
Upper­
Columbia
River
Summer­
and
Fall­
Run
ESU
.
.
.
.
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.
.
.
124
13)
Upper
Columbia
River
Spring­
Run
ESU
.
.
.
.
.
.
.
.
.
.
.
.
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.
125
v
14)
Snake
River
Fall­
Run
ESU
.
.
.
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.
.
126
15)
Snake
River
Spring­
and
Summer­
Run
ESU
.
.
.
.
.
.
.
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.
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.
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.
.
127
Relationship
to
State
Conservation
Management
Units
.
.
.
.
.
.
.
.
.
.
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.
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.
.
127
Relationship
to
ESU
Boundaries
for
other
Anadromous
Pacific
Salmonids
.
.
.
.
.
.
.
.
.
131
Artificial
Propagation
.
.
.
.
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.
.
133
Overview
of
Artificial
Propagation
.
.
.
.
.
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.
.
135
Asia
and
Oceania
.
.
.
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.
.
.
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.
135
Japan
.
.
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.
135
Russia
.
.
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.
135
New
Zealand
.
.
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.
135
North
America
.
.
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135
Alaska
.
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.
135
British
Columbia
.
.
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.
136
Columbia
River
Basin
.
.
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.
138
Scale
of
Hatchery
Production
.
.
.
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.
140
Introduction
of
Non­
Native
Chinook
Salmon
into
Hatcheries
.
.
.
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.
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.
.
149
West
Coast
Artificial
Propagation
Activities
.
.
.
.
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.
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.
150
1)
Sacramento
River
Winter­
Run
ESU
.
.
.
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.
.
150
2)
Central
Valley
Spring­
Run
ESU
.
.
.
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.
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.
.
151
3)
Central
Valley
Fall­
Run
ESU
.
.
.
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.
.
152
4)
Southern
Oregon
and
California
Coast
ESU
.
.
.
.
.
.
.
.
.
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.
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.
.
.
.
.
.
.
.
.
.
153
5)
Upper
Klamath
and
Trinity
Rivers
ESU
.
.
.
.
.
.
.
.
.
.
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.
.
155
6)
Oregon
Coast
ESU
.
.
.
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.
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.
156
7)
Washington
Coast
ESU
.
.
.
.
.
.
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.
.
158
8)
Puget
Sound
ESU
.
.
.
.
.
.
.
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.
.
.
.
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.
.
159
9)
Lower
Columbia
River
ESU
.
.
.
.
.
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.
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.
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.
.
161
10)
Upper
Willamette
River
ESU
.
.
.
.
.
.
.
.
.
.
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.
.
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.
.
.
163
11)
Mid­
Columbia
River
Spring­
Run
ESU
.
.
.
.
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.
.
.
165
12)
Upper
Columbia
Summer­
and
Fall­
Run
ESU
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
167
13)
Upper
Columbia
River
Spring­
Run
ESU
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
.
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.
.
.
.
.
170
14)
Snake
River
Fall­
Run
ESU
.
.
.
.
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.
.
171
15)
Snake
River
Spring­
and
Summer­
Run
ESU
.
.
.
.
.
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.
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.
173
Assessment
of
Risk
Extinction
.
.
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177
Background
.
.
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177
Absolute
Numbers
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178
Historical
Abundance
and
Carrying
Capacity
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180
Trends
in
Abundance
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180
Naturally­
spawning
hatchery
fish
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180
Habitat
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181
Regional
perspective
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182
Factors
Causing
Variability
.
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182
Threats
to
Genetic
Integrity
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183
Recent
Events
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185
Other
Risk
Factors
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186
Approach
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186
vi
Previous
Assessments
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187
Data
Evaluations
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189
Quantitative
methods
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189
Data
types
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189
Computed
statistics
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191
Analysis
of
Biological
Information
.
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192
Central
Valley
Region
.
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192
1)
Sacramento
River
Winter­
Run
ESU
.
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193
2)
Central
Valley
Spring­
Run
ESU
.
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.
196
3)
Central
Valley
Fall­
Run
ESU
.
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198
Southern
Coastal
Region
.
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201
4)
Southern
Oregon
and
California
Coastal
ESU
.
.
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201
5)
Upper
Klamath
and
Trinity
River
ESU
.
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206
Oregon
and
Washington
Coastal
Region
.
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208
6)
Oregon
Coast
ESU
.
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210
7)
Washington
Coast
ESU
.
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.
214
8)
Puget
Sound
ESU
.
.
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.
218
Lower
Columbia
River
Region
.
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.
223
9)
Lower
Columbia
River
ESU
.
.
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.
.
224
10)
Upper
Willamette
River
ESU
.
.
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.
228
Upper
Columbia
and
Snake
Rivers
Region
.
.
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.
229
11)
Middle
Columbia
River
Spring­
Run
ESU
.
.
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.
230
12)
Upper
Columbia
River
Summer­
and
Fall­
Run
ESU
.
.
.
.
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.
.
.
.
.
234
13)
Upper
Columbia
River
Spring­
Run
ESU
.
.
.
.
.
.
.
.
.
.
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.
.
238
14)
Snake
River
Fall­
Run
ESU
.
.
.
.
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.
.
240
15)
Snake
River
Spring­
and
Summer­
Run
ESU
.
.
.
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.
.
241
Discussion
and
Conclusion
on
ESU
Risk
Analysis
.
.
.
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.
.
245
1)
Sacramento
River
Winter­
Run
ESU
.
.
.
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.
.
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.
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.
.
245
2)
Central
Valley
Spring­
Run
ESU
.
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.
.
246
3)
Central
Valley
Fall­
Run
ESU
.
.
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.
246
4)
Southern
Oregon
and
California
Coastal
ESU
.
.
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.
.
247
5)
Upper
Klamath
and
Trinity
Rivers
ESU
.
.
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.
248
6)
Oregon
Coast
ESU
.
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.
249
7)
Washington
Coast
ESU
.
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.
249
8)
Puget
Sound
ESU
.
.
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.
250
9)
Lower
Columbia
River
ESU
.
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.
251
10)
Upper
Willamette
River
ESU
.
.
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.
.
252
11)
Middle
Columbia
River
Spring­
Run
ESU
.
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.
252
12)
Upper
Columbia
River
Summer­
and
Fall­
Run
ESU
.
.
.
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.
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.
.
253
13)
Upper
Columbia
River
Spring­
Run
ESU
.
.
.
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.
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.
.
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.
.
253
14)
Snake
River
Fall­
Run
ESU
.
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.
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.
254
15)
Snake
River
Spring­
and
Summer­
Run
ESU
.
.
.
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.
.
255
Citations
.
.
.
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.
257
Appendix
A:
Age
at
Smoltification
.
.
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.
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.
319
vii
Appendix
B:
Age
at
Maturation
.
.
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.
329
Appendix
C:
Reproductive
Traits
.
.
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.
339
Appendix
D:
Hatchery
Releases
.
.
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347
Appendix
E:
Abundance
Data
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399
Appendix
F:
The
Risk
Matrix
Method
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427
Glossary
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435
viii
ix
List
of
Figures
x
xi
xii
xiii
List
of
Tables
xiv
EXECUTIVE
SUMMARY
In
1994,
the
National
Marine
Fisheries
Service
(
NMFS)
received
a
petition
(
PRO­
salmon
1994)
requesting
the
listing
of
four
populations
of
chinook
salmon
(
Oncorhynchus
tshawytscha)
in
Puget
Sound
as
threatened
or
endangered
species
under
the
federal
Endangered
Species
Act
(
ESA).
In
response
to
this
petition
and
the
more
general
concerns
for
the
status
of
Pacific
salmon
throughout
the
region,
NMFS
announced
that
it
would
initiate
ESA
status
reviews
for
all
species
and
populations
of
anadromous
salmonids
in
the
states
of
Washington,
Idaho,
Oregon,
and
California.
Subsequently,
NMFS
received
a
petition
(
ONRC
and
Nawa
1995)
to
list
all
chinook
salmon
south
of
British
Columbia
under
the
ESA.

The
ESA
allows
the
listing
of
"
distinct
population
segments"
of
vertebrates
as
well
as
named
species
and
subspecies.
The
policy
of
the
NMFS
on
this
issue
for
anadromous
Pacific
salmonids
is
that
a
population
will
be
considered
"
distinct"
for
purposes
of
the
ESA
if
it
represents
an
evolutionarily
significant
unit
(
ESU)
of
the
species
as
a
whole.
To
be
considered
an
ESU,
a
population
or
group
of
populations
must
1)
be
substantially
reproductively
isolated
from
other
populations,
and
2)
contribute
substantially
to
the
ecological
or
genetic
diversity
of
the
biological
species.
Once
an
ESU
is
identified,
a
variety
of
factors
related
to
population
abundance
are
considered
in
determining
whether
a
listing
is
warranted.

West
Coast
Chinook
Salmon
ESUs
Previous
status
reviews
conducted
by
the
NMFS
have
identified
three
ESUs
of
chinook
salmon
in
the
Columbia
River:
Snake
River
fall­
run
(
Waples
et
al.
1991),
Snake
River
spring­
and
summer­
run
(
Matthews
and
Waples
1991),
and
mid­
Columbia
River
summer­
and
fall­
run
chinook
salmon
(
Waknitz
et
al.
1995).
In
addition,
prior
to
development
of
the
ESU
policy,
the
NMFS
recognized
Sacramento
River
winter
chinook
salmon
as
a
"
distinct
population
segment"
under
the
ESA
(
NMFS
1987).
In
reviewing
the
biological
and
ecological
information
concerning
west
coast
chinook
salmon,
the
Biological
Review
Team
(
BRT)
identified
11
additional
ESUs
for
chinook
salmon
from
Washington,
Oregon,
and
California.
Genetic
data
(
from
protein
electrophoresis
and
DNA
analysis)
and
tagging
information
were
key
factors
considered
for
the
reproductive
isolation
criterion,
supplemented
by
inferences
about
barriers
to
migration
created
by
natural
features.
Life­
history
differences
were
another
important
consideration
in
the
designation
of
ESUs.
The
BRT
utilized
the
classification
system
developed
by
Healey
(
1983,
1991)
to
describe
the
two
races
of
chinook
salmon:
1)
ocean­
type
populations
which
typically
migrate
to
seawater
in
their
first
year
of
life
and
spend
most
of
their
oceanic
life
in
coastal
waters,
and
2)
stream­
type
populations
which
migrate
to
sea
as
yearlings
and
often
make
extensive
oceanic
migrations.
Genetic
differences,
as
measured
by
variation
in
allozymes,
indicate
that
the
oceanand
stream­
type
races
represent
two
major
(
and
presumably
monophyletic)
evolutionary
lineages.
A
number
of
additional
factors
were
considered
to
be
important
in
evaluations
of
ecological/
genetic
diversity,
with
data
on
life­
history
characteristics
(
especially
ocean
distribution,
time
of
freshwater
entry,
age
at
smoltification
and
at
maturation)
and
geographic,
hydrological,
and
environmental
characteristics
being
particularly
informative.
xvi
Chinook
Salmon
ESUs
1)
Sacramento
River
Winter­
Run
ESU
This
ESU
includes
the
Upper
Sacramento
River
below
Keswick
Dam.
Historically,
winter­
run
populations
existed
in
the
Upper
Sacramento,
Pit,
McCloud,
and
Calaveras
Rivers.
Winter­
run
chinook
salmon
were
distinguished
from
other
chinook
salmon
populations
in
the
Sacramento
River
Basin
based
on
their
unique
run­
timing
and
genetic
characteristics.
Adult
winter­
run
chinook
salmon
enter
the
Sacramento
River
from
November
to
June
and
spawn
from
late­
April
to
mid­
August,
with
a
peak
from
May
to
June.
No
other
chinook
salmon
population
has
a
similar
life­
history
pattern.
In
general,
winter­
run
chinook
salmon
exhibit
an
ocean­
type
lifehistory
strategy,
and
remain
near
the
coasts
of
California
and
Oregon
during
their
marine
residence.
Winter­
run
chinook
salmon
also
mature
at
a
relatively
young
age
(
2­
3
years
old).
DNA
analysis
indicates
substantial
genetic
differences
between
winter­
run
and
other
chinook
salmon
temporal
runs
in
the
Sacramento
River.

2)
Central
Valley
Spring­
Run
ESU
This
ESU
contains
the
Sacramento
River
Basin
and
includes
chinook
salmon
entering
the
Sacramento
River
from
March
to
July
and
spawning
from
late
August
through
early
October,
with
a
peak
in
September.
Spring­
run
fish
in
the
Sacramento
River
exhibit
an
ocean­
type
life
history,
emigrating
as
fry,
subyearlings,
and
yearlings.
Marine
coded­
wire­
tag
(
CWT)
recoveries
are
primarily
from
fisheries
off
the
California
and
Oregon
coast.
Differences
in
adult
size,
fecundity,
and
smolt
size
were
also
observed
between
spring­
and
fall­
run
chinook
salmon
in
the
Sacramento
River.
DNA
analyses
indicates
moderate
differences
between
the
spring,
fall,
and
late­
fall
runs
in
the
Sacramento
River.

3)
Central
Valley
Fall­
Run
ESU
This
ESU
contains
the
Sacramento
and
San
Joaquin
River
Basins
and
includes
fall
and
late­
fall
run
chinook
salmon.
These
populations
enter
the
Sacramento
and
San
Joaquin
Rivers
from
July
through
March
and
spawn
from
October
through
March.
Fish
in
this
ESU
are
oceantype
chinook
salmon,
emigrating
predominantly
as
fry
and
subyearlings,
remaining
off
the
California
coast
during
their
ocean
migration.
Fall­
run
chinook
salmon
in
the
Sacramento
and
San
Joaquin
River
Basins
are
physically
and
genetically
distinguishable
from
coastal
forms.
xvii
4)
Southern
Oregon
and
California
Coastal
ESU
This
ESU
includes
native
spring
and
fall
runs
of
chinook
salmon
south
of
Cape
Blanco,
Oregon.
Historically,
the
range
may
have
extended
to
the
Ventura
River
in
California,
but
currently
does
not
extend
south
of
San
Francisco
Bay,
California.
Also
included
in
this
ESU
are
populations
in
the
Klamath
River
Basin
from
the
mouth
upriver
to
the
confluence
of
the
Trinity
and
Klamath
Rivers.
Chinook
salmon
in
this
ESU
exhibit
an
ocean­
type
life
history,
with
marine
distribution
predominantly
off
the
California
and
Oregon
coasts.
In
contrast,
populations
north
of
Cape
Blanco
(
ESU
5)
migrate
in
a
northerly
direction,
travelling
as
far
north
as
British
Columbia
and
Alaska.
The
Cape
Blanco
region
is
a
major
biogeographic
boundary
for
numerous
species.
Fall­
run
populations
predominate
in
this
ESU,
with
the
exception
of
the
Rogue
River
Basin
where
there
is
a
substantial
spring
run.
The
status
of
naturally­
spawning
chinook
salmon
in
San
Francisco
Bay
was
not
determined
by
the
BRT
due
to
a
lack
of
information.
Furthermore,
the
BRT
was
unable
to
document
the
existence
of
extant
naturally­
spawning
chinook
salmon
populations
south
of
San
Francisco
Bay.
Ecologically,
the
majority
of
the
river
systems
in
this
ESU
are
relatively
small
and
heavily
influenced
by
a
maritime
climate.

5)
Upper
Klamath
and
Trinity
Rivers
ESU
This
ESU
includes
fall­
and
spring­
run
chinook
salmon
in
the
Klamath
and
Trinity
River
Basin
upstream
of
the
confluence
of
the
Klamath
and
Trinity
Rivers.
Historically,
spring­
run
chinook
salmon
were
probably
the
predominant
run.
This
ESU
still
retains
several
distinct
springrun
populations,
albeit
at
much
reduced
abundance
levels.
As
with
all
chinook
salmon
populations
south
of
the
Columbia
River,
fish
from
this
ESU
exhibit
an
ocean­
type
life
history;
however,
genetically
and
physically,
these
fish
are
quite
distinct
from
coastal
(
ESU
4
and
6)
and
Central
Valley
chinook
salmon
(
ESU
1,
2,
and
3).
Marine
recoveries
of
CWTs
indicate
that
both
the
fall
and
spring
runs
have
a
coastal
distribution
off
the
California
and
Oregon
coasts.

6)
Oregon
Coast
ESU
This
ESU
contains
coastal
basins
north
of,
and
including,
the
Elk
River,
Oregon,
to
the
mouth
of
the
Columbia
River.
This
ESU
includes
fall,
summer,
and
spring
runs
of
chinook
salmon,
with
fall­
run
fish
predominating
in
this
ESU.
With
the
exception
of
the
Umpqua
River
Basin,
the
majority
of
streams
in
the
ESU
are
relatively
short.
The
marine
distribution,
age
structure,
and
genetic
characteristics
of
fish
from
this
ESU
are
very
different
from
neighboring
ESUs
(
ESU
4
and
9),
although
somewhat
similar
to
that
of
fish
from
the
Washington
Coast
(
ESU
7).
xviii
7)
Washington
Coast
ESU
This
ESU
contains
coastal
basins
north
of
the
mouth
of
the
Columbia
River
to,
but
not
including,
the
Elwha
River.
This
ESU
includes
fall,
summer,
and
spring
runs
of
chinook.
These
fish
exhibit
an
ocean­
type
life
history
(
as
do
all
coastal
stocks
in
Washington,
Oregon,
and
California),
but
their
marine
distribution
and
age
structure
differs
considerably
from
fish
in
the
Puget
Sound
(
ESU
8)
and
Lower
Columbia
River
(
ESU
9)
ESUs.
Fish
in
this
ESU
generally
mature
at
3­,
4­,
and
5­
years­
old
and
migrate
in
a
northerly
direction
to
British
Columbian
and
Alaskan
coastal
waters.

8)
Puget
Sound
ESU
This
ESU
contains
coastal
basins
of
the
eastern
part
of
the
Strait
of
Juan
de
Fuca,
Hood
Canal,
and
Puget
Sound.
This
includes
the
Elwha
River
and
extends
to
the
Nooksack
River
Basin
and
the
U.
S.
Canadian
Border.
Spring­,
summer­,
and
fall­
run
chinook
salmon
are
included
in
this
ESU.
Puget
Sound
chinook
salmon
tend
to
mature
at
ages
3
and
4,
and
are
not
recovered
in
Alaskan
waters
to
the
same
extent
as
fish
from
the
Washington
coast
(
ESU
7).
The
genetic
and
life­
history
characteristics
of
Puget
Sound
chinook
salmon
are
very
distinct
from
the
adjacent
Washington
Coast
ESU
(
ESU
7);
however,
the
Elwha
River
chinook
salmon
were
somewhat
intermediate
between
the
two
ESUs.

9)
Lower
Columbia
River
ESU
This
ESU
contains
tributaries
to
the
Columbia
River
from
the
mouth
of
the
Columbia
River
to,
but
not
including,
the
Klickitat
River.
This
includes
natural
fall­
and
spring­
run
chinook
salmon,
with
the
exception
of
spring­
run
chinook
salmon
in
the
Willamette
River
Basin
above
Willamette
Falls
(
see
ESU
10).
Chinook
salmon
in
this
ESU
were
genetically
distinct
from
their
neighboring
ESUs,
and
exhibited
distinctive
life­
history
traits
(
age
at
maturation)
and
oceanmigration
distribution.

10)
Upper
Willamette
River
ESU
This
ESU
contains
the
Willamette
River
Basin
above
the
Willamette
Falls.
The
ESU
includes
natural
spring­
run
chinook
salmon,
but
excludes
fall­
run
chinook
salmon
that
were
introduced
above
the
Willamette
Falls.
These
fish
exhibit
an
ocean­
type
life
history,
and
are
very
distinct
from
adjacent
ESUs
genetically,
in
their
age
structure,
and
in
marine
distribution.
Furthermore,
the
geography
and
ecology
of
the
Willamette
Valley
is
considerably
different
from
surrounding
areas.
Historically,
migratory
access
above
Willamette
Falls
was
only
possible
during
a
narrow
temporal
window,
which
provided
a
powerful
isolating
mechanism
for
upper
Willamette
River
spring­
run
stocks.
xix
11)
Mid­
Columbia
River
Spring­
Run
ESU
This
ESU
includes
tributaries
to
the
Columbia
River
from
the
Klickitat
River
Basin
upstream
to
include
the
Yakima
River
Basin,
excluding
the
Snake
River
Basin.
This
ESU
includes
natural
spring­
run
chinook
salmon
that
exhibit
a
stream­
type
life
history.
Genetically
and
morphologically,
this
ESU
is
very
distinct
from
ocean­
type
spring­
run
chinook
salmon
which
exist
in
the
Lower
Columbia
River
ESU,
and
fall­
run
(
ocean­
type)
fish
which
cohabit
the
same
rivers
as
fish
belonging
to
this
ESU.
Streams
in
this
region
drain
desert
areas
east
of
the
Cascades
(
Columbia
Basin
Ecoregion)
and
are
ecologically
differentiated
from
the
colder,
less
productive,
glacial
streams
of
the
upper­
Columbia
River
Spring­
Run
ESU
and
from
the
generally
higher
elevation
streams
of
the
Snake
River.

12)
Upper­
Columbia
River
Summer­
and
Fall­
Run
ESU
This
ESU
contains
tributaries
to
the
Columbia
River
upstream
of
the
confluence
of
the
Snake
and
Columbia
Rivers
to
the
Chief
Joseph
Dam.
It
includes
fall­
and
summer­
run
(
oceantype
chinook
salmon,
with
the
exception
of
chinook
salmon
which
spawn
in
the
Marion
Drain,
an
irrigation
collection
canal
to
the
Yakima
River
(
see
Status
Review).
Summer­
run
fish
in
this
ESU
were
heavily
influenced
by
the
Grand
Coulee
Fish
Maintenance
Project
(
1939­
43),
whereby
fish
returning
to
spawn
in
the
upper
Columbia
River
were
trapped
at
the
Rock
Island
Dam,
downstream
of
the
Wenatchee
River.
Some
of
these
fish
were
released
into
enclosed
sections
of
the
Wenatchee
and
Entiat
Rivers
to
spawn
naturally,
while
others
were
spawned
in
hatcheries.
The
result
of
this
project
was
the
mixing
of
multiple
populations
into
one
relatively
homogenous
group.

13)
Upper
Columbia
River
Spring­
Run
ESU
This
ESU
includes
tributaries
to
the
Columbia
River
upstream
from
the
Yakima
River
to
the
Chief
Joseph
Dam.
It
includes
spring­
run
chinook
salmon
in
the
Wenatchee,
Entiat,
and
Methow
River
Basins.
These
fish
all
exhibit
a
stream­
type
life
history.
Although
slight
genetic
differences
exist
between
this
ESU
and
the
other
ESUs
containing
stream­
type
fish
(
see
ESU
11
and
15),
ecological
differences
in
spawning
and
rearing
habitats
between
these
stream­
type
ESUs
were
important
in
establishing
the
ESU
boundaries.
Fish
in
this
ESU
were
also
influenced
by
the
Grand
Coulee
Fish
Maintenance
Project
(
1939­
43).
The
result
of
this
project
was
the
mixing
of
multiple
populations
into
one
relatively
homogenous
group.

14)
Snake
River
Fall­
Run
ESU
This
ESU
contains
tributaries
to
the
Columbia
River
from
the
Dalles
Dam
to
the
confluence
of
the
Snake
and
Columbia
Rivers,
including
the
Snake
River
Basin.
It
includes
all
native
populations
of
fall­
run
chinook
salmon
in
the
mainstem
Snake
River
and
the
following
xx
subbasins:
Deschutes,
John
Day,
Tucannon,
Grand
Ronde,
Imnaha,
Salmon,
and
Clearwater
Rivers.
Previously,
this
ESU
had
only
included
fall­
run
chinook
salmon
from
the
Snake
River
Basin,
but
based
on
new
information
presented
in
this
review
the
ESU
was
expanded
to
include
the
Columbia
River
populations
listed
above.
Fish
from
this
ESU
exhibit
an
ocean­
type
life
history.
Genetic­
and
ocean­
migration
differences
contrast
fish
from
this
ESU
with
those
from
ESU
12.
The
BRT
also
noted
ecological
differences
between
the
Snake
River
Basin
and
the
upper­
Columbia
River
(
above
the
confluence
of
the
Snake
River).

15)
Snake
River
Spring­
and
Summer­
Run
ESU
This
ESU
includes
tributaries
to
the
Snake
River
upstream
of
the
Snake
and
Columbia
Rivers'
confluence.
It
includes
all
natural
populations
of
spring­
and
summer­
run
chinook
salmon
in
the
mainstem
Snake
River
and
the
following
subbasins:
Tucannon
River,
Grand
Ronde
River,
Imnaha
River,
and
Salmon
River.
Although
genetic
differences
between
this
and
other
streamtype
ESUs
(
ESU
11
and
13)
are
moderate,
ecological
differences
in
spawning
and
rearing
habitat
were
substantial
enough
to
warrant
the
establishment
of
distinct
ESUs.
Genetically
and
behaviorally,
these
fish
are
very
different
from
the
ocean­
type
fall­
run
fish
that
exist
in
the
Snake
River
Basin.

Assessment
of
Extinction
Risk
The
ESA
(
section
3)
defines
the
term
"
endangered
species"
as
"
any
species
which
is
in
danger
of
extinction
throughout
all
or
a
significant
portion
of
its
range."
The
term
"
threatened
species"
is
defined
as
"
any
species
which
is
likely
to
become
an
endangered
species
within
the
foreseeable
future
throughout
all
or
a
significant
portion
of
its
range."
According
to
the
ESA,
the
determination
as
to
whether
a
species
is
threatened
or
endangered
should
be
made
on
the
basis
of
the
best
scientific
information
available
regarding
its
current
status,
after
taking
into
consideration
conservation
measures
that
are
proposed
or
are
in
place.

For
the
purposes
of
this
review,
the
BRT
did
not
evaluate
likely
or
possible
effects
of
conservation
measures
and
therefore
did
not
make
recommendations
as
to
whether
identified
ESUs
should
be
listed
as
threatened
or
endangered
species.
The
BRT
did,
however,
draw
scientific
conclusions
about
the
risk
of
extinction
faced
by
ESUs
under
the
assumption
that
present
conditions
will
continue.

With
respect
to
the
11
newly­
identified
ESUs,
the
BRT
concluded
that
two
(
Sacramento
River
Spring
Run
and
Upper
Columbia
River
Spring
Run)
are
at
risk
of
extinction,
primarily
due
to
seriously
depressed
abundance.
Five
ESUs
(
Central
Valley
Fall
Run,
Southern
Oregon
and
California
Coast,
Puget
Sound,
Lower
Columbia
River,
and
Upper
Willamette
River)
are
at
risk
of
becoming
endangered,
due
to
a
variety
of
factors.
Only
four
ESUs
(
Upper
Klamath
and
Trinity
xxi
Rivers,
Oregon
Coast,
Washington
Coast,
and
Middle
Columbia
River
Spring
Run)
are
not
at
risk
of
extinction
or
endangerment.

Chinook
Salmon
ESUs
1)
Sacramento
River
Winter­
Run
ESU
Historically,
the
winter
run
was
abundant
and
comprised
populations
in
the
McCloud,
Pit,
Little
Sacramento,
and
Calaveras
Rivers.
Presently,
the
ESU
has
been
reduced
to
a
single
spawning
population
confined
to
the
mainstem
Sacramento
River
below
Keswick
Dam.
Since
counting
began
in
1967,
the
population
has
been
declining
at
an
average
rate
of
18%
per
year,
or
roughly
50%
per
generation.
This
ESU
is
currently
listed
as
endangered
under
the
California
Endangered
Species
Act
and
was
listed
as
threatened
in
1989
and
reclassified
as
endangered
in
1994
under
the
U.
S.
Endangered
Species
Act.

2)
Central
Valley
Spring­
Run
ESU
Spring­
run
chinook
salmon
were
once
the
predominant
run
in
the
Central
Valley.
Dam
construction
and
habitat
degradation
has
eliminated
spring­
run
populations
from
the
entire
San
Joaquin
River
Basin
and
from
many
tributaries
to
the
Sacramento
River
Basin.
Abundance
has
declined
dramatically
from
historical
levels,
and
much
of
the
present
day
production
is
from
artificial
propagation.
There
are
only
a
few
naturally­
spawning
populations
remaining
and
these
all
have
relatively
low
abundances
(<
1000).
Furthermore,
there
is
concern
that
the
hatchery
propagated
spring­
run
fish
have
been
inadvertently
hybridized
with
fall­
run
fish.
Hatchery
release
practices
result
in
high
levels
of
straying
and
an
increased
potential
for
hatchery
strays
spawning
with
native
fish.
The
majority
of
the
BRT
concluded
that
this
ESU
was
at
risk
of
extinction
in
the
foreseeable
future.

3)
Central
Valley
Fall­
Run
ESU
Total
abundance
in
this
ESU
is
relatively
high,
perhaps
near
historical
levels.
However,
the
status
of
populations
in
the
San
Joaquin
River
Basin
are
extremely
depressed.
Spawning
and
rearing
habitat
quality
throughout
the
ESU
are
severely
impacted
by
agricultural
and
municipal
water
use
activities.
Returns
to
the
hatcheries
account
for
20%
of
the
spawning
escapement,
and
hatchery
strays
spawning
in
the
wild
may
account
for
an
further
30%
of
the
spawning
escapement.
The
exchange
of
stocks
between
Central
Valley
hatcheries
may
have
resulted
in
considerable
loss
of
among­
population
genetic
diversity.
Furthermore,
naturally­
spawning
populations
that
are
least
influenced
by
hatchery
strays
are
experiencing
generally
negative
trends
in
abundance.
Finally,
relatively
high
ocean
and
freshwater
harvest
rates
may
threaten
the
sustainability
of
xxii
naturally
spawning
populations.
The
majority
of
the
BRT
felt
that
this
ESU
is
likely
to
become
at
risk
of
extinction
in
the
foreseeable
future.

4)
Southern
Oregon
and
California
Coastal
ESU
Populations
in
this
ESU
have
generally
experienced
declines
in
abundance
from
historical
levels,
with
the
exception
of
populations
in
the
Rogue
River.
Spring­
run
populations
outside
of
the
Rogue
River
have
undergone
severe
declines.
There
is
an
almost
complete
lack
of
data
for
coastal
rivers
south
of
the
Klamath
River,
and
many
rivers
which
historically
sustained
large
populations
of
fall­
run
chinook
salmon
contain
severely
reduced
populations
or
their
populations
have
been
extirpated.
The
BRT
unanimously
concluded
that
this
ESU
was
likely
to
become
at
risk
of
extinction
in
the
foreseeable
future.

5)
Upper
Klamath
and
Trinity
Rivers
ESU
Fall­
run
populations
in
this
ESU
are
at
relatively
high
abundances,
near
historical
levels,
and
trends
are
generally
stable.
Hatchery
production
contributes
significantly
to
total
escapement.
In
contrast,
spring­
run
abundance
is
at
only
10%
of
historical
levels,
and
much
of
the
present
production
is
hatchery­
derived.
Dam
construction
eliminated
much
of
the
historical
spring­
run
spawning
and
rearing
habitat
and
was
responsible,
in
part,
for
the
extirpation
of
at
least
seven
spring­
run
populations.
Due
to
the
disparity
in
risk
status
between
spring
and
fall
runs,
the
BRT
had
considerable
difficulty
in
evaluating
the
status
of
this
ESU.
The
majority
of
the
BRT
concluded
that
this
ESU,
as
a
whole,
was
not
presently
at
significant
risk
of
extinction,
but
there
was
substantial
concern
for
the
status
of
spring­
run
populations.

6)
Oregon
Coast
ESU
Total
abundance
in
this
ESU
is
relatively
high.
Long­
term
trends
for
populations
are
generally
upward,
although
a
number
of
populations
are
experiencing
severe
short­
term
trends
in
abundance.
Spring­
run
populations
are
generally
in
better
condition
in
this
ESU
than
in
other
coastal
ESUs.
Hatchery
production
appears
to
be
a
relatively
minor
component
of
total
escapement.
The
BRT
unanimously
concluded
that
chinook
salmon
in
this
ESU
are
not
in
danger
of
extinction
nor
are
they
likely
to
become
so
in
the
foreseeable
future.

7)
Washington
Coast
ESU
Long­
term
trends
for
most
populations
in
this
ESU
have
been
upward;
however,
several
smaller
populations
are
experiencing
sharply
downward
trends.
Fall­
run
populations
are
predominant
and
tended
to
be
at
a
lower
risk
than
spring
or
summer
runs.
Hatchery
production
is
significant
in
the
southern
portion
of
this
ESU,
whereas
the
majority
of
the
populations
in
the
xxiii
northern
portion
of
the
ESU
have
minimal
hatchery
influence.
The
BRT
unanimously
concluded
that
chinook
salmon
in
this
ESU
are
not
in
danger
of
extinction
nor
are
they
likely
to
become
so
in
the
foreseeable
future.

8)
Puget
Sound
ESU
Total
abundance
in
the
ESU
is
relatively
high;
however,
much
of
this
production
is
hatchery­
derived.
Both
long­
and
short­
term
trends
in
abundance
are
predominantly
downward,
and
several
populations
are
exhibiting
severe
short­
term
declines.
Spring­
run
chinook
salmon
populations
throughout
this
ESU
are
all
depressed.
The
BRT
was
concerned
that
the
high
level
of
hatchery
production
is
masking
more
severe
underlying
trends
in
abundance.
In
many
areas,
spawning
and
rearing
habitats
were
severely
degraded
and
migratory
access
restricted
or
eliminated.
A
majority
of
the
BRT
concluded
that
this
ESU
is
likely
to
become
endangered
in
the
foreseeable
future.

9)
Lower
Columbia
River
ESU
Abundance
in
this
ESU
is
relatively
high;
however,
the
majority
of
the
fish
appear
to
be
hatchery­
produced.
The
chinook
salmon
fall
run
in
the
Lewis
River
appears
to
be
the
only
healthy
naturally­
produced
population
in
this
ESU.
Long­
and
short­
term
trends
in
abundance
are
mostly
negative,
some
severely
so.
The
numbers
of
naturally­
spawning
spring
runs
are
very
low,
in
fact,
the
BRT
was
unable
to
identify
any
healthy
native
spring­
run
populations.
The
pervasive
influence
of
hatchery
fish
in
almost
every
river
in
this
ESU
and
the
degradation
of
freshwater
habitat
suggested
that
many
naturally­
spawning
populations
are
not
able
to
replace
themselves.
The
majority
of
the
BRT
concluded
that
this
ESU
is
likely
to
become
endangered
in
the
foreseeable
future.

10)
Upper
Willamette
River
ESU
Total
abundance
in
this
ESU
is
relatively
high
(
20,000­
30,000
adults)
and
stable;
however,
approximately
10%
of
escapement
spawns
naturally,
and
of
the
natural
spawners
more
than
half
are
first­
generation
hatchery
strays.
The
introduction
of
non­
native
fall­
run
chinook
salmon
above
Willamette
Falls
is
viewed
as
a
potential
risk
to
the
genetic
integrity
of
this
ESU.
Furthermore,
exchanges
of
fish
between
hatcheries
in
this
ESU
has
most
likely
lead
to
the
homogenization
of
populations
within
the
ESU,
although
this
ESU
is
still
quite
distinct
from
adjacent
ESUs.
The
majority
of
the
historical
spawning
habitat
is
now
inaccessible,
and
the
remaining
habitat
is
quite
limited
and
degraded.
The
majority
of
the
BRT
concluded
that
this
ESU
is
likely
to
become
endangered
in
the
foreseeable
future.
xxiv
11)
Mid­
Columbia
River
Spring­
Run
ESU
Total
abundance
in
the
ESU
has
declined
considerably
from
historical
levels,
but
appears
to
be
relatively
stable
during
recent
years.
Natural
production
accounts
for
most
of
the
escapement
in
the
Yakima
and
Deschutes
River
Basins.
Habitat
degradation,
especially
due
to
agricultural
practices,
affects
most
of
the
rivers
in
this
ESU.
The
majority
of
the
BRT
concluded
that
chinook
salmon
in
this
ESU
are
not
in
danger
of
extinction
nor
are
they
likely
to
become
so
in
the
foreseeable
future.

12)
Upper­
Columbia
River
Summer­
and
Fall­
Run
ESU
Total
abundance
in
this
ESU
is
quite
high,
although
naturally
spawning
chinook
salmon
in
the
Hanford
Reach
are
responsible
for
the
vast
majority
of
the
production.
The
BRT
was
concerned
about
the
recent
decline
in
summer­
run
populations
in
this
ESU,
and
the
apparent
increase
in
the
contribution
of
hatchery
return
to
total
escapement.
It
was
unclear
if,
under
current
conditions,
the
naturally
spawning
summer­
run
chinook
salmon
populations
are
selfsustaining
In
an
earlier
review,
this
ESU
was
determined
to
be
neither
at
risk
of
extinction
nor
likely
to
become
so,
and
its
status
was
not
reviewed
in
detail
here.

13)
Upper
Columbia
River
Spring­
Run
ESU
Recent
total
abundance
in
this
ESU
is
quite
low,
and
escapements
from
1994­
96
were
the
lowest
in
60
years.
At
least
6
populations
of
spring­
run
chinook
salmon
in
the
ESU
have
been
extirpated,
and
almost
all
remaining
naturally­
spawning
populations
have
fewer
than
100
spawners.
Hydrosystem
development
has
blocked
access
to
much
historical
habitat
and
directly
impeded
adult
and
smolt
migrations.
The
majority
of
the
BRT
concluded
that
this
ESU
is
currently
at
risk
of
extinction.

14)
Snake
River
Fall­
Run
ESU
Historically
the
Snake
River
component
of
this
ESU
was
the
predominant
source
of
production.
Currently
the
five­
year
average
for
Snake
River
fall­
run
chinook
salmon
is
about
500
adults
(
compared
with
72,000
in
the
1930s
and
1940s).
The
abundance
of
naturally­
spawning
fish
in
the
Deschutes
River
has
averaged
about
6,000
fish
(
1990­
96).
There
is
some
uncertainty
as
to
the
origins
of
fish
spawning
in
the
lower
Deschutes
River,
and
their
relationship
to
fish
in
the
upper
Deschutes
River
(
above
Sherars
Falls).
Extirpated
populations
in
the
John
Day,
Umatilla,
and
Walla
Walla
Rivers
are
believed
to
have
belonged
to
this
ESU.
Hydrosystem
development
blocks
access
to
most
of
the
historical
spawning
habitat
in
the
Snake
River
portion
of
this
ESU,
as
well
as
affecting
migration
corridors.
Snake
River
fall­
run
chinook
salmon
are
currently
listed
as
a
threatened
species
under
the
U.
S.
ESA.
The
BRT
concluded
that
the
newly
defined
ESU
xxv
(
which
includes
the
Deschutes
River
population)
is
likely
to
become
in
danger
of
extinction
in
the
foreseeable
future.

15)
Snake
River
Spring­
and
Summer­
Run
ESU
Recent
abundance
of
the
naturally­
spawning
population
for
this
ESU
has
averaged
about
2,500
fish,
compared
to
historical
levels
of
approximately
1.5
million.
Both
long­
and
short­
term
trends
are
negative
for
all
populations.
A
number
of
populations
have
been
extirpated
in
this
ESU,
primarily
due
to
dam
construction.
This
ESU
is
presently
listed
as
a
threatened
species
under
the
U.
S.
ESA
and
was
not
reviewed
further
in
this
document.
xxvi
xxvii
ACKNOWLEDGMENTS
The
status
review
for
west
coast
chinook
salmon
was
conducted
by
a
team
of
scientists
from
the
National
Marine
Fisheries
Service
(
NMFS)
and
the
U.
S.
Geological
Survey
(
USGS).
The
members
of
the
biological
review
team
(
BRT)
contributed
a
substantial
amount
of
time
and
effort
to
this
process.
The
BRT
included:
Peggy
Busby,
Dr.
Stewart
Grant,
Dr.
Robert
Iwamoto,
Dr.
Robert
Kope,
Dr.
Conrad
Mahnken,
Gene
Matthews,
Dr.
James
Myers,
Philip
Roni,
Dr.
Michael
Schiewe,
David
Teel,
Dr.
Thomas
Wainwright,
F.
William
Waknitz,
Dr.
Robin
Waples,
and
Dr.
John
Williams
of
NMFS
Northwest
Fisheries
Science
Center;
Gregory
Bryant
and
Craig
Wingert
of
NMFS
Southwest
Region;
Dr.
Peter
Adams
and
Dr.
Steve
Lindley
from
NMFS
Southwest
F.
S.
C.
(
Tiburon
Laboratory);
Alex
Wertheimer
of
NMFS
Alaska
Fisheries
Science
Center
(
Auke
Bay
Laboratory);
and
Dr.
Reg
Reisenbichler
from
the
USGS
Biological
Resource
Division.
Their
review
was
dependent
on
information
submitted
directly
to
NMFS,
which
was
presented
at
one
of
the
Biological
and
Technical
Committee
meetings,
provided
in
response
to
queries
by
NMFS
or
previously
published
in
reports
or
the
scientific
literature.
A
number
of
state,
federal,
and
tribal
agencies
actively
provided
information
and
critical
review
during
the
status
review
process.
The
authors
wish
to
acknowledge
in
particular
the
efforts
of
Lisa
Seeb
and
Penny
Crane
of
the
Alaska
Department
of
Fish
and
Game;
Alan
Baracco,
Colleen
Harvey,
Bill
Loudermilk,
Debra
McKee,
Mike
Wallace,
Dave
McLeod,
Larry
Preston,
and
Wade
Sinnen
from
the
California
Department
of
Fish
and
Game;
Kathryn
Kostow
and
Jay
Nicholas
of
the
Oregon
Department
of
Fish
and
Wildlife;
Susan
Bishop,
formerly
of
the
Northwest
Indian
Fisheries
Commission;
Duane
Anderson
and
Gary
Christofferson
of
StreamNet;
Jim
Craig
and
Doug
Olsen
from
U.
S.
Fish
and
Wildlife
Service;
Jerry
Boberg
and
Al
Olsen
of
the
U.
S.
Forest
Service;
and
Anne
Marshall,
Carol
Smith,
Bill
Tweit,
and
Bob
Woodard
of
the
Washington
Department
of
Fish
and
Wildlife.

The
authors
also
wish
to
thank
the
external
reviewers,
Dr.
T.
Bjornn,
Dr.
R.
Hankin,
Dr.
E.
Taylor,
and
Dr.
F.
Utter,
who
provided
considerable
insight
and
clarity
to
the
complex
issues
concerning
chinook
salmon.
Additional
thanks
to
Judith
Larsen,
Tod
McCoy,
Sue
Joerger,
Kathleen
Jewett,
and
JoAnne
Butzerin
for
their
editorial
and
technical
writing
skills.
xxviii
1
The
use
of
the
term
"
spring­
run"
to
describe
the
chinook
salmon
returning
to
the
Dungeness
River
has
been
discontinued
by
state,
tribal,
and
federal
agencies.
It
has
been
replaced
with
the
term
"
native,"
but
in
this
report
the
term
"
spring­
run"
has
been
retained
for
the
purpose
of
maintaining
consistency
with
older
references
to
the
stock.
INTRODUCTION
On
14
March
1994,
the
National
Marine
Fisheries
Service
(
NMFS)
was
petitioned
by
the
Professional
Resources
Organization­
Salmon
(
PRO­
Salmon)
to
list
spring­
run
populations
of
chinook
salmon
(
Oncorhynchus
tshawytscha)
in
the
North
Fork
and
South
Fork
Nooksack
River,
the
Dungeness
River1,
and
the
White
River
(
Fig.
1)
as
threatened
or
endangered
species
under
the
Endangered
Species
Act
(
ESA)
either
singly,
or
in
some
combination
(
PRO­
Salmon
1994).
At
about
the
same
time,
NMFS
also
received
petitions
to
list
additional
populations
of
other
Pacific
salmon
species
in
the
Puget
Sound
area.
In
response
to
these
petitions
and
the
more
general
concerns
for
the
status
of
Pacific
salmon
throughout
the
region,
NMFS
announced
on
12
September
1994
that
it
would
initiate
ESA
status
reviews
for
all
species
of
anadromous
salmonids
in
Washington,
Oregon,
California,
and
Idaho
(
NMFS
1994d).
This
proactive
approach
was
intended
to
facilitate
more
timely,
consistent,
and
comprehensive
evaluations
of
the
ESA
status
of
Pacific
salmonids
than
would
be
possible
through
a
long
series
of
reviews
of
individual
populations.
Subsequent
to
this
announcement,
NMFS
was
petitioned
on
1
February
1995
by
the
Oregon
Natural
Resources
Council
(
ONRC)
and
Siskiyou
Project
Staff
Ecologist
Dr.
Richard
K.
Nawa
to
list
197
stocks
of
chinook
salmon
either
separately
or
in
some
combination.

This
document
reports
results
of
the
comprehensive
ESA
status
review
of
chinook
salmon
from
Washington,
Oregon,
California,
and
Idaho.
To
provide
a
context
for
evaluating
these
populations
of
chinook
salmon,
biological
and
ecological
information
for
chinook
salmon
in
British
Columbia,
Alaska,
and
Asia
were
also
considered.
This
review
thus
encompasses,
but
is
not
restricted
to,
the
populations
identified
in
the
PRO­
Salmon
and
ONRC­
Nawa
petitions.

Because
the
ESA
stipulates
that
listing
determinations
should
be
made
on
the
basis
of
the
best
scientific
information
available,
NMFS
formed
a
team
of
scientists
with
diverse
backgrounds
in
salmon
biology
to
conduct
this
review.
This
Biological
Review
Team
(
BRT)
for
chinook
salmon
included:
Peggy
Busby,
Dr.
Stewart
Grant,
Dr.
Robert
Iwamoto,
Dr.
Robert
Kope,
Dr.
Conrad
Mahnken,
Gene
Matthews,
Dr.
James
Myers,
Philip
Roni,
Dr.
Michael
Schiewe,
David
Teel,
Dr.
Thomas
Wainwright,
F.
William
Waknitz,
Dr.
Robin
Waples,
and
Dr.
John
Williams
of
NMFS
Northwest
Fisheries
Science
Center;
Gregory
Bryant
and
Craig
Wingert
of
NMFS
Southwest
Region;
Dr.
Steve
Lindley
and
Dr.
Peter
Adams
from
NMFS
Southwest
Region
(
Tiburon
Laboratory);
Alex
Wertheimer
of
NMFS
Alaska
Fisheries
Science
Center
(
Auke
Bay
Laboratory);
and
Dr.
Reg
Reisenbichler
from
the
USGS
Biological
Resource
Division.
NMFS
received
scientific
and
technical
information
from
Pacific
Salmon
Biological
and
Technical
Committees
(
PSBTCs)
convened
in
Washington,
Oregon,
and
California.
Meetings
of
the
PSBTC
were
not
held
in
Idaho
because
all
chinook
salmon
populations
in
Idaho
2
Figure
1.
Map
showing
major
rivers
and
other
key
geographic
features
discussed.
3
are
already
listed
under
the
ESA.
The
BRT
discussed
and
evaluated
scientific
information
gathered
at
the
PSBTC
meetings,
and
also
reviewed
information
submitted
to
the
ESA
administrative
record
for
chinook
salmon,
including
specific
comments
by
co­
managing
agencies
on
a
draft
version
of
this
document
(
CDFG
1997b,
HVTC
1997,
IDFG
1997,
LIBC
1997,
NWIFC
1997a,
ODFW
1997a,
and
WDFW
1997a,
YTFP
1997a).

In
determining
whether
a
listing
under
the
ESA
is
warranted,
two
key
questions
must
be
addressed:

1)
Is
the
entity
in
question
a
"
species"
as
defined
by
the
ESA?
2)
If
so,
is
the
"
species"
threatened
or
endangered?

These
two
questions
are
addressed
in
separate
sections
of
this
report.
If
it
is
determined
that
a
listing(
s)
is
warranted,
then
NMFS
is
required
by
law
(
1973
ESA
Sec.
4(
a)(
1))
to
identify
one
or
more
of
the
following
factors
responsible
for
the
species'
threatened
or
endangered
status:
1)
destruction
or
modification
of
habitat,
2)
overutilization
by
humans,
3)
disease
or
predation,
4)
inadequacy
of
existing
regulatory
mechanisms,
or
5)
other
natural
or
human
factors.
This
status
review
does
not
formally
address
factors
for
decline;
except
insofar
as
they
provide
information
about
the
degree
of
risk
faced
by
the
species
in
the
future
if
current
conditions
continue.
A
separate
document
identifies
factors
for
decline
of
chinook
salmon
from
Washington,
Oregon,
California,
and
Idaho,
and
is
presented
subsequent
to
any
proposed
listing
recommendation.

The
"
Species"
Question
As
amended
in
1978,
the
ESA
allows
listing
of
"
distinct
population
segments"
of
vertebrates
as
well
as
named
species
and
subspecies.
However,
the
ESA
provides
no
specific
guidance
for
determining
what
constitutes
a
distinct
population,
and
the
resulting
ambiguity
has
led
to
the
use
of
a
variety
of
criteria
in
listing
decisions
over
the
past
decade.
To
clarify
the
issue
for
Pacific
salmon,
NMFS
published
a
policy
document
describing
how
the
agency
will
apply
the
definition
of
"
species"
in
the
ESA
to
anadromous
salmonid
species,
including
sea­
run
cutthroat
trout
and
steelhead
(
NMFS
1991).
A
more
detailed
discussion
of
this
topic
appeared
in
the
NMFS
"
Definition
of
Species"
paper
(
Waples
1991b).
The
NMFS
policy
stipulates
that
a
salmon
population
(
or
group
of
populations)
will
be
considered
"
distinct"
for
purposes
of
the
ESA
if
it
represents
an
evolutionarily
significant
unit
(
ESU)
of
the
biological
species.
An
ESU
is
defined
as
a
population
that
1)
is
substantially
reproductively
isolated
from
conspecific
populations
and
2)
represents
an
important
component
of
the
evolutionary
legacy
of
the
species.

The
term
"
evolutionary
legacy"
is
used
in
the
sense
of
"
inheritance,"
that
is,
something
received
from
the
past
and
carried
forward
into
the
future.
Specifically,
the
evolutionary
legacy
of
a
species
is
the
genetic
variability
that
is
a
product
of
past
evolutionary
events
and
that
represents
4
the
reservoir
upon
which
future
evolutionary
potential
depends.
Conservation
of
these
genetic
resources
should
help
to
ensure
that
the
dynamic
process
of
evolution
will
not
be
unduly
constrained
in
the
future.

The
NMFS
policy
identifies
a
number
of
types
of
evidence
that
should
be
considered
in
the
species
determination.
For
each
of
the
criteria,
the
NMFS
policy
advocates
a
holistic
approach
that
considers
all
types
of
available
information
as
well
as
their
strengths
and
limitations.
Isolation
does
not
have
to
be
absolute,
but
it
must
be
strong
enough
to
permit
evolutionarily
important
differences
to
accrue
in
different
population
units.
Important
types
of
information
to
consider
include
natural
rates
of
straying
and
recolonization,
evaluations
of
the
efficacy
of
natural
barriers,
and
measurements
of
genetic
differences
between
populations.
Data
from
protein
electrophoresis
or
deoxyribonucleic
acid
(
DNA)
analyses
can
be
particularly
useful
for
this
criterion
because
they
reflect
levels
of
gene
flow
that
have
occurred
over
evolutionary
time
scales.

The
key
question
with
respect
to
the
second
ESU
criterion
is,
if
the
population
became
extinct,
would
this
represent
a
significant
loss
to
the
ecological/
genetic
diversity
of
the
species?
Again,
a
variety
of
types
of
information
should
be
considered.
Phenotypic
and
life­
history
traits
such
as
size,
fecundity,
migration
patterns,
and
age
and
time
of
spawning
may
reflect
local
adaptations
of
evolutionary
importance,
but
interpretation
of
these
traits
is
complicated
by
their
sensitivity
to
environmental
conditions.
Data
from
protein
electrophoresis
or
DNA
analyses
provide
valuable
insight
into
the
process
of
genetic
differentiation
among
populations
but
little
direct
information
regarding
the
extent
of
adaptive
genetic
differences.
Habitat
differences
suggest
the
possibility
for
local
adaptations
but
do
not
prove
that
such
adaptations
exist.

Background
of
Chinook
Salmon
under
the
ESA
On
7
November
1985,
NMFS
received
a
petition
from
the
American
Fisheries
Society
(
AFS)
to
list
the
winter­
run
chinook
salmon
in
the
Sacramento
River
as
a
threatened
species
under
the
federal
ESA.
NMFS
initially
announced
its
decision
not
to
list
this
population
as
threatened
or
endangered
on
27
February
1987
(
NMFS
1987).
Subsequently,
the
winter­
run
chinook
salmon
population
experienced
a
further
decline,
and
an
emergency
listing
to
list
the
population
as
threatened
was
made
on
4
August
1989
(
NMFS
1989);
the
listing
was
extended
on
2
April
1990
(
NMFS
1990a).
A
final
rule
to
list
the
Sacramento
River
winter­
run
chinook
salmon
as
threatened
was
made
on
5
November
1990
(
NMFS
1990b).
The
winter
run
continued
to
decline
and
was
subsequently
listed
as
endangered
4
January
1994
(
NMFS
1994b).

On
7
June
1990,
NMFS
received
a
petition
from
Oregon
Trout
and
five
co­
petitioners
to
list
Snake
River
spring­
run
chinook
salmon,
Snake
River
summer­
run
chinook
salmon,
and
Snake
River
fall­
run
chinook
salmon
under
the
ESA.
A
final
rule
was
announced
on
22
April
1992
(
NMFS
1992),
which
determined
that
Snake
River
chinook
salmon
should
be
listed
as
threatened
under
the
ESA.
Furthermore,
it
was
determined
that
the
spring­
and
summer­
run
5
2
Mid­
Columbia
was
used
by
the
petitioners
to
refer
to
the
Columbia
River
Basin
between
Priest
Rapids
and
Chief
Joseph
Dams.
populations
collectively
constituted
a
separate
ESU
from
the
fall­
run
chinook
salmon
under
the
ESA.
As
a
result
of
record
low
adult
returns
in
1994
and
projected
returns
for
1995,
an
emergency
interim
rule
was
announced
18
August
1994
to
reclassify
the
Snake
River
spring/
summer
run
and
Snake
River
fall
run
as
endangered
(
NMFS
1994c);
however,
both
Snake
River
chinook
salmon
ESUs
were
subsequently
classified
(
17
April
1995)
in
a
final
ruling
as
being
threatened
(
NMFS
1995a).

A
petition
for
the
listing
of
summer­
run
chinook
salmon
in
the
mid­
Columbia
River2
was
submitted
to
NMFS
on
3
June
1993,
by
the
American
Rivers
and
ten
co­
petitioners.
On
23
September
1994,
NMFS
determined
that
the
mid­
Columbia
River
summer­
run
chinook
salmon
stocks
petitioned
did
not
constitute
an
ESU,
but
belonged
to
a
larger
fall­
and
summer­
run
chinook
salmon
ESU
located
along
the
mainstem
Columbia
River
between
the
Chief
Joseph
and
McNary
Dams
(
NMFS
1994a).
NMFS
concluded
that
this
ESU
did
not
warrant
a
listing
of
endangered
or
threatened.

Summary
of
Information
Presented
by
the
Petitioners
This
section
briefly
summarizes
information
presented
by
the
petitioners
(
Professional
Resources
Organization
(
PRO)­
Salmon
1994,
Oregon
National
Resources
Council
(
ONRC)
and
Nawa
1995)
to
support
their
arguments
that
specific
chinook
salmon
stocks
in
Washington,
Oregon,
Idaho,
and
California
qualify
as
threatened
or
endangered
species
under
the
ESA.
Previous
ESA
petitions
for
chinook
salmon
under
the
ESA
have
been
evaluated
and
summarized
in
elsewhere
(
NMFS
1987,
Matthews
and
Waples
1991,
Waples
et
al.
1991b,
Waknitz
et
al.
1995).

Distinct
Population
Segments
The
PRO­
Salmon
(
1994)
petition
requested
that
NMFS
evaluate
four
stocks
of
chinook
salmon
in
Washington
state
for
listing
as
threatened
or
endangered
under
the
ESA:
the
North
Fork
Nooksack
River
spring
run,
South
Fork
Nooksack
River
spring
run,
Dungeness
River
spring
run,
and
White
River
spring
run.
The
petitioners
presented
several
alternative
groupings
of
these
stocks
into
one
or
more
ESUs,
which
might
also
include
stocks
not
specifically
mentioned
in
their
petition.
The
ONRC
and
Nawa
(
1995)
petition
listed
197
"
stocks"
in
Washington,
Oregon,
California,
and
Idaho
to
be
considered
for
listing
as
threatened
or
endangered,
either
separately
or
in
one
or
more
ESUs.
The
authors
specifically
included
non­
native
stocks,
such
as
Clearwater
River
spring­
run
chinook
salmon,
which
contains
components
of
other
spring­
run
stocks
from
the
6
Snake
River
spring­
and
summer­
run
ESU.
They
argued
that
if
an
ESU
that
contains
the
original
components
of
a
mixed
stock
is
identified
and
listed
as
threatened
or
endangered,
then
the
mixed
stock
should
be
included
in
the
ESU.

ONRC
and
Nawa
suggested
several
alternative
scenarios
for
chinook
salmon,
specifically,
to
list:

°
chinook
salmon
and
their
critical
habitat
as
an
ESU
in
Washington,
Oregon,
California,
and
Idaho;
or
°
spring,
summer,
fall,
and
winter
chinook
salmon
and
their
critical
habitat
as
four
distinct
ESUs;
or
°
ESUs
which
comprise
one
or
more
of
the
197
stocks
of
chinook
salmon
(
listed
in
the
petition),
the
four
stocks
previously
petitioned
by
PRO­
Salmon
in
addition
to
stocks
which
belong
to
the
four
existing
chinook
salmon
ESUs
identified
by
NMFS,
and
their
critical
habitat;
or
°
each
of
the
197
stocks
of
chinook
salmon
(
listed
in
the
petition)
and
the
4
stocks
previously
petitioned
by
PRO­
Salmon
as
separate
ESUs,
in
addition
to
the
4
existing
chinook
salmon
ESUs
identified
by
NMFS;
or
°
regional
ESUs:
(
a)
spring­
and
summer­
run
chinook
salmon
in
Washington,
Oregon,
California,
and
Idaho;
(
b)
coastal
fall
chinook
salmon
that
spawn
in
rivers
and
creeks
south
of
Cape
Blanco,
Oregon
(
excluding
Rogue
River
fall
chinook
salmon);
(
c)
Columbia
River
fall
chinook
salmon,
which
spawn
in
tributaries
below
McNary
Dam;
(
d)
Puget
Sound
fall
and
summer/
fall
chinook
salmon
(
including
Sooes
River
fall
chinook
salmon
on
the
Washington
Coast);
and
(
e)
fall
chinook
salmon
from
the
Central
Valley
of
California
(
including
"
wild"
fall
chinook
salmon
that
spawn
in
small
tributaries
to
San
Francisco
Bay)
and
their
critical
habitat.

Population
Abundance
Both
the
PRO­
Salmon
(
1994)
and
ONRC
and
Nawa
(
1995)
petitions
cited
extensive
information
to
document
the
decline
of
specific
chinook
salmon
stocks.
PRO­
Salmon
(
1994)
cited
the
work
of
Nehlsen
et
al.
(
1991),
who
considered
the
four
stocks
of
chinook
salmon
in
the
petition
to
be
at
a
high
or
moderate
risk
of
extinction,
and
WDF
et
al.
(
1993),
who
identified
the
status
of
the
four
stocks
as
"
critical,"
based
on
"
chronically
low"
escapement
or
redd
counts.
The
spring
run
on
the
White
River
had
declined
from
5,432
in
1942
to
a
low
of
66
in
1977,
and
return
numbers
have
averaged
less
than
200
fish
from
1978­
91
(
PRO­
Salmon
1994).
Escapement
estimates
for
the
North
Fork
Nooksack
River
spring
run
are
less
accurate
because
of
unfavorable
7
river
conditions
for
sampling.
Spawner/
redd
surveys
nevertheless
indicate
a
considerable
decrease
in
stock
size.

ONRC
and
Nawa
(
1995)
surveyed
and
categorized
417
stocks
of
chinook
salmon,
of
which
they
considered
67
(
16.1%)
to
be
extinct,
21
(
5.0%)
nearly
extinct,
95
(
22.8%)
declining,
75
(
18.0%)
composite
production
[
in
which
the
hatchery
contribution
exceeds
natural
production],
and
a
further
37
(
8.9%)
of
unknown
status.
Using
information
from
a
number
of
sources,
the
petitioners
presented
overall
and
regional
estimates
of
the
decline
of
chinook
salmon
stocks.
Nehlsen
et
al.
(
1991)
listed
64
stocks
of
chinook
salmon
that
they
determined
to
be
at
a
high
or
moderate
risk
of
extinction
or
of
special
concern.
WDF
et
al.
(
1993)
determined
the
status
of
40
of
the
108
(
37.0%)
chinook
salmon
stocks
in
Washington
State
to
be
"
critical"
or
"
depressed."
The
Wilderness
Society
(
1993)
reported
that
63%
of
spring­
and
summer­
run
chinook
salmon
stocks
in
Washington,
Oregon,
California,
and
Idaho
were
considered
to
be
extinct,
with
a
further
24%
being
endangered
or
threatened.
Similarly,
among
fall
chinook
salmon
stocks,
19%
were
extinct,
and
25%
endangered
or
threatened.

On
a
regional
basis,
the
Central
Valley
of
California
had
the
highest
percentage
of
extinct
stocks
(
40%),
with
only
one
wild
stock
classified
as
not
declining
according
to
ONRC
and
Nawa
(
1995).
Stocks
within
the
coastal
basins
south
of
Cape
Blanco,
Oregon
had
also
experienced
a
similar
decrease
in
abundance,
with
67%
of
the
stocks
classified
as
extinct,
nearly
extinct,
or
declining.
Within
the
Columbia
River
Basin,
chinook
salmon
stocks
below
McNary
Dam
(
River
Kilometer
[
RKm]
470)
have
been
heavily
influenced
by
artificial
propagation,
and
only
six
wild
stocks
were
identified
that
were
not
declining.
According
to
ONRC
and
Nawa,
the
Columbia
River
chinook
salmon
stocks
above
McNary
Dam
have
experienced
the
second
highest
level
of
extinction
(
28%),
with
44%
of
the
stocks
being
classified
as
declining.
In
the
Snake
River,
the
petitioners
identified
13
stocks
(
28%)
as
being
extinct
and
22
stocks
(
47%)
to
be
in
decline.
No
wild
stocks
were
found
that
were
not
declining.
Among
chinook
salmon
stocks
in
Puget
Sound,
50%
of
the
spring­
run
stocks
were
extinct.
Only
coastal
stocks
north
of
Cape
Blanco,
Oregon
were
not
found
to
be
seriously
declining.
ONRC
and
Nawa
(
1995)
presented
individual
stock
historical
abundance
information
for
many
of
the
417
stocks
surveyed.
This
information
further
documented
many
of
the
regional
declines
noted
above.

Causes
of
Decline
for
Chinook
Salmon
The
petitioners
identified
several
factors
which
they
believe
have
either
singly
or
in
combination
resulted
in
the
chinook
salmon
stock
declines
in
abundance
described
above.
Because
the
petitions
cover
such
a
wide
geographic
area,
encompassing
several
terrestrial
and
marine
ecological
regions,
and
because
the
populations
surveyed
have
been
impacted
by
varying
anthropogenic
factors,
only
a
very
generalized
review
of
this
topic
will
be
given.
8
3
The
term
dams
includes
the
physical
presence
of
mainstem
dams,
the
operation
of
the
hydropower
system,
reservoir
storage,
and
water
withdrawal
associated
with
dams.

4
Logging
activities
include
tree­
cutting,
road
building,
and
splash­
damming
(
historically).
PRO­
Salmon
(
1994)
and
ONRC
and
Nawa
(
1995)
both
cited
references
indicating
that
habitat
degradation
is
the
major
cause
for
the
decline
in
the
petitioned
chinook
salmon
stocks.
The
influence
of
dams3
was
most
commonly
implicated
by
ONRC
and
Nawa
(
1995)
as
being
responsible
for
the
decline
or
extinction
of
chinook
salmon
stocks.
Of
the
stock
extinctions
surveyed
in
the
coastwide
region,
76%
were
dam
related.
This
was
most
noticeable
in
the
Central
Valley,
California
where
100%
of
the
extinctions
surveyed
were
dam
related
(
Campbell
and
Moyle
1990).
Furthermore,
48
of
the
spring­
and
summer­
run
stocks
found
to
be
in
decline
were
affected
by
dams.
Two
of
the
four
chinook
salmon
stocks
petitioned
by
PRO­
Salmon
(
1994)
were
impacted
to
some
extent
by
dam
operation,
but
logging4
and
agricultural
land
use/
water
diversion
(
including
diking)
also
figured
as
major
factors
in
all
four
stocks.
The
Nooksack
Technical
Group
(
1987)
indicated
that
sedimentation
from
logging
activities
had
seriously
impacted
the
quality
of
the
spawning
habitats
in
both
the
North
and
South
Forks
of
the
Nooksack
River.
PRO­
Salmon
(
1994)
considered
water
diversion
for
agricultural
use
to
be
a
major
contributor
to
the
decline
of
the
Dungeness
River
spring
run.
Overall,
ONRC
and
Nawa
(
1995)
estimated
that
logging
was
responsible,
in
part,
for
60%
of
the
declines
and
6%
of
the
extinctions
among
the
stocks
surveyed.
Similarly,
agriculture,
water
withdrawal,
mining
and
urbanization
factors
were
implicated
in
58%
of
the
declines
and
9%
of
the
extinctions
among
the
417
stocks
surveyed.
Both
petitioners
also
presented
evidence
that
the
exploitation
rates
on
the
stocks
were
sufficiently
high
to
have
seriously
depleted
stocks
or
been
partially
responsible
for
the
extinction
of
stocks
(
Dosewallips,
Duckabush,
and
Mokelumne
Rivers
spring­
run
chinook
salmon
(
ONRC
and
Nawa
1995)).

The
other
major
concern
of
the
petitioners
was
the
impact
of
introduced
and/
or
artificially
propagated
fish
on
indigenous
stocks.
Potentially
deleterious
impacts
of
artificial
propagation
presented
by
ONRC
and
Nawa
(
1995)
include:
interbreeding
of
fall
and
spring
runs
in
California
due
to
habitat
alterations
(
Campbell
and
Moyle
1990),
interspecies
hybridization
between
chinook
and
coho
salmon
(
Oncorhynchus
kisutch
Walbaum)
(
Bartley
et
al.
1990),
competition
between
hatchery
and
native
stocks,
interbreeding
between
hatchery
and
native
chinook
salmon
stocks,
disease
introductions
by
artificially
propagated
fish,
and
the
unsustainability
of
hatchery
stocks
in
general.
Finally,
ONRC
and
Nawa
(
1995)
suggested
the
"
inadequacy
of
existing
regulatory
mechanisms"
was
a
general
reason
for
the
overall
decline
in
abundance
of
chinook
salmon.
9
INFORMATION
RELATING
TO
THE
SPECIES
QUESTION
In
this
section,
we
summarize
biological
and
environmental
information
and
consider
the
relevancy
of
each
in
determining
the
nature
and
extent
of
West
Coast
chinook
salmon
ESUs.
ESU
boundaries
were
determined
by
the
BRT
on
the
basis
of
the
team's
professional
opinion
of
the
degree
to
which
environmental
and
biological
attributes
exhibited
significant
changes
with
respect
to
the
reproductive
isolation
and
ecological/
genetic
diversity
of
West
Coast
chinook
salmon.

General
Biology
of
Chinook
Salmon
Chinook
salmon,
also
commonly
referred
to
as
king,
spring,
quinnat,
Sacramento,
California,
or
tyee
salmon,
is
the
largest
of
the
Pacific
salmon
(
Netboy
1958).
The
species
distribution
historically
ranged
from
the
Ventura
River
in
California
to
Point
Hope,
Alaska
in
North
America,
and
in
northeastern
Asia
from
Hokkaido,
Japan
to
the
Anadyr
River
in
Russia
(
Healey
1991).
Additionally,
chinook
salmon
have
been
reported
in
the
Mackenzie
River
area
of
northern
Canada
(
McPhail
and
Lindsey
1970).
Of
the
Pacific
salmon,
chinook
salmon
exhibit
arguably
the
most
diverse
and
complex
life
history
strategies
Healey
(
1986)
described
16
age
categories
for
chinook
salmon,
7
total
ages
with
3
possible
freshwater
ages.
This
level
of
complexity
is
roughly
comparable
to
sockeye
salmon
(
O.
nerka),
although
sockeye
salmon
have
a
more
extended
freshwater
residence
period
and
utilize
different
freshwater
habitats
(
Miller
and
Brannon
1982,
Burgner
1991).
Two
generalized
freshwater
life­
history
types
were
initially
described
by
Gilbert
(
1912):
"
stream­
type"
chinook
salmon
reside
in
freshwater
for
a
year
or
more
following
emergence,
whereas
"
ocean­
type"
chinook
salmon
migrate
to
the
ocean
within
their
first
year.
Healey
(
1983,
1991)
has
promoted
the
use
of
broader
definitions
for
"
ocean­
type"
and
"
stream­
type"
to
describe
two
distinct
races
of
chinook
salmon.
This
racial
approach
incorporates
life
history
traits,
geographic
distribution,
and
genetic
differentiation
and
provides
a
valuable
frame
of
reference
for
comparisons
of
chinook
salmon
populations.
For
this
reason,
the
BRT
has
adopted
the
broader
"
racial"
definitions
of
ocean­
and
stream­
type
for
this
review.

The
generalized
life
history
of
Pacific
salmon
involves
incubation,
hatching,
and
emergence
in
freshwater,
migration
to
the
ocean,
and
subsequent
initiation
of
maturation
and
return
to
freshwater
for
completion
of
maturation
and
spawning
(
Fig.
2).
Juvenile
rearing
in
freshwater
can
be
minimal
or
extended.
Additionally,
some
male
chinook
salmon
mature
in
freshwater,
thereby
foregoing
emigration
to
the
ocean.
The
timing
and
duration
of
each
of
these
stages
is
related
to
genetic
and
environmental
determinants
and
their
interactions
to
varying
degrees.
Salmon
exhibit
a
high
degree
of
variability
in
life­
history
traits;
however,
there
is
considerable
debate
as
to
what
degree
this
variability
is
the
result
of
local
adaptation
or
the
general
plasticity
of
the
salmonid
genome
(
Ricker
1972,
Healey
1991,
Taylor
1991).
10
11
Several
types
of
biological
evidence
were
considered
in
evaluating
the
contribution
of
West
Coast
chinook
salmon
to
ecological/
genetic
diversity
of
the
biological
species
under
the
ESA.
Life­
history
traits
examined
for
naturally
spawning
chinook
salmon
populations
included
smolt
size
and
outmigration
timing,
age
and
size
at
spawning,
river­
entry
timing,
spawn
timing,
fecundity,
and
ocean
migration.
These
traits
are
believed
to
have
both
a
genetic
and
environmental
basis,
and
similarities
among
populations
could
indicate
either
a
shared
genetic
heritage
or
similar
responses
to
shared
environmental
conditions.

The
analysis
of
life­
history
trait
information
is
complicated
by
several
factors.
Data
collected
from
different
locations
during
different
years
are
confounded
by
spatial
and
temporal
environmental
variability.
This
variability
creates
considerable
"
noise,"
which
may
be
as
large
as
differences
between
geographically
distant
populations,
and
may
mask
subtle
regional
patterns.
High
interannual
variability
also
complicates
the
comparison
of
results
from
studies
conducted
during
different
time
periods.
For
chinook
salmon,
for
which
a
single
broodyear
may
return
from
the
ocean
over
a
5­
or
6­
year
period,
variations
in
ocean
productivity
due
to
events
such
as
the
1983
El
Niño
(
Johnson
1988b)
may
bias
estimates
of
age
distribution,
age­
size
relationships,
and/
or
age
and
size­
related
fecundity
estimates.
Furthermore,
it
may
be
difficult
to
distinguish
between
fish
from
different
runs
emigrating
from,
or
returning
to,
the
same
river
system.
Direct
comparisons
of
chinook
salmon
life­
history
traits
between
stocks
under
controlled
conditions
are
limited
in
number,
and
the
extent
to
which
inference
can
be
made
to
wild
populations
is
uncertain.

A
third
confounding
complication
is
that
the
expression
of
life­
history
traits
may
be
altered
by
anthropogenic
activities
such
as
land­
use
practices
(
Hartman
et
al.
1984,
Holtby
1987),
harvest
(
Ricker
1981),
or
artificial
propagation
(
Steward
and
Bjornn
1990,
Flagg
et
al.
1995b).
To
help
limit
any
bias
introduced
by
artificial
propagation,
life­
history
trait
comparisons
in
this
status
review
have
focused
on
naturally
spawning
populations.
However,
because
of
the
widespread
practice
of
off­
station
plants
of
hatchery­
reared
fry
and
smolts,
many
studies
of
naturally
spawning
populations
may
have
inadvertently
included
first­
generation
hatchery
fish
or
fish
whose
ancestors
have
been
hatchery
reared.
Life­
history
trait
information
from
hatchery
populations
was
used
only
when
insufficient
information
from
naturally
spawning
populations
was
available,
as
in
the
case
of
ocean
migration
patterns.
As
with
environmental
variability,
the
effects
of
anthropogenic
activities
may
confound
the
expression
of
life­
history
traits
and
are
difficult
to
factor
out.

Because
of
these
potential
sources
of
variability,
we
felt
that
statistical
analyses
of
lifehistory
trait
variability
would
not
be
particularly
informative.
Instead,
data
were
collected
from
as
many
sources
as
possible
from
each
system
to
give
some
indication
of
the
mean
and
range
in
character
traits.
Older
data
sets
were
especially
sought
to
provide
insight
into
chinook
salmon
population
characteristics
prior
to
the
proliferation
of
hatchery
programs,
which
have
produced
fish
with
relatively
high
juvenile
survival
and
growth
rates
and
modified
saltwater
entry
dates.

Ecological
Features
12
Geological
Events
The
geologic
events
of
the
last
20,000
years
have
provided
mechanisms
for
genetic
isolation,
colonization,
and
population
interbreeding.
In
determining
ESU
boundaries
it
is
useful
to
understand
the
factors
that
may
have
shaped
present
day
chinook
salmon
population
distributions.
Much
of
the
present
distribution
of
aquatic
and
terrestrial
species
in
western
North
America
is
a
legacy
of
the
volcanic,
tectonic,
and
glacial
forces
that
have
shaped
this
region.
Events
such
as
headwater
transfer
or
stream
capture
have
altered
the
flow
of
major
rivers
and
the
aquatic
species
that
inhabit
them.
The
Cordilleran
ice
sheet
was
the
last
major
glacial
event
to
affect
the
distribution
of
chinook
salmon.
At
its
height
some
10,000­
15,000
years
ago,
vast
areas
of
Southeast
Alaska,
British
Columbia,
Washington,
and
Idaho
were
covered
with
ice
(
McPhail
and
Lindsey
1970).
This
created
a
discontinuous
distribution
of
chinook
salmon
stocks.
Two
major
ice­
free
refugia
existed:
Beringia,
composed
of
the
Bering
land
bridge
connecting
Eastern
Siberia
and
Western
Alaska;
and
Cascadia,
composed
of
the
lands
south
of
the
mid­
Columbia
River
drainage
(
McPhail
and
Lindsey
1970).
An
additional
ice­
free
refuge
existed
on
the
coast
of
the
Olympic
Peninsula
in
the
area
of
the
Chehalis
River.
The
drop
in
sea
level
during
the
glacial
periods
may
have
created
minor
refugia
along
the
coast
of
Vancouver
Island
or
the
present­
day
Queen
Charlotte
Islands
(
McPhail
and
Lindsey
1986).
As
the
ice
sheet
receded,
the
colonization
of
newly
exposed
freshwater
habitat
began
from
the
two
refugia.

Chinook
salmon
colonization
during
the
postglacial
period
(
approximately
beginning
10,000
years
ago)
occurred
through
a
number
of
possible
pathways.
Straying
adults
could
invade
coastal
river
systems,
as
could
salmon
that
moved
farther
upriver
to
headwaters
exposed
by
the
receding
glaciers.
Ice
dams
and
land
expansion
after
the
retreat
of
glacial
ice
sheets
caused
rivers
to
alter
course
and
change
watersheds.
Watershed
capture
has
resulted
in
the
exchange
of
aquatic
organisms
between
several
major
river
systems.
Parts
of
the
present
day
Fraser
River
drainage
flowed
into
the
Columbia
River
via
the
Okanogan
River
and
Shuswap
Creek
during
the
last
deglaciation
(
McPhail
and
Lindsey
1986).
Species
that
moved
into
the
Upper
Fraser
River
from
the
Columbia
River
also
gained
access
to
southeastern
Alaskan
coastal
rivers.
The
Stikine,
Skeena,
and
Nass
Rivers
at
various
times
drained
east
into
the
Fraser
River
Basin
relative
to
their
current
westerly
flow
to
the
Gulf
of
Alaska
(
McPhail
and
Lindsey
1986).
Similarly,
the
Alsek
River
in
Alaska,
which
also
flows
to
the
Gulf
of
Alaska,
drained
what
is
now
part
of
the
Yukon
River
headwaters
(
Lindsey
and
McPhail
1986).
Presently,
the
headwaters
of
the
Taku,
Stikine,
and
Yukon
Rivers
lie
within
50
miles
of
one
another.
Chinook
salmon
populations
from
Beringia
also
had
access
to
the
Mackenzie
River
in
Canada
during
the
deglaciation,
which
may
explain
recurring
reports
of
chinook
salmon
in
that
river
system
(
McPhail
and
Lindsey
1970).

Ecoregions
13
The
fidelity
with
which
chinook
salmon
return
to
their
natal
stream
implies
a
close
association
between
a
specific
stock
and
its
freshwater
environment.
The
selective
pressures
of
different
freshwater
environments
may
be
responsible
for
differences
in
life­
history
strategies
among
stocks.
Miller
and
Brannon
(
1982)
hypothesized
that
local
temperature
regimes
are
the
major
factor
influencing
life­
history
traits.
If
the
boundaries
of
distinct
freshwater
habitats
coincide
with
differences
in
life
histories
it
would
suggest
a
certain
degree
of
local
adaptation.
Therefore,
identifying
distinct
freshwater,
terrestrial,
and
climatic
regions
may
be
useful
in
identifying
chinook
salmon
ESUs.
The
Environmental
Protection
Agency
(
EPA)
has
established
a
system
of
ecoregion
designations
based
on
soil
content,
topography,
climate,
potential
vegetation,
and
land
use
(
Omernik
1987).
These
ecoregions
are
similar
to
the
physiographic
provinces
determined
by
the
Pacific
Northwest
River
Basins
Commission
(
PNRBC
1969)
for
the
Pacific
Northwest.
Historically,
the
distribution
of
chinook
salmon
in
Washington,
Oregon,
California,
and
Idaho
would
have
included
13
of
the
present
day
EPA
ecoregions
(
Fig.
3).
Similarly,
there
is
a
strong
relationship
between
ecoregions
and
freshwater
fish
assemblages
(
Hughes
et
al.
1987).
We
have
retained
the
ecoregion
names
and
numbers
used
by
Omernik
(
1987)
and
included
physiographic
information
presented
by
PNRBC
(
1969),
present
day
water
use
information
(
USGS
1993),
river
flow
information
(
Hydrosphere
Products,
Inc.
1993),
and
climate
data
from
the
U.
S.
Department
of
Commerce
(
1968)
into
the
appropriate
ecoregion
description
(
Omernik
and
Gallant
1986,
Omernik
1987).
Additional
information
for
British
Columbia
(
Environment
Canada
1977,
1991)
and
Alaska
(
Hydrosphere
Products,
Inc.
1993)
is
included
for
comparative
purposes.
The
following
ecoregions
are
wholly
or
partially
contained
within
the
historical
natural
range
of
chinook
salmon
in
Washington,
Oregon,
California,
and
Idaho.

Coastal
Range
(#
1)

Extending
from
the
Olympic
Peninsula
through
the
Coast
Range
proper
and
down
to
the
Klamath
Mountains
and
the
San
Francisco
Bay
area,
this
region
is
influenced
by
medium
to
high
rainfall
levels
due
to
the
interaction
between
marine
weather
systems
and
the
mountainous
nature
of
the
region.
Topographically,
the
region
averages
about
500
m
in
elevation,
with
mountain
tops
under
1,200
m.
These
mountains
are
generally
rugged
with
steep
canyons.
Between
the
ocean
and
the
mountains
lies
a
narrow
coastal
plain
composed
of
sand,
silt,
and
gravel.
Tributary
streams
are
short
and
have
a
steep
gradient;
therefore,
surface
runoff
is
rapid
and
water
storage
is
relatively
short
term
during
periods
of
no
recharge.
These
rivers
are
especially
prone
to
low
flows
during
times
of
drought.
Regional
rainfall
averages
200­
240
cm
per
year
(
Fig.
4),
with
generally
lower
levels
along
the
southern
Oregon
coast.
Average
annual
river
flows
for
most
rivers
in
this
region
are
among
the
highest
found
on
the
West
Coast
when
adjusted
for
watershed
area
(
Fig.
5).
River
flows
peak
during
winter
rain
storms
common
in
December
and
January
(
Fig.
6).
Snow
melt
adds
to
the
surface
runoff
in
the
spring,
providing
a
second
flow
peak,
and
14
Figure
3.
U.
S.
Environmental
Protection
Agency
ecoregions
for
California,
Idaho,
Oregon,
and
Washington
(
Omernik
and
Gallant
198,
Omernik
1987).
Regions
are
based
on
land
use,
climate,
topography,
potential
natural
vegetation,
and
soils.
Ecoregions
with
number
designations
are
described
in
the
text.
15
Figure
4.
Average
annual
precipitation
(
cm)
for
selected
areas
of
Washington,
Oregon,
California,
and
Idaho
(
U.
S.
Dep.
Commerce
1968).
16
Figure
5.
Average
annual
flow
per
area
(
m
³
seconds(
s)­
1km­
2)
for
selected
river
basins
in
Alaska,
British
Columbia,
Washington,
Oregon,
California,
and
Idaho.
Values
were
calculated
as
the
average
annual
flow
for
each
gauging
station
divided
by
the
reported
gauged
area.
Based
on
USGS
streamflow
data
(
Hydrosphere
Data
Products,
Inc.
1993)
and
Inland
Water
Directorate
streamflow
data
(
Environment
Canada
1991)
(
modified
from
Weitkamp
et
al.
1995).
17
Figure
6.
Timing
of
annual
peak
flow
(
by
month)
for
selected
river
basins
in
Alaska,
British
Columbia,
Washington,
Oregon,
California,
and
Idaho.
If
two
peaks
in
flow
occur,
the
higher
of
the
two
peaks
is
represented.
Based
on
USGS
streamflow
data
(
Hydrosphere
Data
Products,
Inc.
1993)
and
Inland
Water
Directorate
streamflow
data
(
Environment
Canada
1991)
(
modified
from
Weitkamp
et
al.
1995).
18
there
are
long
periods
when
the
river
flows
are
maintained
at
least
50%
of
peak
flow
(
Fig.
7).
During
July
or
August
there
is
usually
no
precipitation;
this
period
may
expand
to
2
or
3
months
every
few
years.
River
flows
are
correspondingly
at
their
lowest
(
Fig.
8)
and
temperatures
at
their
highest
during
August
and
September
(
Fig.
9).
Oregon
coastal
rivers
have
the
largest
relative
difference
in
minimum
and
maximum
flows,
where
minimum
flows
are
2­
5%
of
the
maximum
flows.

The
region
is
heavily
forested
primarily
with
Sitka
spruce,
western
hemlock,
and
western
red
cedar.
Forest
undergrowth
is
composed
of
numerous
types
of
shrubs
and
herbaceous
plants.

Puget
Lowland
(#
2)

Situated
between
the
Coast
Range
and
Cascade
Range
Ecoregion,
this
region
experiences
reduced
rainfalls
(
50­
120
cm)
from
the
rainshadow
effect
of
the
Coast
Mountains.
The
area
is
generally
flat
with
high
hills
(
600
m)
at
the
southern
margin
of
the
ecoregion.
Soils
are
composed
of
alluvial
and
lacustrine
deposits.
These
deposits
are
glacial
in
origin
north
of
Centralia,
Washington.
This
area
tends
to
have
large
groundwater
resources,
with
groundwater
from
the
bordering
mountain
ranges
helping
sustain
river
flows
during
drought
periods.
Peak
river
flow
varies
from
December
to
June
depending
on
the
contribution
of
snowpack
to
surface
runoff
for
each
river
system.
Rivers
tend
to
have
sustained
flows
(
5
to
8
months
of
flows
at
50%
of
the
peak
or
more),
and
low
flows
are
generally
10­
20%
or
more
of
the
peak
flows.

Douglas
fir
represent
the
primary
subclimax
forest
species,
with
other
coniferous
species
(
lodgepole,
western
white,
and
ponderosa
pines)
locally
abundant.
Prairie,
swamp,
and
oak,
birch,
or
alder
woodlands
are
also
common.
The
land
is
heavily
forested,
and
wood­
cutting
activities
(
including
road
building,
etc.)
contribute
to
soil
erosion,
river
siltation,
and
river
flow
and
temperature
alteration.

The
region
is
heavily
urbanized,
and
domestic
and
industrial
wastes
impact
local
water
systems.
Urban
run­
off
and
sewage
treatment
influence
water
quality
west
of
the
Cascade
Mountains,
with
the
exception
of
the
Olympic
Peninsula
coastal
and
northern
Puget
Sound
rivers.
Glacial
sediment
also
influences
water
quality,
especially
in
the
Skagit,
North
Fork
Nooksack,
Nisqually,
and
Puyallup/
White
River
Basins.

Willamette
Valley
(#
3)

Adjoining
the
southern
border
of
the
Puget
Sound
Lowland
Ecoregion
at
the
Lewis
River,
this
region
was
not
glacially
influenced.
A
rainshadow
effect,
similar
to
the
one
influencing
the
Puget
Sound
Lowlands,
limits
rainfall
to
about
120
cm
per
year.
River
flows
peak
in
December
and
January
and
are
sustained
for
6
or
7
months
of
the
year.
Low
flows
occur
in
August
and
September,
although
the
volume
is
generally
20%
of
the
peak
flow.
19
Figu
re
7.
Duration
of
high
flows
(
number
of
months
when
flow
is
equal
to
or
exceeds
50%
of
peak
monthly
flow)
for
selected
river
basins
in
Alaska,
British
Columbia,
Washington,
Oregon,
California,
and
Idaho.
Based
on
USGS
streamflow
data
(
Hydrosphere
Data
Products,
Inc.
1993)
and
Inland
Water
Directorate
streamflow
data
(
Environment
Canada
1991)
(
modified
from
Weitkamp
et
al.
1995).
20
Figure
8.
Timing
of
annual
low
flow
(
by
month)
for
selected
river
basins
in
Alaska,
British
Columbia,
Washington,
Oregon,
California,
and
Idaho.
If
two
peaks
in
flow
occur,
(
Hydrosphere
Data
Products,
Inc.
1993)
and
Inland
Water
Directorate
streamflow
data
(
Environment
Canada
1991)
(
modified
from
Weitkamp
et
al.
1995).
21
Figure
9.
Annual
maximum
monthly
stream
temperatures
(
0C)
for
selected
river
basins
in
Alaska,
British
Columbia,
Washington,
California,
Oregon,
and
Idaho.
Based
on
USGS
streamflow
data
(
Hydrosphere
Data
Products,
Inc.
1993)
and
Inland
Water
Directorate
temperature
data
(
Environment
Canada
1991)
(
modified
from
Weitkamp
et
al.
1995).
22
Much
of
the
land
has
been
converted
to
agricultural
use,
with
Douglas
fir
and
Oregon
white
oak
stands
present
in
less­
developed
areas.
Irrigation
is
commonly
employed,
and
stream
flows,
especially
in
the
southern
portion
of
this
region,
can
be
significantly
affected.
Agricultural
and
livestock
practices
contribute
to
soil
erosion
and
fertilizer/
manure
deposition
into
stream
systems.

Water
quality
is
impacted
by
agricultural
and
urban
activities.
Many
water
quality
problems
are
exacerbated
by
low
water
flows
and
high
temperatures
during
the
summer.
Pulp
and
paper
mill
discharges
of
dioxin
into
the
Columbia
and
Willamette
Rivers
were
cited
as
another
water
quality
concern,
although
this
situation
has
been
much
more
serious
in
the
past
(
USGS
1993).

Cascades
(#
4)

This
region
is
composed
of
the
Cascade
Range
in
Washington
and
Oregon
and
the
Olympic
Mountains
in
Washington
state.
Peaks
above
3,000
m
are
distributed
throughout
the
region.
The
crest
of
the
Cascade
Range
(
averaging
1,500
m)
captures
much
of
the
ocean
moisture
moving
eastward
in
addition
to
providing
a
biological
barrier.
Rainfalls
can
average
280
cm
per
year
(
up
to
380
cm
in
the
Olympic
Mountains),
much
of
which
is
in
the
form
of
heavy
snowpack.
Intensive
rainstorms,
those
depositing
more
than
2.5
cm
per
hour,
are
rare.
Rainfall
is
generally
spread
over
the
year
with
the
majority
occurring
between
October
and
March.
Except
where
porous
rock
substrate
exists,
there
is
little
capacity
for
long­
term
groundwater
storage.
In
these
porous
rock
areas,
streams
receive
75­
95%
of
their
average
discharge
as
groundwater,
and
are
able
to
maintain
their
flows
during
dry
periods.
Surface
water
flow
originating
in
the
Cascades
and
Olympic
Mountains
influences
river
flows
throughout
this
region.

Currently
the
area
is
primarily
forested
with
Douglas
fir,
noble
fir,
and
Pacific
silver
fir
(
all
subclimax
species),
whereas
western
hemlock
and
red
cedar
are
common
climax
species.
At
higher
elevations,
these
trees
are
replaced
by
Englemann
spruce,
whitebark
pine,
and
mountain
hemlock.
Forest
undergrowth
tends
to
be
dense
on
the
western
slopes
of
this
region
and
rather
sparse
on
the
eastern
slopes.
Heavy
rainfall,
combined
with
woodcutting
activities,
has
resulted
in
increased
soil
erosion.

Sierra
Nevada
(#
5)

To
the
south
of
the
Cascades
Ecoregion
lies
a
similar
mountainous
ecoregion,
comprised
of
portions
of
the
Klamath,
Sierra,
Trinity,
and
Siskiyou
Mountains.
Annual
rainfall
varies
considerably,
from
40
cm
to
over
150
cm,
depending
on
elevation
and
the
degree
of
rainshadowing.
Most
of
the
rain
comes
in
the
winter
months,
with
summers
being
hot
and
dry.
Topographically,
the
region
rises
to
over
2,000
m
with
an
average
elevation
of
1,000
m.
This
region
contains
the
headwaters
for
the
Rogue,
Klamath,
and
Sacramento
Rivers.
Peak
flows
23
occur
in
February,
with
low
flows
in
August,
September,
or
October.
As
a
result
of
water
diversion
and
impoundment
activities,
flows
are
now
more
evenly
apportioned
throughout
the
year.
This
has
occurred
primarily
through
irrigation/
flood
mitigation­
related
reductions
in
peak
flows
and
less
so
through
increased
spillage
during
the
historical
time
of
minimum
flows.

Douglas
fir
is
the
predominant
tree
species,
but
mixed
coniferous­
oak
stands
are
common.
Soils
tend
to
be
unstable,
and
timber
harvest
or
livestock
grazing
can
result
in
severe
erosion.
Hydraulic
placer
mining
has
had
a
considerable
impact
on
stream
quality
and
hillslope
stability.

Southern
and
Central
California
Plains
and
Hills
(#
6)

To
the
east
and
in
the
rainshadow
of
the
Coastal
Mountain
range,
the
tablelands
and
hills
of
this
region
have
generally
low
levels
of
annual
rainfall
(
40­
100
cm).
Tributary
rivers
to
the
Sacramento
and
San
Joaquin
Rivers
flow
through
this
region.
Vegetation
is
composed
of
California
oaks
and
manzanita
chaparral
with
extensive
needlegrass
steppe.
Livestock
grazing
in
the
open
woodlands
is
the
predominant
land
use.

Central
California
Valley
(#
7)

The
Sacramento
and
San
Joaquin
Rivers
are
the
key
features
of
the
Central
California
Valley
Ecoregion.
The
broad
flat
lands
that
border
the
river
naturally
support
needlegrass
and
marshgrasses,
although
much
of
the
region
has
been
extensively
converted
to
agricultural
use.
The
annual
rainfall
for
the
region
is
40­
80
cm.
The
Sacramento
and
San
Joaquin
Rivers
peak
in
February
with
a
6­
month
period
of
high
flows
(>
50%
of
peak
flow).
Low
flows
occur
in
September
and
October.
Changes
in
the
hydrology
of
tributaries
and
irrigation
withdrawals
from
the
mainstem
rivers
have
drastically
altered
the
flow
characteristics
of
these
rivers
over
the
course
of
the
last
100
years.
An
estimated
90%
of
the
surface
water
withdrawals
were
used
for
irrigation
in
1990
(
USGS
1990).
The
maintenance
of
livestock
and
cultivation,
irrigation,
and
chemical
treatment
of
crop
land
has
resulted
in
increases
in
fecal
coliform,
dissolved
nitrate,
nitrite,
phosphorus,
and
sulfate
concentration
levels
(
USGS
1993).
Industrial
and
mining
runoff
from
sites,
such
as
the
copper
mines
near
Spring
Creek
in
the
Sacramento
River
Basin,
also
impact
water
quality
in
the
immediate
area.

Eastern
Cascades
Slopes
and
Foothills
(#
9)

This
ecoregion
marks
the
transition
between
the
high
rainfall
areas
of
the
Cascades
Ecoregion
and
the
drier
basin
ecoregions
to
the
east.
The
area
receives
30
cm
to
60
cm
of
rainfall
per
year.
Streamflow
is
intermittent,
especially
during
the
summer
dry
season.
Surface
and
groundwater
contributes
to
flows
in
the
Yakima,
Deschutes,
Klickitat,
and
White
Salmon
Rivers.
24
Ponderosa
and
lodgepole
pine
are
common
throughout
the
region,
with
little
forest
undergrowth.
Soils
tend
to
be
volcanic,
young,
and
highly
erodible.
Primary
land
uses
are
timber
harvest
and
mixed
grazing/
timber
areas.
Agriculture
is
limited
to
valleys
and
irrigation
is
commonly
employed.

Columbia
Basin
(#
10)

This
ecoregion
is
typified
by
irregular
plains,
tablelands,
and
high
hills/
low
mountains.
The
plateau
spans
from
the
Cascade
Mountains
to
the
Blue
Mountains
in
the
south
and
southeast.
Much
of
the
basin
is
covered
with
glacial
and
alluvial
deposits.
The
loose
surface
substrate
is
prone
to
erosion.
There
is
little
rainfall
and
the
majority
of
the
water
discharge
comes
from
the
mountains
that
border
the
basin.
Because
tributaries
to
the
mid­
and
upper
Columbia
River
receive
much
of
their
water
from
snowmelt,
peak
river
flows
are
in
May
and
June,
except
for
the
Deschutes,
John
Day,
and
Umatilla
Rivers,
which
peak
in
April.
Peak
flows
are
not
as
sustained
as
on
the
coast,
generally
lasting
2­
3
months.
Annual
rainfalls
of
20­
60
cm
support
sagebrush
and
wheatlands.
Most
smaller
streams
are
ephemeral,
partially
due
to
irrigation
withdrawals
(
Omernik
and
Gallant
1986).
The
Columbia
Plateau
experiences
a
prolonged
drought
of
1
to
3
months
every
year,
with
longer
events
occurring
frequently.
Low
river
flows
occur
during
the
late
summer
and
early
fall,
August­
October,
when
irrigation
demand
is
heavy.
Nitrates,
sulfites,
and
pesticides
commonly
associated
with
crop
irrigation
are
found
in
most
of
the
rivers
in
the
Columbia
River
Basin.
Heavy
metal
contamination
from
Canadian
mining
operations
has
been
detected
at
several
downstream
sites
on
the
Columbia
River
(
USGS
1993).

Sagebrush
and
wheatgrass
constitute
the
primary
natural
vegetation
for
this
region.
Much
of
the
land
has
been
converted
to
dryland
wheat
agriculture,
with
smaller
irrigated
areas
supporting
the
cultivation
of
peas
and
potatoes.
Irrigation
and
agriculture
have
changed
the
flow
and
course
of
smaller
rivers
and
streams
(
Omernik
and
Gallant
1986).

Blue
Mountains
(#
11)

The
Blue,
Wallowa,
Ochoco,
Strawberry,
and
Aldrich
Mountains
are
contained
in
this
ecoregion.
The
mountains
are
a
mix
of
older
sedimentary
and
younger
volcanic
peaks.
Mountainous
regions
contain
ponderosa
pine,
grand
fir
and
Douglas
fir,
and
Englemann
spruce
stands.
Rainfall
varies
from
25­
50
cm
in
the
lowlands,
and
as
much
as
100
cm
in
the
mountains,
most
of
which
falls
as
snow.
The
aquifers
that
develop
in
these
mountains
feed
into
numerous
river
systems:
the
John
Day,
Umatilla,
and
Walla
Walla
Rivers,
which
flow
into
the
Columbia
River,
and
the
Tucannon,
Grande
Ronde
and
Imnaha
Rivers,
which
flow
into
the
Snake
River.
Peak
flows
occur
from
April
to
June,
but
only
last
2
to
4
months;
however,
flood
events
historically
have
occurred
from
December
through
February
as
rain
on
snow
events
(
WDFW
1997a).
Minimum
flows
occur
predominantly
in
August
or
September,
except
in
the
mountains
where
flows
are
at
a
minimum
in
January
and
February.
25
Lowlands
contain
sagebrush,
wheatgrass,
and
bluegrass.
Land­
use
activities
correspond
to
vegetation,
with
timber
harvest
more
prevalent
in
the
mountains
and
grazing
prevalent
in
the
lowlands.
Both
of
these
activities
have
led
to
considerable
localized
stream­
side
erosion.

Snake
River
Basin/
High
Desert
(#
12)

This
region
spans
southeastern
Oregon,
southern
Idaho,
northeastern
California,
and
northern
Nevada.
Passage
of
chinook
salmon
into
most
of
the
region
has
been
blocked
by
dams,
but
the
region
still
exerts
a
considerable
influence
on
downstream
habitat.
This
area
is
geologically
very
new
and
contains
extensive
areas
of
lava
and
other
volcanic
material.
The
rock
substrate
is
very
permeable,
streams
tend
to
lose
much
of
their
flow
through
percolation
and
evaporation,
and
only
the
larger
rivers
that
lie
below
the
water
table
contain
substantial
flows
year
round.
Rainfalls
are
generally
less
than
30
cm
annually,
but
may
be
as
high
as
60
cm
on
the
borders
of
the
ecoregion.
Extended
dry
intervals
are
very
common
in
the
Snake
River
Plateau.

Sagebrush
and
wheatgrass
are
prevalent
with
much
of
the
area
utilized
as
rangeland.
Agriculture
(
potatoes,
corn,
grains)
is
sustained
where
water
resources
are
available.
Rivers
in
the
southern
half
of
Idaho
are
affected
by
agricultural
and
urban
development.
Irrigation
return
flows,
livestock
grazing,
and
urban
activities
were
associated
with
high
nutrient
concentrations
in
the
Boise
and
Snake
Rivers
(
USGS
1993).

Northern
Rockies
(#
15)

Forming
the
northeast
boundary
of
the
Columbia
Basin
Ecoregion,
this
region
is
a
mosaic
of
mountain
crestlines
(
up
to
2,500
m)
and
valleys.
Rainfall
varies
accordingly
from
50
to
150
cm
or
more
per
year,
some
of
which
falls
in
intense
local
storms.
Winter
snowpack
is
the
major
contributor
to
the
streamflows;
river
flows
peak
with
the
spring
melt
in
May
or
June
lasting
only
2­
3
months.
One­
and
2­
month
drought
periods
are
fairly
common;
however,
longer
periods
are
quite
rare,
especially
in
the
higher
mountains,
where
drought
periods
of
even
1
month
are
rare
(
once
in
5
years).
Low
flows
correspond
with
low
periods
of
precipitation
in
August
and
September
except
in
the
higher
elevations,
where
winter
temperatures
limit
flow.
In
many
areas,
soil
and
subsoil
development
have
created
important
areas
for
water
storage.
Seepage
is
an
important
water
source
for
major
rivers
in
this
area.
The
Salmon
and
Clearwater
Rivers
drain
the
southern
portion
of
this
region
and
are
the
only
major
tributaries
to
which
chinook
salmon
still
have
access.
The
Spokane,
Kootenai,
and
Pend
Oreille
Rivers
drain
into
the
Columbia
River
from
the
eastern
and
northern
portions
of
this
ecoregion;
however,
runs
that
historically
existed
on
these
rivers
have
been
eliminated
by
impassable
dams
(
Fulton
1968).

Forests
are
dominated
by
conifers:
western
white
pine,
lodgepole
pine,
western
red
cedar,
western
hemlock,
western
larch,
Englemann
spruce,
subalpine
fir,
and
Douglas
fir.
Prairie
and
mixed
forest/
grassland
are
also
common.
Forestry
is
the
primary
land­
use
activity,
although
26
mining
and
grazing
activities
are
commonplace.
Water
systems
in
the
northern
half
of
Idaho,
the
Coeur
d'Alene
and
Clearwater
Rivers,
are
impacted
by
mining
and
logging
operations;
however,
containment
ponds
appear
to
limit
metal
concentrations
downstream
(
USGS
1993).

Marine
Habitat
The
marine
habitat
can
be
subdivided
into
three
general
regions
 
estuary,
coastal,
and
ocean.
Chinook
salmon
with
different
life­
history
strategies
use
these
regions
to
different
extents;
therefore,
changes
in
the
conditions
in
one
region
may
selectively
affect
some
populations
more
than
others.

Ocean­
type
chinook
salmon
reside
in
estuaries
for
longer
periods
as
fry
and
fingerlings
than
do
with
yearling,
stream­
type,
chinook
salmon
smolts
(
Reimers
1973,
Kjelson
et
al.
1982,
Healey
1991).
The
diet
of
outmigrating
ocean­
type
chinook
salmon
varies
geographically
and
seasonally,
and
feeding
appears
to
be
opportunistic
(
Healey
1991).
Aquatic
insect
larvae
and
adults,
Daphnia,
amphipods
(
Eogammarus
and
Corophium
spp.),
and
Neomysis
have
been
identified
as
important
food
items
(
Kjelson
et
al.
1982,
Healey
1991).
Rivers
with
well
developed
estuaries
are
able
to
sustain
larger
ocean­
type
populations
than
those
without
(
Levy
and
Northcote
1982).
Juvenile
chinook
salmon
growth
in
estuaries
is
often
superior
to
river­
based
growth
(
Rich
1920a,
Reimers
1971,
Schluchter
and
Lichatowich
1977).
Stream­
type
chinook
salmon
move
quickly
through
the
estuary,
into
coastal
waters,
and
ultimately
to
the
open
ocean
(
Healey
1983,
Healey
1991).
Very
limited
data
are
available
concerning
the
ocean
migration
of
stream­
type
chinook
salmon;
they
apparently
move
quickly
offshore
and
into
the
central
North
Pacific,
where
they
make
up
a
disproportionately
high
percentage
of
the
commercial
catch
relative
to
ocean­
type
fish
(
Healey
1983,
Myers
et
al.
1987).
The
Stikine,
King
Salmon,
and
Chilkat
Rivers
are
notable
exceptions
to
this
general
stream­
type
migration
pattern.
Apparently,
a
portion
of
fish
from
these
stocks
remain
in
the
coastal
waters
of
southeast
Alaska
throughout
their
lives
(
ADFG
1997).
In
contrast,
throughout
their
ocean
residence
ocean­
type
chinook
salmon
inhabit
coastal
waters,
where
coded­
wire
tag
(
CWT)­
marked
fish
are
recovered
in
substantial
numbers
(
Healey
and
Groot
1987).

The
utilization
of
estuaries
by
ocean­
type
chinook
salmon
makes
them
more
susceptible
to
changes
in
the
productivity
of
that
environment
than
stream­
type
chinook
salmon.
Estuaries
may
be
"
overgrazed"
when
large
numbers
of
ocean­
type
juveniles
enter
the
estuary
en
masse
(
Reimers
1973,
Healey
1991).
The
potential
also
exists
for
large­
scale
hatchery
releases
of
fry
and
fingerling
ocean­
type
chinook
salmon
to
overwhelm
the
production
capacity
of
estuaries
(
Lichatowich
and
McIntyre
1987).
The
loss
of
coastal
wetlands
to
urban
or
agricultural
development
may
more
directly
impact
ocean­
type
populations.
Dahl
(
1990)
reported
that
California
has
lost
94%
of
its
wetlands.
Furthermore,
an
estimated
80­
90%
of
the
undiked
tidal
marshlands
in
the
Sacramento
River
Delta
area,
the
major
nursery
area
for
Central
Valley
chinook
salmon
stocks,
has
been
lost
(
Nichols
et
al
1986,
Lewis
1992).
A
similar
reduction
has
been
27
reported
in
Washington
and
Oregon
wetlands:
a
70%
loss
in
the
Puget
Sound,
50%
in
Willapa
Bay,
and
85%
in
Coos
Bay
(
Refalt
1985).

The
ocean
migrations
of
chinook
salmon
extend
well
into
the
North
Pacific
Ocean.
The
productivity
of
various
ocean
regions
has
been
correlated
with
the
degree
of
wind­
driven
upwelling
(
Bakun
1973,
1975).
Under
normal
conditions
this
upwelling
decreases
along
the
coast
from
California
to
Washington
and
British
Columbia
(
Bakun
1973).
Changes
in
wind
directions
related
to
sea
level
pressure
(
SLP)
systems,
most
notably
the
Aleutian
low
pressure
(
ALP)
or
Central
North
Pacific
(
CNP)
pressure
indices,
can
greatly
alter
upwelling
patterns
(
Ware
and
Thompson
1991,
Beamish
and
Bouillon
1993).
Upwelling
brings
cold,
nutrient­
rich
waters
to
the
surface,
resulting
in
an
increase
in
plankton
and
ultimately
salmon
production
(
Beamish
and
Bouillon
1993).
Strong
ALP
measurements
(
high
pressure
readings)
tend
to
result
in
minimal
upwelling
in
the
North
Pacific.
Similarly,
atmospheric
pressure
systems
in
the
Central
Pacific
can
alter
trade
wind
patterns
to
bring
warmer
water
up
along
the
California
coast;
this
occurrence
is
better
known
as
an
El
Niño.
El
Niño
events
suppress
coastal
upwelling
off
the
Washington,
Oregon,
and
California
coasts
and
tend
to
bring
warmer
water
and
warm­
water
species
northward
(
McLain
1984).
One
difference
between
El
Niño
events
and
ALP
events
is
that
the
northerly
flow
of
warm
waters
associated
with
El
Niño
events
may
stimulate
ocean
productivity
off
Alaska
(
McLain
1984).
Ocean
migratory
pattern
differences
between
and
within
ocean­
and
stream­
type
chinook
salmon
stocks
may
be
responsible
for
fluctuations
in
abundance.
Moreover,
the
evolution
of
life­
history
strategies
has,
in
part,
been
a
response
to
long­
term
geographic
and
seasonal
differences
in
marine
productivity
and
estuary
availability.

Chinook
Salmon
Life
History
and
Ecology
Juvenile
Life
History
The
most
significant
process
in
the
juvenile
life
history
of
chinook
salmon
is
smoltification,
the
physiological
and
morphological
transition
from
a
freshwater
to
marine
existence.
The
emigration
from
river
to
ocean
is
thought
to
have
evolved
as
a
consequence
of
differences
in
food
resources
and
survival
probabilities
in
the
two
environments
(
Gross
1987).
Salmon
juvenile
lifehistory
patterns
are
usually
deduced
by
examining
the
developmental
pattern
of
circuli
on
juvenile
and
adult
fish
scales
(
Gilbert
1912,
Rich
1920a,
Koo
and
Isarnkura
1967).
Within
the
ocean­
type
(
subyearling)
and
stream­
type
(
yearling)
migrant
designations,
several
subtypes
have
been
described
(
Gilbert
1912,
Reimers
1973,
Schluchter
and
Lichatowich
1977,
Fraser
et
al.
1982).
Ocean­
type
juveniles
enter
saltwater
during
one
of
three
distinct
phases.
"
Immediate"
fry
migrate
to
the
ocean
soon
after
yolk
resorption
at
30­
45
mm
in
length
(
Lister
et
al.
1971,
Healey
1991).
In
most
river
systems,
however,
fry
migrants,
which
migrate
at
60­
150
days
post­
hatching,
and
fingerling
migrants,
which
migrate
in
the
late
summer
or
autumn
of
their
first
year,
represent
the
majority
of
ocean­
type
emigrants.
When
environmental
conditions
are
not
conducive
to
28
subyearling
emigration,
ocean­
type
chinook
salmon
may
remain
in
freshwater
for
their
entire
first
year.
Stream­
type
chinook
salmon
migrate
during
their
second
or,
more
rarely,
their
third
spring.
Under
natural
conditions
stream­
type
chinook
salmon
appear
to
be
unable
to
smolt
as
subyearlings.
The
underlying
biological
bases
for
differences
in
juvenile
life
history
appear
to
be
both
environmental
and
genetic
(
Randall
et
al.
1987).
Distance
of
migration
to
the
marine
environment,
stream
stability,
stream
flow
and
temperature
regimes,
stream
and
estuary
productivity,
and
general
weather
regimes
have
been
implicated
in
the
evolution
and
expression
of
specific
emigration
timing.

The
success
of
different
juvenile
life­
history
strategies
is
linked
to
the
coordinated
expression
of
other
traits.
Gilbert
(
1912)
noted
that
ocean­
type
fish
exhibited
a
faster
growth
rate
relative
to
stream­
type
fish.
The
growth
difference
between
ocean­
and
stream­
type
juveniles
has
also
been
observed
by
other
researchers
(
Carl
and
Healey
1984,
Cheng
et
al.
1987,
Taylor
1990a).
Some
of
this
difference
may
be
related
to
differences
in
rearing
environment,
although
under
standardized
conditions
there
was
still
a
significant
growth
difference
between
ocean­
and
streamtype
juveniles
(
Taylor
1990b).
Clarke
et
al.
(
1992)
demonstrated
that
the
growth
of
stream­
type
juveniles
was
strongly
associated
with
photoperiod,
while
ocean­
type
juvenile
growth
appeared
to
be
independent
of
photoperiod.
Juvenile
life
history
appears
to
be
a
heritable
trait.
Hybridization
experiments
indicated
that
the
stream­
type
smoltification
and
growth
pattern
are
recessive
relative
to
the
ocean­
type
pattern
(
Clarke
et
al.
1992).
Juvenile
stream­
type
chinook
salmon
have
also
been
shown
to
be
more
aggressive
than
ocean
types.
This
may
be
a
territorial
defense
mechanism
for
resource
limited
freshwater
systems
(
Taylor
and
Larkin
1986,
Taylor
1988,
Taylor
1990b).
Morphometric
differences,
such
as
larger
and
more
colorful
fins,
observed
in
some
stream­
type
populations
may
be
related
to
social
displays
that
maintain
territories
(
Carl
and
Healey
1984,
Taylor
and
Larkin
1986).
Thus,
the
timing
of
parr­
smolt
transition
appears
to
be
associated
with
the
expression
of
a
number
of
other
traits
in
order
to
maximize
individual
survival.

Juvenile
stream­
and
ocean­
type
chinook
salmon
have
adapted
to
different
ecological
niches.
Ocean­
type
chinook
salmon
tend
to
utilize
estuaries
and
coastal
areas
more
extensively
for
juvenile
rearing.
In
general,
the
younger
(
smaller)
juveniles
are
at
the
time
of
emigrating
to
the
estuary,
the
longer
they
reside
there
(
Kjelson
et
al.
1982,
Levy
and
Northcote
1982,
Healey
1991).
There
is
also
an
apparent
positive
relationship
between
rivers
with
large
estuary
systems
and
the
number
of
fry
migrants
(
Fraser
et
al.
1982).
Brackish
water
areas
in
estuaries
also
moderate
physiological
stress
during
parr­
smolt
transition.
The
development
of
the
ocean­
type
life­
history
strategy
may
have
been
a
response
to
the
limited
carrying
capacity
of
smaller
stream
systems
and
glacially
scoured,
unproductive
watersheds,
or
a
means
of
avoiding
the
impact
of
seasonal
floods
in
the
lower
portion
of
many
watersheds
(
Miller
and
Brannon
1982).
In
the
Sacramento
River
and
coastal
California
rivers,
subyearling
emigration
is
related
to
the
avoidance
of
high
summer
water
temperatures
(
Calkins
et
al.
1940,
Gard
1995).
Ocean­
type
chinook
salmon
may
also
use
seasonal
flood
cycles
as
a
cue
to
volitionally
begin
downstream
emigration
(
Healey
1991).
Migratory
behavior
in
ocean­
type
chinook
salmon
juveniles
is
also
positively
correlated
with
water
flow
(
Taylor
1990a).
29
Stream­
type
juveniles
are
much
more
dependent
on
freshwater
stream
ecosystems
because
of
their
extended
residence
in
these
areas.
A
stream­
type
life
history
may
be
adapted
to
those
watersheds,
or
parts
of
watersheds,
that
are
more
consistently
productive
and
less
susceptible
to
dramatic
changes
in
water
flow,
or
which
have
environmental
conditions
that
would
severely
limit
the
success
of
subyearling
smolts
(
Miller
and
Brannon
1982,
Healey
1991).
Stream­
type
chinook
salmon
juveniles
exhibit
downstream
dispersal
and
utilize
a
variety
of
habitats
during
their
freshwater
residence.
This
dispersal
appears
to
be
related
to
resource
allocation
and
migration
to
overwintering
habitat
and
is
not
associated
with
saltwater
osmoregulatory
competence
(
Hillman
et
al.
1987,
Levings
and
Lauzier
1989,
Taylor
1990a,
Healey
1991).
For
example,
the
migration
of
subyearling
juvenile
spring­
run
chinook
salmon
in
the
Wenatchee
River
(
a
stream­
type
population)
may
be
due
to
competition
with
hatchery
releases
or
the
interspecific
interaction
between
steelhead
and
chinook
salmon
juveniles
(
Hillman
and
Chapman
1989).
There
was
a
tendency
for
juveniles
to
move
into
deeper
water,
farther
from
the
bank
shelter,
as
they
grew
older.
If
suitable
overwintering
habitat,
such
as
large
cobble,
is
not
available
then
the
fish
will
tend
to
migrate
downstream
(
Bjornn
1971,
Bustard
and
Narver
1975,
Hillman
et
al.
1987).
At
the
time
of
saltwater
entry,
stream­
type
(
yearling)
smolts
are
much
larger,
averaging
73­
134
mm
depending
on
the
river
system,
than
their
ocean­
type
(
subyearling)
counterparts
and
are
therefore
able
to
move
offshore
relatively
quickly
(
Healey
1991).

The
variability
in
the
time
of
emigration
to
the
marine
environment
among
stocks
of
chinook
salmon,
combined
with
geographic
and
yearly
differences
in
freshwater
productivity,
make
comparisons
of
the
sizes
of
smolts
among
different
stocks
difficult.
Size
data
may
be
confounded
by
the
presence
within
a
watershed
of
multiple
native
stocks
that
exhibit
different
lifehistory
strategies.
The
possible
inclusion
of
hatchery­
reared
fish
in
smolt
samples
is
a
further
confounding
factor.
Smolt
size,
therefore,
was
not
emphasized
among
the
life­
history
traits
used
to
determine
ESU
boundaries.

Ocean­
and
stream­
type
chinook
salmon
populations
exhibit
a
geographical
distribution
that
further
underscores
the
ecological
adaptation
of
these
two
races.
Chinook
salmon
stocks
in
Asia,
Alaska,
and
Canada
north
of
the
55th
parallel,
and
in
the
headwaters
(
upper
elevations)
of
the
Fraser
River
and
the
Columbia
River
Basins,
exhibit
a
stream­
type
life
history:
emigrating
to
sea
in
their
second
or
third
spring
and
generally
entering
freshwater
several
months
prior
to
spawning
(
Healey
1991).
A
notable
exception
to
this
trend
includes
populations
in
the
Situk
River
and
several
Yakutat
foreland
River
Basins
in
Alaska,
which
emigrate
primarily
as
subyearlings
(
Johnson
et
al
1992a,
ADFG
1997).
Ocean­
type
chinook
salmon
are
predominant
in
coastal
regions
south
of
55
E
N,
in
Puget
Sound,
in
the
lower
reaches
of
the
Fraser
and
Columbia
Rivers,
and
in
California's
Central
Valley
(
Gilbert
1912,
Rich
1920a,
Healey
1983,
Taylor
1990b).
One
analysis
of
principal
components
influencing
life­
history
type
(
distance
to
the
sea,
daylight
hours
during
the
growing
season
and
air
temperature)
accounted
for
96%
of
the
total
observed
variation
in
age
at
smoltification
(
Taylor
1990a).
However,
the
abrupt
change
between
streamand
ocean­
type
life
histories
at
55
E
N
occurs
in
the
absence
of
a
similarly
abrupt
change
in
environmental
conditions
(
Healey
1983)
and
may
be
related
to
patterns
of
colonization
following
deglaciation
(
Taylor
1990b).
30
Stream­
type
life
histories
are
most
commonly
associated
with
early
timed
runs
of
fish
(
Rich
1920a,
Healey
1983).
This
is
partially
because
the
headwater
regions
south
of
55
E
N
are
only
accessible
during
peak
spring
stream
flows,
additionally,
temperatures
in
more
northerly
streams
and
headwater
areas
are
much
colder
than
in
other
areas
and
require
early
deposition
of
eggs
to
allow
for
proper
developmental
timing.
Overall,
juvenile
smoltification
strategies
are
one
expression
of
a
more
complicated,
genetically
based
life­
history
adaptation
to
ecological
conditions
(
Taylor
1990a,
Clarke
et
al.
1992).
Differences
in
juvenile
life­
history
strategies
among
chinook
salmon
stocks
were
a
useful
component
in
helping
to
determine
boundaries
between
ESUs.

Ocean
Distribution
Coastwide,
chinook
salmon
remain
at
sea
from
1
to
6
years
(
more
commonly
2
to
4
years),
with
the
exception
of
a
small
proportion
of
yearling
males
which
mature
in
freshwater
or
return
after
2
or
3
months
in
salt
water
(
Rutter
1904,
Gilbert
1912,
Rich
1920a,
Mullan
et
al.
1992).
Differences
in
the
ocean
distribution
of
specific
stocks
may
be
indicative
of
resource
partitioning
and
may
be
important
to
the
success
of
the
species
as
a
whole.
Current
migratory
patterns
may
have
evolved
as
a
balance
between
the
relative
benefits
of
accessing
specific
feeding
grounds
and
the
energy
expenditure
necessary
to
reach
them.
If
the
migratory
pattern
for
each
population
is,
in
part,
genetically
based,
then
the
efficiency
with
which
subsequent
generations
reach
and
return
from
their
traditional
feeding
grounds
will
be
increased.

The
vast
majority
of
CWT­
marked
chinook
salmon
come
from
hatchery
populations;
therefore,
the
migratory
routes
of
many
wild
fish
stocks
must
be
inferred
from
their
corresponding
hatchery
populations.
Furthermore,
CWT
ocean
recoveries
are
obtained
through
commercial
and
sport
fishery
samples;
therefore,
the
relative
intensity
of
each
fishery
can
bias
the
interpretation
of
the
oceanic
distribution
of
each
stock.
Comparisons
of
oceanic
distributions
across
years
can
also
be
influenced
by
changes
in
fishing
regulations
and
ocean
conditions
(
such
as
during
an
El
Niño).
Confounding
effects
were
considered
in
the
interpretation
of
CWT
recoveries,
and
small
differences
in
CWT
ocean
recoveries
between
stocks
were
not
considered
as
a
distinguishing
factor.

The
genetic
basis
for
ocean
distribution
has
been
supported
by
a
number
of
different
studies
involving
the
monitoring
of
CWT­
marked
fish
caught
in
the
ocean
fisheries.
The
relative
influence
of
genetic
vs.
environmental
factors
on
migratory
pattern
can
be
deduced
from
transplantation
studies.
Transplanted
Elwha
River
chinook
salmon
continued
to
follow
their
traditional
migratory
pattern
after
being
reared
and
released
at
a
site
150
km
to
the
east,
except
that
the
actual
route
had
also
been
shifted
150
km
eastward
(
Brannon
and
Hershberger
1984).
Additionally,
hybrids
between
the
Elwha
River
and
Green
River
(
University
of
Washington)
stocks
exhibited
an
intermediate
ocean
migration
pattern.
Transplantation
studies
with
coastal
stocks
in
Oregon
have
yielded
similar
results
(
Nicholas
and
Hankin
1988).
Chinook
salmon
31
whose
natal
stream
lies
south
of
Cape
Blanco
tend
to
migrate
to
the
south,
while
those
to
the
north
of
Cape
Blanco
tend
to
migrate
in
a
northerly
direction.
Transplants
of
south
migrating
stocks
to
release
sites
north
of
Cape
Blanco
do
not
alter
the
basic
southerly
direction
of
ocean
migration
(
Nicholas
and
Hankin
1988).
Recoveries
of
CWT­
marked
fish
from
ocean
fisheries
indicate
that
fish
stocks
follow
predicable
ocean
migration
patterns,
and
that
these
are
based
on
"
ancestral"
feeding
routes
(
Brannon
and
Setter
1987).

Ocean­
and
stream­
type
chinook
salmon
are
recovered
differentially
in
coastal
and
midocean
fisheries,
indicating
divergent
migratory
routes
(
Healey
1983,
1991).
Ocean­
type
chinook
salmon
tend
to
migrate
along
the
coast,
while
stream­
type
chinook
salmon
are
found
far
from
the
coast
in
the
central
North
Pacific
(
Healey
1983,
1991;
Myers
et
al.
1984).
Studies
of
CWTmarked
prerecruit
(<
71
cm)
fish
in
the
marine
fisheries
off
of
Southeastern
Alaska
indicated
that
differences
in
migration
speed,
timing,
and
growth
were
related
to
the
life
history,
age,
and
general
geographic
origin
of
the
stocks
(
Orsi
and
Jaenicke
1996).
The
causal
basis
for
this
difference
in
migration
pattern
is
unknown,
but
may
be
related
to
poor
coastal
feeding
conditions
during
past
glacial
events
for
the
more
northerly
(
stream­
type)
populations.

The
freshwater
component
of
the
adult
returning
migratory
process
is
also
under
a
significant
genetic
influence.
In
one
experiment,
"
upriver
bright"
chinook
salmon
were
captured,
spawned,
and
the
subsequent
progeny
reared
and
released
from
a
downriver
site
(
McIsaac
and
Quinn
1988).
A
significant
fraction
of
the
returning
adults
from
the
"
upriver
bright"
progeny
group
bypassed
their
rearing
site
and
returned
to
their
"
traditional"
spawning
ground
370
km
further
upriver.
The
high
degree
of
fidelity
with
which
chinook
salmon
return
to
their
natal
stream
has
been
shown
in
a
number
of
studies
(
Rich
and
Holmes
1928,
Quinn
and
Fresh
1984,
McIsaac
and
Quinn
1988).
Returning
to
the
"
home
stream"
provides
a
mechanism
for
local
adaptation
and
reproductive
isolation.

Ocean
migration
patterns
represent
an
important
form
of
resource
partitioning
and
are
important
to
the
evolutionary
success
of
the
species;
therefore,
differences
in
ocean
migratory
pattern
were
an
important
consideration
in
the
determination
of
ESU
boundaries.

Size
and
Age
at
Maturation
The
age
at
which
chinook
salmon
begin
sexual
maturation
and
undertake
their
homeward
migration
is
dependent
on
a
number
of
different
factors.
Age,
body
size
and
composition,
and
fecundity
traits
in
salmonids
have
all
been
shown
to
be
partially
under
genetic
control
(
Ricker
1972)
and
genetically
and
phenotypically
correlated
(
Gall
1975).
Because
of
genetic
correlations
between
these
traits,
natural
selection
on
one
or
more
of
these
traits
may
affect
the
expression
of
other
traits.
The
confounding
effects
of
correlated
traits
make
it
difficult
to
identify
specific
selective
(
ecologically
important)
criteria
that
influence
size
and
age
at
maturity.
32
5
J.
D.
Hubble,
Biologist,
Yakama
Tribal
Fisheries,
P.
O.
Box
151,
Toppenish,
WA
98948.
Pers.
Commun.,
April
1996.
Adult
body
size
in
chinook
salmon
does
not
appear
to
be
strongly
correlated
to
latitude;
however,
there
appears
to
be
a
slight
negative
correlation
between
adult
body
size
and
length
of
migration
(
Roni
and
Quinn
1995).
The
relationship
between
size
and
length
of
migration
may
also
reflect
the
earlier
timing
of
river
entry
and
the
cessation
of
feeding
for
chinook
salmon
stocks
that
migrate
to
the
upper
reaches
of
river
systems.
Juvenile
life
history
has
an
apparent
influence
on
the
size
of
returning
spawners.
Ocean­
type
fish
that
have
been
at
sea
from
1
to
2
years
are
generally
larger
than
their
respective
stream­
type
counterparts
(
Roni
and
Quinn
1995).
This
may
reflect
the
more
productive
feeding
conditions
that
exist
in
the
marine
environment
and/
or
the
additional
3
to
5
months
that
ocean­
type
fish
remain
in
the
marine
environment
before
beginning
their
spawning
migration.

Body
size,
which
is
correlated
with
age,
may
be
an
important
factor
in
migration
and
redd
construction
success.
Beacham
and
Murray
(
1987)
reported
a
correlation
between
body
size
and
large
(<
100
km2
watershed
area)
and
small
river
size
in
chum
salmon
(
O.
keta).
Roni
and
Quinn
(
1995)
reported
that
under
high
density
conditions
on
the
spawning
ground,
natural
selection
may
produce
stocks
with
exceptionally
large­
sized
returning
adults.
Spawning
aggregations
may
select
for
large
body
size
in
males
due
to
competition
between
males
for
females
and
the
"
attractiveness"
of
large
males
to
females
(
Foote
1990).
Large
body
size
may
be
advantageous
for
females
because
of
the
success
of
larger
fish
in
establishing,
digging,
and
protecting
their
redds
(
Healey
and
Heard
1984).
Competition
for
redd
sites,
stream
flow,
and
gravel
conditions
are
also
thought
to
influence
adult
size
in
coho
salmon
(
Holtby
and
Healey
1986).

An
alternative
strategy
for
chinook
salmon
is
for
males
to
mature
at
an
early
age.
"
Minijack
or
"
jack"
chinook
salmon
males
mature
in
their
first
or
second
ocean
years,
respectively.
Early
maturation
among
male
chinook
salmon
was
first
described
by
Rutter
(
1904).
Early
maturation
offers
a
reduced
risk
of
mortality,
but
younger
(
smaller)
males
may
be
at
a
competitive
disadvantage
in
securing
a
mate
(
Gross
1987).
The
incidence
of
jack
males
has
underlying
genetic
determinants
and
appears
to
be,
in
part,
a
response
to
favorable
growing
conditions.
A
variant
of
this
life­
history
strategy
is
maturation
without
emigrating
to
the
ocean.
Rich
(
1920a)
estimated
that
10­
12%
of
the
juvenile
males
on
the
McCloud
River
were
maturing
without
leaving
the
river.
Mullan
et
al.
(
1992)
found
that
early
maturing
resident
males
were
common
in
both
hatchery
and
wild
populations
in
the
Wenatchee
River.
Non­
migrating
mature
males
have
also
been
observed
in
the
Snake
River
Basin
(
Gebhards
1960,
Burck
1967,
Sankovich
and
Keefe
1996),
Methow
and
Yakima
Rivers
(
Hubble5),
and
the
Deschutes
River.
Resident
males
have
been
observed
among
some
stream­
and
ocean­
type
chinook
salmon
stocks
in
the
Fraser
River
above
Hell's
Gate,
which
would
have
historically
been
a
potential
barrier
to
small
migrating
early
maturing
males,
but
not
among
lower
river
or
coastal
populations
(
Taylor
1989,
Foote
et
al.
1991).
The
location
and
physical
characteristics
of
each
river
may
determine
the
expression
of
this
life­
history
trait.
It
is
33
unlikely
that
small
jack
males
would
be
physically
able
to
undertake
the
arduous
return
migration
to
many
upriver
areas
(
Mullan
et
al.
1992)
or
that
sufficient
time
exists
for
the
completion
of
the
smolt
emigration
and
return
migration.
Nonmigrating
early
maturing
males
may
have
a
good
chance
of
mating
success,
especially
during
poor
return
years
when
there
may
be
a
shortage
of
large
males
on
the
spawning
grounds.
The
modification
of
smoltification,
a
major
physiological
process,
to
produce
early
maturing
males
in
a
population
is
indicative
of
the
importance
of
this
life­
history
trait
to
the
reproductive
success
of
specific
populations.

The
heritability
of
body
size
and
age
has
been
more
extensively
studied
in
chinook
salmon
than
have
other
traits.
Crosses
between
different
aged
parents
have
demonstrated
that
the
ages
of
maturity
for
parents
and
progeny
were
strongly
correlated
(
Ellis
and
Noble
1961,
Donaldson
and
Bonham
1970,
Hershberger
and
Iwamoto
1984,
Withler
et
al.
1987,
Hankin
et
al.
1993).
The
expression
of
early
maturation
in
chinook
salmon
was
found
to
have
a
significant
genetic
component;
moreover,
different
stocks
exhibited
different
levels
of
early
maturation
in
response
to
environmental
changes
(
Heath
et
al.
1994).
The
positive
response
of
chinook
salmon
to
selective
breeding
experiments
is
indicative
of
a
significant
genetic
component
to
body
size
(
Donaldson
and
Menasveta
1961).
Chinook
salmon
stocks
exhibit
considerable
variability
in
size
and
age
of
maturation,
and
at
least
some
portion
of
this
variation
is
genetically
determined.

From
an
evolutionary
standpoint,
the
potential
increases
in
size,
fecundity,
and
egg
size
gained
from
remaining
on
the
marine
feeding
grounds
an
additional
year
must
be
weighed
against
the
chances
of
mortality
during
that
year
(
Healey
and
Heard
1984,
Healey
1986).
The
specific
conditions
that
exist
in
each
river
must
also
influence,
in
part,
the
expression
of
these
characteristics.
The
size
and
age
of
spawning
chinook
salmon
in
any
given
population
may
have
a
significant
impact
on
their
survival,
and
trends
in
size
and
age
were
utilized
in
determining
ESU
boundaries.
However,
the
large
environmental
influence
(
on
a
regional
and
annual
basis)
on
chinook
salmon
size
and
age,
as
well
as
possible
biases
resulting
from
different
fishery
harvest
techniques
and
the
inclusion
of
hatchery
reared
fish,
would
suggest
that
available
size
and
age
data
be
used
with
caution.

Run
Timing
Early
researchers
recorded
the
existence
of
different
temporal
"
runs"
or
modes
in
the
migration
of
chinook
salmon
from
the
ocean
to
freshwater.
Two
major
influxes
of
chinook
salmon
were
observed
returning
to
the
Sacramento­
San
Joaquin
River
system,
although
"...
there
is
no
definite
distinction
between
spring
and
fall
runs;
there
is
no
time
during
the
summer
when
there
are
no
salmon
running"
(
Rutter
1904,
p.
122).
It
was
also
reported
that
spring­
run
fish
tended
to
migrate
to
the
upriver
portions
of
the
Sacramento
River
and
spawn
earlier
than
the
fall
run,
which
spawned
in
the
lower
regions
of
tributaries
and
in
mainstem
river
areas.
A
similar
distinction
was
made
between
spring,
summer,
and
fall
or
"
snow"
salmon
runs
in
the
Klamath
River
(
Snyder
1931).
The
underlying
genetic
influence
on
run
timing
was
initially
demonstrated
34
by
Rich
and
Holmes
(
1928),
when
spring­
run
chinook
salmon
from
the
MacKenzie
River
were
reared,
marked,
and
released
from
a
predominantly
fall­
run
watershed.
The
transplanted
chinook
salmon
displayed
no
apparent
alteration
in
their
normal
time
of
return
or
spawning,
although
there
was
an
increase
in
straying.
Subsequent
stock
transplantations
have
further
substantiated
the
heritable
nature
of
run
timing.
Heritability
estimates
for
return
timing
among
early­
and
latereturning
pink
salmon
(
Oncorhynchus
gorbuscha)
runs
in
Alaska
were
0.4
and
0.2
for
females
and
males,
respectively
(
Gharrett
and
Smoker
1993).

Freshwater
entry
and
spawning
timing
are
generally
thought
to
be
related
to
local
temperature
and
water
flow
regimes
(
Miller
and
Brannon
1982).
Temperature
has
a
direct
effect
on
the
development
rate
of
salmonids
(
Alderdice
and
Velsen
1978).
Only
one
run
timing
for
chinook
salmon
is
found
in
most
rivers
in
Alaska
and
northern
British
Columbia,
where
summers
are
short
and
water
temperatures
cold
(
Burger
et
al.
1985).
The
Kenai
River
in
Alaska
is
an
exception
to
this
trend,
having
mid­
June
and
mid­
July
runs
that
ultimately
spawn
in
areas
with
distinct
thermal
regimes
(
Burger
et
al.
1985).
Asian
rivers
are
thought
to
contain
only
one
run
of
chinook
salmon,
with
the
possible
exception
of
the
Kamchatka
and
Bol'shaya
Rivers
(
Vronskiy
1972,
Smirnov
1975).
Among
stream­
type
stocks,
the
King
Salmon
River
in
Alaska
differs
from
the
general
trend
in
that
adults
return
in
a
relatively
mature
condition
and
spawn
in
the
lower
river,
extending
down
to
the
intertidal
area
(
Kissner
1985,
ADFG
1997).
The
majority
of
multiple
run
rivers
are
found
south
from
the
Bella
Coola
and
Fraser
Rivers.

Runs
are
designated
on
the
basis
of
adult
migration
timing;
however,
distinct
runs
also
differ
in
the
degree
of
maturation
at
the
time
of
river
entry,
thermal
regime
and
flow
characteristics
of
their
spawning
site,
and
actual
time
of
spawning.
Early,
spring­
run
chinook
salmon
tend
to
enter
freshwater
as
immature
or
"
bright"
fish,
migrate
far
upriver,
and
finally
spawn
in
the
late
summer
and
early
autumn.
Late,
fall­
run
chinook
salmon
enter
freshwater
at
an
advanced
stage
of
maturity,
move
rapidly
to
their
spawning
areas
on
the
mainstem
or
lower
tributaries
of
the
rivers,
and
spawn
within
a
few
days
or
weeks
of
freshwater
entry
(
Fulton
1968,
Healey
1991).
Summer­
run
fish
show
intermediate
characteristics
of
spring
and
fall
runs,
spawning
in
large
and
medium­
sized
tributaries,
and
not
showing
the
extensive
delay
in
maturation
exhibited
by
spring­
run
chinook
salmon
(
Fulton
1968).
Winter­
run
chinook
salmon
(
which
presently
exist
only
in
the
Sacramento
River)
begin
their
freshwater
migration
at
an
immature
stage
and
travel
to
the
upper
portions
of
the
watershed
to
spawn
in
the
spring.
All
stocks,
and
especially
those
that
migrate
into
freshwater
well
in
advance
of
spawning,
utilize
resting
pools.
These
pools
provide
an
energetic
refuge
from
river
currents,
a
thermal
refuge
from
high
summer
and
autumn
temperatures,
and
a
refuge
from
potential
predators
(
Berman
and
Quinn
1991,
Hockersmith
et
al.
1994).
Furthermore,
the
utilization
of
resting
pools
may
maximize
the
success
of
the
spawning
migration
through
decreases
in
metabolic
rate
and
the
potential
reduction
in
susceptibility
to
pathogens
(
Bouck
et
al.
1975,
Berman
and
Quinn
1991).
In
the
Stilliguamish
River,
there
was
a
high
correlation
between
the
location
of
pools
and
redds,
suggesting
that
the
pool
abundance
may
limit
the
amount
of
spawning
habitat
available
(
PSSSRG
1997).
35
Run
timing
is
also,
in
part,
a
response
to
streamflow
characteristics.
Rivers
such
as
the
Klickitat
or
Willamette
Rivers
historically
had
waterfalls
which
blocked
upstream
migration
except
during
high
spring
flows
(
WDF
et
al.
1993).
Low
river
flows
on
the
south
Oregon
coast
during
the
summer
result
in
barrier
sandbars
which
block
migration
(
Kostow
1995).
The
timing
of
migration
and,
ultimately,
spawning
must
also
be
cued
to
the
local
thermal
regime.
Egg
deposition
must
be
timed
to
ensure
that
fry
emerge
during
the
following
spring
at
a
time
when
the
river
or
estuary
productivity
is
sufficient
for
juvenile
survival
and
growth.
The
strong
association
between
run
timing
and
ecological
conditions
made
this
trait
useful
in
considering
potential
ESU
boundaries.

Straying
The
high
degree
of
fidelity
with
which
chinook
salmon
return
to
their
natal
stream
has
been
shown
in
a
number
of
studies
(
Rich
and
Holmes
1928,
Quinn
and
Fresh
1984,
McIsaac
and
Quinn
1988).
Returning
to
one's
natal
stream
may
have
evolved
as
a
method
of
ensuring
an
adequate
incubation
and
rearing
habitat.
It
also
provides
a
mechanism
for
reproductive
isolation
and
local
adaptation.
Conversely,
returning
to
a
stream
other
than
that
of
one's
origin
is
important
in
colonizing
new
areas
and
responding
to
unfavorable
or
perturbed
conditions
at
the
natal
stream
(
Quinn
1993).
High
rates
of
straying
by
returning
Umatilla
River
fall
chinook
salmon
(
an
introduced
upriver
bright
stock)
into
the
Snake
River
in
1987­
89
were
apparently
related
to
poor
acclimation,
high
water
temperatures,
and
lack
of
water
in
the
Umatilla
River
(
Waples
et
al.
1991b).
Straying
coho
salmon
(
O.
kisutch)
and
sockeye
salmon
have
rapidly
colonized
newly
deglaciated
habitat
(
Milner
and
Bailey
1989),
and
summer­
run
chinook
salmon
may
have
recolonized
the
Okanogan
River
following
the
cessation
of
trapping
operations
at
Rock
Island
Dam,
which
blocked
entry
from
1939­
43
(
Waknitz
et
al.
1995).
The
degree
of
straying
in
wild
populations
determines
the
extent
of
reproductive
isolation
and
the
potential
for
the
formation
of
ESUs.

Available
information
on
straying
rates
primarily
involves
hatchery­
reared,
transplanted,
or
transported
fish.
Rich
and
Holmes
(
1928),
in
one
of
the
earliest
studies
of
homing,
released
marked
chinook
salmon
juveniles
from
a
number
of
hatcheries
along
the
lower
Columbia
River.
Of
the
104
chinook
salmon
that
were
recovered
in
spawning
areas
or
at
hatchery
racks,
only
5
(
4.8
%)
had
strayed
to
areas
other
than
their
release
sites
(
Rich
and
Holmes
1928).
Quinn
and
Fresh
(
1984)
reported
that
only
1.4%
of
the
returning
spring­
run
chinook
salmon
from
the
Cowlitz
River
Hatchery
were
recovered
outside
of
their
natal
watershed,
and
it
was
suggested
that
straying
was
more
frequent
in
older
fish
and
in
years
when
the
run­
size
was
low.
Olfactory
cues
provided
by
conspecifics
on
spawning
grounds,
especially
large
aggregations,
may
be
a
powerful
attractant
to
returning
salmon
(
Duker
1981).
If
these
spawning
aggregations
are
an
attractant,
it
may
explain
the
negative
correlation
between
run­
size
and
straying
as
well
as
explaining
the
observed
straying
of
naturally­
produced
salmon
into
hatcheries.
Chapman
et
al.
(
1991,
1994)
suggested
that
straying
is
more
common
among
fall­
run
fish
than
among
spring­
run
36
fish.
Quinn
et
al.
(
1991)
found
that
straying
rates
differed
considerably
(
10­
27.5%)
between
hatcheries
releasing
fall
chinook
salmon
on
the
lower
Columbia
River.

The
adult
returning
migratory
process
has
been
shown
to
be
under
a
significant
genetic
influence.
In
one
experiment,
"
upriver
bright"
chinook
salmon
were
captured,
spawned,
and
the
subsequent
progeny
reared
and
released
from
a
downriver
site
(
McIsaac
and
Quinn
1988).
A
significant
fraction
of
the
returning
adults
from
the
upriver
bright
progeny
group
bypassed
their
rearing
site
and
returned
to
their
"
traditional"
spawning
ground
370
km
further
upriver.

Hatchery
rearing
and
release
procedures
may
increase
the
rate
of
straying.
Wild
chinook
salmon
had
significantly
lower
straying
rates
than
did
hatchery­
reared
fish
from
the
Lewis
River
(
McIsaac
1990).
Releasing
fish
even
a
short
distance
from
the
hatchery
can
dramatically
increase
the
straying
rate
(
Quinn
1993,
Heard
1996).
Straying
rates
as
high
as
86%
resulted
from
the
long­
distance
transportation
and
release
of
fall
chinook
salmon
in
the
Sacramento
River
(
Cramer
1989).
Unfavorable
conditions
(
high
water
temperature
and
low
flow)
at
hatchery
return
facilities
may
further
increase
straying
rates
(
Quinn
1993).
The
use
of
hatchery
stocks
founded
from
a
composite
of
wild
stocks
(
e.
g.,
upriver
bright
fall
chinook
salmon)
may
increase
straying
if
the
genetic
component
to
homing
is
more
important
than
the
olfactory
(
learned)
component.
Chapman
et
al.
(
1994)
indicated
that
Columbia
River
fall
chinook
salmon
upriver
bright
hatchery
stocks
did
have
a
relatively
high
straying
rate.
However,
Pascual
and
Quinn
(
1994)
found
similar
homing
success
rates
for
local
and
introduced
stocks
of
chinook
salmon
released
in
the
Columbia
River.

Any
interpretation
of
straying
rates
should
consider
the
way
in
which
strays
were
enumerated.
Chapman
et
al.
(
1991)
made
a
distinction
between
"
legitimate"
strays
and
"
wanderers,"
those
fish
that
enter
non­
native
streams
as
a
part
of
their
homing
search
or
as
a
temporary
refuge
from
unfavorable
river
conditions.
Wanderers
will
normally
retreat
from
these
non­
native
streams
and
continue
their
return
migration;
however,
where
weirs
or
hatchery
traps
are
present,
wanderers
will
be
unable
to
return
and
are
often
considered
strays.
Additionally,
straying
rates
can
be
influenced
by
the
effort
placed
on
surveying
sites
other
than
the
release
site.

The
use
of
cut­
off
dates
by
hatcheries
to
separate
run­
times
can
result
in
"
temporal"
straying.
Cope
and
Slater
(
1957)
found
that
16%
of
the
fish
returning
as
"
spring­
run"
adults
to
Coleman
NFH
were
produced
from
fall­
run
parents,
and
19%
of
the
returning
"
fall­
run"
adults
came
from
spring­
run
parents.
The
use
of
fixed
return
or
spawning
dates
to
distinguish
runs
at
adult
collection
facilities
may
have
resulted
in
the
introgression
of
previously
distinct
stocks
(
Mullan
1987,
WDF
et
al.
1993,
Waknitz
et
al.
1995).

Straying
by
hatchery
fish,
especially
those
from
non­
native
hatchery
stocks,
increases
the
potential
for
interbreeding
and
genetic
homogenization.
This
may
result
in
the
loss
of
regionally
distinct
life­
history
characteristics.
37
Fecundity
and
Egg
Size
Fecundity
and
egg
size
differences
between
stocks
of
salmon
occur
on
a
geographic
basis.
In
salmon,
fecundity
tends
to
increase
while
egg
size
decreases
with
latitude
(
Healey
and
Heard
1984,
Kaev
and
Kaeva
1987,
Fleming
and
Gross
1990).
Variation
between
and
within
regions
can
be
considerable.

The
anadromous
life
history
of
salmon
is
thought
to
be
a
response
to
the
relatively
poor
productivity
of
glacially
influenced
or
unstable
freshwater
environments
relative
to
the
nearby
marine
habitat
(
Neave
1958,
Miller
and
Brannon
1982).
In
order
to
maximize
the
success
of
their
emigration
to
saltwater,
salmon
juveniles
must
obtain
a
relatively
large
size
in
productivity­
limited
freshwater
environments.
One
strategy
for
accomplishing
this
is
through
the
production
of
large
eggs
and
thereby
large
embryos
(
Taylor
1991,
Kreeger
1995).
Larger
eggs
produce
larger
fry
(
Fowler
1972),
which
may
be
more
successful
at
migrating
to
saltwater
than
smaller
fry
(
Kreeger
1995).
Ocean­
type
chinook
salmon
stocks
in
British
Columbia
were
reported
to
have
larger
eggs
than
stream­
type
stocks
(
Lister
1990).
Rich
(
1920b)
found
that
some
chinook
salmon
returning
to
coastal
streams
in
Oregon
and
Washington
had
larger
eggs
than
fish
returning
to
the
Columbia
River.
In
general,
Smironov
(
1975)
suggested
that
latitudinal
differences
existed
in
egg
size,
with
southern
stocks
having
larger
eggs.
Furthermore,
he
speculated
that
this
was
because
embryonic
development
at
higher
temperatures
is
less
efficient;
southern
stocks
need
more
energy
stores
(
larger
eggs)
to
complete
development.
Alternatively,
this
trend
may
be
related
to
the
need
for
more
southerly,
predominantly
ocean­
type,
chinook
salmon
to
produce
larger­
sized
fry
for
migration
to
estuary
areas.
In
general,
stream­
type
stocks
of
chinook
salmon
have
smaller
eggs
than
ocean­
type
stocks.
However,
there
is
no
apparent
latitudinal
cline
in
egg
size
among
streamtype
nor
ocean­
type
stocks
(
Appendix
C).

Older
(
larger)
year
classes
of
salmon
tend
to
produce
larger
sized
eggs
but
not
proportionately
larger
numbers
of
eggs
than
their
younger
(
smaller)
counterparts;
this
may
be
a
life­
history
strategy
to
improve
the
survival
of
individual
progeny
rather
than
producing
more
of
them
(
Gray
1965,
Iwamoto
1982,
Beacham
and
Murray
1985,
Healey
1986,
Nicholas
and
Hankin
1988).
Factors
affecting
egg
size
in
chinook
salmon
appear
to
be
operating
on
a
between­
and
within­
population
basis.
Variability
in
egg
size
within
populations
appears
to
be
most
directly
related
to
fish
size
and,
to
a
lesser
extent,
age
(
Healey
and
Heard
1984,
Hankin
and
McKelvey
1985),
whereas
between­
population
differences
may
represent
an
adaptation
to
regional
environmental
and
geographic
conditions.

Physiological
and
ecological
factors
have
been
identified
that
may
limit
the
potential
minimum
and
maximum
egg
sizes,
0.12
and
0.47
g,
respectively
(
Quinn
and
Bloomberg
1992).
The
physical
limitations
of
large
eggs
in
absorbing
oxygen
due
to
a
reduced
surface
area­
tovolume
ratio
and
the
generally
high
physiological
oxygen
demands
of
salmonids
may
limit
the
maximum
size
of
chinook
salmon
eggs.
Stream
flow,
gravel
quality,
and
silt
load
all
significantly
influence
the
survival
of
developing
chinook
salmon
eggs.
Therefore,
behavioral
traits
such
as
38
spawning
site
selection
would
need
to
be
correlated
with
physical
fecundity
traits.
Healey
(
1991)
showed
that
suboptimum
habitat
conditions
delay
or
discourage
spawning
at
a
specific
site.

Variation
in
fecundity
and
egg
size
among
different
stocks
of
chinook
salmon
appears
to
be
related
to
geography
and
life­
history
strategy.
Chinook
salmon
females
sampled
from
the
Sacramento
River
had
68%
more
eggs
than
females
from
the
Klamath
River,
after
adjusting
for
differences
in
body
size
(
Snyder
1931,
Healey
and
Heard
1984).
Fecundity
is
related
to
body
size,
although
this
relationship
is
also
dependent
on
a
number
of
other
factors
 
age,
migration
distance,
latitude
 
and
varies
between
stocks
(
Healey
and
Heard
1984,
Kaev
and
Kaeva
1987,
Fleming
and
Gross
1990).
Galbreath
and
Ridenhour
(
1964)
found
that
linear
length­
fecundity
regressions
for
the
Columbia
River
chinook
salmon
stocks
were
not
significantly
different
when
compared
on
a
seasonal
(
monthly)
run
timing,
total
age,
or
smolt
age
basis;
however,
differences
in
body
size
and
a
small
sample
size
may
have
obscured
racial
differences
in
fecundity.
A
further
complication
in
the
analysis
of
fecundity
traits
is
the
difference
in
body
weight
devoted
to
gonadal
tissue
in
coastal
and
inland
populations.
Populations
which
undertake
extended
migrations
may
not
be
able
to
devote
the
same
percentage
of
body
weight
toward
gonad
(
especially
ovary)
development
(
Lister
1990).
Linley
(
1993)
found
a
significant
negative
correlation
for
adult
sockeye
salmon
between
the
percentage
of
body
weight
devoted
to
gonads
and
the
length
and
duration
of
the
freshwater
migration.
Ivankov
(
1983)
determined
that
differences
in
the
fecundity
of
masu
salmon
(
O.
masu)
females
within
and
among
rivers
were
correlated
with
juvenile
growth
rate
and
the
rate
of
gonadal
development
prior
to
saltwater
emigration,
although
he
did
not
specifically
evaluate
the
relative
contributions
of
genetic
and
environmental
effects.

Correlations
between
fecundity
and
body
size
and
age,
in
addition
to
environmental
fluctuations
over
several
years,
complicate
the
interpretation
of
fecundity
differences.
Furthermore,
the
majority
of
fecundity
information
comes
from
hatchery
populations.
Differences
in
selection
on
fecundity
and
egg
size
traits
under
hatchery
conditions
relative
to
the
natural
environment
may
limit
the
representative
value
of
hatchery
populations
for
their
wild
counterparts
(
Fleming
and
Gross
1990).

Other
Life­
History
Traits
Information
concerning
the
variability,
adaptiveness,
and
heritability
of
other
life­
history
traits
in
salmon
is
extremely
limited.
Genetically
based
differences
in
the
rate
of
Pacific
salmon
embryonic
and
alevin
development
between
run
times
in
the
same
river
(
Tallman
1986),
and
between
rivers
(
Iwamoto
1982,
Beacham
and
Murray
1987,
1989)
represent
important
adaptations
to
ensure
emergence
occurs
at
a
time
for
optimal
survival.
The
heritability
estimates
for
embryonic
development
to
hatch
in
chinook
salmon
range
from
0.25
to
0.40
(
Hickey
1983).
Smirnov
(
1975)
suggested
significant
differences
in
the
embryonic
development
exist
between
Asian
and
North
American
stocks
of
chinook
salmon.
39
Pathogen
resistance
is
another
locally
adapted
trait.
Chinook
salmon
from
the
Columbia
River
drainage
exhibited
reduced
susceptibility
to
Ceratomyxa
shasta,
an
endemic
pathogen,
relative
to
stocks
from
coastal
rivers
where
the
disease
is
not
known
to
occur
(
Zinn
et
al.
1977).
Differences
in
susceptibility
to
the
infectious
hematopoietic
necrosis
virus
(
IHNV)
were
detected
between
Alaskan
and
Columbia
River
stocks
of
chinook
salmon
(
Wertheimer
and
Winton
1982).
Variability
in
temperature
tolerance
between
populations
is
also
probably
due
to
adaptation
to
local
conditions;
however,
information
on
the
genetic
basis
of
this
trait
is
lacking
(
Levings
1993).

Regional
Variation
in
Life­
History
Traits
Comparisons
of
life­
history
traits
among
chinook
salmon
populations
revealed
regional
differences
in
many
traits.
The
definition
of
geographic
regions
which
contained
populations
with
similar
life­
history
attributes
was
an
important
step
in
the
establishment
of
tentative
ESU
boundaries.
The
following
discussion
includes
information
on
anthropogenic
changes
in
habitat
quality,
stock
transfers,
and
artificial
propagation
efforts.
The
impacts
of
these
activities
on
genetic
integrity,
abundance,
and
other
potential
risks
to
chinook
salmon
populations
are
discussed
in
later
sections
in
more
detail
and
are
included
here
only
to
the
extent
that
these
activities
may
have
altered
the
expression
of
life­
history
traits
in
presumptive
native
populations.

Puget
Sound
to
the
Strait
of
Juan
de
Fuca
Chinook
salmon
are
found
in
most
of
the
rivers
in
this
region.
WDF
et
al.
(
1993)
recognizes
27
distinct
stocks
of
chinook
salmon:
8
spring­
run,
4
summer­,
and
15
summer/
falland
fall­
run
stocks.
The
existence
of
an
additional
five
spring­
run
stocks
has
been
disputed
among
different
management
agencies
(
WDF
et
al.
1993).
The
Skagit
River
and
its
tributaries
 
the
Baker,
Sauk,
Suiattle,
and
Cascade
Rivers
 
constitute
what
was
historically
the
predominant
system
in
Puget
Sound
containing
naturally
spawning
populations
(
WDF
et
al.
1993).
Spring­
run
chinook
salmon
are
present
in
the
North
and
South
Fork
Nooksack
Rivers,
the
Skagit
River
Basin,
the
White,
and
the
Dungeness
Rivers
(
WDF
et
al.
1993).
Spring­
run
populations
in
the
Stillaguamish,
Skokomish,
Dosewallips,
and
Elwha
Rivers
are
thought
to
be
extinct
(
Nehlsen
et
al.
1991).
Summer­
run
chinook
salmon
are
present
in
the
Upper
Skagit
and
Lower
Sauk
Rivers
in
addition
to
the
Stilliguamish
and
Snohomish
Rivers
(
WDF
et
al.
1993).
Fall­
run
stocks
(
also
identified
by
management
agencies
as
summer/
fall
runs
in
Puget
Sound)
are
found
throughout
the
region
in
all
major
river
systems.
The
artificial
propagation
of
fall­
run
stocks
is
widespread
throughout
this
region.
Summer/
fall
chinook
salmon
transfers
between
watersheds
within
and
outside
the
region
have
been
commonplace
throughout
this
century;
thus,
the
purity
of
naturally
spawning
stocks
varies
from
river
to
river.
Captive
broodstock/
recovery
programs
for
spring­
run
chinook
salmon
have
been
undertaken
on
the
White
River
(
Appleby
and
Keown
1994),
and
the
Dungeness
River
(
Smith
and
Sele
1995b).
Supplementation
programs
currently
exist
for
spring­
run
chinook
salmon
on
North
Fork
Nooksack
River
and
summer­
run
40
chinook
salmon
on
the
Stillaguamish
and
Skagit
Rivers
(
Marshall
et
al.
1995,
Fuss
and
Ashbrook
1995).
Hatchery
programs
also
release
Suiattle
River
spring­
run
chinook
salmon
and
Snohomish
River
(
Wallace
River)
summer­
run
chinook
salmon
(
Marshall
et
al.
1995,
Fuss
and
Ashbrook
1995).
The
potential
impacts
of
artificial
propagation
and
rearing
programs
(
especially
delayedrelease
programs)
on
the
expression
of
life­
history
traits
were
taken
into
account
when
comparing
the
characteristics
of
each
stock.

Adult
spring­
run
chinook
salmon
in
the
Puget
Sound
typically
return
to
freshwater
in
April
and
May
(
Table
1)
and
spawn
in
August
and
September
(
Fig.
10)
(
Orrell
1976,
WDF
et
al.
1993).
Adults
migrate
to
the
upper
portions
of
their
respective
river
systems
and
hold
in
pools
until
they
mature.
In
contrast,
summer­
run
fish
begin
their
freshwater
migration
in
June
and
July
and
spawn
in
September,
while
summer/
fall­
run
chinook
salmon
begin
to
return
in
August
and
spawn
from
late
September
through
January
(
WDF
et
al.
1993).
Studies
with
radio­
tagged
fish
in
the
Skagit
River
indicated
that
river­
entry
time
was
not
an
accurate
predictor
of
spawning
time
or
location
(
SCC
1995).
In
rivers
with
an
overlap
in
spawning
time,
temporal
runs
on
the
same
river
system
maintain
a
certain
amount
of
reproductive
isolation
through
geographic
separation.
For
example,
an
18­
km
river
section
(
at
river
kilometer
(
RKm)
35­
53)
of
poor
spawning
habitat
separates
the
spawning
areas
for
summer
and
spring
runs
on
the
Sauk
River
(
Williams
et
al.
1975).
Table
1.
Freshwater
migration
(
hatched
areas)
and
spawning
timing
(
gray
areas)
for
selected
chinook
salmon
from
Washington,
Oregon,
California,
and
Idaho.
Run
designations
are
Sp­
spring,
Su­
summer,
F­
Fall,
LF­
late
fall,
and
W­
winter.
Spring
run
designations
for
White
and
Dungeness
River
stocks
have
been
reclassified
by
local
management
agencies,
but
"
sp"
labels
have
been
retained
for
historical
consistency.
The
designation
"
P"
represents
peak
spawning.
Due
to
variability
in
spawning
times
within
a
stock,
some
fish
may
still
be
entering
freshwater
during
the
spawning
time
intervals.
Stocks
in
italics
are
thought
to
be
extinct
but
are
included
for
comparative
purposes.

MONTH
Stock
Run
March
April
May
June
July
Aug.
Sept.
Oct.
Nov.
Dec.
Jan.
Feb.
Reference
1.
Puget
Sound
and
Hood
Canal
N.
F.
Nooksack
R.
Sp
P
WDF
et
al.
1993
S.
F.
Nooksack
R.
Sp
P
WDF
et
al.
1993
Upper
Skagit
R.
Su
P
Orrell
1976,
WDF
et
al.
1993
Lower
Skagit
R.
F
P
WDF
et
al.
1993
Upper
Sauk
R.
Sp
P
Orrell
1976,
WDF
et
al.
1993
Lower
Sauk
R.
Su
P
WDF
et
al.
1993,
WDFW
1995
Suiattle
R.
Sp
P
WDF
et
al.
1993,
WDFW
1995
Upper
Cascade
R.
Sp
P
WDF
et
al.
1993,
WDFW
1995
Stillaguamish
R.
Su
P
WDF
et
al.
1993,
WDFW
1995
Stillaguamish
R.
F
P
WDF
et
al.
1993
Snohomish
R.
Su
WDF
et
al.
1993
Snohomish
R.
F
P
WDF
et
al.
1993
Cedar
R.
F
WDF
et
al.
1993
Green
R.
F
P
WDF
et
al.
1993
White
R.
Sp
WDF
et
al.
1993
Nisqually
R.
F
WDF
et
al.
1993
Duckabush/
Dosewalips
R.
F
P
PNPTC
1995
Skokomish
R.
F
P
WDF
et
al.
1993
2.
Washington
Coast
and
the
Strait
of
Juan
de
Fuca
Dungeness
R.
Sp
P
PNPTC
1995,
WDFW
1995
Elwha
R.
F
P
PNPTC
1995,
WDFW
1995
Hoko
R.
F
P
WDF
et
al.
1993,
WDFW
1995
Sooes
R.
F
P
P
WDF
et
al.
1993
Sol
Duc
R.
Sp
P
WDF
et
al.
1993,
QTNR
1995
Sol
Duc
R.
F
P
WDF
et
al.
1993
Bogachiel
R.
Su
P
QTNR
1995
Bogachiel
R.
F
P
WDF
et
al.
1993
Calawah
R.
Su
P
WDF
et
al.
1993
Calawah
R.
F
P
WDF
et
al.
1993
Table
1
(
Cont.).

MONTH
Stock
Run
March
April
May
June
July
Aug.
Sept.
Oct.
Nov.
Dec.
Jan.
Feb.
Reference
Hoh
R.
Sp
P
WDF
et
al.
1993,
HIT
1995
Hoh
R.
F
P
WDF
et
al.
1993
Queets
R.
Sp
P
WDF
et
al.
1993,
QTNR
1995
Queets
R.
F
WDF
et
al.
1993,
QTNR
1995
Quinault
R.
Sp
WDF
et
al.
1993,
QTNR
1995
Quinault
R.
F
WDF
et
al.
1993,
QTNR
1995
Chehalis
R.
Sp
P
WDF
et
al.
1993
Chehalis
R.
F
WDF
et
al.
1993
Wynoochee
R.
Sp
P
Wynoochee
R.
F
WDF
et
al.
1993
Satsop
R.
Su
WDF
et
al.
1993
Satsop
R.
F
P
WDF
et
al.
1993
Elk
R.
F
P
WDF
et
al.
1993
Wilapa
Bay
R.
F
P
WDF
et
al.
1993
North
R.
F
P
WDF
et
al.
1993
3.
Columbia
River
Basin
(
excluding
the
Snake
River
Basin)
Lower
Col
R.
F
P
P
Howell
et
al.
1985,
WDF
et
al.
1993
Cowlitz
R.
Sp
P
Howell
et
al.
1985,
WDF
et
al.
1993
Kalama
R.
Sp
P
Howell
et
al.
1985,
WDF
et
al.
1993
Kalama
R.
F
Howell
et
al.
1985,
WDF
et
al.
1993
Lewis
R.
Sp
P
Howell
et
al.
1985,
WDF
et
al.
1993
Lewis
R.
F
P
WDF
et
al.
1993,
WDFW
1995
Washougal
R.
F
P
Howell
et
al.
1985,
WDF
et
al.
1993
Clackamas
R.
Sp
P
Galbreath
1965,
Howell
et
al.
1985
Santiam
R.
Sp
P
Howell
et
al.
1985,
Olsen
et
al.
1992
Willamette
R.
Sp
P
Howell
et
al.
1985,
Bennett
1988
Sandy
R.
(
Late)
F
Howell
et
al.
1985
Wind
R.
Sp
P
Schreck
et
al.
1986,
WDF
et
al.
1986
Klickitat
R.
Sp
P
Howell
et
al.
1995,
WDF
et
al.
1993
Deschutes
R.
Sp
P
Lindsay
et
al.
1989,
Olsen
et
al.
1992
Deschutes
R.
F
P
Jonasson
and
Lindsay
1988
Table
1
(
Cont.).

MONTH
Stock
Run
March
April
May
June
July
Aug.
Sept.
Oct.
Nov.
Dec.
Jan.
Feb.
Reference
John
Day
R.
Sp
P
Burck
et
al.
1979,
Olsen
1994d
John
Day
R.
F
Howell
et
al.
1985
Yakima
R.
Sp
P
Howell
et
al.
1985,
WDF
et
al.
1993
Naches
R.
Sp
P
P
Major
and
Mighell
1969,
WDFW
1995
American
R.
Sp
P
Major
and
Mighell
1969,
WDFW
1995
Yakima
R.
F
P
WDF
et
al.
1993,
WDFW
1995
Marion
Drain
F
P
WDF
et
al.
1993,
WDFW
1995
Hanford
Reach
F
P
Howell
et
al.
1985,
WDF
et
al.
1993
Wenatchee
R.
Sp
P
French
and
Wahle
1959,
Chapman
et
al.
1995
Wenatchee
R.
Su
P
P
WDF
et
al.
1993,
Peven
and
Truscott
1995
Entiat
R.
Sp
P
WDF
et
al.
1993,
Chapman
et
al.
1995
Methow
R.
Sp
P
WDF
et
al.
1993,
Chapman
et
al.
1995,
USFS
1995
Methow
R.
Su
P
P
WDF
et
al.
1993,
Chapman
et
al.
1994
Okanogan
R.
Su
P
P
WDF
et
al.
1993,
Chapman
et
al.
1994
4.
Snake
River
Tucannon
R.
Sp
WDF
et
al.
1993
M.
S.
Snake
R.
Sp
Keifer
et
al.
1992
Snake
R.
F
P
Chapman
et
al.
1991,
Garcia
et
al.
1996
Grande
Ronde
R.
Sp
P
Howell
et
al.
1985
Grande
Ronde
R.
F
Olsen
et
al.
1992
Wenaha
R.
Sp
?
P
Chapman
et
al.
1990
Imnaha
R.
Sp
P
Howell
et
al.
1985
M.
F.
Clearwtr.
R.
Sp
Keifer
et
al.
1992
Rapid
R.
Sp
P
P
Howell
et
al.
1985,
Schreck
et
al.
1986
M.
F.
Salmon
R.
Sp
?
P
Keifer
et
al.
1992
Little
Salmon
R.
Su
P
Keifer
et
al.
1992
Salmon
R.
Su
Keifer
et
al.
1992
Pahsimeroi
R.
Su
Keifer
et
al.
1992
5.
Oregon
Coast
(
to
the
Elk
River
and
Cape
Blanco)
Table
1
(
Cont.).

MONTH
Stock
Run
March
April
May
June
July
Aug.
Sept.
Oct.
Nov.
Dec.
Jan.
Feb.
Reference
Nehalem
R.
Su
P
Nicholas
and
Hankin
1988
Miami
R.
F
P
Nicholas
and
Hankin
1988
Klichis
R.
F
P
Nicholas
and
Hankin
1988
Nicholas
and
Hankin
1988
Wilson
R.
F
P
Nicholas
and
Hankin
1988
Nicholas
and
Hankin
1988
Trask
R.
Sp
P
P
Nicholas
and
Hankin
1988
Trask
R.
F
Nicholas
and
Hankin
1988
Nicholas
and
Hankin
1988
Tillamook
R.
F
P
Nicholas
and
Hankin
1988
Nestucca
R.
Sp
P
Nicholas
and
Hankin
1988
Nestucca
R.
F
P
Nicholas
and
Hankin
1988
Salmon
R.
F
P
Nicholas
and
Hankin
1988
Siletz
R.
Sp
P
Nicholas
and
Hankin
1988
Siletz
R.
F
P
Nicholas
and
Hankin
1988
Yaquina
R.
F
P
Nicholas
and
Hankin
1988
Alsea
R.
Sp
P
Nicholas
and
Hankin
1988
Alsea
R.
F
P
Nicholas
and
Hankin
1988
Suislaw
R.
F
P
Nicholas
and
Hankin
1988
Umpqua
R.
(
Up.)
F
P
Nicholas
and
Hankin
1988
Umpqua
R.
(
Smith)
F
P
Nicholas
and
Hankin
1988
Umpqua
R.
Sp
P
Nicholas
and
Hankin
1988
Coos
R.
F
P
Nicholas
and
Hankin
1988
Coquille
R.
F
P
Nicholas
and
Hankin
1988
Euchre
Ck.
F
Nicholas
and
Hankin
1988
Floras
Ck.
F
P
Nicholas
and
Hankin
1988
Sixes
R.
F
P
Uremovich
1977,
Nicholas
and
Hankin
1988
Elk
R.
F
P
P
Burck
and
Reimers
1978
Nicholas
and
Hankin
1988
6.
Southern
Oregon
and
California
Coast
and
Klamath
River
Basin
Rogue
R.
Sp
P
Nicholas
and
Hankin
1988,
ODFW
1991
Rogue
R.
F
P
Nicholas
and
Hankin
1988,
ODFW
1991
Hunter
Ck.
F
P
Nicholas
and
Hankin
1988,
ODFW
1991
Pistol
R.
F
P
Nicholas
and
Hankin
1988,
ODFW
1991
Chetco
R.
F
P
Nicholas
and
Hankin
1988,
ODFW
1991
Table
1
(
Cont.).

MONTH
Stock
Run
March
April
May
June
July
Aug.
Sept.
Oct.
Nov.
Dec.
Jan.
Feb.
Reference
Winchuck
R.
F
P
McLeod
1995
Smith
R.
Sp
Leidy
and
Leidy
1984
Smith
R.
F
P
Waldvogel
1995
Klamath
R.
Basin
Sp
HVTC
1997
Klamath
R.
Basin
F
HVTC
1997
Klamath
R.
Sp
P
Snyder
1931,
USFWS
1994,
Tuss
et
al.
1987
Klamath
R.
F
P
Leidy
and
Leidy
1984,
Synder
1931,
USFWS
1994
Klamath
R.
LF
P
Synder
1931
Shasta
R.
F
P
CDFG
1995
Trinity
R.
Sp
Moffett
and
Smith
1950,
CDFG
1995,
Dean
1995
Trinity
R.
F
P
USFWS
1994
Little
R.
F
P
Mosser
1995
Mad
R.
F
P
McLeod
1995
Eel
R.
F
P
Grass
1995
Mattole
R.
F
Young
1987,
Busby
1991
Garcia
R.
F
P
P
Nielsen
et
al.
1995
Russian
R.
F
P
P
Gunter
1995
7.
Sacramento
and
San
Joaquin
Rivers
San
Joaquin
R.
F
P
Neillands
1995
San
Joaquin
R.
Sp
P
Hallock
and
Van
Woert
1959
Mokelumne
R.
F
P
EBMOD
1995,
CDFG
1997f
Stanislaus
R.
F
P
Fisher
1994,
CDFG
1997f
Merced
R.
F
P
Neillands
1995,
CDFG
1997f
Sacramento
R.
Sp
P
P
Calkins
et
al.
1940,
Sacramento
R.
F
P
Calkins
et
al.
1940,
Kjelson
et
al.
1982
American
R.
F
P
Clark
1929,
Ducey
1995
Sacramento
R.
LF
Clark
1929,
Fisher
1994
Sacramento
R.
W
P
P
Fisher
1994
Deer
Ck.
Sp
P
46
Figure
10.
Month
of
peak
spawning
activity
for
spring­,
summer­,
fall­,
and
winter­
run
chinook
salmon
in
Washington,
Oregon,
California,
and
Idaho.
Shapes
with
two
shades
or
patterns
indicate
that
the
peak
occurs
at
the
end
of
the
earlier
month
and
the
beginning
of
the
later
month.
47
The
majority
of
Puget
Sound
fish
emigrate
to
the
ocean
as
subyearlings.
Many
of
the
rivers
have
well­
developed
estuaries
that
are
important
rearing
areas
for
emigrating
ocean­
type
smolts.
Puget
Sound
stocks
also
tend
to
have
relatively
large
eggs,
with
average
diameter
being
greater
than
8.0
mm,
which
may
be
an
adaptation
for
their
subyearling
smolting
strategy.
In
contrast,
the
Suiattle
and
South
Fork
Nooksack
Rivers
have
been
characterized
as
producing
a
majority
of
yearling
smolts
(
Fig.
11)
(
Marshall
et
al.
1995).
Analysis
of
scales
from
adults
returning
to
the
South
Fork
Nooksack
in
1994
and
1995
indicated
that
69.1%
of
the
fish
had
emigrated
as
yearlings
(
WDFW
1995);
however,
analysis
of
adults
returning
in
1980­
85
showed
only
16.4%
of
the
fish
had
emigrated
as
yearlings
and
75%
of
these
were
hatchery
fish
(
WDFW,
unpublished).
The
reason
for
this
difference
is
unknown.
Glacially
influenced
conditions
on
the
Suiattle
River
may
be
responsible
for
limiting
juvenile
growth,
delaying
smolting,
and
producing
a
higher
proportion
of
4­
and
5­
year­
olds
compared
to
other
chinook
salmon
stocks
in
Puget
Sound,
which
mature
predominantly
as
3­
and
4­
year­
olds
(
Fig.
12).
Puget
Sound
stocks
exhibit
a
similarity
in
marine
distribution
based
on
CWT
recoveries
in
ocean
fisheries.
Tagged
fish
have
been
primarily
captured
in
Canadian
coastal
and
Puget
Sound
waters
(
Fig.
13).
Marine
recoveries
of
CWTs
from
Nooksack
River
spring­
run
chinook
salmon
have
occurred
to
a
lesser
extent
in
the
Puget
Sound
fishery
than
in
other
Puget
Sound
stocks.
This
may
be
due
to
the
geographical
position
of
the
Nooksack
River
Basin
at
the
northern
end
of
Puget
Sound
and/
or
the
allocation
of
effort
by
fishers
in
Puget
Sound.
Additionally,
Elwha
River
summer/
fall
chinook
salmon
CWT
recoveries
in
Alaska
and
Puget
Sound
appear
to
be
intermediate
in
their
frequencies
between
Puget
Sound
stocks
and
Washington
coast
stocks.

Anthropogenic
activities
have
limited
the
access
to
historical
spawning
grounds
and
altered
downstream
flow
and
thermal
conditions.
Water
diversion
and
hydroelectric
dams
haveprevented
access
to
portions
of
several
rivers.
Furthermore,
the
construction
of
Cushman
Dam
on
the
North
Fork
Skokomish
River
may
have
resulted
in
a
residualized
population
of
chinook
salmon
in
Lake
Cushman.
Watershed
development
and
activities
throughout
Puget
Sound,
Hood
Canal,
and
Strait
of
Juan
de
Fuca
regions
have
resulted
in
increased
sedimentation,
higher
water
temperatures,
decreased
large
woody
debris
(
LWD)
recruitment,
decreased
gravel
recruitment,
a
reduction
in
river
pools
and
spawning
areas,
and
a
loss
of
estuarine
rearing
areas
(
Bishop
and
Morgan
1996).
These
impacts
on
the
spawning
and
rearing
environment
may
also
have
had
an
impact
on
the
expression
of
many
life­
history
traits
and
masked
or
exaggerated
the
distinctiveness
of
many
stocks.

Life­
history
similarities
 
emigration
timing,
age
at
maturation,
and
ocean
migration
 
among
spring­,
summer­,
and
fall­
run
chinook
salmon
may
be
related
to
the
relatively
recent
deglaciation
(
10,000
b.
p.)
of
the
Puget
Sound
region.
It
is
unclear
when
suitable
freshwater
habitats
for
chinook
salmon
became
available
in
the
Puget
Sound
area
following
deglaciation
(
Busack
and
Marshall
1995).
However,
chinook
salmon
in
Oregon
coastal
rivers,
which
were
not
glaciated,
also
show
little
differentiation
in
life­
history
characteristics,
except
for
run
timing.
The
life
history
exhibited
may
instead
represent
an
optimized
strategy
for
stocks
in
48
Figure
11.
Proportional
distribution
of
subyearling
and
yearling
smolts
for
selected
runs
of
chinook
salmon
in
Washington,
Oregon,
California,
and
Idaho.
References
for
data
points
can
be
found
in
Appendix
A.
49
50
51
52
53
54
55
the
Puget
Sound
area
regardless
of
run
timing
or
simply
the
homogenization
of
stocks
due
to
artificial
propagation.

Washington
and
Oregon
coasts
(
Hoko
River
to
Cape
Blanco)

Fall­,
summer­,
and
spring­
run
chinook
salmon
are
found
in
this
region.
Rivers
in
this
region
tend
to
be
short
with
low
gradients
near
the
coast.
These
low
gradient
areas
are
preferred
spawning
sites
for
chinook
salmon.
The
relatively
small
size
of
the
rivers
limits
the
amount
of
spawning
habitat
available
and
minimizes
the
likelihood
of
spatial
separation
of
run
times.
The
Chehalis
and
Umpqua
Rivers
are
physically
much
larger
than
any
of
the
other
basins,
although
they
do
not
maintain
proportionately
larger
chinook
salmon
runs.
WDF
et
al.
(
1993)
recognized
2
spring­
run,
4
summer­
run,
4
spring/
summer­
run,
and
23
fall­
run
"
stocks"
on
the
Washington
coast.
According
to
the
Oregon
Department
of
Fish
and
Wildlife
(
ODFW),
the
Oregon
coast
from
the
mouth
of
the
Columbia
River
to
Cape
Blanco
contains
11
spring­
run,
1
summer­
run,
and
33
fall­
run
populations
(
Kostow
1995).
Peak
spawning
periods
for
spring,
spring/
summer,
and
summer­
run
populations
occur
from
mid­
September
to
early
October
which
is
somewhat
later
than
in
Puget
Sound
and
the
Strait
of
Juan
de
Fuca.
Peak
river­
entry
times
for
spring­
and
summer­
run
stocks
range
from
May
to
August.
In
general,
populations
considered
spring,
spring/
summer,
and
summer
runs
return
to
the
river
at
an
immature
stage
and
hold
in
the
river
for
an
extended
period
before
spawning.
In
contrast,
fall­
run
fish
enter
freshwater
at
an
advanced
stage
of
maturation.
Peak
spawning
periods
for
coastal
fall
runs
occur
from
late­
October
to
early­
December,
with
a
tendency
for
later
spawning
in
more
southerly
rivers.
The
existence
of
multiple
runs
on
many
of
the
smaller
coastal
river
systems
is
associated
with
low
summer
flows
that
physically
limit
access
or
result
in
high
summer
water
temperatures
in
the
lower
river
reaches
(
Nicholas
and
Hankin
1988).

Chinook
salmon
from
the
Washington
and
Oregon
coasts
emigrate
to
saltwater
primarily
as
subyearlings
and
utilize
the
productive
estuary
and
coastal
areas
as
rearing
habitat.
The
limited
size
of
many
coastal
watersheds
mandates
the
reliance
on
extended
estuary
or
coastal
rearing
by
juveniles.
Furthermore,
high
summer
water
temperatures
and
related
low
flows
may
be
responsible
for
early
emigration.
Chinook
salmon
from
coastal
populations
(
ocean­
type)
tend
to
have
much
larger
eggs
than
inland,
predominantly
stream­
type,
populations
(
Rich
1920b
,
Nicholas
and
Hankin
1988,
Lister
1990).
Larger
eggs
result
in
larger
juveniles
and
may
enable
an
earlier
and
more
successful
emigration
to
marine
rearing
habitat
(
Fowler
1972,
Kreeger
1995).
The
Washington
and
Oregon
coasts
contain
numerous
large
estuary
areas:
Grays
Harbor,
Willapa
Bay,
Tillamook
Bay,
Coos
Bay,
Winchester
Bay
(
Umpqua
R.),
and
Yaquina
Bay.
Emigrating
juveniles
from
rivers
without
well­
developed
estuary
systems
may
undertake
coastal
migrations
to
estuary
feeding
areas
or
find
sufficient
rearing
habitat
in
coastal
areas,
but
it
is
unclear
which
strategy
they
undertake.
Coastal
chinook
salmon
from
this
region
also
mature
at
a
later
age
than
stocks
from
Puget
Sound,
the
lower
Columbia
River
and
southern
Oregon
coastal
areas
(
Nicholas
and
Hankin
1988,
SCC
1995,
QFD
1995,
WDFW
1995).
The
majority
of
the
56
runs
are
composed
of
4­
and
5­
year­
old
fish,
with
a
small
proportion
of
6­
year­
olds.
The
numerically
large
populations
of
chinook
salmon
on
smaller
coastal
rivers
may
create
competition
for
mates
and
select
for
larger
(
older)
male
chinook
salmon
(
Roni
and
Quinn
1995).

Marine
recoveries
of
CWTs
indicate
a
similar
ocean
migration
distribution
for
Washington
and
northern
Oregon
coastal
stocks.
The
majority
of
the
recoveries
are
from
4­
and
5­
year­
old
fish
in
British
Columbia
and
Alaska
fisheries.
This
is
a
more
northerly
oceanic
distribution
than
is
observed
for
Puget
Sound,
Lower
Columbia
River,
and
Southern
Oregon
and
California
stocks.
A
proportion
of
fish
from
stocks
in
the
vicinity
of
Cape
Blanco
tend
to
exhibit
a
"
north­
andsouth
migration
pattern,
with
a
proportion
of
recoveries
occurring
in
Oregon
and
California
coastal
waters
(
Nicholas
and
Hankin
1988).
The
existence
of
a
transition
zone
in
migratory
patterns
may
be
due
to
natural
and/
or
anthropogenic
factors.
CWT
ocean
recoveries
of
Umpqua
River
spring­
run
chinook
salmon,
specifically
Rock
Creek
Hatchery
fish,
show
a
north
and
south
distribution.
The
mouth
of
the
Umpqua
River
is
almost
100
km
north
of
Cape
Blanco;
however,
the
Umpqua
River
has
received
transfers
of
Rogue
River
spring­
run
chinook
salmon,
a
south
migrating
stock,
during
rebuilding
programs
over
the
past
decades.
The
north­
south
migratory
pattern
may
be
the
result
of
hybridization
of
Rogue
and
Umpqua
River
stocks.
Differences
in
age
and
oceanic
migration
pattern
between
the
Washington
and
Oregon
coast
and
neighboring
regions
were
among
the
most
pronounced
of
any
life­
history
comparisons.

California
and
southern
Oregon
coast
(
south
of
Cape
Blanco)

The
coastal
drainages
south
of
Cape
Blanco
are
dominated
by
the
Rogue,
Klamath,
and
Eel
Rivers.
The
Chetco,
Smith,
Mad,
Mattole,
and
Russian
Rivers
and
Redwood
Creek
are
smaller
systems
that
contain
sizable
populations
of
fall­
run
chinook
salmon
(
Campbell
and
Moyle
1990,
ODFW
1995).
Presently,
spring
runs
are
found
in
the
Rogue,
Klamath,
and
Trinity
Rivers;
additionally,
a
vestigial
spring
run
may
still
exist
on
the
Smith
River
(
Campbell
and
Moyle
1990,
USFS
1995).
Historically,
fall­
run
chinook
salmon
were
predominant
in
most
coastal
river
systems
south
to
the
Ventura
River;
however,
their
current
distribution
only
extends
to
the
Russian
River
(
Healey
1991).
There
have
also
been
spawning
fall­
run
chinook
salmon
reported
in
small
rivers
draining
into
San
Francisco
Bay
(
Nielsen
et
al.
1994).

Chinook
salmon
populations
south
of
Cape
Blanco
all
exhibit
an
ocean­
type
life
history.
The
majority
of
fish
emigrate
to
the
ocean
as
subyearlings,
although
yearling
smolts
can
constitute
up
to
approximately
a
fifth
of
outmigrants
from
the
Klamath
River
Basin,
and
to
a
lesser
proportion
in
the
Rogue
River
Basin;
however,
the
proportion
of
fish
which
smolted
as
subyearling
vs.
yearling
varies
from
year
to
year
(
Snyder
1931,
Schluchter
and
Lichatowich
1977,
Nicholas
and
Hankin
1988,
Barnhart
1995).
This
fluctuation
in
age
at
smoltification
is
more
characteristic
of
an
ocean­
type
life
history.
Furthermore,
the
low
flows,
high
temperatures,
and
barrier
bars
that
develop
in
smaller
coastal
rivers
during
the
summer
months
would
favor
an
ocean­
type
(
subyearling
smolt)
life
history
(
Kostow
1995).
57
Run
timing
for
spring­
run
chinook
salmon
in
this
area
typically
begins
in
March
and
continues
through
July,
with
peak
migration
occurring
in
May
and
June.
Spawning
begins
in
late
August
and
can
continue
through
October,
with
a
peak
in
September.
Historically,
spring­
run
spawning
areas
were
located
in
the
river
headwaters
(
generally
above
400
m).
Run
timing
for
fallrun
chinook
salmon
varies
depending
on
the
size
of
the
river.
Adult
Rogue,
Upper
Klamath,
and
Eel
River
fall
chinook
salmon
return
to
freshwater
in
August
and
September
and
spawn
in
late
October
and
early
November
(
Stone
1897,
Snyder
1931,
Nicholas
and
Hankin
1988,
Barnhart
1995).
In
other
coastal
rivers
and
the
lower
reaches
of
the
Klamath
River,
fall­
run
freshwater
entry
begins
later
in
October,
with
peak
spawning
in
late
November
and
December
 
often
extending
into
January
(
Leidy
and
Leidy
1984,
Nicholas
and
Hankin
1988,
Barnhart
1995).
Latefall
or
"
snow"
chinook
salmon
from
Blue
Creek,
on
the
lower
Klamath
River,
were
described
as
resembling
the
fall­
run
fish
from
the
Smith
River
in
run
and
spawning
timing,
as
well
as
the
degree
of
sexual
maturation
at
the
time
of
river
entry
(
Snyder
1931).

Populations
in
this
region
are
readily
distinguished
from
more
northerly
coastal
populations
by
their
oceanic
migration
patterns.
Recoveries
of
CWTs
in
ocean
fisheries
occur
primarily
off
the
Oregon
and
California
coasts.
The
majority
of
the
spring
and
fall
runs
are
composed
of
3­
and
4­
year­
old
fish,
with
a
small
proportion
of
5­
year­
olds
(
Snyder
1931,
Kutkuhn
1963,
Nicholas
and
Hankin
1988,
Barnhart
1995).
Analysis
of
scales
from
"
late­
fall
run"
fish
returning
to
the
lower
Klamath
River
indicated
that
there
was
a
higher
proportion
of
5­
yearold
fish
(
up
to
51%)
compared
with
spring­
or
fall­
run
fish
returning
to
the
upper
Klamath
River
(
Snyder
1931).
In
general,
fish
from
coastal
populations
south
of
Cape
Blanco
mature
earlier
than
those
to
the
north.

Other
morphological
and
physiological
differences
between
geographic
regions
have
been
observed.
McGregor
(
1923a)
and
Snyder
(
1931)
described
significant
differences
between
Klamath
and
Sacramento
River
fish
in
gill
arch
and
pyloric
caeca
counts,
in
addition
to
body
size
and
fecundity.
Dorsal
fin
ray,
anal
fin
ray,
and
branchiostegal
counts
for
the
Klamath
River
chinook
salmon
were
significantly
lower
than
for
Columbia
River
ocean­
or
stream­
type
chinook
salmon
stocks
(
Snyder
1931,
Schreck
et
al.
1986).
Rich
(
1920b)
found
that
coastal
stocks
from
the
Umpqua
and
Rogue
Rivers
had
larger
eggs
than
Columbia
River
stocks.
Egg
diameters
for
fall­
run
chinook
salmon
on
the
Klamath
River
averaged
9
mm
(
Snyder
1931),
which
is
similar
to
ranges
presented
by
Nicholas
and
Hankin
(
1988)
for
Oregon
coast
chinook
salmon
but
much
larger
than
for
populations
in
the
Sacramento
River
(
see
California
Central
Valley
section).
Furthermore,
data
collected
by
McGregor
(
1922,
1923b)
indicated
that
for
a
given
length,
Sacramento
River
fish
have
a
higher
average
fecundity
and
smaller
egg
size
than
fish
from
the
Klamath
River.
While
coastal
populations
south
of
Cape
Blanco
are
substantially
different
from
those
to
the
north,
there
is
some
finer
scale
differentiation
between
shorter
coastal
system
and
the
two
larger
river
basins,
the
Rogue
and
Klamath
Rivers.

Agricultural,
logging,
and
mining
activities,
in
combination
with
periodic
flood
events
(
e.
g.
1955,
1969),
have
affected
all
of
the
coastal
river
systems
to
some
degree.
Mining
activities
58
have
also
caused
severe
habitat
degradation.
The
construction
of
dams
on
the
Rogue,
Klamath,
and
Eel
River
Basins
has
restricted
the
distribution
and
potentially
altered
the
life
history
of
chinook
salmon,
especially
spring­
run
fish
that
historically
utilized
upstream
habitat.
Lost
Creek
Dam
(
RKm
253)
eliminated
one­
third
of
the
spawning
habitat
of
spring­
run
chinook
salmon
in
the
Rogue
River
(
Kostow
1995).
Additionally,
changes
in
river
flow
and
temperature
have
allowed
fall­
run
chinook
salmon
to
spawn
in
more
upstream
locations
and
increased
the
opportunities
for
interbreeding
between
fall
and
spring
runs
(
ODFW
1990).
Similarly,
dam
construction
on
the
Klamath
River
Basin
has
eliminated
much
of
the
spawning
habitat
for
spring­
run
fish
and
increased
the
potential
for
interbreeding
between
spring
and
fall
runs.
Fish
passage
to
the
upper
Klamath
River
was
blocked
at
Klamath
Falls
by
the
Link
River
hydroelectric
dam
in
1895.
Several
dams
have
subsequently
been
constructed
on
the
mainstem
Klamath
River.
Historically,
the
largest
spring­
run
population
in
the
Klamath
River
Basin
was
in
the
Shasta
River;
however,
this
population
was
extirpated
in
the
early
1930s
as
a
result
of
land
use
practices
and
water
diversion
dams.
Since
1962,
the
upper
limit
to
anadromous
migration
has
been
the
Iron
Gate
Dam
(
RKm
306).
Additionally,
the
Lewiston
water
diversion
dam
(
RKm
249)
on
the
Trinity
River
has
prevented
access
of
spring­
run
chinook
salmon
to
their
historical
spawning
grounds
on
the
East
Fork,
Stuart
Fork,
and
Upper
Trinity
River
and
Coffee
Creek
(
Campbell
and
Moyle
1990).
Hatchery­
reared
smolts,
especially
yearling
smolts,
from
mitigation
hatcheries
on
the
Klamath
River
(
Iron
Gate
Hatchery)
and
Trinity
River
(
Trinity
River
Hatchery)
have
probably
altered
age
of
maturation
and
smoltification
estimates
derived
from
the
scales
of
unmarked
returning
adults.
The
life­
history
attributes
of
coastal
chinook
salmon
south
of
Cape
Blanco
are
quite
distinct
from
those
to
the
north,
in
the
Upper
Klamath
River
Basin,
and
those
in
the
Central
Valley.
These
differences
exist
in
spite
of
artificial
propagation
and
the
loss
of
ecologically
distinct
spawning
and
rearing
habitat
areas.

California
Central
Valley
The
Sacramento
and
San
Joaquin
Rivers
and
their
tributaries
contain
several
different
groups
of
chinook
salmon
based
on
run
timing
and
habitat
utilization.
Historically,
spring­
run
fish
were
predominant
throughout
the
Central
Valley,
occupying
the
upper
and
middle
reaches
(
450­
1,600
m
in
elevation)
of
the
San
Joaquin,
American,
Yuba,
Feather,
Sacramento,
McCloud,
and
Pit
Rivers,
with
smaller
populations
in
most
other
tributaries
with
sufficient
cold­
water
flow
to
maintain
spring­
run
adults
through
the
summer
prior
to
spawning
(
Stone
1874,
Rutter
1904,
Clark
1929).
Winter­
run
populations
historically
utilized
the
upper
watersheds
(
450­
900
m
in
elevation)
of
the
upper
Sacramento,
Pit,
McCloud,
and
Calaveras
Rivers
and
were
not
as
numerous
as
the
spring
or
fall
runs
(
Slater
1963,
Reynolds
et
al.
1993).
Fall
and
late­
fall
runs
spawn
in
the
lower
reaches
(
60­
600
m)
of
most
rivers
and
streams
in
the
Central
Valley
(
Clark
1929,
Hallock
and
Fry
1967,
Reynolds
et
al.
1993).
Fall­
run
chinook
salmon
are
currently
the
most
numerous
of
the
runs
in
the
Central
Valley.
Habitat
degradation
due
to
dams,
water
diversions,
and
placer
mining,
as
well
as
past
and
present
land­
use
practices
have
severely
reduced
the
range
and
number
of
spring­
and
winter­
run
chinook
salmon
and
to
a
lesser
extent
fall
and
late­
fall
runs
(
Clark
1929,
Needham
et
al.
1940,
Reynolds
et
al.
1993,
Fisher
1994).
59
Central
Valley
chinook
salmon
exhibit
an
ocean­
type
life
history.
Large
numbers
of
fry
have
been
observed
emigrating
during
the
winter
and
spring
(
Rutter
1904,
Rich
1920a,
Calkins
et
al.
1940,
Kjelson
et
al.
1982,
Gard
1995).
High
summer
water
temperatures
in
the
lower
Sacramento
River
(
temperatures
in
the
Sacramento­
San
Joaquin
Delta
can
exceed
22
E
C)
present
a
thermal
barrier
to
up­
and
downstream
migration
and
may
be
partially
responsible
for
the
evolution
of
the
fry
migration
life
history
(
Rich
1920a,
Kjelson
et
al.
1982).
Water
withdrawals
for
agricultural
and
municipal
purposes,
have
occasionally
been
of
a
sufficient
magnitude
to
result
in
reverse
flows
in
the
lower
San
Joaquin
River.

Age
estimates
from
scales
of
returning
adults
in
1919
and
1921
indicated
that
89%
of
the
fish
had
emigrated
as
subyearlings
(
Clark
1929).
Scale
samples
in
Clark's
study
were
from
returning
adults
taken
below
the
confluence
of
the
Sacramento
and
San
Joaquin
Rivers.
Scale
samples
were
made
throughout
the
year
during
the
course
of
the
in­
river
fishing
season
(
there
were
two
closures
during
early
June
to
early
July
and
late
September
to
early
November)
and
would
have
included
all
of
the
runs.
Calkins
et
al.
(
1940)
sampled
both
the
fall
and
spring
runs
on
the
upper
Sacramento
River
and
determined
that
the
proportion
of
adults
that
emigrated
as
subyearlings
in
both
runs
was
90%.
Gard
(
1995)
stated
that
the
majority
of
smolts
from
all
four
runs
on
the
upper
Sacramento
River
currently
emigrate
as
subyearlings.
The
emigration
of
spring,
fall,
and
late­
fall
runs
is
completed
prior
to
high
summer
temperatures
in
the
lower
river,
while
winter­
run
emigration
does
not
begin
until
after
the
summer
temperatures
have
started
to
diminish
in
August
(
Fig.
14).
In
contrast,
Fisher
(
1994)
suggested
that
a
large
proportion
of
late­
fall
and
spring­
run
juveniles
emigrate
as
yearlings,
the
average
length
for
late­
fall­
run
and
spring­
run
smolts
being
160
and
115
mm,
respectively.
Using
scales
from
returning
adults,
Calkins
et
al.
(
1940)
estimated
that
the
average
size
of
subyearling
fall­
and
spring­
run
smolts
at
the
time
of
ocean
entrance
was
88
and
83
mm,
respectively.
Emigrating
juveniles
sampled
in
the
upper
Sacramento
River
are,
on
average,
less
than
70
mm
in
length
(
Gard
1995).
Vast
numbers
of
fry
(<
70
mm)
were
observed
rearing
in
the
Sacramento­
San
Joaquin
River
estuary,
but
relatively
few
larger
smolts
were
found
in
the
late
spring
or
fall
(
Kjelson
et
al.
1982).
Fry
tend
to
remain
in
the
estuary
for
an
extended
period
of
almost
2
months
(
Kjelson
et
al.
1982).
The
tendency
for
fish
to
emigrate
as
fry
appears
to
be
characteristic
of
this
region
and
is
linked
to
summer
water
conditions
(
low
flow
and
high
temperatures).

As
with
the
timing
of
smolt
emigration,
the
timing
of
the
adult
return
migration
and
spawning
is
dictated
by
high
summer
temperatures.
Fall­
and
late­
fall
runs
enter
freshwater
at
an
advanced
stage
of
maturity
and
move
quickly
to
their
spawning
sites.
The
return
migration
does
not
begin
until
late
August
or
September
(
fall
run)
or
December
(
late­
fall
run)
after
summer
temperatures
have
declined
(
Hallock
and
Fry
1967).
Fall­
run
and
late­
fall­
run
chinook
salmon
peak
spawning
occurs
in
late
October
and
early
February,
respectively
(
Fisher
1994).
Winter­
run
and
spring­
run
fish
enter
freshwater
well
in
advance
of
spawning.
Winter­
run
adults
historically
60
Figure
14.
Percentage
passage
(
shaded
area)
of
emigrating
juvenile
chinook
salmon
and
their
corresponding
length
(
mm)
for
spring,
fall,
late­
fall,
and
winter
runs
on
the
Sacramento
River.
Downstream
migrants
were
sampled
at
Red
Bluff
Diversion
Dam
(
Rkm
391)
and
assigned
to
specific
run
designations
based
on
growth
models
for
each
run
timing
(
Gard
1995).
Summer
high­
water
temperatures
in
the
lower
Sacramento
River
create
a
thermal
block
to
downstream
migration.
61
would
have
migrated
upstream
at
a
time
of
high
river
flows
in
late
November
through
January
and
held
in
upriver
areas
until
spawning
sometime
in
April­
July
(
Slater
1963,
Fisher
1994).
The
eggs
deposited
would
have
developed
during
the
summer
months
in
the
cold
headwaters
of
the
Sacramento,
Pit,
McCloud,
and
Calaveras
Rivers.
Fry
would
then
emigrate
in
the
fall
after
temperatures
in
the
lower
river
had
cooled.
The
migration
of
the
spring
run
began
in
March
and
April,
later
than
the
winter
run,
when
river
flows
were
still
sufficient
for
these
fish
to
gain
access
to
the
cool,
spring­
and
snow­
fed
upper
reaches
of
rivers.
Spawning
did
not
typically
start
until
late
August
(
lasting
through
early
October),
and
fry
did
not
emigrate
until
river
flows
had
risen
in
early
winter.
Winter­
and
spring­
run
fish
no
longer
have
access
to
the
vast
majority
of
their
historical
spawning
and
juvenile
rearing
grounds,
but
their
migration
and
spawning
timing
still
reflect
the
appropriate
timetable
to
utilize
these
areas.

Estimates
of
the
age
at
maturation
for
Central
Valley
stocks
differ
between
studies;
this
may
be
due
to
differences
in
scale
pattern
interpretation,
or
there
may
have
been
a
shift
to
younger
spawners.
Fish
gill­
netted
in
1919
and
1921
below
the
confluence
of
the
Sacramento
and
San
Joaquin
Rivers
were
primarily
4
years
old
(
46.5%),
with
5­
and
3­
year
olds
comprising
32.5
and
17.0%
of
the
spawners,
respectively.
The
use
of
fish
collected
in
gill
nets
introduces
a
considerable
bias;
differences
observed
in
the
percentage
of
5­
year­
olds
between
1919
and
1921
(
24.0%
vs.
41.0%),
was
thought
to
be
due
to
a
change
in
the
gill­
net
mesh
size
from
14
cm
to
19
cm.
Additionally,
the
large
mesh
size
would
potentially
explain
the
low
incidence,
1.1%,
of
2­
year­
old
fish
in
1921.
Rich
(
1921)
estimated
females
caught
in
the
troll
fishery
off
Monterey
Bay
in
1918
would
mature
in
their
third
or
fourth
year.
The
predominant
age
classes
among
returning
fall­
and
spring­
run
adults
sampled
at
Redding
in
1939
were
3­
and
4­
year­
old
fish
(
Calkins
et
al.
1940).
Furthermore,
the
incidence
of
2­
year­
old
males
(
jacks)
was
8.8
and
27.3%
for
the
springand
fall­
run
fish,
respectively.
Five­
and
6­
year
old
fish
contributed
less
than
5%
of
the
return
for
both
runs
(
Calkins
et
al.
1940).
Near
the
turn
of
the
century,
Rutter
(
1904)
observed
large
numbers
of
small
male
"
grilse"
(
jacks)
in
Battle
Creek,
a
tributary
to
the
upper
Sacramento
River.
Samples
taken
from
the
McCloud
River
from
1909­
12
suggested
that
approximately
10%
of
the
males
matured
as
2­
year
olds
without
leaving
freshwater
(
Rich
1920a).
The
mean
age
composition
for
fall­
run
chinook
salmon
from
the
upper
Sacramento
River,
for
the
1973­
79
brood
years,
was
24,
57,
19,
and
<
1%
for
2­,
3­,
4­,
and
5­
year­
olds,
respectively
(
Reisenbichler
1986).
Hallock
and
Fisher
(
1985)
estimated
that
for
winter­
run
chinook
salmon,
3­
year­
old
returning
adults
constituted
the
majority
of
returning
fish
(
67%),
with
2­
year­
old
and
4­
year­
old
fish
representing
the
remainder
of
the
age
classes
(
25
and
8%,
respectively).
More
recently,
Fisher
(
1994)
estimated
that
the
3­
year­
old
age
class
was
predominant
among
all
runs,
being
77,
57,
91,
and
87%
of
each
run
for
fall­,
late­
fall­,
winter­,
and
spring­
runs,
respectively.
The
age
structure
of
fish
from
the
San
Joaquin
River
Basin
appears
to
be
much
younger
than
that
of
the
Sacramento
River
(
Neillands
1995).
Up
to
30%
of
the
returning
adults
in
the
Merced
and
Tuolumne
Rivers
are
2
years
of
age;
this
includes
a
number
of
2­
year­
old
females,
"
Jills,"
which
are
not
normally
observed
in
other
river
systems.
The
younger
age
of
maturation
is
probably
related
to
warmer
water
temperatures
in
the
San
Joaquin
River
rather
than
being
genetically
influenced,
given
the
genetic
similarity
between
Sacramento
and
San
Joaquin
River
fall­
runs.
62
Furthermore,
analysis
of
chinook
salmon
age
structure
in
the
San
Joaquin
River
is
complicated
by
the
influence
of
river
flow
on
the
survival
of
emigrating
juveniles.
During
extreme
drought
years,
there
has
been
a
near
failure
of
the
corresponding
year
class
of
smolts.
It
has
yet
to
be
determined
whether
the
shift
toward
a
younger
age
structure
in
the
Central
Valley
during
this
century
is
environmentally­
mediated,
due
to
the
selective
harvest
of
older
(
larger)
adults,
or
reflects
an
underlying
genetic
change.

Sacramento
River
chinook
salmon
reproductive
traits
are
very
different
from
coastal
California
and
the
Klamath
River
populations.
Information
on
Sacramento
River
chinook
salmon
eggs
sizes
is
limited.
Page
(
1888)
estimated
the
average
egg
diameter
was
6.7
mm
for
eggs
collected
at
the
Baird
NFH
on
the
McCloud
River.
The
average
egg
diameter
for
winter­
run
eggs
in
1992
was
6.91
mm
(
USFWS
1996a).
Quinn
and
Bloomberg
(
1992)
found
that
chinook
salmon
in
New
Zealand
(
from
Sacramento
River
transplants
in
1901­
07)
have
considerably
smaller
eggs,
(
0.17
g),
relative
to
coastal
stocks
in
British
Columbia,
(
0.47
g).
The
fecundity
of
Central
Valley
females
was
also
considerably
higher
for
a
given
body
size
than
for
females
from
the
Klamath
River
(
Snyder
1931).

Historically,
low
summer
flows
and
associated
high
temperatures
have
been
major
factors
in
determining
the
life­
history
characteristics
for
each
of
the
four
runs
in
the
Central
Valley.
Winter­
and
spring­
run
adults
utilized
colder
mountain
streams
to
provide
a
suitable
holding,
incubation,
and
fry­
rearing
environment
during
months
when
the
environment
on
the
lower
river
was
inhospitable.
Fall­
and
late­
fall­
run
fish
delayed
the
adult
return
migration
and
spawning
until
temperatures
had
declined
to
acceptable
levels.
Differences
in
habitat
utilization
provided
a
spatial
separation
between
runs
in
addition
to
temporal
differences.
The
duration
of
freshwater
rearing
appears
to
have
been
minimized
to
allow
emigration
to
estuarine
rearing
habitat
before
temperatures
rose
to
deleterious
levels.

Anthropogenic
activities
have
primarily
affected
the
spring
and
winter
runs.
Placer
mining
in
the
1800s
destroyed
spawning
and
rearing
habitats
either
directly
or
through
increased
sedimentation.
Mine
wastes
still
affect
water
quality.
Water
diversion
and
hydroelectric
dams
have
limited
or
prevented
access
to
most
of
the
upriver
areas
that
were
historically
utilized
by
spring
and
winter
runs
(
Clark
1929).
Agricultural
and
municipal
water
withdrawals
have
reduced
river
flows
and
increased
temperatures
during
the
critical
summer
months,
or
in
some
cases
even
reversed
river
flows
(
Reynolds
et
al.
1993).
Changes
in
the
thermal
and
water
flow
profiles
for
Central
Valley
rivers
have
presumably
subjected
chinook
salmon
to
strong
selective
forces.
The
degree
to
which
current
life­
history
traits
reflect
predevelopment
characteristics
is
largely
unknown,
especially
since
most
of
the
habitat
degradation
occurred
before
chinook
salmon
studies
were
undertaken
late
in
the
nineteenth
century.

One
consequence
of
dam
construction
has
been
alteration
of
the
river
thermal
profile.
The
completion
of
Shasta
Dam
(
RKm
505)
in
1944
eliminated
access
to
the
McCloud,
Pit,
and
Upper
Sacramento
Rivers.
However,
water
subsequently
released
from
Shasta
Dam
has
had
a
63
more
uniform,
cooler,
thermal
regime,
12­
15
E
C,
than
prior
to
dam
construction
(
Moffett
1949).
This
cool
water
provided
new
spawning
habitat
for
spring­
and
winter­
run
adults
attempting
to
migrate
to
their
historical
spawning
grounds.
The
released
water
was
also
significantly
warmer
than
historical
levels
during
the
autumn
and
winter,
thereby
accelerating
egg
development
and
fry
emergence
(
Moffett
1949).
Accelerated
embryonic
development
may
effect
subsequent
smolt
emigration
timing
and
reduce
estuarine
survival.
Additionally,
dam
construction
has
eliminated
the
spatial
and
temporal
barriers
that
once
separated
the
fall
run
from
the
spring
run
and
increase
the
potential
for
hybridization.
The
expected
loss
of
spawning
habitat
above
Shasta
Dam
led
to
efforts
to
salvage
fall­
and
spring­
run
adults
destined
for
the
upper
Sacramento
River
(
Calkins
et
al.
1940).
In
a
program
that
paralleled
the
GCFMP
recovery
effort,
fish
were
intercepted
at
Balls
Ferry
(
RKm
446)
or
Keswick
Dam
(
RKm
486)
and
transferred
to
the
Coleman
NFH
for
spawning,
to
Deer
Creek
(
RKm
353)
for
natural
spawning
(
spring
run
only),
or
allowed
to
remain
in
the
Sacramento
River
(
primarily
fall
run)
to
spawn
naturally.
The
primary
criteria
for
separating
spring
and
fall
runs
was
a
late
June
cut­
off
date
that
varied
from
year
to
year
(
Moffett
1949).
In
all,
some
15,972
"
spring­
run"
chinook
salmon
were
hauled
to
Deer
Creek
from
1941­
46.
A
considerable
proportion
of
transferred
fish
died
shortly
after
transfer
to
Deer
Creek
because
of
high
water
temperatures
(
Moffett
1949).
There
was
no
provision
in
the
plan
to
identify
winter­
run
adults,
and
a
number
were
incidentally
hauled
to
Deer
Creek
(
Slater
1963).
The
absence
of
baseline
information
on
spring­
run
fish
from
the
mainstem
Sacramento
River
and
Deer
Creek
prevents
any
estimate
of
the
impact
of
these
fish
transfers,
nor
is
there
any
information
for
estimating
potential
interbreeding
between
winter
and
spring
runs.
The
loss
of
spring­
run
spawning
habitat
in
the
headwater
areas
has
eliminated
the
spatial
separation
that
once
maintained
the
genetic
isolation
between
spring­
and
fall­
run
populations,
and
a
certain
amount
of
mixing
has
probably
occurred
in
both
hatchery
and
naturally
spawning
populations
(
Fisher
1994).
Stock
transfers
and
high
straying
rates
may
have
resulted
in
the
loss
of
distinctive
life­
history
characteristics
between
fall­
run
populations.
Perhaps
because
fall­
run
fish
utilize
mainstem
areas
and
rear
in
freshwater
for
a
limited
period,
there
has
been
little
selective
pressure
for
geographic
adaptation
within
the
Central
Valley.
Alternatively,
local
extinctions
and
recolonizations
due
to
natural
drought
cycles
may
have
prevented
distinct
populations
from
forming
among
fall­
run
chinook
salmon.
Nevertheless,
differences
in
the
life­
history
traits
of
winter,
spring,
fall,
and
latefall
runs
are
still
apparent
in
spite
of
massive
changes
in
their
spawning
and
rearing
habitat,
and
these
differences
underscore
the
distinctiveness
of
these
stocks.

Columbia
River
ocean
type
Lower
Columbia
River
(
to
the
Cascade
Crest)
 
The
Columbia
River
is
the
third
largest
river
system
in
the
United
States.
The
Columbia
River
exerts
a
dominant
influence
on
the
biota
of
the
Pacific
Northwest,
although
smaller,
regional,
distinctions
exist
within
the
basin.
In
the
lower
Columbia
River,
the
Cowlitz,
Kalama,
Lewis,
White
Salmon,
and
Klickitat
Rivers
are
the
major
river
systems
on
the
Washington
State
side,
while
the
Willamette
and
Sandy
Rivers
are
foremost
on
the
Oregon
State
side.
Spring­
run
chinook
salmon,
which
spawn
above
the
Willamette
Falls,
will
be
discussed
separately
because
of
their
geographic
and
life­
history
distinctiveness.
The
64
Clackamas
River
is
the
major
tributary
to
the
Willamette
River
below
the
Willamette
Falls
and
is
included
in
the
discussion
of
this
region.

The
fall
run
is
predominant
in
this
region.
Fall­
run
fish
return
to
the
river
in
mid­
August
and
spawn
within
a
few
weeks
(
WDF
et
al.
1993,
Kostow
1995).
These
fall­
run
chinook
salmon
are
often
called
"
tules"
and
are
distinguished
by
their
dark
skin
coloration
and
advanced
state
of
maturation
at
the
time
of
freshwater
entry.
Tule
fall­
run
chinook
salmon
populations
may
have
historically
spawned
from
the
mouth
of
the
Columbia
River
to
the
Klickitat
River
(
RKm
290).
Whatever
spawning
grounds
were
accessible
to
fall­
run
chinook
salmon
on
the
Klickitat
River
(
below
Lyle
Falls
at
RKm
3)
would
have
been
inundated
following
the
construction
of
Bonneville
Dam
(
RKm
243)
in
1938
(
Bryant
1949,
Hymer
et
al.
1992a,
WDF
et
al.
1993).
There
is
no
record
of
fall
chinook
salmon
utilizing
this
lower
portion
of
the
Klickitat
River
(
Fulton
1968).
A
significant
fall
run
once
existed
on
the
Hood
River
(
RKm
272)
prior
to
the
construction
of
Powerdale
Dam
(
1929)
and
other
diversion
and
irrigation
dams
(
Fulton
1968);
however,
this
run
has
become
severely
depleted
and
may
have
been
extirpated
(
Howell
et
al.
1985,
Nehlsen
et
al.
1991,
Theis
and
Melcher
1995).
The
Big
White
Salmon
River
(
RKm
270)
supported
runs
of
chinook
salmon
prior
to
the
construction
of
Condit
Dam
(
RKm
4)
in
1913
(
Fulton
1968).
Although
some
fall­
run
salmon
spawning
occurs
below
Condit
Dam,
there
have
been
substantial
introductions
of
non­
native
stocks
(
WDF
et
al.
1993),
and
the
persistence
of
a
discrete
native
stock
is
unlikely.
Fall­
run
fish
from
the
Big
White
Salmon
River
were
used
to
establish
the
nearby
Spring
Creek
National
Fish
Hatchery
(
NFH)
in
1901
(
Hymer
et
al.
1992a).
Spring
Creek
NFH
is
one
component
of
the
extensive
hatchery
system
in
Washington
and
Oregon
producing
fall
chinook
salmon
(
Howell
et
al.
1985).
"
Tule
fall­
run"
chinook
salmon
begin
the
freshwater
phase
of
their
return
migration
in
late
August
and
October
and
the
peak
spawning
interval
does
not
occur
until
November
(
WDF
et
al.
1993).

Among
other
fall­
run
populations,
a
later
returning
component
of
the
fall
chinook
salmon
run
exists
in
the
Lewis
and
Sandy
Rivers
(
WDF
et
al.
1993,
Kostow
1995,
Marshall
et
al.
1995).
Because
of
the
longer
time
interval
between
freshwater
entry
and
spawning,
Lewis
and
Sandy
River
fall
chinook
salmon
are
less
mature
at
freshwater
entry
than
tule
fall
chinook
salmon
and
are
commonly
termed
lower
river
"
brights"
(
Marshall
et
al.
1995).

The
Cowlitz,
Kalama,
Lewis,
Clackamas,
and
Sandy
Rivers
presently
contain
both
spring
and
fall
runs,
while
the
Big
White
Salmon
River
historically
contained
both
spring
and
fall
runs
but
presently
only
contains
fall­
run
fish
(
Fulton
1968,
WDF
et
al.
1993).
The
Klickitat
River
probably
contained
only
spring­
run
chinook
salmon
due
to
falls
that
blocked
access
to
fall­
run
chinook
salmon
during
autumn
low
flows
(
Fulton
1968).
The
spring
run
on
the
Big
White
Salmon
River
was
extirpated
following
construction
of
Condit
Dam
(
Fulton
1968),
while
a
variety
of
factors
may
have
caused
the
decline
and
extinction
of
spring­
run
chinook
salmon
on
the
Hood
River
(
Nehlsen
et
al.
1991,
Kostow
1995).

Spring­
run
chinook
salmon
on
the
lower
Columbia
River,
like
those
from
coastal
stocks,
enter
freshwater
in
March
and
April
well
in
advance
of
spawning
in
August
and
September.
65
Historically,
fish
migrations
were
synchronized
with
periods
of
high
rainfall
or
snowmelt
to
provide
access
to
upper
reaches
of
most
tributaries
where
fish
would
hold
until
spawning
(
Fulton
1968,
Olsen
et
al.
1992,
WDF
et
al.
1993).
Dams
have
reduced
or
eliminated
access
to
upriver
spawning
areas
on
the
Cowlitz,
Lewis,
Clackamas,
Sandy,
and
Big
White
Salmon
Rivers.
A
distinct
winter­
spawning
run
may
have
existed
on
the
Sandy
River
(
Mattson
1955)
but
is
believed
to
have
been
extirpated
(
Kostow
1995).

Hatchery
programs
are
widespread
throughout
the
region,
and
most
populations,
with
the
possible
exception
of
fall
chinook
salmon
on
the
Lewis
and
Sandy
Rivers,
are
maintained
to
a
significant
extent
via
artificial
propagation
(
Howell
et
al.
1985,
WDF
et
al.
1993,
Kostow
1995).
The
life­
history
characteristics
of
spring­
and
fall­
run
populations
in
many
rivers
have
probably
been
influenced,
to
varying
degrees,
by
transfers
of
non­
indigenous
stocks.
This
is
especially
true
of
the
stream­
type
chinook
salmon
spring­
run
established
in
the
Wind
River
at
the
Carson
NFH
and
of
upriver
bright
fall­
run
chinook
salmon
transferred
into
various
systems.

The
majority
of
fall­
run
chinook
salmon
emigrate
to
the
marine
environment
as
subyearlings
(
Reimers
and
Loeffel
1967,
Howell
et
al.
1985,
Hymer
et
al.
1992a,
Olsen
et
al.
1992,
WDF
et
al.
1993).
A
portion
of
returning
adults
whose
scales
indicate
a
yearling
smolt
migration
may
be
the
result
of
extended
hatchery­
rearing
programs
rather
than
of
natural,
volitional
yearling
emigration.
It
is
also
possible
that
modifications
in
the
river
environment
may
have
altered
the
duration
of
freshwater
residence.
The
natural
timing
of
spring­
run
chinook
salmon
emigration
is
similarly
obscured
by
hatchery
releases
of
spring­
run
chinook
salmon
juveniles
late
in
their
first
autumn
or
early
in
their
second
spring.
Age
analysis
based
on
scales
from
naturally
spawning
spring­
run
adults
from
the
Kalama
and
Lewis
Rivers
indicated
a
significant
contribution
to
escapement
by
fish
that
entered
saltwater
as
subyearlings
(
Hymer
et
al.
1992a).
This
subyearling
smoltification
pattern
may
also
be
indicative
of
life­
history
patterns
for
the
Cowlitz
River
spring
run,
because
both
the
Kalama
and
Lewis
Rivers
have
received
considerable
numbers
of
transplanted
fish
from
the
Cowlitz
River.
Life­
history
data
from
the
Clackamas
and
Sandy
Rivers
is
very
limited,
and
transplantation
records
indicated
that
these
rivers
have
received
overwhelmingly
large
numbers
of
upper
Willamette
River
spring­
run
chinook
salmon
(
Nicholas
1995).
In
1898,
eggs
from
returning
spring­
run
chinook
salmon
were
collected
from
the
Clackamas
River
(
near
Clear
Creek)
from
15
September
to
24
October,
and
from
the
upper
Clackamas
River
from
17
July
to
26
August
(
Ravenel
1899).
The
upper
Clackamas
River
spring­
run
chinook
salmon
spawning
peak
has
apparently
shifted
from
mid­
August
(
1899)
to
the
present
day
peak
interval
from
late
September
to
early
October
(
Nicholas
1995,
Willis
et
al.
1995).
This
later
spawning
peak
is
more
consistent
with
upper
Willamette
River
stocks
(
Nicholas
1995,
Willis
et
al.
1995).
Smoltification
patterns
for
fish
from
the
upper
Willamette
River
are
discussed
in
a
later
section.

Comparisons
of
historical
data
on
the
age
structure
of
fish
returning
to
the
Columbia
River
are
also
informative
in
analyzing
natural
smoltification
traits
without
the
impact
of
large
hatchery
programs.
Analysis
of
scales
from
returning
adult
chinook
salmon
sampled
in
the
lower
Columbia
66
River
and
at
Bonneville
Dam
indicate
that
the
proportion
of
yearling
migrants
contributing
to
escapement
was
much
lower
for
spring­
run
fish
in
the
1920s
than
at
present
(
Fig.
15)
(
Rich
1925;
Young
and
Robinson
1974;
Fryer
and
Schwartzberg
1991a,
1991b,
1992,
1993,
1994;
Fryer
et
al.
1992).
This
decrease
over
time
in
the
proportion
of
subyearling
smolts
may
be
due
to
increased
hatchery
releases
of
yearling
smolts,
increased
use
of
stream­
type
springrun
stocks
in
hatcheries,
decline
in
Columbia
River
summer­
run
populations,
or
the
decreased
survival/
abundance
of
naturally­
reared
subyearling
smolts
related
to
changing
freshwater
habitat
or
smolt
passage
problems.

Adults
return
to
tributaries
in
the
lower
Columbia
River
at
3
and
4
years
of
age
for
fall­
run
fish
and
4
to
5
years
of
age
for
spring­
run
fish.
This
may
be
related
to
the
predominance
of
yearling
smolts
among
spring­
run
stocks.
Marine
CWT
recoveries
for
lower
Columbia
River
stocks
tend
to
occur
off
the
British
Columbia
and
Washington
coasts,
with
a
small
proportion
of
tags
recovered
from
Alaska.

Upper
Willamette
River
 
Willamette
Falls
(
RKm
42)
has
historically
limited
access
to
the
upper
river
and
thus
defines
the
boundary
of
a
distinct
geographic
region.
High
flows
over
the
falls
provided
a
window
for
returning
chinook
salmon
in
the
spring,
while
low
flows
prevented
fish
from
ascending
the
falls
in
the
autumn
(
Howell
et
al.
1985).
The
predominant
tributaries
to
the
Willamette
River
that
historically
supported
spring­
run
chinook
salmon
 
the
Molalla
(
Rkm
58),
Santiam
(
RKm
174),
McKenzie
(
RKm
282),
and
Middle
Fork
Willamette
Rivers
(
RKm
301)
 
all
of
which
drain
the
Cascades
to
the
east
(
Mattson
1948,
Nicholas
1995).
Since
the
Willamette
Valley
was
not
glaciated
during
the
last
epoch
(
McPhail
and
Lindsey
1970),
the
reproductive
isolation
provided
by
the
falls
probably
has
been
uninterrupted
for
a
considerable
time
period.
This
isolation
has
provided
the
potential
for
significant
local
adaptation
relative
to
other
Columbia
River
populations.

Three
major
populations
of
spring­
run
chinook
salmon
are
presently
located
above
Willamette
Falls
(
McKenzie
River,
and
North
and
South
Forks
of
the
Santiam
River)
(
Kostow
1995).
Within­
basin
transfers
associated
with
increased
artificial
propagation
efforts
since
the
turn
of
the
century
have
reduced
the
genetic
diversity
between
upper
Willamette
River
stocks
(
Kostow
1995,
Nicholas
1995).
Fall­
run
chinook
salmon
are
present
in
the
upper
Willamette
River,
but
these
fish
are
the
result
of
transplants
subsequent
to
the
construction
of
fish
passage
facilities
in
1971
and
1975
(
Bennett
1988).
Adult
spring­
run
chinook
salmon
enter
the
Columbia
River
in
March
and
April,
but
they
do
not
ascend
the
Willamette
Falls
until
May
or
June.
The
migration
past
the
falls
generally
coincides
with
a
rise
in
river
temperatures
above
10
E
C
(
Mattson
1948,
Howell
et
al.
1985,
Nicholas
1995).
Spawning
generally
begins
in
late
August
and
continues
into
early
October,
with
spawning
peaks
in
September
(
Mattson
1948,
Nicholas
1995,
Willis
et
al.
1995).
Recent
analysis
of
scales
from
returning
adults
indicated
that
the
67
Figure
15.
Percentage
of
adults
sampled
at
various
times
during
their
return
migration
to
the
Lower
Columbia
River
that
had
emigrated
as
yearling
smolts.
Age
at
smoltification
was
estimated
by
analysis
of
scales
removed
from
returning
adults
sampled
weekly
in
the
fishery
or
at
the
Bonneville
Dam
ladder.
Samples
were
taken
from
different
locations
during
different
time
periods:
1920,
1960­
63,
1990­
93
(
Rich
1925;
Young
and
Robinson
1974;
Fryer
and
Schwartzberg
1991a,
1991b,
1992,
1993,
1994;
Fryer
et
al.
1992).
68
6
B.
Beckman,
Fisheries
Biologist,
National
Marine
Fisheries
Service,
2725
Montlake
Blvd.
E.,
Seattle,
Washington,
98122.
Pers.
Commun.,
July
1996.
majority
of
fish
had
emigrated
to
saltwater
as
yearlings,
but
this
is
certainly
biased
by
the
overwhelming
hatchery
contribution
to
escapement
(
90+%)
and
the
hatchery
strategy
of
releasing
fish
late
in
their
first
autumn
or
in
their
second
spring
(
Nicholas
1995,
Willis
et
al.
1995).
Scales
sampled
from
returning
adults
in
1941
indicated
that
the
fish
had
entered
saltwater
during
the
autumn
of
their
first
year
(
Craig
and
Townsend
1946).
Mattson
(
1963)
found
that
returning
adults
which
had
emigrated
as
"
fingerling"
(
subyearling)
smolts
made
up
a
significant
proportion
of
the
3­
year­
old
age
class,
with
fingerling
emigrants
making
up
a
smaller
proportion
of
the
older
age
classes.
A
recent
study
indicated
that
Willamette
River
spring­
run
chinook
salmon
have
a
physiological
smoltification
window
during
their
first
autumn
(
Beckman6).
Large
numbers
of
fry
and
fingerlings
have
been
observed
migrating
downriver
from
the
Willamette
River
and
its
tributaries
(
Craig
and
Townsend
1946,
Mattson
1962,
Howell
et
al.
1988).
Based
on
the
examination
of
scale
patterns
from
returning
adults,
it
would
appear
that
these
fry
do
not
immediately
enter
the
estuary
or
do
not
survive
the
emigration.
Emigrating
fry
would
have
been
severely
affected
by
the
high
water
temperatures
and
industrial
waste
discharges
that
were
common
throughout
much
of
this
century
in
the
lower
Willamette
River,
especially
during
periods
of
low
river
flow
in
the
late
spring
and
early
summer
(
Craig
and
Townsend
1946,
Mattson
1962,
USGS
1993).
More
recently,
fry
migrants
constitute
a
relatively
small
proportion
of
the
smolt
emigration
(
especially
when
compared
to
the
artificially
propagated
fingerling
and
yearling
contribution);
thus
their
potential
contribution
to
returning
adults
would
be
expected
to
be
quite
low.
Alternatively,
these
fry
migrants
could
be
rearing
in
the
Columbia
River
prior
to
emigrating
to
the
marine
environment
(
Craig
and
Townsend
1946,
Mattson
1962).

In
general,
Willamette
River
spring­
run
chinook
salmon
mature
in
their
fourth
and
fifth
year
of
life,
with
the
majority
maturing
at
age
4.
Historically,
5­
year­
old
fish
comprised
the
dominant
portion
of
the
run
(
Nicholas
1995,
Willis
et
al.
1995).
Marine
recoveries
of
CWTmarked
fish
occur
off
the
British
Columbia
and
Alaska
coasts,
and
a
much
larger
component
(>
30%)
of
the
recoveries
is
from
Alaska
relative
to
other
lower
Columbia
River
stocks.
Age
of
release
(
subyearling
vs.
yearling)
does
not
appear
to
influence
the
general
oceanic
distribution
of
fish.
Morphologically,
Willamette
River
spring­
run
fish
are
similar
to
other
lower
Columbia
River
chinook
salmon
(
Schreck
et
al.
1986).
Vertebral
counts
for
several
Willamette
River
"
wild"
and
hatchery
samples
average
68.3­
69.5,
which
is
similar
to
other
ocean­
type
chinook
salmon
from
the
Columbia
River,
but
it
is
significantly
less
than
vertebral
counts
for
upper
Columbia
River
stream­
type
spring­
and
summer­
run
chinook
salmon,
71.3­
72.5
(
Schreck
et
al.
1986).
These
vertebral
counts
suggest
that
past
transplants
of
Carson
NFH
spring­
run
chinook
salmon
(
a
stream­
type
stock)
did
not
have
a
significant
genetic
impact
on
Willamette
River
stocks.
Although
Willamette
River
spring­
run
chinook
salmon
can
generally
be
categorized
as
Columbia
River
ocean­
type
chinook
salmon,
they
do
exhibit
some
distinct
life­
history
attributes
relative
to
other
stocks
in
this
general
group.
69
Water
diversions,
dam
placements,
and
river
channelizations
may
have
altered
the
abundance,
spawning
and
rearing
distribution,
and
smolt
timing
of
populations
of
spring­
run
chinook
salmon
from
historical
levels.
Although
the
Willamette
River
was
once
highly
braided
with
numerous
side
channels
offering
ideal
rearing
habitat
for
juvenile
salmonids
(
Kostow
1995),
approximately
75%
of
that
river
shoreline
has
been
lost
(
Sedell
and
Froggatt
1984).
Irrigation
withdrawals
began
in
the
1800s;
additionally,
timber
harvest
activities
and
the
construction
of
splash
dams
had
a
severe
impact
on
spawning
and
rearing
habitat
access
and
quality
(
Kaczynski
and
Palmisano
1993).
Water
diversion
and
hydroelectric
dam
construction
in
the
1950s
and
1960s
limited
access
to
significant
portions
of
the
major
spring­
run
chinook
salmon
bearing
tributaries
to
the
Willamette
River.
In
all,
water
storage
projects
eliminated
access
to
707
stream
kilometers
(
Cramer
et
al.
1996).
In
addition
to
loss
of
habitat,
the
dams
have
altered
the
natural
thermal
regime.
The
premature
emergence
of
spring­
run
chinook
salmon
fry
due
to
releases
of
warmer
reservoir
water
in
the
autumn
may
have
caused
high
mortalities
among
naturally
spawning
fish
(
Kostow
1995).
Furthermore,
cooler
than
normal
waters
released
in
the
spring
limit
the
growth
of
naturally
rearing
fish.
Habitat
changes
may
have
created
selective
pressures
that
would
alter
the
expression
of
historical
life­
history
traits,
primarily
impacting
naturally
spawning
and
rearing
salmonids.

Despite
the
homogenization
of
spring­
run
chinook
salmon
stocks
through
intrabasin
transfers
and
the
impact
of
large
scale
artificial
propagation
efforts,
the
distinctiveness
of
Willamette
River
spring­
run
chinook
salmon
life­
history
traits
relative
to
other
ocean­
type
populations
appears
to
have
been
retained
Columbia
River
(
east
of
the
Cascade
Crest)
 
East
of
the
Cascade
Crest,
many
river
systems
support
populations
of
both
ocean­
and
stream­
type
chinook
salmon.
Fall­
run
(
ocean­
type)
fish
return
to
spawn
in
the
mainstem
Columbia
and
Snake
Rivers
and
their
tributaries,
primarily
the
Deschutes
and
Yakima
Rivers
(
Hymer
et
al.
1992b,
Olsen
1992).
Historically,
numerous
other
Columbia
River
tributaries
in
Washington,
Oregon,
and
Idaho
supported
fall
runs,
but
for
a
variety
of
reasons
these
are
now
extinct
(
Fulton
1968,
Nehlsen
et
al.
1991,
Hymer
et
al.
1992a,
Olsen
et
al.
1992,
WDF
et
al.
1993).
Fall­
run
salmon
historically
migrated
as
far
as
Kettle
Falls
(
RKm
1,090)
on
the
Columbia
River
prior
to
the
completion
of
Grand
Coulee
Dam
(
RKm
961)
in
1941
(
Mullan
1987).
Chapman
(
1943)
observed
chinook
salmon
spawning
in
deep
water
just
below
Kettle
Falls
in
October
1938.
Similarly,
fall­
run
chinook
salmon
migrated
up
the
Snake
River
to
Shoshone
Falls
(
RKm
976),
although
Augur
Falls
(
RKm
960)
probably
blocked
the
passage
of
most
fish
(
Evermann
1896,
Fulton
1968).

Summer­
run
chinook
salmon
populations
on
the
Columbia
River
exhibit
an
ocean­
type
life
history,
while
summer­
run
fish
on
the
Snake
River
exhibit
a
stream­
type
life
history
(
Taylor
1990a,
Chapman
et
al.
1991,
Chapman
et
al.
1994,
Matthews
and
Waples
1991,
Waknitz
et
al.
1995).
Summer­
run
fish
return
to
freshwater
in
June
through
mid­
August
 
slightly
earlier
than
the
fall­
run
fish,
which
return
from
mid­
August
through
October
(
Fulton
1968).
Summer­
run
fish
were
able
to
ascend
Kettle
Falls
(
Evermann
1896,
Bryant
and
Parkhurst
1950)
and
probably
70
migrated
as
far
as
Lake
Windermere
in
British
Columbia
(
Hymer
et
al.
1992b,
Chapman
et
al.
1994).
With
the
completion
of
the
Grand
Coulee
Dam
in
1941
(
RKm
961)
and
Chief
Joseph
Dam
in
1955
(
RKm
877),
the
farthest
that
summer­
run
chinook
salmon
can
migrate
upriver
is
the
Okanogan
River
(
RKm
859).
Currently,
naturally
spawning
ocean­
type
summer­
run
chinook
salmon
are
also
found
in
the
Wenatchee
(
RKm
753)
and
Methow
Rivers
(
RKm
843)
(
Waknitz
et
al.
1995).
Summer­
run
chinook
salmon
are
also
reported
to
spawn
in
the
lower
Entiat
and
Chelan
Rivers,
in
addition
to
below
mainstem
Columbia
River
dams
(
Marshall
et
al.
1995);
however,
it
has
not
been
determined
whether
or
not
these
are
self­
staining
populations.

There
are
numerous
differences
between
ocean­
type
fish
east
and
west
of
the
Cascade
Crest.
Celilo
Falls
(
RKm
320),
which
was
submerged
under
Lake
Celilo
following
the
building
of
the
Dalles
Dam
(
RKm
309)
in
1957,
was
located
where
the
Cascade
Crest
line
intersects
the
Columbia
River
and
may
have
historically
been
a
barrier
to
returning
tule
(
lower
river)
fall­
run
chinook
salmon.
The
Cascade
Crest
also
marks
the
boundary
between
the
maritime
ecoregions
to
the
west
and
the
arid
ecoregions
to
the
east.
Historically,
summer­
run
and
"
upriver
bright"
fallrun
fish
in
the
Columbia
River
were
not
found
below
this
demarcation
(
Fulton
1968).
"
Upriver
brights"
are
so
named
because
they
enter
freshwater
prior
to
the
expression
of
secondary
maturation
characteristics
(
darkening
of
skin
and
formation
of
the
kype)
and
1
to
3
months
prior
to
actual
spawning
(
WDF
et
al.
1993,
Marshall
et
al.
1995).
Among
ocean­
type
Columbia
River
populations
above
Celilo
Falls,
summer­
run
chinook
salmon
spawn
in
the
mid­
and
lower
reaches
of
tributaries
with
peak
spawning
occurring
in
October,
whereas
fall­
run
chinook
salmon
spawn
in
the
mainstem
Columbia
and
Snake
Rivers
and
the
lower
reaches
of
the
Deschutes
and
Yakima
Rivers
with
peak
spawning
occurring
in
November
(
Howell
et
al.
1985,
Marshall
et
al.
1995,
Mullan
1987,
Garcia
et
al.
1996).
Additionally,
fall­
run
chinook
salmon
in
the
mainstem
Columbia
and
Snake
Rivers
have
been
observed
spawning
in
water
10
m
deep
or
more
(
Chapman
1943,
Bruner
1951,
Swan
et
al.
1988,
Hymer
et
al.
1992b,
Dauble
et
al.
1995).

Ocean­
type
fry
west
of
the
Cascade
Crest
emerge
in
April
and
May,
and
the
majority
rear
from
1
to
4
months
in
freshwater
prior
to
emigrating
to
the
ocean
(
Mullan
1987,
Olsen
et
al.
1992,
Hymer
et
al.
1992a,
WDF
et
al.
1993,
Chapman
et
al.
1994,
Marshall
et
al.
1995).
A
small
proportion
of
summer­
and
fall­
run
fish
remain
in
freshwater
until
their
second
spring
and
emigrate
as
yearlings
(
Chapman
et
al.
1994,
Waknitz
et
al.
1995).
The
proportion
of
yearling
outmigrants
varies
from
year
to
year
due,
perhaps,
to
environmental
fluctuations.
Among
summer­
run
populations,
the
lowest
incidence
of
yearling
outmigrants
is
found
in
the
Okanogan
River,
where
the
waters
are
relatively
warm
and
highly
productive
(
Chapman
et
al.
1994).

The
age
of
maturation
for
ocean­
type
chinook
salmon
varies
considerably
among
rivers
in
this
region.
Naturally
spawning
summer­
run
fish
in
the
Wenatchee,
Methow,
and
Okanogan
Rivers
mature
primarily
in
their
fourth
or
fifth
year
(
Chapman
et
al.
1994,
Waknitz
et
al.
1995,
Marshall
et
al.
1995).
The
age
distribution
for
fall­
run
chinook
salmon
returning
to
the
Hanford
Reach
section
of
the
Columbia
River
(
RKm
292)
and
the
lower
Yakima
River
(
below
Prosser
Dam
RKm
75.8)
includes
higher
proportions
of
2­
year­
old
"
jacks"
and
3­
year­
old
adults
relative
71
to
summer­
run
fish
(
Hymer
et
al.
1992b,
WDFW
1995).
However,
the
Hanford
Reach
and
lower
Yakima
River
populations
contain
higher
proportions
of
4­
and
5­
year­
old
spawners
than
other
fall­
run
stocks
(
the
Deschutes
River
and
the
Marion
Drain)
found
above
the
Cascade
Crest
(
Hymer
et
al.
1992b,
WDFW
et
al.
1995).
The
Deschutes
River
and
Marion
Drain
systems
support
fall­
runs
with
very
high
incidences
of
2­
year­
old
"
jack"
chinook
salmon
(
Hymer
et
al.
1992b,
ODFW
1995,
WDFW
1995).
A
significant
proportion
of
the
Snake
River
fall
run
is
presently
reared
at
the
Lyons
Ferry
Hatchery
and
limited
information
is
available
on
naturally
spawning
fish.
The
age
distribution
for
fish
returning
to
Lyons
Ferry
includes
a
large
proportion
(
20%)
of
2­
year­
old
jacks
relative
to
other
stocks,
although
the
majority
return
as
4­
and
5­
year
olds
(
Hymer
et
al.
1992b,
Marshall
et
al.
1995).
The
high
incidence
of
jacks
may
be
related
to
the
release
of
yearling
smolts,
which
constitute
approximately
one­
half
of
all
releases
(
Howell
et
al.
1985,
Chapman
et
al.
1991);
however,
size
distributions
for
Snake
River
fall­
run
fish
intercepted
at
Little
Goose
Dam
(
RKm
113)
in
1976
(
NMFS
1996a)
and
at
Salmon
Falls
(
RKm
922)
in
1894
(
Evermann
1896)
were
very
similar
(
Fig.
16)
and
included
a
large
number
of
smaller
jacks.

Ocean
recoveries
of
CWTs
describe
two
basic
patterns.
Fall­
run
fish
from
the
lower
Yakima
River
and
summer­
and
fall­
run
fish
from
the
mainstem
Columbia
River
and
its
tributaries
(
above
the
confluence
of
the
Yakima
and
Columbia
Rivers)
are
recovered
primarily
in
Alaska
and
British
Columbia
coastal
waters.
In
contrast,
a
significant
number
of
tagged
fall­
run
chinook
salmon
from
the
Snake
and
Deschutes
Rivers
are
recovered
in
southerly
waters
off
the
Oregon
and
California
Coast,
and
recovery
of
CWT­
marked
Snake
and
Deschutes
River
fall­
run
chinook
salmon
off
Alaska
is
not
large
(
Howell
et
al.
1985,
Waples
et
al.
1991b).
Thus,
among
oceantype
populations
east
of
the
Cascade
Crest,
there
appears
to
be
some
degree
of
divergence
in
maturation
rates
and
migration.

Anthropogenic
influences
have
had
a
great
impact
on
the
life
history
and
distribution
of
ocean­
type
chinook
salmon
in
the
Columbia
River
Basin.
Access
to
spawning
habitat
on
the
mainstem
Snake
River
was
blocked
to
migrating
salmonids
beginning
in
1910
with
Swan
Falls
Dam
(
RKm
734)
and
most
recently
by
the
Hells
Canyon
Dam
(
RKm
459)
in
1967
(
Fulton
1968,
Waples
et
al.
1991b).
An
additional
four
mainstem
dams
(
Ice
Harbor
Dam
[
1961;
RKm
16],
Lower
Monumental
Dam
[
1969;
RKm
67],
Little
Goose
Dam
[
1970;
RKm
113],
and
Lower
Granite
Dam
[
1975;
RKm
173])
on
the
Snake
River
have
inundated
spawning
areas
and
impeded
adult
and
smolt
migrations
(
Fulton
1968,
Chapman
et
al.
1991,
Waples
et
al.
1991b).
Nine
dams
exist
on
that
portion
of
the
mainstem
Columbia
River
that
is
still
accessible
to
migrating
salmon,
and
numerous
historical
spawning
sites
were
probably
inundated
by
reservoirs
created
by
those
dams
upriver
from
the
present
Dalles
Dam
(
Smith
1966,
Waknitz
et
al.
1995).

The
construction
of
Grand
Coulee
Dam
and
the
concurrent
Grand
Coulee
Fish
Maintenance
Project
(
GCFMP)
also
influenced
the
present
distribution
of
summer/
fall­
run
chinook
salmon.
To
compensate
for
the
loss
of
spawning
habitat
above
the
dam,
spring­
and
summer­
run
chinook
salmon
were
intercepted
at
Rock
Island
Dam
(
RKm
730)
from
1939­
43
and
72
Figure
16.
Length
distribution
(
cm)
for
Snake
River
male
and
female
chinook
salmon
sampled
at
Salmon
Falls,
Rkm
922
in
Sept./
Oct.
1894
(
Evermann
1986)
and
Little
Goose
Dam,
Rkm
113
in
Sept./
Oct.
9176
(
NMFS
1996a).
Salmon
Falls
distributions
are
based
on
732
males
and
170
females;
Little
Goose
Dam
distributions
are
based
on
48
males
and
91
females.
73
either
transported
to
surrogate
spawning
sites
or
held
in
hatchery
facilities
for
artificial
propagation
(
Fish
and
Hanavan
1948).
Returning
summer­
run
adults
were
transported
to
enclosed
sections
of
the
Wenatchee
or
Entiat
Rivers
to
spawn
naturally
(
Fish
and
Hanavan
1948).
Captive
spawning
began
in
1940
at
the
Leavenworth
NFH
on
Icicle
Creek
and
subsequently
at
other
facilities
on
the
Entiat
and
Methow
Rivers.
Artificially
propagated
fry
and
fingerlings
were
planted
in
the
Wenatchee,
Entiat,
and
Methow
Rivers
during
the
GCFMP,
but
neither
adults
nor
juveniles
were
introduced
into
the
Okanogan
River.
The
reintroduction
of
summer­
run
fish
into
the
Okanogan
River
resulted
from
later
transplantations
or
recolonization
by
straying
fish
after
the
termination
of
trapping
activities
at
Rock
Island
Dam
in
late
1943
(
Waknitz
et
al.
1995).
Prior
to
the
GCFMP,
Craig
and
Suomela
(
1941)
reported
that
summer­
run
chinook
salmon
above
Rock
Island
Dam
were
found
in
fairly
low
numbers
in
the
Wenatchee
and
Okanogan
Rivers.
Emigrating
young­
of­
year
chinook
salmon
trapped
in
the
Methow
River
in
1937
(
WDF
1938)
may
have
been
ocean­
type
summer­
run
juveniles
migrating
to
the
ocean
or
stream­
type
spring­
run
juveniles
moving
to
winter
feeding
ground
downstream.
Given
the
small
numbers
of
returning
adults
reported
by
WDF
(
1938)
and
Craig
and
Suomela
(
1941)
native
fish
populations
were
probably
swamped
by
later
releases.
Another
consequence
of
the
GCFMP
was
the
potential
mixing
of
spring­
run
(
stream­
type)
and
summer/
fall­
run
(
ocean­
type)
fish.
Runs
were
discriminated
based
on
a
9
July
cut­
off
date
at
the
Rock
Island
Dam
trap,
and
no
distinction
was
made
between
later
returns
of
summer­
and
fall­
run
fish
(
Fish
and
Hanavan
1948).

Historically,
a
substantial
population
of
summer­
run
chinook
salmon
once
existed
on
the
Yakima
River;
however,
the
last
summer­
run
redd
was
observed
in
1970
and
this
stock
appears
to
be
extirpated
(
BPA
et
al.
1996).
A
summer
run
may
also
have
existed
on
the
Deschutes
River.
Recoveries
of
returning
adults
tagged
at
Bonneville
Dam
in
June
and
July
(
a
migration
timing
that
is
generally
associated
with
summer
runs)
were
made
in
the
Deschutes
and
Metolius
(
a
tributary
to
the
upper
Deschutes
River)
Rivers
(
Galbreath
1966).
Jonasson
and
Lindsay
(
1988)
speculated
that
a
distinct
summer
run
spawned
in
the
upper
Deschutes
River
prior
to
the
construction
of
Pelton
Dam
(
RKm
166)
in
1958
and
Round
Butte
Dam
(
RKm
177)
in
1964,
and
that
subsequently
the
run
was
eliminated
or
assimilated
into
the
fall­
run.
Presently,
fall­
run
chinook
salmon
on
the
Deschutes
River
return
much
earlier
than
any
other
fall­
run
stock
on
the
Columbia
River
(
Olsen
et
al.
1992),
suggesting
that
some
assimilation
may
have
taken
place.

Fall­
run
chinook
salmon
populations
have
been
extirpated
in
the
John
Day,
Umatilla,
and
Walla
Walla
Rivers
(
Kostow
1995).
Information
on
the
historical
life­
history
traits
for
these
rivers
is
limited.
Rich
(
1920b)
remarked
that
Umatilla
River
fall
chinook
salmon
were
unusually
small,
with
average
weights
of
4.5­
5.5
kg
compared
to
9.0
kg
for
the
fall
run
in
the
Columbia
River.
Deschutes
River
fall­
run
chinook
salmon
are
similarly
described
as
having
a
small
size
for
their
age
(
Kostow
1995)
which
suggests
some
degree
of
relatedness
with
the
extirpated
Umatilla
River
fish.

The
expression
of
fall­
run
life­
history
strategies
in
the
Yakima
River
are
potentially
biased
by
changes
in
spawning
and
rearing
habitat
and
introductions
of
non­
native
populations.
74
7
B.
D.
Watson,
Yakama
Fisheries
Project,
771
Pence
Rd,
Yakima
WA
98902.
Pers.
commun.,
February
1996.
The
development
of
agricultural
irrigation
projects
on
the
Yakima
River
during
the
last
century
has
resulted
in
lower
river
flows,
higher
water
temperatures,
river
eutrophication,
and
limited
or
impeded
migration
access
(
Davidson
1953,
BPA
et
al.
1996).
Several
million
"
upriver
brights"
and
smaller
numbers
of
lower
Columbia
River
fall­
run
hatchery
chinook
salmon
have
been
released
into
the
Yakima
River
(
Howell
et
al.
1985,
Hymer
et
al
1992b).
The
"
upriver
brights"
stocks
represent
a
composite
of
Columbia
and
Snake
River
populations
and
were
generally
founded
by
random
samples
of
fall­
run
chinook
salmon
intercepted
at
a
number
of
mainstem
dams
(
Howell
et
al.
1985).
The
majority
of
these
introductions
on
the
Yakima
River
have
occurred
below
Prosser
Dam
(
RKm
76)
and
may
be
responsible
for
genetic
and
life­
history
differences
between
Marion
Drain
and
lower
Yakima
River
fall­
run
fish
(
Marshall
et
al.
1995).
Water
temperatures
in
the
Yakima
River
have
increased
significantly,
such
that
returning
fall­
run
adults
must
delay
river
entry,
and
juveniles
must
emigrate
from
the
river
sooner
than
occurred
historically
(
Watson7).
Conditions
above
Prosser
Dam
are
such
that
only
in
the
Marion
Drain
(
RKm
134),
a
27­
km
long
irrigation
return
water
canal
which
is
supplied
with
more
thermally
stable
groundwater,
is
it
possible
for
fall­
run
chinook
salmon
to
naturally
produce
smolts
in
any
number
(
BPA
et
al.
1996,
Watson
see
footnote
7).
It
has
been
speculated
that
the
Marion
Drain
fish
are
representative
of
"
native"
Yakima
River
fish
(
Marshall
et
al.
1995);
if
this
is
the
case,
then
the
phenotypic
expression
of
their
life­
history
traits
(
spawn
timing,
age
at
smoltification,
age
at
maturation,
size
at
maturation)
may
have
been
altered
by
the
artificial
environment
in
which
they
currently
exist.
For
example,
warmer
winter
temperatures
and
high
stream
productivity
contribute
to
the
production
of
large,
95
mm,
outmigrating
subyearling
smolts
in
late
April
(
Watson
see
footnote
7)
which,
in
turn,
result
in
the
high
incidence
of
2­
year­
old
mature
males
observed.
The
persistence
of
life­
history
differences
among
some
populations
of
ocean­
type
chinook
salmon
in
the
Columbia
River
Basin,
despite
extensive
stock
transfers
and
geographic
constriction
of
available
habitat,
is
indicative
of
the
significance
of
these
traits.

Columbia
River
Stream
Type
 
Stream­
type
chinook
salmon
in
the
Columbia
River
are
represented
by
spring­
run
fish
from
the
Klickitat
River
upriver
to
the
accessible
tributaries
of
the
Columbia
and
Snake
Rivers
and
summer­
run
fish
in
the
Snake
River
Basin.
With
the
exception
of
the
Klickitat
River,
all
of
these
rivers
are
located
upriver
from
the
historical
location
of
Celilo
Falls,
near
the
present
Dalles
Dam.

In
the
Columbia
Basin,
the
Klickitat,
Deschutes,
John
Day,
Yakima,
Wenatchee,
Entiat,
and
Methow
Rivers
contain
"
native"
stream­
type
chinook
salmon.
Marshall
et
al.
(
1995)
reported
that
the
spring
run
on
the
Klickitat
River
has
some
genetic
and
life­
history
similarities
to
lower
Columbia
River
(
ocean­
type)
spring­
runs.
However,
this
run
exhibits
classical
stream­
type
characteristics
 
yearling
smolt
migration
and
limited
recoveries
of
CWTs
from
coastal
fisheries
(
Howell
et
al.
1985,
Hymer
et
al.
1992b,
WDF
et
al.
1993).
Scale
samples
taken
from
Klickitat
River
spring­
run
fish
early
in
the
1900s
(
prior
to
extensive
artificial
propagation
efforts)
indicated
a
1­
year
freshwater
residence
prior
to
emigration
to
the
ocean
(
Rich
1920b).
Transplants
of
75
Cowlitz
and
Willamette
River
spring­
run
chinook
salmon
to
the
Klickitat
River
(
Howell
et
al.
1985)
may
be
responsible
for
the
few
ocean
recoveries
of
CWT­
marked
fish
released
from
the
Klickitat
River
Hatchery.
Finally,
vertebral
counts
from
Klickitat
River
spring­
run
fish
(
average
71.3)
clustered
with
stream­
type
(
71­
73
vertebrae)
and
not
ocean­
type
populations
(
66­
69
vertebrae)
(
Schreck
et
al.
1986).

Tributaries
to
the
Snake
River
that
contain
"
native"
stream­
type
populations
include
the
Tucannon,
Grande
Ronde,
Imnaha,
and
Salmon
Rivers.
A
stream­
type
run
in
Asotin
Creek
existed
until
recently,
but
may
now
be
extinct
(
WDFW
1997a).
In
a
previous
status
review,
stream­
type
chinook
salmon
in
the
Clearwater
River
system
were
determined
to
have
been
introduced
from
a
number
of
Snake
River
and
Columbia
River
sources
(
see
Appendix
D)
and
were
not
considered
for
listing
under
the
ESA
(
Matthews
and
Waples
1991).
Stream­
type
fish
in
the
Columbia
River
and
Snake
River
Basins
spawn
across
a
large
geographic
area
that
encompasses
several
diverse
ecosystems.

Stream­
type
fish
remain
in
freshwater
throughout
their
first
year
and
sometimes
second
year
following
emergence
(
Healey
1991).
Typically,
stream­
type
chinook
salmon
undertake
extensive
offshore
ocean
migrations;
therefore,
few
CWT­
marked
fish
from
stream­
type
stocks
are
recovered
in
coastal
or
high
seas
fisheries
(
Healey
1983,
Howell
et
al.
1985,
Olsen
et
al.
1992,
Hymer
et
al.
1992b).
Spring
runs
enter
the
Columbia
River
from
March
through
mid­
May,
and
summer
runs
from
mid­
May
to
mid­
July
(
Galbreath
1966).
Fish
passing
over
Bonneville
Dam
(
RKm
235)
prior
to
1
June
are
designated
by
the
U.
S.
Army
Corps
of
Engineers
(
USACE)
as
belonging
to
the
spring­
run,
although
there
is
considerable
overlap
(
Galbreath
1966).
The
majority
of
stream­
type
fish
mature
at
4
years
of
age,
with
the
exception
of
fish
returning
to
the
American
and
upper
Salmon
Rivers,
which
return
predominantly
as
5­
year­
olds.
Fish
ascend
to
the
upper
reaches
of
most
river
systems,
and
in
some
cases
access
to
these
areas
is
only
possible
during
the
high
spring
river
flows
from
snowmelt
and
spring
storms.
The
return
migration
and
spawning
timing
for
summer­
run
(
stream­
type)
fish
on
the
Snake
River
is
somewhat
later
than,
and
in
somewhat
lower
reaches
than
used
by
the
spring
runs,
although
this
distinction
is
apparently
not
always
clear
(
Chapman
et
al.
1991).
The
use
of
smaller
tributaries
for
spawning
and
extended
juvenile
rearing
by
stream­
type
chinook
salmon
increases
the
potential
for
adaptation
to
local
ecosystems
through
natural
selection
relative
to
ocean­
type
populations
(
which
spawn
in
mainstem
areas
and
migrate
more
quickly
to
the
marine
environment).

An
important
adaptation
by
stream­
type
chinook
salmon
in
the
Columbia
and
Snake
River
Basins
is
the
early
maturation
of
resident
males
(
Gebhards
1960,
Burck
1967,
Mullan
et
al.
1992,
Sankovich
and
Keefe
1996).
These
resident
males
may
play
a
crucial
role
during
years
with
low
numbers
of
returning
adults
by
ensuring
returning
females
spawn
successfully.
The
expression
of
this
life­
history
trait
may
vary
depending
on
the
location
and
physical
characteristics
of
each
river,
but
the
fact
that
all
stream­
type
populations
appear
to
express
this
trait
is
indicative
of
its
importance.
Additionally,
stream­
type
females
produce
much
smaller
eggs,
generally
less
than
8
mm
in
diameter,
than
Columbia
River
or
coastal
ocean­
type
females.
Reductions
in
egg
size
are
compensated
for
by
increases
in
total
egg
number;
however,
perhaps
76
due
to
the
energetic
costs
of
their
extensive
migrations
and/
or
their
prolonged
residence
in
freshwater
prior
to
spawning,
the
percentage
of
body
weight
devoted
to
gonads
appears
to
be
less
in
stream­
type
stocks
than
in
coastal
ocean­
type
stocks
(
Lister
1990,
Bartlett
1995).
Producing
a
greater
number
of
smaller
eggs
may
be
an
appropriate
strategy
to
maximize
long­
term
survival
in
response
to
the
environmental
fluctuations
of
high­
altitude
spawning
habitats.
Furthermore,
large
eggs
may
not
be
as
important
to
stream­
type
fish,
which
smolt
as
yearlings.

Comparisons
of
chinook
salmon
populations
in
the
Columbia
River
Basin
indicated
some
morphological
differences
between
life­
history
types
(
Schreck
et
al.
1986).
Samples
showed
stream­
type
populations
averaged
71.2­
72.5
vertebrae,
significantly
more
than
the
typical
oceantype
population
with
65.9­
69.45
vertebrae,
except
for
"
fall­
run"
fish
taken
from
the
lower
Yakima
River
(
70.6
vertebrae).
Electrophoretic
analysis
of
these
fish
by
Schreck
et
al.
(
1986)
placed
the
lower
Yakima
River
fall­
run
with
Snake
River
stream­
type
populations,
in
contrast
to
subsequent
studies
by
other
researchers.
When
the
lower
Yakima
River
sample
is
excluded,
there
is
a
clear
distinction
in
the
average
vertebral
counts
of
ocean­
and
stream­
type
populations.

Stream­
type
chinook
salmon
spawn
in
rivers
whose
headwaters
are
located
in
one
of
three
major
mountain
systems:
the
Cascade,
Blue,
and
Rocky
Mountains.
The
Salmon
River
lies
in
the
Northern
Rockies
Ecoregion
and
spawning
areas
for
stream­
type
fish
are
predominantly
above
1,000
m
and
average
approximately
1,500
m.
The
Grande
Ronde
and
Imnaha
Rivers,
tributaries
to
the
Snake
River,
originate
in
the
Blue
Mountains
with
spawning
areas
at
approximately
1,000
m
and
higher.
The
John
Day
River,
a
tributary
to
the
Columbia
River,
has
its
headwaters
in
the
Strawberry
Mountains
and
contains
spawning
areas
on
the
North,
Middle,
and
South
Forks
at
approximately
1,000
m.
Even
prior
to
the
construction
of
Pelton
Dam,
spawning
areas
for
springrun
chinook
salmon
on
the
Deschutes
River
lay
below
1,000
m
(
Nehlsen
1995).
The
Klickitat,
Yakima,
Wenatchee,
Entiat,
and
Methow
Rivers
all
contain
stream­
type
spawning
areas
at
relatively
lower
elevations,
500­
1,000
m.
Differences
in
elevation
and
geography
are
correlated
with
differences
in
temperature,
rainfall,
and
productivity,
with
obvious
impacts
on
salmon
development
rate,
growth,
and
carrying
capacity.
Schreck
et
al.
(
1986)
analyzed
several
aspects
of
spawning
and
rearing
habitat
for
different
rivers
in
the
Columbia
River
Basin.
Differences
were
most
apparent
between
upper
(
Klickitat
River
and
upstream)
and
lower
Columbia
River
tributaries.
There
are
two
geographically­
defined
clusters
of
stream­
type
chinook
salmon
rivers:
relatively
low
elevation
rivers
in
the
Columbia
River
Basin
and
the
higher
elevation
rivers
in
the
Snake
River
Basin.

Anthropogenic
activities
have
significantly
influenced
the
distribution
of
stream­
type
chinook
salmon.
Not
included
in
this
review
is
the
spring
run
on
the
Wind
River,
which
is
a
hatchery
stock
founded
by
intercepting
spring­
run
fish
at
Bonneville
Dam
destined
for
upriver
tributaries
(
Howell
et
al.
1985,
Hymer
et
al.
1992b,
Marshall
et
al.
1995).
Stream­
type
chinook
salmon
on
the
Methow,
Entiat,
and
Wenatchee
Rivers
were
influenced
by
GCFMP
transfers
of
fish
destined
for
rivers
above
Rock
Island
Dam.
River
surveys
undertaken
prior
to
the
onset
of
the
GCFMP
indicated
that
spring­
run
(
stream­
type)
fish
historically
existed
in
the
Wenatchee,
Entiat,
and
Methow
Rivers,
but
the
run
size
had
diminished
considerably
by
the
1930s,
and
the
77
run
on
the
Entiat
River
may
have
been
extirpated
(
Craig
and
Suomela
1941,
Mullan
1987).
Returning
adults
intercepted
at
Rock
Island
Dam
each
year
prior
to
9
July
were
classified
as
spring
run
and
either
transferred
to
spawning
sites
on
the
Wenatchee
or
Entiat
River,
or
to
hatcheries
for
spawning
(
Fish
and
Hanavan
1948).
Hybridizations
between
late­
returning
streamtype
(
spring­
run)
and
early­
returning
ocean­
type
(
summer­
run)
fish
probably
occurred
under
this
system
(
Chapman
et
al.
1991,
Waknitz
et
al.
1995).
Alternatively,
Fish
and
Hanavan
(
1948)
observed
that
presumptive
spring­
run
fish
transferred
to
impounded
stream
sections
and
allowed
to
naturally
spawn
all
did
so
within
the
normal
spawning
period
recorded
for
spring­
run
chinook
salmon.
Given
the
small
size
of
the
spring­
run
populations
that
existed
on
these
rivers
prior
to
the
GCFMP,
the
majority
of
the
fish
intercepted
at
Rock
Island
Dam
were
probably
destined
for
rivers
above
Grand
Coulee
Dam
(
Fish
and
Hanavan
1948,
Chapman
et
al.
1991).
Subsequent
increases
in
run­
size
in
the
Wenatchee,
Entiat,
and
Methow
Rivers
following
the
GCFMP
suggest
that
introduced
fish
became
established
in
these
rivers
(
Mullan
1987).

The
construction
of
the
Hermiston
Power
and
Light
(
1910)
and
Three
Mile
Dams
(
1914)
on
the
Umatilla
River
and
the
Lewiston
Dam
(
1927)
on
the
Clearwater
River
were
largely
responsible
for
the
extirpation
of
native
stocks
of
stream­
type
chinook
salmon
on
those
systems
(
Olsen
et
al
1992,
Keifer
et
al.
1992).
Fish
from
a
number
of
sources
have
since
been
used
to
reestablish
stream­
type
chinook
salmon
stocks
on
the
Umatilla
and
Clearwater
Rivers.
Certain
spring­
run
chinook
salmon
stocks,
such
as
the
Carson
NFH
stock,
have
been
widely
transferred
to
rivers
throughout
the
Columbia
and
Snake
River
Basins,
and
their
integration
into
many
local
populations
is
likely.

Hydroelectric
dams
and/
or
irrigation
diversions
affect
virtually
every
river
containing
stream­
type
chinook
salmon
(
although
irrigation
effects
are
less
significant
in
much
of
the
Snake
River
Basin)
and
have
produced
changes
in
thermal
regime,
loss
of
spawning
and
rearing
habitat,
or
direct
mortality
by
stranding
or
upstream
and
downstream
passage
injury
(
Lindsay
et
al.
1989,
Matthews
and
Waples
1991).
Identifying
regional
life­
history
differences
among
stream­
type
populations
is
complicated
by
stock
transfers
and
the
difficulty
in
separating
hatchery
and
naturally
produced
fish.
Culture
practices
and
differences
in
water
conditions,
primarily
temperature,
may
alter
the
observed
expression
of
numerous
life­
history
traits,
such
as
body
size
and
age
of
smoltification
and
maturation.

Genetic
Information
Background
78
The
previous
section
examined
evidence
for
phenotypic
and
life­
history
differences
between
populations
or
groups
of
populations
that
might
be
used
to
identify
distinct
population
segments.
The
genetic
basis
of
many
phenotypic
and
life­
history
traits,
however,
is
weak
or
unknown,
and
it
is
difficult
to
infer
the
amount
of
reproductive
isolation
from
population
differences
in
these
traits.
In
this
section,
we
consider
biochemical
and
molecular
genetic
evidence
that
might
be
used
to
define
reproductively
isolated
populations
or
groups
of
populations
of
chinook
salmon.
We
focus
on
genetic
markers
that
have
been
shown
to
follow
or
are
assumed
to
follow
Mendelian
inheritance,
so
that
an
analysis
of
the
geographical
distributions
of
these
markers
can
reveal
historical
levels
of
gene
flow
and
isolation.
The
bulk
of
this
evidence
consists
of
frequencies
of
protein
variants
(
allozymes),
or
of
naturally
occurring
mutations
in
minisatellite
and
microsatellite
loci
(
variable
numbers
of
short
tandem
repeats)
and
mitochondrial
(
mt)
DNA.
Because
of
high
mutation
rates
in
minisatellite
and
microsatellite
loci,
and
in
some
sections
of
mtDNA,
the
analysis
of
these
loci
permits
a
greater
resolution
of
the
effects
of
more
recent
population
events
than
does
the
analysis
of
allozyme
loci,
which
generally
have
lower
mutation
rates.
The
different
temporal
perspectives
of
population
structure
from
these
various
techniques
were
considered
in
our
attempts
to
define
distinct
population
segments.
Analyses
of
populations
of
chinook
salmon
have
been
examined
for
genetic
variability
throughout
most
of
the
geographical
distribution
of
this
species
with
allozyme
electrophoresis,
and
in
some
regions
with
the
analysis
of
mtDNA
or
microsatellite
loci.

Statistical
Methods
Several
standard
statistical
methods
have
been
used
to
analyze
molecular
genetic
data
to
test
various
hypotheses
of
reproductive
isolation.
Comparisons
between
observed
genotypic
frequencies
in
a
sample
with
frequencies
expected
with
random
mating
(
Hardy­
Weinberg
proportions)
can
be
used
to
infer
the
breeding
structure
of
a
population
or
to
detect
population
mixing.
Contingency­
table
comparisons
of
allozyme
or
microsatellite
allele
frequencies
among
population
samples
with
the
chi­
square
statistics
or
G­
statistic
have
been
widely
used
to
detect
significant
differences
between
populations.
The
finding
of
significant
frequency
differences
between
populations
may
be
evidence
of
reproductive
isolation.

Another
way
of
measuring
genetic
isolation
between
populations
is
to
calculate
genetic
distances
from
allele­
frequency
estimates.
Several
genetic
distance
measures
(
e.
g.
Cavalli­
Sforza
and
Edwards
1967,
Rogers
1972,
Nei
1972,
1978)
have
been
used
to
study
the
population
genetic
structure
of
chinook
salmon.
It
is
unclear,
however,
which
measure
is
best,
or
whether
there
is
one
measure
that
is
always
best.
An
attractive
feature
of
Rogers'
and
Cavalli­
Sforza
and
Edwards'
distances
is
that
they
satisfy
the
triangle
inequality;
that
is,
given
three
populations
(
A,
B,
C),
the
sum
of
the
distances
between
A
and
B
and
between
B
and
C
is
always
greater
than
or
equal
to
the
distance
between
A
and
C.
On
the
other
hand,
neither
of
these
genetic­
distance
measures
employs
a
correction
for
sample
size,
so
distances
are
biased
upward,
especially
for
small
sample
sizes.
In
contrast,
Nei's
(
1978)
distance
(
D)
is
unbiased,
but
does
not
always
satisfy
79
the
triangle
inequality.
When
sample
sizes
used
to
estimate
allelic
frequencies
are
50
individuals
or
more,
the
difference
between
Nei's
genetic
distance
(
Nei
1972)
and
Nei's
unbiased
genetic
distance
(
Nei
1978)
is
small,
but
still
might
be
a
substantial
proportion
of
D,
if
D
is
small.
Another
consideration
is
that
Nei's
and
Rogers'
distance
measures
can
be
affected
by
different
levels
of
heterozygosity
between
populations,
whereas
Cavalli­
Sforza
and
Edwards'
measure
is
not.
Discussions
of
these
and
other
features
of
genetic
distances
appear
in
Nei
(
1978),
Hillis
et
al.
(
1996),
and
Rogers
(
1991).

Most
of
the
discussion
on
genetic
distances
has
focused
on
the
merits
of
the
various
measures
for
phylogenetic
reconstruction
among
species
and
higher
taxa.
No
one
has
quantitatively
evaluated
the
performances
of
these
distances
in
assessing
the
genetic
population
structures
of
species
like
salmon,
which
typically
show
relatively
small
genetic
distances
between
conspecific
populations.
Since
it
is
unclear
which
distance
measure
is
"
best"
in
any
given
application,
we
analyzed
each
set
of
data
with
Nei's
unbiased,
Rogers',
and
Cavalli­
Sforza
and
Edwards'
genetic
distances
to
identify
results
that
were
robust
to
the
choice
of
the
distance
measure.
In
most
cases,
the
different
genetic­
distance
measures
yielded
highly
correlated
results.
For
simplicity,
we
report
only
results
based
on
Cavalli­
Sforza
and
Edwards'
distance
measure.
This
measure
ranges
from
0.0
(
identity)
to
1.0
(
complete
dissimilarity).

The
degree
of
reproductive
isolation
was
inferred
from
an
analysis
of
the
pattern
of
genetic
distances
between
populations.
Clustering
methods,
such
as
the
unweighted
pair
group
method
with
arithmetic
averages
(
UPGMA;
Sneath
and
Sokal
1963)
and
the
neighbor­
joining
method
(
Saitou
and
Nei
1987),
produce
hierarchical
groupings
of
genetically
similar
populations.
Multivariate
methods,
such
as
multidimensional
scaling
(
MDS;
Kruskal
1964)
or
principal
components
analysis
(
PCA)
cluster
populations
in
two
or
three
dimensions.
When
the
geographical
distribution
of
genetic
variability
is
continuous
and
not
hierarchical
or
disjunct,
such
as
in
a
clinal
or
reticulate
pattern,
MDS
and
PCA
more
accurately
depict
relationships
among
samples
than
does
agglomerative
clustering
such
as
the
UPGMA
(
Lessa
1990).
Since
the
latter
algorithm
compares
the
genetic
distance
of
an
incoming
sample
to
the
average
genetic
distance
between
samples
already
in
a
cluster,
the
information
about
the
relationship
between
the
incoming
sample
and
the
samples
already
in
the
cluster
is
lost.
MDS,
on
the
other
hand,
is
a
non­
metric
ordination
technique
that
minimizes
the
distortion
of
pairwise
genetic
distances
between
samples
in
n­
dimensional
space
without
averaging.
Principal
component
analysis
of
allelic
frequencies
can
also
be
used
to
examine
genetic
relationships
among
populations.
In
the
present
analyses,
the
results
of
a
PCA
were
usually
similar
to
MDS
ordinations
for
a
set
of
data.
Reproductive
isolation
between
populations
was
inferred
from
a
visual
examination
of
these
plots,
whenever
clusters
of
related
populations
were
consistent
with
the
geographies
of
the
samples
in
the
clusters.

Levels
of
genetic
variability
within
populations
were
also
considered,
because
the
level
of
within­
population
variability
may
reflect
evolutionary
or
historical
differences
in
population
size
and
migration
patterns
between
populations.
Within­
population
genetic
diversity
(
H)
is
usually
measured
by
the
expected
(
with
random
mating)
proportion
of
heterozygous
individuals
in
a
population
and
is
averaged
over
the
number
of
loci
examined.
Estimates
of
heterozygosity
based
80
on
a
small
number
of
individuals
are
usually
accurate,
as
long
as
a
large
number
of
loci
(>
30
loci)
are
surveyed
for
variability
(
Nei
1978).

Genetic
differentiation
between
populations
at
various
hierarchical
levels
has
been
estimated
in
many
studies
with
a
gene
diversity
analysis
(
Nei
1973,
Charkraborty
1980),
which
apportions
allele­
frequency
variability
among
populations
into
its
geographical
or
temporal
components.
For
example,
the
proportion
of
genetic
subdivision
among
populations
may
be
estimated
with
G
ST
=
(
H
T
­
H
S)/
H
T,
where
H
S
is
the
average
within­
population
heterozygosity
and
H
T
is
the
total
heterozygosity
disregarding
geographical
subdivision.
F
ST
is
equivalent
to
G
ST
when
there
are
only
two
alleles
at
a
locus.
Most
genetic
variability
in
salmonids
occurs
as
genotypic
differences
among
individuals
within
a
population
(
Ryman
1983).
A
smaller
proportion
of
the
total
variability
is
due
to
hierarchical
differences
between
regions,
river
systems,
tributaries
and
streams
within
a
river
system,
between
years,
or
between
run
types.
Estimates
of
G
ST
or
F
ST
among
natural
populations
ranges
from
0.0
(
no
genetic
differentiation
among
populations)
to
about
0.25
(
strong
differentiation
among
populations).
These
statistics
facilitate
comparisons
among
groups
of
populations
that
may
reveal
regional
differences
in
gene
flow
between
populations,
or
the
effects
of
hatchery
strays
on
levels
of
differentiation
between
populations.

In
the
present
status
review,
we
first
present
the
results
of
previous
population
genetic
studies
of
chinook
salmon,
then
present
the
results
of
an
analysis
of
allele­
frequency
data
that
constitute
an
interagency,
coast­
wide
data
base.
The
primary
purpose
of
the
review
is
to
present
genetic
evidence
of
reproductive
isolation
between
populations
or
groups
of
populations.
Allelefrequency
differentiation
among
populations
and
differences
in
levels
of
gene
diversity
constitute
the
bulk
of
this
evidence.

Previous
Genetic
Studies
Alaska
Gharrett
et
al.
(
1987)
studied
genetic
variability
among
populations
of
chinook
salmon
in
13
river
drainages
in
western,
south­
central,
and
southeastern
Alaska.
They
examined
electrophoretic
variability
in
proteins
encoded
by
28
loci,
8
of
which
had
at
least
moderate
levels
of
polymorphism
(
frequency
of
the
common
allele
less
than
0.90
in
at
least
1
of
the
population
samples).
In
most
drainages,
collections
were
made
at
more
than
one
site
or
in
more
than
one
year,
or
both.
Allele­
frequency
heterogeneity
was
observed
among
three
areas
in
the
Yukon
River
drainage,
and
among
lower
and
upper
Stikine
River
samples.
On
a
larger
geographic
scale,
significant
overall
heterogeneity
was
present
among
tributaries
of
western,
south­
central,
and
southeastern
Alaska.
A
gene
diversity
analysis
showed
that
94.1%
of
the
total
variability
over
samples
was
contained,
on
average,
within
the
genetically­
homogeneous
river
drainages,
3.3%
was
due
to
differences
among
river
drainages
within
the
three
regions,
and
2.6%
was
due
to
differences
among
regions.
A
comparison
of
these
results
with
other
studies
(
Pacific
Northwest,
Utter
et
al.
1989;
Oregon­
California,
Bartley
and
Gall
1990),
indicates
the
amount
of
genetic
81
differentiation
between
Alaskan
populations
may
be
smaller
than
that
for
chinook
salmon
populations
in
other
regions.
A
maximum­
likelihood
cluster
analysis
of
Cavalli­
Sforza
and
Edwards
(
1967)
genetic
distances
between
samples
showed
that
populations
in
western
and
south­
central
Alaska
were
closely
related
to
one
another,
but
were
distinct
from
southeastern
Alaska
populations.
Samples
from
southeastern
Alaskan
populations
were
genetically
intermediate
between
samples
from
western
and
south­
central
Alaska
as
well
as
those
from
southern
British
Columbia
and
Washington.

Pacific
Northwest
overview
Utter
et
al.
(
1989)
examined
allozyme
variability
at
25
polymorphic
loci
in
samples
from
86
populations
extending
from
the
Skeena
River,
British
Columbia
to
the
Sacramento
and
San
Joaquin
Rivers,
California.
Geographically
proximate
samples
not
showing
significant
allelefrequency
differences
(
P<
0.01)
were
pooled,
and
this
reduced
the
data
set
to
65
units
for
geographical
analyses.
A
PCA
of
allelic
frequencies
and
cluster
analysis
of
Nei's
(
1972)
genetic
distances
between
samples
indicated
the
existence
of
nine
genetically
distinct
regional
groups
of
populations
(
Fig.
17).
The
first
region
consisted
of
populations
in
the
upper
Fraser
River
and
tentatively
included
a
single
sample
from
the
Babine
River,
a
tributary
of
the
Skeena
River.
A
second
region
included
populations
in
rivers
draining
into
Georgia
Strait
in
southern
British
Columbia.
Region
3
included
populations
around
Puget
Sound,
and
a
fourth
group
included
populations
on
the
west
coast
of
Vancouver
Island,
along
the
Strait
of
Juan
de
Fuca,
and
on
the
coasts
of
Washington,
Oregon,
and
California.
In
the
Columbia
River
basin,
Region
5
included
populations
in
the
lower
Columbia
River
and
its
tributaries,
and
Region
6
included
populations
in
rivers
above
Bonneville
Dam,
except
those
in
the
Snake
River,
which
constituted
Region
7.
Farther
to
the
south,
Region
8
consisted
of
populations
in
the
Klamath
River
Basin,
and
Region
9
included
populations
in
the
Sacramento
and
San
Joaquin
Rivers.

A
gene
diversity
analysis
of
the
65
population
units
in
the
9
regions
indicated
that
87.7%
of
the
total
observed
variability
was
contained,
on
average,
within
the
units.
Of
the
remaining
12.3%,
1.5%
was
due
to
differences
among
the
9
regions,
6.2%
was
due
to
differences
among
or
between
river
drainages
within
regions,
and
4.6%
was
due
to
genetic
differences
among
82
Figure
17.
The
nine
genetically
defined
regional
groups
of
chinook
salmon
proposed
by
Utter
et
al.
(
1989).
Number
designations
are
further
explained
in
the
text.
83
populations
within
areas.
Utter
et
al.
(
1989)
re­
analyzed
the
same
set
of
allelic
frequencies
to
estimate
the
gene
diversity
components
due
to
differences
among
adult
run
times
(
spring,
summer,
and
fall).
Allele­
frequency
differences
among
populations
within
the
run
times
accounted
for
11.4%
of
the
total
variability,
whereas
only
0.9%
of
the
total
variability
was
due
to
differences
among
run
times.
The
authors
concluded
that
neither
clustering
nor
the
gene
diversity
analyses
supported
the
concept
that
chinook
salmon
adult
run
times
represented
distinct
"
races"
with
separate
ancestries,
but
rather
that
"
genetic
divergence
into
temporally
distinct
units
tend[
ed]
to
occur
within
an
area
from
a
common
ancestral
stock
..."
(
p.
247).

The
genetic
survey
of
Utter
et
al.
(
1989)
failed
to
distinguish
clearly
between
Snake
River
(
Region
7)
and
Klamath
River
(
Region
8)
populations
of
chinook
salmon,
even
though
the
mouths
of
these
rivers
are
geographically
widely
separated,
and
recent
gene
flow
between
them
is
unlikely.
The
authors
speculated
that
this
similarity
was
an
artifact
that
would
be
resolved
as
more
data
became
available.
Subsequently,
Utter
et
al.
(
1992)
added
allelic
frequencies
for
15
additional
polymorphic
loci
to
the
data
of
Utter
et
al.
(
1989)
and
included
allelic
frequencies
of
Bartley
et
al.
(
1992)
and
Waples
et
al.
(
1991b).
The
re­
analysis
indicated
a
clear
genetic
separation
between
populations
in
the
Snake
and
Klamath
River
Basins.

In
a
regional
study
of
mitochondrial
DNA
variability,
Wilson
et
al.
(
1987)
used
14
type
II
restriction
enzymes
(
enzymes
with
cleavage
sites
located
within
the
recognition
sequence)
to
survey
geographical
variability
in
6
samples
from
wild
and
hatchery
populations
of
chinook
salmon
extending
from
Bristol
Bay,
Alaska
to
southern
British
Columbia.
Four
of
the
enzymes
showed
restriction
fragment
length
polymorphisms
(
RFLPs),
and
6
composite
haplotypes
were
found
among
76
fish.
The
most
abundant
haplotype
occurred
in
43
of
the
55
(
79%)
fish
from
southern
British
Columbia.
The
second
most
abundant
haplotype
(
N=
20)
was
shared
between
Alaskan
(
N=
4)
and
British
Columbian
(
N=
6)
samples.
A
third
haplotype
was
found
only
in
Alaska
(
N=
10).
Three
additional
haplotypes
were
found
in
single
fish
from
three
different
localities.
Although
the
lack
of
sharing
of
5
of
6
haplotypes
between
Alaska
and
British
Columbia
indicated
substantial
reproductive
isolation
between
these
populations,
average
sequence
divergence
between
haplotypes
from
Alaska
and
British
Columbia
(
P=
0.43%)
was
not
greater
than
that
between
haplotypes
within
Alaska
(
P=
0.45%)
and
within
British
Columbia
(
P=
0.54%).
A
comparison
with
the
RFLP
haplotypes
for
10
restriction
enzymes
that
were
in
common
with
those
of
Berg
and
Ferris
(
1984)
in
a
study
of
chinook
salmon
in
California
indicated
a
sequence
divergence
of
2.2%,
a
value
as
large
as
the
sequence
divergence
between
chinook
salmon
and
coho
salmon
reported
by
Thomas
et
al.
(
1986).

Yukon
and
British
Columbia
Beacham
et
al.
(
1989)
examined
genetic
variability
at
20
allozyme
loci
among
samples
from
15
populations
of
chinook
salmon
in
the
Canadian
Yukon
River
system,
and
one
sample
from
the
Alsek
River
drainage.
Chinook
salmon
returning
to
natal
spawning
sites
in
the
upper
reaches
of
the
Yukon
River
in
Canada
must
travel
at
least
1,200
km.
Tests
for
allele­
frequency
heterogeneity
at
16
polymorphic
loci
showed
a
highly
significant
difference
between
the
Yukon
84
River
samples
and
the
sample
from
the
Alsek
River
system.
Although
the
headwaters
of
these
two
river
systems
are
in
close
proximity,
the
Yukon
River
flows
into
the
Bering
Sea
and
the
Alsek
River
flows
into
the
Gulf
of
Alaska
several
hundreds
of
kilometers
away.
Among
the
upper
Yukon
River
samples,
the
samples
from
Whitehorse
and
Takhini
Rivers
were
genetically
distinct
from
the
other
samples.
The
rest
of
the
Yukon
River
samples
were
not
clustered
into
clear
geographical
groups.
These
results
show
that
many
of
the
geographically
isolated
populations
in
major
tributaries
of
the
upper
Yukon
River
are
also
genetically
distinct
from
one
another.

In
another
study,
Beacham
et
al.
(
1996)
surveyed
variability
at
three
minisatellite
loci
among
populations
of
chinook
salmon
extending
from
the
Nass
River
in
northern
British
Columbia,
through
the
mainland
to
the
Fraser
River,
and
to
eastern
and
western
Vancouver
Island.
Minisatellite
loci
are
segments
of
DNA
consisting
of
tandomly
repeated
sequences
10­
75
base
pairs
in
length,
and
alleles
consist
of
different
numbers
of
these
repeats.
Alleles
detected
with
one
probe,
pSsa­
A34,
were
previously
shown
to
follow
Mendelian
inheritance
(
Stevens
et
al.
1993).
Band
counts
were
binned
into
size
classes,
because
it
was
not
always
possible
to
establish
the
homologies
of
electrophoretically
similar
fragments.
The
frequencies
of
these
size
classes
were
used
to
assess
population
genetic
structure
in
the
same
way
allozyme
alleles
were
used
to
test
for
Hardy­
Weinberg
proportions
or
reproductive
isolation
among
populations.
Beacham
et
al.
(
1996)
found
strong
frequency
differences
between
northern
and
southern
populations
of
chinook
salmon
in
British
Columbia,
and
also
between
Fraser
River,
West
Vancouver
Island,
and
East
Vancouver
Island
populations.
A
neighbor­
joining
tree
of
Mahalanobis
generalized
distances
between
samples
showed
two
major
clusters
consisting
of
samples
from
northern
British
Columbia
and
those
from
southern
British
Columbia
and
Vancouver
Island.
A
PCA
analysis,
however,
indicated
a
major
genetic
discontinuity
between
mainland
populations
and
populations
on
Vancouver
Island.
In
the
PCA,
samples
of
mainland
populations
fell
into
a
linear
array
reflecting
isolation
by
distance,
a
feature
of
population
genetic
structure
that
was
not
apparent
in
the
neighbor­
joining
tree.
The
genetic
distinction
of
southern
mainland
populations
of
chinook
salmon
(
excluding
the
Fraser
River)
and
eastern
Vancouver
Island
populations
was
not
previously
detected
by
the
analysis
of
allozyme
variability
(
Utter
et
al.
1989).

In
a
study
of
chinook
salmon
in
southwestern
British
Columbia,
Heath
et
al.
(
1995),
examined
variability
among
seven
populations
on
the
eastern
side
of
Vancouver
Island
and
two
populations
in
the
Fraser
River
with
the
analysis
of
a
single­
locus
minisatellite
gene
with
the
probe
OtSL1.
Alleles
with
similar
allelic
mobilities
after
electrophoresis
were
binned
and
the
frequencies
of
the
binned
classes
were
analyzed
with
a
PCA.
The
principal
components
were
tested
for
significance
with
a
one­
way
ANOVA,
and
significant
components
were
used
in
a
discriminant
function
analysis
to
produce
estimates
of
population
differentiation.
They
found
a
52%
overall
success
rate
of
assigning
sampled
fish
to
the
locations
from
which
they
had
been
drawn.
Populations
that
had
received
transplants
tended
to
show
the
least
amount
of
discrimination,
and
this
was
attributed
to
the
homogenizing
effects
of
gene
flow
from
the
transfers.
These
results
are
consistent
with
allozyme
studies
for
this
area
in
showing
detectable
genetic
differences
between
populations
over
a
restricted
area.
The
analysis
of
minisatellite
loci,
85
however,
may
have
more
discriminating
power
than
allozymes,
because
of
the
higher
mutation
rate
for
minisatellite
loci.

Washington
Reisenbichler
and
Phelps
(
1987)
examined
chinook
salmon
allozyme
variability
in
four
river
drainages
on
the
north
coast
of
Washington.
Six
of
the
55
enzyme­
encoding
loci
examined
for
genetic
variability
were
polymorphic
with
frequencies
of
common
alleles
less
than
0.95,
and
hence
were
useful
for
depicting
population
structure.
Juveniles
and
adults
were
sampled
in
the
lower
portions
of
rivers,
so
intra­
river
variability
could
not
be
estimated.
The
variance
in
allelic
frequencies
between
brood
years
1981
and
1982
at
four
localities
was
used
as
an
error
term
in
an
ANOVA
of
arcsine
transformed
common­
allele
frequencies.
The
ANOVA
failed
to
detect
significant
allele­
frequency
heterogeneity
among
the
four
drainages
for
the
fall­
run
samples;
that
is,
the
amount
of
allele­
frequency
variability
among
drainages
along
the
coast
was
no
greater
than
variability
between
years
within
rivers,
on
average.
The
comparison
between
summer­
and
fallrun
adult
chinook
salmon
in
four
rivers,
however,
approached
significance
(
P=
0.07).
Comparisons
between
summer­
run
hatchery
and
summer­
run
wild
fish,
and
between
fall­
run
hatchery
and
fall­
run
wild
fish,
were
both
significant.
These
results
show
that
in
this
relatively
small
area
on
the
Washington
coast
a
greater
amount
of
reproductive
isolation
appeared
between
run
types
than
between
populations
within
run
types.
Significant
frequency
differences
between
hatchery
and
wild
populations
indicated
minimal
mixing
between
these
groups
of
fish
in
this
area.

Marshall
et
al.
(
1995)
examined
allele­
frequency
variability
at
42
loci
in
58
chinook
salmon
populations
representing
major
spawning
areas
in
Washington.
They
defined
two
nested
levels
of
population
units
from
the
results
of
UPGMA
clustering
and
multidimensional
scaling
of
Cavalli­
Sforza
and
Edwards'
genetic
distances
between
samples.
The
more
inclusive
units,
major
ancestral
lineages
(
MAL),
were
defined
by
four
clusters:
1)
upper
Columbia
and
Snake
River
(
spring
run)
samples,
2)
upper
Columbia
River
(
summer­
and
fall­
run
"
brights"),
mid­
and
lower
Columbia
River
(
spring­
and
fall­
run
"
tules"
and
"
brights"),
and
Snake
River
(
fall
run)
samples,
3)
Washington
coastal
and
Strait
of
Juan
de
Fuca
(
spring
and
fall
run)
samples,
and
4)
Puget
Sound
(
spring,
summer,
and
fall
run)
samples.
Each
of
these
four
groups
were
further
distinguished
by
characteristic
levels
of
allozyme
polymorphism
and
by
shared
occurrences
of
rare
or
private
alleles
among
populations
within
the
clusters.
Finer
scale
genetic
diversity
units
(
GDUs)
were
designated
within
each
of
the
four
groups
by
considering
life
history,
ecological,
and
physiographic
information
in
addition
to
allelic
frequencies
and
genetic
distances
between
samples.

Columbia
River
Basin
One
of
the
earliest
studies
of
chinook
salmon
genetics
in
the
Columbia
River
was
by
Kristiansson
and
McIntyre
(
1976),
who
reported
allelic
frequencies
for
4
polymorphic
loci
in
samples
from
10
hatcheries,
5
of
which
were
located
along
the
coast
and
5
in
the
lower
Columbia
River
Basin.
Significant
frequency
differences
for
SOD*
were
detected
between
spring­
and
fall­
86
run
samples
collected
at
the
Little
White
Salmon
Hatchery
on
the
Columbia
River,
but
not
for
spring­
and
fall­
run
samples
from
the
Trask
River
Hatchery
along
the
northern
coast
of
Oregon.
Significant
allele­
frequency
differences
were
also
found
between
Columbia
River
samples
as
a
group
and
Oregon
coastal
samples
for
PGM*
and
MDH*.

Utter
et
al.
(
1982)
compared
allelic
frequencies
at
12
polymorphic
loci
in
samples
of
fallrun
chinook
salmon
from
the
Priest
Rapids
Hatchery
in
the
mid­
Columbia
River
and
from
Ice
Harbor
Dam
on
the
Snake
River.
These
samples
were
taken
over
four
years
at
each
locality.
Significant
allele­
frequency
differences
between
populations
were
detected
for
5
loci.

Schreck
et
al.
(
1986)
examined
allele­
frequency
variability
at
18
polymorphic
loci
to
infer
genetic
relationships
among
56
Columbia
River
Basin
chinook
salmon
populations.
A
hierarchical
cluster
analysis
of
genetic
correlations
between
populations
identified
two
major
groups.
The
first
contained
spring­
run
chinook
salmon
east
of
the
Cascade
Mountains
and
summer­
run
fish
in
the
Salmon
River.
Within
this
group
they
found
three
subclusters:
1)
wild
and
hatchery
spring­
run
chinook
salmon
east
of
the
Cascade
Mountains,
2)
spring­
run
chinook
salmon
in
Idaho,
and
3)
widely
scattered
groups
of
spring­
run
chinook
salmon
in
the
White
Salmon
River
Hatchery,
the
Marion
Forks
Hatchery,
and
the
Tucannon
River.
A
second
major
group
consisted
of
spring­
run
chinook
salmon
west
of
the
Cascade
Crest,
summer­
run
fish
in
the
upper
Columbia
River,
and
all
fall­
run
fish.
Three
subclusters
also
appeared
in
this
group:
1)
spring­
and
fall­
run
fish
in
the
Willamette
River,
2)
spring­
and
fall­
run
chinook
salmon
below
Bonneville
Dam,
and
3)
summer­
and
fall­
run
chinook
salmon
in
the
upper
Columbia
River.
Schreck
et
al.
(
1986)
also
surveyed
morphological
variability
among
areas,
and
these
results
were
reviewed
in
the
Life
History
section
of
this
status
review.

Waples
et
al.
(
1991a)
examined
21
polymorphic
loci
in
samples
from
44
populations
of
chinook
salmon
in
the
Columbia
River
Basin.
A
UPGMA
tree
of
Nei's
(
1978)
genetic
distances
between
samples
showed
three
major
clusters
of
Columbia
River
Basin
chinook
salmon:
1)
Snake
River
spring­
and
summer­
run
chinook
salmon,
and
mid­
and
upper
Columbia
River
spring­
run
chinook
salmon,
2)
Willamette
River
spring­
run
chinook
salmon,
3)
mid­
and
upper
Columbia
River
fall­
and
summer­
run
chinook
salmon,
Snake
River
fall­
run
chinook
salmon,
and
lower
Columbia
River
fall­
and
spring­
run
chinook
salmon.
These
results
indicate
that
the
timing
of
chinook
salmon
returns
to
natal
rivers
was
not
necessarily
consistent
with
genetic
subdivisions.
For
example,
summer­
run
chinook
salmon
in
the
Snake
River
were
genetically
distinct
from
summer­
run
chinook
salmon
in
the
mid
and
upper
Columbia
River,
but
still
had
similar
adult
run
timings.
Spring­
run
populations
in
the
Snake,
Willamette
and
lower,
mid,
and
upper
Columbia
Rivers
were
also
genetically
distinct
from
each
other
but
had
similar
run
timings.
Conversely,
some
populations
with
similar
run
timings,
such
as
lower
Columbia
River
"
tule"
fallrun
fish
and
upper
Columbia
River
"
bright"
fall­
run
fish,
were
genetically
distinct
from
one
another.
Juvenile
outmigration
also
differed
among
some
groups
with
similar
adult
run
timing.
For
example,
summer­
run
juveniles
in
the
upper
Columbia
River
exhibit
ocean­
type
life­
history
characteristics,
but
summer­
run
chinook
salmon
in
the
Snake
River
migrate
exhibit
stream­
type
life­
history
characteristics.
87
In
a
status
review
of
Snake
River
fall
chinook
salmon,
Waples
et
al.
(
1991b)
examined
genetic
relationships
among
fall­
run
chinook
salmon
in
the
Columbia
and
Snake
Rivers
(
Group
3
of
Waples
et
al.
1991a)
in
more
detail.
A
UPGMA
cluster
analysis
of
Nei's
unbiased
genetic
distance,
based
on
21
polymorphic
loci,
indicated
that
"
bright"
fall­
run
chinook
salmon
in
the
upper
Columbia
River
were
genetically
distinct
from
those
in
the
Snake
River.
Populations
in
the
two
groups
were
characterized
by
allele­
frequency
differences
of
about
10­
20%
at
several
loci,
and
these
differences
remained
relatively
constant
from
year
to
year
in
the
late
1970s
and
early
1980s.
However,
allele­
frequency
shifts
from
1985
to
1990
for
samples
of
fall­
run
chinook
salmon
at
Lyons
Ferry
Hatchery
in
the
Snake
River
suggested
that
mixing
with
upper
Columbia
River
fish
had
occurred.
This
is
consistent
with
reports
that
stray
hatchery
fish
from
the
upper
Columbia
River
were
inadvertently
used
as
brood
stock
at
the
Lyons
Ferry
Hatchery.
Samples
of
"
bright"
fall­
run
chinook
salmon
from
the
Deschutes
River
and
the
Marion
Drain
irrigation
channel
in
the
Yakima
River
Basin
also
appeared
in
the
same
cluster
with
samples
of
fall­
run
chinook
salmon
from
the
Snake
River.

Genetic
analysis
of
oceanic
mixed­
stock
harvests
indicated
differences
in
ocean
distributions
between
"
bright"
and
"
tule"
fall­
run
chinook
salmon
from
the
Columbia
River.
Utter
et
al.
(
1987)
estimated
allelic
frequencies
for
17
polymorphic
loci
in
baseline
samples
from
88
localities
extending
from
southern
British
Columbia
(
except
1
sample
from
northern
British
Columbia)
through
Washington
and
Oregon
to
northern
California.
These
data
were
pooled
on
the
basis
of
contingency­
table
tests
of
allelic
frequencies
into
65
groups
with
genetically
homogeneous
populations.
These
groups
were
used
to
estimate
the
stock
composition
of
fishery
samples
taken
at
ports
of
landing
from
the
mouth
of
the
Strait
of
Juan
de
Fuca
to
northern
Oregon.
Tagging
returns
(
Table
5
in
Utter
et
al.
1987)
indicated
that
"
tule"
fish
tended
to
be
caught
in
the
coastal
waters
of
Washington,
whereas
"
upriver
brights"
tended
to
be
caught
in
the
commercial
harvests
of
Alaska
and
British
Columbia.
The
results
of
the
mixed­
stock
analysis
for
samples
collected
in
1982
and
1983
were
consistent
with
tagging
returns
in
indicating
different
ocean
distributions
of
"
tule"
and
upriver
"
bright"
Columbia
River
chinook
salmon.

In
a
study
of
genetic
effects
of
hatchery
supplementation
on
naturally
spawning
populations
in
the
upper
Snake
River
Basin,
Waples
et
al.
(
1993)
examined
allele­
frequency
variability
at
35
polymorphic
loci
in
14
wild
(
no
hatchery
supplementation),
naturally
spawning
(
some
hatchery
supplementation),
and
hatchery
populations
of
spring­
and
summer­
run
chinook
salmon.
Most
populations
were
sampled
over
two
years.
An
analysis
of
these
data
indicated
that
96.6%
of
the
genetic
diversity
existed
as
genetic
differences
among
individuals
within
populations.
Most
of
the
remaining
3.4%
was
due
to
differences
between
localities,
and
only
a
negligible
amount
was
due
to
allele­
frequency
differences
between
spring­
and
summer­
run
chinook
salmon.
Results
reveal
a
close
genetic
affinity
in
the
upper
Snake
River
between
natural
spawners
that
suggests
either
gene
flow
between
populations
or
a
recent
common
ancestry.
Comparisons
between
hatchery
and
natural
populations
in
the
same
river
indicated
that
the
degree
of
genetic
similarity
between
them
reflected
the
source
of
the
brood
stock
in
the
hatchery.
As
expected,
the
genetic
similarity
between
wild
and
hatchery
fish,
for
which
local
wild
fish
were
used
as
brood
stock,
was
high.
88
In
a
study
of
upper
Columbia
River
chinook
salmon,
Utter
et
al.
(
1995)
examined
allelefrequency
variability
at
36
loci
in
samples
of
16
populations.
A
UPGMA
tree
of
Nei's
(
1972)
genetic
distances
between
samples
indicated
that
spring­
run
populations
were
distinct
from
summer­
and
fall­
run
populations.
The
average
genetic
distance
between
samples
from
the
two
groups
was
about
eight
times
the
average
of
genetic
distances
between
samples
within
each
group.
Allele­
frequency
variability
among
spring­
run
populations
was
considerably
greater
than
that
among
summer­
and
fall­
run
populations
in
the
upper
Columbia
River.
The
lack
of
strong
allele­
frequency
differentiation
between
summer­
and
fall­
run
samples
indicated
minimal
reproductive
isolation
between
these
two
groups
of
fish.
Hatchery
populations
of
spring­
run
chinook
salmon
were
genetically
distinct
from
wild
spring­
run
populations,
but
hatchery
populations
of
fall­
run
chinook
salmon
were
not
genetically
distinct
from
wild
fall­
run
populations.

Some
studies
have
indicated
that
Snake
River
spring­
and
summer­
run
chinook
salmon
have
reduced
levels
of
genetic
variability.
Utter
et
al.
(
1989)
estimated
gene
diversities
with
25
polymorphic
loci
for
65
population
units
and
found
that
gene
diversities
in
the
Snake
River
were
lower
than
those
in
the
Columbia
River.
Winans
(
1989)
estimated
levels
of
gene
diversity
with
33
loci
for
spring­,
summer­,
and
fall­
run
chinook
salmon
at
28
localities
in
the
Columbia
River
Basin.
Fall­
run
chinook
salmon
tended
to
have
significantly
greater
levels
of
gene
diversity
(
N=
12,
mean
H=
0.081)
than
both
spring­
(
N=
17,
H=
0.065)
and
summer­
run
(
N=
3,
mean
H=
0.053)
chinook
salmon.
Spring­
run
fish
in
the
Snake
River
had
the
lowest
gene
diversities
(
N=
4,
mean
H=
0.044).
However,
Waples
et
al.
(
1991a)
found
that,
with
a
larger
sample
of
65
loci,
gene
diversities
in
Snake
River
spring­
run
and
summer­
run
chinook
salmon
were
not
as
low
as
that
suggested
by
earlier
studies.

Recent,
but
unpublished,
data
are
available
for
chinook
salmon
and
will
be
discussed
in
the
next
section.
However
the
results
of
the
foregoing
studies
of
Columbia
and
Snake
River
chinook
salmon
permit
the
following
generalizations:

1)
Populations
of
chinook
salmon
in
the
Columbia
and
Snake
Rivers
are
genetically
discrete
from
populations
along
the
coasts
of
Washington
and
Oregon.

2)
Strong
genetic
differences
exist
between
populations
of
spring­
run
and
fall­
run
fish
in
the
upper
Columbia
and
Snake
Rivers.
In
the
lower
Columbia
River,
however,
springrun
fish
are
genetically
more
closely
allied
with
nearby
fall­
run
fish
in
the
lower
Columbia
River
than
with
spring­
run
fish
in
the
Snake
and
upper
Columbia
Rivers.

3)
Summer­
run
fish
are
genetically
related
to
spring­
run
fish
in
some
areas
(
e.
g.,
Snake
River),
but
to
fall­
run
fish
in
other
areas
(
e.
g.,
upper
Columbia
River).

4)
Populations
of
fall­
run
fish
are
subdivided
into
several
genetically
discrete
geographical
groups
in
the
Columbia
and
Snake
Rivers
(
these
populations
will
be
discussed
in
detail
in
the
next
section).
89
5)
Hatchery
populations
of
chinook
salmon
tend
to
be
genetically
similar
to
the
respective
source
populations
used
to
found
or
augment
the
hatchery
populations.

California
and
Oregon
Bartley
and
Gall
(
1990)
surveyed
samples
from
35
populations
in
the
Sacramento
and
San
Joaquin
Rivers
and
along
the
coast
of
northern
California
for
genetic
variability
at
up
to
53
loci.
Overall,
genetic
variability
was
detected
at
40%
(
21)
of
the
loci
with
the
0.95
criterion
of
polymorphism,
but
varied
from
3
(
5.8%)
to
17
(
32%)
loci
among
samples.
Cluster
analysis
of
Nei's
(
1978)
unbiased
genetic
distances
between
samples
revealed
three
major
clusters
roughly
corresponding
to
1)
the
Klamath
and
Trinity
Rivers
populations,
2)
Eel
River
populations,
and
3)
the
Sacramento
and
San
Joaquin
River
populations.
Samples
from
eight
coastal
populations
did
not
cluster
together,
but
were
scattered
among
samples
in
the
three
major
clusters.
One
sample
from
the
Omagar
Creek
pond­
rearing
facility
in
the
lower
Klamath
River
drainage
did
not
fall
into
any
of
the
three
major
clusters.
The
average
percentage
of
the
total
genetic
variability
contained
within
samples
was
82.3%,
and
the
remainder
was
due
to
differences
among
samples
on
various
geographical
scales.
The
greatest
sources
of
geographical
subdivision
were
among
rivers
within
a
drainage
(
6.1%)
and
among
drainages
within
a
region
(
5.4%),
on
average.
Differences
among
samples
within
rivers
(
3.3%)
and
among
regions
(
2.9%)
represented
smaller
amounts
of
geographical
heterogeneity.
The
authors
did
not
distinguish
among
adult
run
times
in
their
analyses.

Bartley
et
al.
(
1992)
expanded
the
study
of
Bartley
and
Gall
(
1990)
and
surveyed
up
to
78
loci
in
samples
from
37
chinook
salmon
populations
in
the
Sacramento
and
San
Joaquin
Rivers,
northern
coastal
California,
the
Klamath
and
Trinity
Rivers,
and
rivers
along
southern
to
middle
coastal
Oregon.
The
authors
detected
genetic
variation
at
47
(
60.3%)
loci.
They
found
significant
departures
of
genotypic
proportions
from
Hardy­
Weinberg
proportions
in
8%
of
the
samples
overall,
5%
(
13
of
252
tests)
in
samples
from
wild
populations,
but
11%
(
24
of
210
tests)
in
samples
of
hatchery­
spawned
juveniles.
They
also
found
a
larger
than
expected
number
of
departures
from
Hardy­
Weinberg
proportions
(
13%,
13
of
97
tests)
in
wild
and
hatchery
samples
from
the
Klamath
River
Basin.
In
a
large
number
of
tests,
5%
are
expected
to
be
"
significant"
because
of
Type
I
error,
but
a
larger
proportion
of
significant
tests
may
indicate
that
juveniles
with
limited
numbers
of
parents
had
been
collected,
or
that
juveniles
from
genetically
distinct
subpopulations
had
been
included
in
a
sample,
or
that
the
genetic
model
or
interpreting
electrophoretic
banding
patterns
was
incorrect,
or
that
natural
selection
was
occurring
on
some
genotypes.
Allelic
frequencies
estimated
from
some
of
these
samples
may,
therefore,
not
represent
discrete
randomly
mating
populations.

From
these
data,
Bartley
et
al.
(
1992)
calculated
Nei's
(
1972)
genetic
distances
between
populations
and
produced
a
UPGMA
tree
consisting
of
five
clusters,
each
with
a
strong
geographical
component.
One
cluster
included
samples
from
populations
in
the
lower
Klamath
and
Smith
Rivers
of
northern
California
and
the
Chetco
and
Rogue
Rivers
of
southern
Oregon,
but
also
included
a
sample
from
Rock
Creek
Hatchery,
which
is
located
along
the
mid­
Oregon
90
coast.
A
second
cluster
included
samples
from
the
Eel
River
and
from
coastal
rivers
of
northern
California.
A
third
cluster
included
samples
from
the
upper
Klamath
and
Trinity
Rivers.
A
more
distantly
related
cluster
contained
samples
from
the
Oregon
coast
north
of
the
Rogue
River.
The
most
distinct
cluster
included
samples
from
the
Sacramento
and
San
Joaquin
Rivers,
which
were
not
well
differentiated
from
each
other.
A
hierarchical
gene
diversity
analysis,
modeled
a
posteriori
after
the
geographical
subdivisions
found
in
the
cluster
analysis
of
genetic
identities,
showed
that
89.4%
of
the
total
genetic
variability
observed
in
the
study
was
contained
on
average
within
subpopulations,
7.4%
was
due
to
differences
among
the
5
major
groups
detected
in
the
UPGMA
tree,
and
3.2%
was
due
to
differences
among
populations
within
the
groups
on
average.
These
results
indicate
that
the
major
drainages
from
mid
Oregon
south
each
contain
genetically
distinct
populations
of
chinook
salmon.

Yip
(
1994)
examined
allozyme
variability
at
53
enzyme
loci
in
398
fish
collected
between
September
and
December
1992
at
the
Trinity
River
Hatchery
in
the
Klamath
River
drainage.
About
40
fish
returning
to
the
hatchery
were
sampled
each
week
for
11
weeks
during
the
spawning
season.
Average
heterozygosities
in
these
samples
ranged
from
0.021
to
0.035
with
a
mean
of
0.029.
These
low
values
were
similar
to
the
low
values
in
Klamath
River
populations
found
by
(
Utter
et
al.
1987)
and
are
well
below
the
average
of
0.102
for
80
populations
of
chinook
salmon
(
Utter
et
al.
1987).
The
entry
timing
of
spring­
and
fall­
run
fish
into
the
Trinity
River
Hatchery
was
estimated
from
fish
with
coded
wire
tags
in
the
years
1989­
92
and
1994.
Based
on
these
returns,
the
weekly
samples
for
genetic
analysis
were
divided
a
priori
into
two
groups,
weeks
1­
4
and
weeks
5­
11.
Tests
for
allele­
frequency
differences
were
made
with
5
polymorphic
loci.
Not
all
of
the
fish
used
in
the
genetic
analysis
had
coded
wire
tags,
so
there
may
have
been
a
some
overlap
between
spring­
and
fall­
run
fish
in
the
middle
of
the
spawning
season
when
they
entered
the
hatchery.
The
sums
of
the
G­
statistics
for
individual
tests
were
not
significant
for
weekly
samples
within
either
group,
but
were
highly
significant
(
P<
0.01)
for
the
between­
group
comparisons.
These
results
were
interpreted
to
indicate
that
spring­
and
fall­
run
chinook
salmon
returning
to
the
hatchery
were
genetically
different.
The
analysis
of
temporal
run­
time
differences
was
continued
in
1994
with
allele
frequencies
for
three
polymorphic
loci,
GPI­
B2*,
sMEP­
1*,
and
PGK­
2*.
(
Yip
et
al.
1996).
As
in
1992,
comparisons
of
allele
frequencies
between
dates
within
the
1994
spring
and
fall
runs
were
not
significant.
Comparisons
between
allele
frequencies
between
1992
and
1994
for
the
spring
run
were
not
significant,
but
there
was
a
significant
overall
difference
between
1992
and
1994
fall­
run
fish.
An
approximate
F
ratio,
based
on
the
sums
of
the
G­
tests
for
within­
group
allele­
frequency
heterogeneity,
was
used
to
test
whether
between­
run
heterogeneity
was
greater
than
temporal
differences
within
runs.
This
test
was
significant
and
was
concordant
with
the
conclusions
of
the
earlier
study
that
spring­
and
fall­
run
chinook
salmon
were
genetically
discrete.

Vilkitis
et
al.
(
1994)
used
RFLP
analysis
of
internal
transcribed
spacers
of
ribosomal
DNA,
and
randomly
amplified
polymorphic
DNA
(
RAPD)
to
measure
the
level
of
divergence
between
the
spring
and
fall
runs
at
4
locations
in
the
Salmon
River,
California.
This
preliminary
study
of
samples,
collected
during
1992­
93,
found
distinct
genotypes
in
spring­
and
fall­
run
91
chinook
salmon
that
indicated
there
were
differences
between
locations,
yet
did
not
present
any
quantitative
information
on
the
actual
level
of
divergence.

In
tests
for
between­
year
differences
in
allele
frequencies
at
an
average
of
10
polymorphic
loci
in
samples
from
hatchery
and
wild
populations
in
Oregon,
Waples
and
Teel
(
1990)
found
a
greater
number
of
significant
tests
between
years
for
hatchery
samples
than
for
samples
from
naturally
spawning
populations.
The
greater
allele­
frequency
instability
between
years
in
the
hatcheries
was
attributed
to
the
use
of
an
effective
number
of
parents
less
than
50
in
many
hatchery
propagation
programs,
even
though
the
numbers
of
returning
adults
was
much
higher.

Populations
of
chinook
salmon
in
California
have
also
been
examined
for
repeat
length
polymorphisms
at
microsatellite
loci.
Hedgecock
et
al.
(
1995)
analyzed
samples
of
fall­,
late
fall­,
winter­,
and
spring­
run
chinook
salmon
populations
in
the
Sacramento
River
for
variability
at
a
single
locus.
Winter­
run
samples
included
fish
from
1)
1995
brood
stock
from
the
Coleman
National
Fish
Hatchery
(
CNFH),
2)
1995
carcasses
from
the
Sacramento
River,
and
3)
1991­
94
CNFH
brood
stock.
Spring­
run
fish
were
sampled
at
Deer
Creek,
and
fall­
and
late
fall­
run
fish
were
sampled
from
Battle
Creek
Hatchery
stock.
The
authors
concluded
that
winter­
run
fish
were
distinct
from
spring­,
fall­
and
late
fall­
run
fish
but
that
winter­
run
brood
stock
in
CNFH
may
have
included
a
genetic
contribution
from
spring­
run
fish,
not
only
in
1995,
but
also
in
previous
years.
Banks
et
al.
(
Bodega
Marine
Laboratory,
Bodega
Bay,
CA.
Unpublished,
1996.)
extended
the
study
of
these
samples
with
an
analysis
of
four
additional
microsatellite
loci.
A
UPGMA
tree
of
Nei's
(
1978)
genetic
distance
showed
that
fall­
and
late
fall­
run
fish
were
most
similar
among
run
types.
Even
so,
a
randomized
chi­
square
test
(
Roff
and
Bentzen
1989)
showed
that
allele
frequencies
for
1
of
the
5
loci
in
fall­
and
late
fall­
run
fish
were
significantly
different.
Spring­
run
fish
were
the
next
most
closely
related
to
fall­
and
late
fall­
run
fish,
but
showed
significant
allele­
frequency
differences
with
fall­
or
late
fall­
run
fish
at
7
of
the
10
possible
comparisons.
Winter­
run
chinook
salmon
was
a
distant
outlier
to
the
three
other
runs,
and
showed
significant
allele­
frequency
differences
for
13
of
the
possible
15
comparisons
with
the
other
run
types.
The
average
F
ST
over
the
5
loci
was
0.084
and
represents
considerable
divergence
among
the
run
types.
These
results
demonstrate
significant
levels
of
reproductive
isolation
between
winter­
run
fish
and
the
other
three
run
types,
and
between
spring­
run
fish
and
fall­
and
late
fall­
run
fish
in
the
Sacramento
River.
It
is
difficult,
however,
to
evaluate
the
importance
of
these
run­
time
differences
relative
to
run­
time
differences
in
populations
elsewhere,
because
of
the
lack
of
a
coast­
wide
data
base
for
these
microsatellite
loci.

Nielsen
(
1995)
surveyed
sequence
variability
in
a
164­
base­
pair
segment
of
the
control
region
of
mtDNA
in
California
Central
Valley
chinook
salmon
from
8
rivers,
5
hatcheries,
and
the
Guadalupe
Slough.
These
samples
included
spring­,
fall­,
late­
fall­,
and
winter­
run
fish.
Ten
haplotypes
were
defined
by
7
nucleotide
substitutions:
4
transversions,
2
transitions,
and
an
81
base­
pair
insertion.
Although
the
analysis
of
a
single
locus
should
be
used
cautiously,
the
relatively
large
sample
sizes
in
this
study
provided
considerable
power
to
test
some
hypotheses
of
population
structure.
A
significant
haplotypic
frequency
difference
was
found
between
two
successive
years
for
returning
adults
at
one
of
two
hatcheries.
None
of
the
tests
for
haplotype­
92
frequency
differences
between
pairs
of
wild
fall­
run
samples
was
significant.
However,
frequencies
in
some
fall­
run
wild
samples
were
significantly
different
from
frequencies
in
samples
of
fall­
run
hatchery
populations.
Haplotypic
frequencies
in
samples
from
Guadalupe
Slough
were
significantly
different
from
each
of
the
four
run
types,
but
were
not
significantly
different
from
haplotype
frequencies
at
the
Feather
and
Merced
River
hatcheries.
Significant
differences
appeared
between
each
of
the
four
run
types.
Nucleotide
diversity,
the
average
level
of
sequence
divergence
between
haplotypes,
was
small,
ranging
from
0.001
to
0.009
between
run
types
and
averaging
0.004
in
the
pooled
sample.
Haplotype
diversity
(
analogous
to
single­
locus
heterozygosity)
ranged
from
0.07
in
winter­
run
chinook
salmon
to
0.64
in
late
fall­
run
chinook
salmon,
and
averaged
0.42
over
samples.
A
gene
diversity
analysis
of
haplotypic
frequencies
indicated
that
84.7%
of
the
total
variability
was
contained,
on
average,
within
run
time
and
15.3%
was
due
to
differences
between
run
times.
This
level
of
differentiation
among
run
types
is
high,
but
is
similar
to
differentiation
between
run
types
in
some
other
regions
based
on
allozyme
frequencies.

Levels
of
Genetic
Differentiation
among
Populations
A
summary
of
representative
estimates
of
gene
diversity
statistics
appears
in
Table
2
for
chinook
salmon
and
other
species
of
salmon
and
sea
run
trout.
The
geographical
areas
covered
in
the
studies
listed
in
the
table
are
similar,
except
for
the
studies
of
coho
salmon
(
Wehrhahn
and
Powell
1987,
Reisenbichler
and
Phelps
1987),
which
were
conducted
over
smaller
areas.
Genetic
subdivision
among
populations
within
drainages
or
among
drainages
(
or
adult
run
type)
was
estimated
with
G
ST=
H
S/
H
T,
where
H
S
is
the
average
within­
population
gene
diversity
and
H
T
is
the
total
gene
diversity,
disregarding
genetic
subdivision.
The
percentage
of
gene
diversity
contained
within
populations,
on
average
over
loci,
ranges
from
about
80%
to
about
98%
in
93
Table
2.
Gene
diversity
structure
(
within
and
among
populations
in
drainages,
and
among
drainages
or
run
types)
for
chinook
salmon
(
Oncorhynchus
tshawytscha)
and
other
species
of
salmon.

Region
Within
Pop.
Among
Pop.
in
Drainages
Among
Drainages
or
Run
Types
Reference
Chinook
Salmon
(
Oncorhynchus
tshawytscha))
Alaska
(
AK)
94.1
5.9
Gharrett
et
al.
1987
Pacific
Northwest
87.7
4.6
7.7
Utter
et
al.
1989
Oregon
(
OR)­
California
(
CA)
82.3
3.3
14.4
Bartley
and
Gall
1990
OR­
CA
89.4
10.6
Bartley
et
al.
1992
CA
84.7
15.3
Nielsen
1995
Chum
Salmon
(
O.
keta)
Japan­
Russia
96.2
3.8
Winans
et
al.
1994
SE
AK­
British
Columbia
(
BC)
97.3
2.7
Kondzela
et
al.
1994
BC­
WA
97.2
0.3
2.5
Phelps
et
al.
1994
Coho
Salmon
(
O.
kisutch)
Southern
B.
C.
91.4
8.6
Wehrhahn
and
Powell
1987
Northern
WA
95.1
9.0
4.0
Reisenbichler
and
Phelps
1987
Pink
Salmon
(
O.
gorbuscha)
(
Even
Year)
B.
C.­
WA
98.5
1.5
Hard
et
al.
1996
AK
96.4
1.3
2.3
Gharrett
et
al.
1988
Pink
Salmon
(
Odd
year)
B.
C.­
WA
97.9
2.1
Hard
et
al.
1996
Sockeye
Salmon
(
O.
nerka)
B.
C.
82.8
8.0
9.2
Wood
et
al.
1994
WA,
B.
C.,
Idaho
84.7
15.3
Winans
et
al.
1996
Steelhead
(
O.
mykiss)
WA
98.2
1.8
Reisenbichler
and
Phelps
1987
OR­
CA
98.3
1.7
Reisenbichler
and
Phelps
1987
94
species
of
salmon
and
anadromous
trouts.
Chinook
salmon
in
the
Pacific
Northwest
tend
to
show
greater
levels
of
genetic
subdivision
among
populations
(
G
ST
11­
18%)
than
do
chum,
coho,
pink
salmon
(
G
ST
2­
9%),
and
steelhead
(
G
ST
1.7%)
in
many
of
the
same
areas.
Like
chinook
salmon,
sockeye
salmon
(
O.
nerka)
tend
to
show
a
greater
degree
of
genetic
subdivision
among
populations
(
G
ST
18%)
than
do
other
species
of
salmon.
Chinook
salmon
populations
in
Alaska
tend
to
show
less
genetic
differentiation
(
G
ST
5.9%)
than
do
southern
populations
in
British
Columbia,
Washington,
Oregon,
and
California.

New
Studies
To
examine
evidence
for
reproductively
isolated
populations
or
groups
of
populations,
we
analyzed
allelic
frequencies
collected
over
15
years
by
geneticists
at
NMFS,
University
of
California
at
Davis,
Washington
Department
of
Fish
and
Wildlife,
and
the
Alaska
Department
of
Fish
and
Game.
This
set
of
data
included
both
published
and
unpublished
allelic
frequencies
collected
with
standardized
laboratory
procedures
and
compiled
for
use
by
participating
fishery
management
agencies.
Complete
sets
of
data
were
available
for
31
polymorphic
loci:
mAAT­
1*,
sAAT­
1,2*,
sAAT­
3*,
sAAT­
4*,
ADA­
1*,
ADA­
2*,
mAH­
4*,
sAH*,
GPI­
A*,
GR*,
HAGH*,
mIDHP­
2*,
sIDHP­
1*,
sIDHP­
2*,
LDH­
B2*,
LDH­
C*,
mMDH­
2*,
sMDH­
A1,2*,
sMDHB1,2
sMEP­
1*,
MPI*,
PEPA*,
PEPB­
1*,
PEPD­
2*,
PEPLT*,
PGDH*,
PGK­
2*,
PGM­
1*,
PGM­
2*,
sSOD­
1*,
TPI­
4*.
Two
loci,
mAH­
4*
and
GR*,
were
not
available
for
Alaska
chinook
salmon
samples,
so
analyses
including
these
samples
were
based
on
only
29
loci.
For
populations
sampled
more
than
1
year
 
some
as
many
as
3
or
4
years
 
allelic
frequencies
for
each
locus
were
combined,
and
the
pooled
frequencies
were
used
to
represent
the
population
frequencies.
In
several
instances,
allelic
frequencies
for
neighboring
populations
were
also
combined,
if
the
sum
of
the
individual
G­
tests
of
frequencies
between
samples,
divided
by
the
sum
of
the
degrees
of
freedom
was
not
significant.
(
This
data
set
also
serves
as
a
population
baseline
for
estimating
the
stock
contributions
of
chinook
salmon
to
mixed­
population
ocean
or
river­
mouth
harvests,
chiefly
along
the
coasts
of
Washington
and
Oregon.)
A
total
of
193
populations
extending
from
Alaska
to
California
were
included
in
the
present
analyses
(
Table
3
and
Fig.
18).
We
calculated
Rogers'
(
1972),
Nei's
unbiased
(
1978),
and
Cavalli­
Sforza
and
Edwards'
(
1967)
chord
distances
between
samples,
and
searched
for
genetically­
discrete
geographical
groups
with
multidimensional
scaling
in
three
dimensions
and
with
the
UPGMA
tree
algorithm.

Regional
patterns
of
genetic
variability
All
193
population
units
were
included
in
the
first
analysis
to
examine
large­
scale
geographical
patterns
of
genetic
structure
among
chinook
salmon
populations
from
Alaska
to
California.
A
major
feature
of
the
UPGMA
tree
and
MDS
analysis
(
Fig.
19)
of
these
samples
was
a
clear
genetic
separation
between
populations
with
stream­
type
life
histories
and
those
with
ocean­
type
life
histories.
Stream­
type
populations
extend
from
Alaska,
through
northern
British
