# Updated Status of Federally Listed ESUs 

# of West Coast Salmon and Steelhead 

# 

# 

# 

# West Coast Salmon Biological Review Team

# 

# Northwest Fisheries Science Center

2725 Montlake Boulevard East

Seattle, WA 98112

**Southwest Fisheries Science Center**

Santa Cruz Laboratory\
110 Shaffer Road\
Santa Cruz, CA 95060

# 

# 

# July 2003

This is a scientific report. It does not represent or set policy for
NMFS or NOAA, regardless of whether any statements contained herein may
appear to do so.

Table of Contents

Executive Summary **5**

Introduction **7**

Methods **24**

References **30**

**A. CHINOOK**

A. 1 Background and History of Listings **1**

A.2.1 Snake River Fall-Run Chinook **3**

A.2.2 Snake River Spring/Summer-Run Chinook **11**

A.2.3 Upper Columbia River Spring-Run Chinook **28**

A.2.4 Puget Sound Chinook **41**

A.2.5 Lower Columbia River Chinook **78**

A.2.6 Upper Willamette River Chinook **104**

A.2.7 California Coastal Chinook **113**

A.2.8 Sacramento River Winter-Run Chinook **124**

A.2.9 Central Valley Spring-Run Chinook **131**

A.3 Chinook BRT Conclusions **143**

A.4 References **149**

A.5 Appendices **160**

**B. STEELHEAD**

B.1 Background and History of Listings **1**

B.2.1 Snake River Basin Steelhead **7**

B.2.2 Upper Columbia River Steelhead **24**

B.2.3 Middle Columbia River Steelhead **34**

B.2.4 Lower Columbia River Steelhead **50**

B.2.5 Upper Willamette River Steelhead **73**

B.2.6 Northern California Steelhead **84**

B.2.7 Central California Coast Steelhead **97**

B.2.8 South-Central California Coast Steelhead **106**

B.2.9 Southern California Steelhead **114**

B.2.10 California Central Valley Steelhead **123**

B.2.11 Steelhead BRT Conclusions **134**

B.3 References **142**

B.4 Appendices **157**

**C. COHO**

C.1 Background and History of Listings **1**

C.2.1 Oregon Coast Coho **3**

C.2.2 Southern Oregon/Northern California Coasts Coho **30**

C.2.3 Central California Coho **54**

C.2.4 Lower Columbia River Coho **71**

C.2.5 Coho BRT Conclusions **90**

C.3 References **94**

C.4 Appendices **107**

**D. SOCKEYE**

D.1 Background and History of Listings **1**

D.2.1 Snake River Sockeye **4**

D.2.2 Ozette Lake Sockeye **9**

D.3 Sockeye BRT Conclusions **15**

D.4 References **17**

D.5 Appendices **20**

**E. CHUM**

E.1 Background and History of Listings **1**

E.2.1 Hood Canal Summer-Run Chum **3**

E.2.2 Lower Columbia River Chum **20**

E.3 Chum BRT Conclusions **32**

E.4 References **34**

E.5 Appendices **36**

ACKNOWLEDGMENTS

We are grateful to the large number of regional biologists who provided
raw data and information used in this report. This report was improved
as a result of comments provided by state, tribal, and federal
comanagers on an earlier draft. The effort to update the status of all
listed ESUs of west coast salmon and steelhead would not have been
possible without the help of many, including Andrew Albaugh, Charlene
Bergeron, Ronda Carbary, Henry Carson, Kurt Davis, Christopher Donohoe,
Tamara Harms, Christine Holt, Andrea Jarvela, Laura Johnston, Jenny
Moslemi, Jessica Piasecke, Cory Ruedebusch, Brycen Swart, JJ Westfall,
and Thomas Williams.

EXECUTIVE SUMMARY

During the 1990s, the National Marine Fisheries Service (NMFS; NOAA
Fisheries) conducted a series of reviews of the status of West Coast
populations of Pacific salmon and steelhead (*Oncorhynchus* spp.) with
respect to the U.S. Endangered Species Act (ESA). This report summarizes
scientific conclusions of the NMFS Biological Review Team (BRT)
regarding the updated status of 26 ESA-listed ESUs of salmon and
steelhead (and one candidate species ESU) from Washington, Oregon,
Idaho, and California. These ESUs were listed following a series of
status reviews conducted during the 1990s. The status review updates
were undertaken to allow consideration of new data that accumulated over
the various time periods since the last updates and to address issues
raised in recent court cases regarding the ESA status of hatchery fish
and resident (nonanadromous) populations.

This report represents the first major step in the agency's efforts to
review and update the listing determinations for all listed ESUs of
salmon and steelhead. By statute, ESA listing determinations must take
into consideration not only the best scientific information available,
but also those efforts being made to protect the species. After
receiving the BRT report and considering the conservation benefits of
protective efforts, NMFS will determine what changes, if any, to propose
to the listing status of the affected ESUs.

As in the past, the BRT used a risk-matrix method to quantify risks in
different categories within each ESU. In the current report, the method
was modified to reflect the four major criteria identified in the NMFS
viable salmonid populations (VSP) document (McElhany et al. 2000):
abundance, growth rate/productivity, spatial structure, and diversity.
These criteria are being used as a framework for approaching formal ESA
recovery planning for salmon and steelhead. Tabulating mean risk scores
for each element allowed the BRT to identify the most important concerns
for each ESU and to compare relative risk across ESUs and species. The
BRT considered these data and other information in making their overall
risk assessments. Based on provisions in the draft revised NMFS policy
on consideration of artificial propagation in salmon listing
determinations, the BRT's risk analyses focused on the viability of
populations sustained by natural production.

Based on the criterion of self-sustainability, for the following ESUs
the majority BRT conclusion was "in danger of extinction:" Upper
Columbia River spring-run chinook, Sacramento River winter-run chinook,
Upper Columbia River steelhead, Southern California steelhead,
California Central Valley steelhead, Central California Coast coho,
Lower Columbia River coho, Snake River sockeye. For the following ESUs,
the majority BRT conclusion was "likely to become endangered in the
foreseeable future:" Snake River fall-run chinook, Snake River
spring/summer-run chinook, Puget Sound chinook, Lower Columbia River
chinook, Upper Willamette River chinook, California Coastal chinook,
Central Valley spring-run chinook, Snake River steelhead, Lower Columbia
River steelhead, Upper Willamette River steelhead, Northern California
steelhead, Central California Coast steelhead, South-Central California
Coast steelhead, Oregon Coast coho, Southern Oregon/Northern California
Coasts coho, Ozette Lake sockeye, Hood Canal summer-run chum, and Lower
Columbia River chum. In one case (Middle Columbia River steelhead), the
BRT was nearly evenly split on the question of whether the ESU was or
was not likely to become endangered in the foreseeable future (a slight
majority concluded that the ESU was likely to become endangered) (Table
1).

Table 1.  BRT conclusions regarding updated status of salmon and
steelhead ESUs; X indicates the majority vote; (X) indicates a
substantial minority (\>40% of the vote).

  ----------- ----------------------------- ------------ ------------ ------------
  Species     ESU                           Danger of\   Likely to    Not Likely
                                            Extinction   Become\      to Become
                                                         Endangered   Endangered

  Chinook     Snake River fall-run                       X            

              Snake River spring/summer-run              X            

              Upper Columbia River          X            \(X\)        
              spring-run                                              

              Puget Sound                                X            

              Lower Columbia                             X            

              Upper Willamette                           X            

              California Coastal                         X            

              Sacramento River winter-run   X                         

              Central Valley spring-run                  X            

  Steelhead   Snake River Basin                          X            

              Upper Columbia River          X            \(X\)        

              Middle Columbia River                      X            \(X\)

              Lower Columbia River                       X            

              Upper Willamette River                     X            

              Northern California                        X            

              Central California Coast                   X            

              South Central California                   X            
              Coast                                                   

              Southern California           X                         

              California Central Valley     X                         

  Coho        Oregon Coast                               X            \(X\)

              Southern Oregon / Northern                 X            
              California Coasts                                       

              Central California            X                         

              Lower Columbia                X                         

  Sockeye     Snake River                   X                         

              Ozette Lake                                X            

  Chum        Hood Canal summer-run                      X            

              Lower Columbia River                       X            
  ----------- ----------------------------- ------------ ------------ ------------

INTRODUCTION

# Primary contributors: Robin S. Waples and Thomas C. Wainwright (Northwest Fisheries Science Center) {#primary-contributors-robin-s.-waples-and-thomas-c.-wainwright-northwest-fisheries-science-center .Author}

During the 1990s, the National Marine Fisheries Service (NMFS; NOAA
Fisheries) conducted a series of reviews of the status of West Coast
populations of Pacific salmon and steelhead (*Oncorhynchus* spp.) with
respect to the U.S. Endangered Species Act (ESA). Initially, these
reviews were in response to petitions for populations of a particular
species within a particular geographic area, but in 1994, the agency
began a series of proactive, comprehensive ESA status reviews of all
populations of anadromous Pacific salmonids from Washington, Idaho,
Oregon, and California (Federal Register, Vol. 59, No. 175, September
12, 1994, p. 46808).

The first step in these reviews is to determine the units that can be
considered "species" under the ESA and, hence, listed as threatened or
endangered, if warranted, based on their status. The ESA allows listing
not only of full species, but also named subspecies and "distinct
population segments" (DPSs) of vertebrates (including fish). The ESA
petitions and status reviews for Pacific salmonids have focused
primarily on the DPS level. To guide DPS evaluations of Pacific salmon,
NMFS has used the policy developed in 1991 (NMFS 1991, Waples 1991,
1995), which is described in the next section. As a result of these
status reviews, NMFS has identified over 50 evolutionary significant
units (ESUs) of salmon and steelhead from California and the Pacific
Northwest, of which 26 are listed as threatened or endangered species
under the ESA. A complete list of these evaluations can be found at
(http://www.nwr.noaa.gov/ 1salmon/salmesa/fractlist.htm), and the
technical documents representing results of the status reviews can be
accessed online at web sites of the Northwest Fisheries Science Center
(http://www.nwfsc.noaa.gov/pubs/), the Southwest Regional Office
(http://swr.nmfs.noaa.gov/ salmon.htm), the Santa Cruz Laboratory
(http://www.pfeg.noaa.gov/tib/esa/salmonids/esa_docs/ index.html), and
the Northwest Regional Office (http://www.nwr.noaa.gov/1habcon/habweb/
listnwr.htm).

In 2000, NMFS initiated formal ESA recovery planning for listed salmon
and steelhead ESUs. Recovery efforts are organized into a series of
geographic areas or domains. Within each domain, a technical recovery
team (TRT) has been (or is in the process of being) formed to develop a
sound scientific basis for recovery planning. Regional planners will use
the information provided by the TRTs to craft comprehensive recovery
plans for all listed ESUs within each domain. For more information about
the ESA recovery planning process for salmon and steelhead and the TRTs,
see the NMFS Northwest Salmon Recovery Planning web site
(http://www.nwfsc.noaa.gov/cbd/trt/).

Recently, several factors led NMFS to conclude that the ESA status of
listed salmon and steelhead ESUs should be reviewed at this time. First,
a September 2001 court ruling called into question the NMFS decision to
not list several hatchery populations considered to be part of the
Oregon Coast coho salmon ESU (Alsea Valley Alliance v. Evans \[161 F.
Supp. 2d 1154, D. Oreg. 2001\]; Alsea decision). The ruling held that
the ESA does not allow listing of any unit smaller than a DPS (or ESU),
and that NMFS had violated that provision of the act by listing only
part of an ESU. Although this legal case applied directly only to the
Oregon Coast coho salmon ESU, the same factual situation (hatchery
populations considered part of listed ESUs, but not listed) also applied
to most other listed ESUs of salmon and steelhead. Second, two
additional lawsuits currently pending that involve California ESUs of
steelhead (EDC v. Evans, SACV-00-1212-AHS (EEA); MID v. Evans,
CIV-F-02-6553 OWW DLB (E.D. Cal)) raised a similar issue---NMFS
concluded that resident fish were part of the ESU, but only the
anadromous steelhead were listed. Again, this same factual situation is
found in most, if not all, listed steelhead ESUs. Finally, at least
several years of new data are available for most ESUs, and up to a
decade has passed since the first populations were listed in the
Sacramento and Snake Rivers. Furthermore, in some (but not all) areas,
adult returns in the last few years have been considerably higher than
have been seen for several decades.

As a result of these factors, NMFS committed to a systematic updating of
the ESA status of all listed ESUs of Pacific salmon and steelhead
(Federal Register Vol. 67, No. 28, February 11, 2002). This report
summarizes updated biological information for the 26 listed salmon and
steelhead ESUs and one candidate ESU (Lower Columbia coho salmon), and
presents the Biological Review Team's (BRT's) conclusions regarding
these ESUs' current risk status. The BRT consisted of a core group of
scientists from the NMFS Northwest and Southwest Fisheries Science
Centers, supplemented by experts on particular species from NMFS and
other federal agencies. BRT membership is indicated in the sections for
each species. The BRT met in January, March, and April 2003 to review
information related to the updated status reviews.

ESU Determinations

As amended in 1978, the ESA allows listing of "distinct population
segments" of vertebrates as well as named species and subspecies.
However, the ESA provided no specific guidance for determining what
constitutes a distinct population segment, and the resulting ambiguity
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 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 description of this
topic appeared in the NMFS "Definition of Species" paper (Waples 1991).
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 ESU of the biological species. An ESU is defined as a
population that: 1) is substantially reproductively isolated from
conspecific population, and 2) represents an important component in the
evolutionary legacy of the species. Information that can be useful in
determining the degree of reproductive isolation includes incidence of
straying, rates of recolonization, degree of genetic differentiation,
and the existence of barriers to migration. Insight into evolutionary
significance can be provided by data on genetic and life-history
characteristics, habitat differences, and the effects of stock transfers
or supplementation efforts. The NMFS BRTs have used a comprehensive
approach that utilized all available scientific information to define
ESUs. A discussion of how the NMFS policy was applied in a number of ESA
status reviews can be found in Waples (1995).

Geographic Boundaries

The status review updates focused primarily on risk assessments, and
(apart from the discussion of resident fish in steelhead ESUs) the BRT
did not consider issues associated with the geographic boundaries of
ESUs. If significant new information arises to indicate that specific
ESU boundaries should be reconsidered, that would be done at a later
time.

Artificial Propagation

Most salmon and steelhead ESUs have hatchery populations associated with
them, and it is important for administrative, management, and
conservation reasons to determine the biological relationship between
these hatchery fish and natural populations within the ESU. The ESA
status reviews conducted since 1993 have been guided by the NMFS ESA
policy for artificial propagation of Pacific salmon and steelhead (NMFS
1993). That policy recognizes that "genetic resources important to the
species' evolutionary legacy may reside in hatchery fish as well as in
natural fish, in which case, the hatchery fish can be considered part of
the "biological ESU in question." As part of the coastwide status
reviews, the NMFS BRTs applied this principle in evaluating the ESU
status of hatchery populations associated with all listed salmon and
steelhead ESUs, with the result being that many hatchery populations are
currently considered to be part of the ESUs. However, only a small
fraction of these hatchery populations have been listed---generally,
those associated with natural populations or ESUs considered at high
risk of extinction. NMFS felt that listing other hatchery populations in
the ESUs would provide little or no additional conservation benefit
beyond that conferred by the listing of natural fish, but would greatly
increase the regulatory burden on stakeholders, researchers, and the
general public.

As discussed above, a recent court decision has determined that this
approach is inconsistent with the act---an ESU must be listed or not
listed in its entirety. At the same time that NMFS announced the status
review updates, the agency committed to revising the ESA artificial
propagation policy for Pacific salmon and using the revised policy to
guide the hatchery ESU determinations and consideration of artificial
propagation in the risk analyses (Federal Register Vol. 67, No. 28,
February 11, 2002). Although a revised policy has not yet been proposed
through formal rulemaking, a draft has been publicly available on the
agency's web site since August 2002
(http://www.nwr.noaa.gov/HatcheryListingPolicy/DraftPolicy.pdf). That
draft indicates that hatchery populations that have "diverged
substantially from the evolutionary lineage represented by the ESU" will
not be considered part of the ESU. The draft policy is currently under
revision, and one issue that remains to be resolved is how "substantial"
the divergence must be before a hatchery population should no longer be
considered part of a salmon or steelhead ESU, even if it was originally
derived from populations within the ESU. Due to the lack of resolution
of this issue, the BRT has not attempted to revisit the ESU
determinations for hatchery populations in this report. However, a
separate working group has updated the stock histories and biological
information for every hatchery population associated with each listed
ESU (SSHAG 2003) and has also assigned each hatchery population to one
of four categories, as described below. How these categories relate to
ESU membership remains to be determined. A table showing the SSHAG
categories appears in the Appendix to the section of the report for each
species. The BRT reviewed the information in these appendices, along
with other hatchery information, to obtain a better understanding of the
nature and role of hatcheries associated with each listed ESU.

In the SSHAG document, each hatchery stock was assigned to a category
based on variation across three axes (Figure 1): 1) the degree of
genetic divergence between the hatchery stock and the natural
population(s) that occupy the watershed into which the hatchery stock is
released; 2) the origin of the hatchery stock; and 3) the status of the
natural population(s) in the watershed. There are four categories of
divergence: minimal, moderate, substantial, and extreme. Minimal
divergence means that based on the best information available, there is
no appreciable genetic divergence between the hatchery stock and the
natural population(s) in the watershed (e.g., because the hatchery and
wild populations are well mixed each generation). Moderate divergence
means the level of divergence between the hatchery stocks and the local
natural populations is no more than what would be expected between
closely related populations within the ESU. Substantial divergence is
roughly the level of divergence expected between more distantly related
populations within the ESU. Extreme divergence is divergence greater
than what would be expected among natural populations in the ESU, such
as that caused by deliberate artificial selection or inbreeding. The
second axis describes the origin of the hatchery stock, and can either
be local, nonlocal but predominantly from within the ESU, or
predominantly from outside of the ESU. The third axis describes the
status of the natural population(s) in the watershed of the same species
as the hatchery stock, which can either be native or nonnative.

*Category 1* stocks are characterized by no more than minimal divergence
between the hatchery stock and the local natural population(s) and
regular, substantial incorporation of natural-origin fish into the
hatchery broodstock. Within Category 1, Category 1a stocks are
characterized by the existence of a native natural population of the
same species in the watershed, while Category 1b stocks are
characterized by the lack of such a population (i.e., the local
naturally spawning population was introduced from elsewhere). Note that
a Category 1a designation can describe a range of biological scenarios,
and does not necessarily imply that the hatchery stock and the
associated natural population are close to a "pristine" state. For
example, a hatchery program that started many years ago with local
broodstock and regularly incorporated local natural-origin fish in
substantial proportions thereafter would likely be a Category 1a, even
if both the hatchery stock and the local natural population have
diverged from what the natural population was like historically.

*Category 2* stocks are no more than moderately diverged from the local,
natural population(s) in the watershed. Category 2a stocks were founded
from a local, native population in the watershed in which they are
released. Category 2b stocks were founded nonlocally but from within the
ESU, and are released in a watershed that does not contain a native
natural population. Category 2c stocks were founded nonlocally but from
within the ESU, and are released in a watershed that contains a native
natural population.

*Category 3* stocks are substantially diverged from the natural
population(s) in the watershed in which they are released. The "a", "b,"
and "c" designations are the same as described for Category 2 above.

*Category 4* stocks characterized either by being founded predominantly
from sources that are not considered part of the ESU in question, or by
extreme divergence from the natural population(s) in the watershed in
which they are released, regardless of founding source.

![](media/image1.wmf){width="6.204166666666667in" height="5.28125in"}

Figure 1. Summary of hatchery categorization system (SSHAG 2003).

Resident Fish

In addition to the anadromous life history, sockeye salmon (*O. nerka*)
and steelhead (*O. mykiss*) have nonanadromous or resident forms,
generally referred to as kokanee and rainbow trout, respectively. (At
least one resident population of chinook salmon also occurs, in Lake
Cushman, Washington.) As is the case with hatchery fish, it is important
to determine the relationships of these resident fish to anadromous
populations in listed ESUs. This issue is complicated by the complexity
of jurisdictional responsibilities---NMFS has ESA responsibility for
anadromous Pacific salmonids, but the U.S. Fish and Wildlife Service
(USFWS) has ESA jurisdiction for resident fish. At the time this report
was prepared, the two agencies had not developed a general policy on how
to determine the ESU/DPS status of resident fish or how to make the
listing determinations for the overall ESU/DPSs.

Resident (kokanee) populations in the two ESA-listed sockeye salmon ESUs
(Redfish Lake and Lake Ozette) have been genetically characterized and
determined not to be part of the sockeye salmon ESUs. However, the ESU
status of many resident populations of *O. mykiss* remains in doubt. For
the purposes of this status review update, therefore, the BRT adopted a
working framework for determining the ESU/DPS status of *O. mykiss* that
are geographically associated with listed steelhead ESUs. These
evaluations were guided by the same biological principles used to define
ESUs of natural fish and determine ESU membership of hatchery fish: the
extent of reproductive isolation from, and evidence of biological
divergence from, other populations within the ESU. These principles are
comparable to the "discreteness" and "significance" criteria of the
joint DPS policy of the two listing agencies (61 FR 4722, 7 February
1996). Ideally, each resident population would be evaluated individually
on a case-by-case basis using all available biological information. In
practice, little or no information is available for most resident
salmonid populations.

To facilitate conclusions about the ESU/DPS status of resident fish,
NMFS and USFWS have identified three different cases, reflecting the
range of geographic relationships between resident and anadromous forms
within different watersheds:

> Case 1: No obvious physical barriers to interbreeding exist between
> resident and anadromous forms.
>
> Case 2: Long-standing natural barriers (e.g., a waterfall) separate
> resident forms upstream from anadromous forms downstream.
>
> Case 3: Relatively recent (e.g., within last 100 years) human actions
> or man-made barriers (e.g., construction of a dam without provision
> for upstream fish passage) separate resident and anadromous forms.

The BRT reviewed available information about individual resident
populations of *O. mykiss* to determine which case each population fits
into. The BRT also adopted, for the purpose of the updated status
reviews and extinction risk assessments, the following working
assumptions about ESU membership of resident *O. mykiss* falling in each
of these categories:

> Case 1: Resident fish were assumed provisionally to be part of the
> ESU. Rationale: Empirical studies show that resident and anadromous
> *O. mykiss* are typically very similar genetically when they co-occur
> in sympatry, with no physical barriers to migration or interbreeding
> (Chilcote 1976, Currens et al. 1987, Leider et al. 1995, Pearsons et
> al. 1998). (Note: This assumption is not necessarily applicable to *O.
> nerka*, because sockeye and kokanee can show substantial divergence,
> even in sympatry.)
>
> Case 2: Resident fish were assumed provisionally not to be part of the
> ESU. Rationale: Many populations in this category have been isolated
> from contact with anadromous populations for thousands of years.
> Empirical studies (Chilcote 1976, Currens et al. 1990) show that, in
> these cases, the resident fish typically show substantial genetic and
> life-history divergence from the nearest downstream anadromous
> populations.
>
> Case 3: No default assumption was made about ESU status of resident
> fish.

The default assumptions about ESU membership for Case 1 and Case 2
populations can be overridden by specific information for individual
populations. For example, as noted above, anadromous and resident *O.
nerka* can diverge substantially in sympatry, and it is possible the
same may be true for some *O. mykiss* populations.

The BRT discussed Case 3 populations at some length. Case 3 populations
were, most likely, Case 1 populations (and hence presumably part of the
ESU) prior to construction of the artificial barrier. Some BRT members
felt that, in the absence of information to the contrary, it is
reasonable to assume that Case 3 populations of *O. mykiss* are still in
the ESU, given that the time since erection of the artificial barriers
has been relatively short for substantial evolutionary divergence.
However, the majority of the BRT members preferred to make no particular
assumption regarding Case 3 populations. They reached this conclusion
for two major reasons. First, Case 3 populations that historically were
part of the ESU may no longer represent the ESU biologically because of
(a) bottlenecks and/or local adaptation and rapid evolutionary
divergence in a novel environment; or (b) displacement or introgression
from nonnative, hatchery-origin rainbow trout. Notably, releases of
hatchery rainbow trout have been widespread in the Pacific Northwest and
California, including areas impounded by dams that block access to
anadromous fish (Ludwig 1995, Van Vooren 1995). Empirical studies
(Wishard et al. 1984, Williams et al. 1997, Utter 2001) have shown that
the results of such releases can be quite variable, ranging from
replacement of the native gene pool to hybridization to no detectable
genetic effect. Therefore, the current relationship between Case 3
populations and anadromous populations in the ESU is difficult to
evaluate without empirical data and historical stocking records for the
population in question. Second, identifying a default assumption for
Case 3 populations in the face of considerable biological uncertainty
requires consideration of other factors that are not entirely scientific
(such as, What is the appropriate burden of proof? and What are the
biological, economic, and political consequences of making a wrong
assumption?). Therefore, in this report the BRT did not suggest a
default assumption regarding the ESU status of Case 3 populations.
Instead, this report summarizes empirical information that does exist
for specific Case 3 populations and discusses its relevance to ESU
determinations. As new biological information relevant to the ESU status
of individual Case 3 populations is developed as part of the overall
recovery planning process for West Coast salmon and steelhead described
in the Background and Introduction section, that information will be
passed on to NMFS Regional Office Staff for consideration.

Genetic data can provide a powerful means for determining the
evolutionary origin of a sampled population, and such data can therefore
be very useful in evaluating the extent to which native resident *O.
mykiss* populations have been affected by releases of nonnative hatchery
rainbow trout. The steelhead ESU reports in Section B of this report
summarize this information as it applies to specific Case 3 populations.
As discussed above, rapid genetic changes associated with human impacts
can also occur within populations in the absence of stock transfers, and
these changes are unlikely to be detected with standard molecular
genetic techniques. Evaluating the importance of such effects is very
difficult. Phenotypic and life-history traits can serve as proxies for
genetically based, adaptive differences among populations; however, such
traits can also be affected by environmental conditions, which confounds
their interpretation. These confounding effects can generally be teased
apart only with very detailed experiments. It is therefore likely that
the evolutionary relationships of many Case 3 populations will remain
uncertain for the foreseeable future.

In response to a request for additional information about listed ESUs of
steelhead (67 FR 79898-79900; 31 December 2002), NMFS received two
comments relevant to the ESU status of resident *O. mykiss*. The Center
for Biological Diversity (CBD 2003) argued that NMFS erred in referring
to *O. mykiss* trapped above dams as "resident" fish and excluding them
from the steelhead listings. According to CBD, the distinction between
anadromous and resident populations should be based not on circumstances
of geography (i.e., whether the fish are currently above or below a
recent man-made barrier), but rather on biological attributes of the
populations---specifically, the "genetic trait expressed in
smoltification." They argued that resident populations that are
genetically (i.e., historically) anadromous, but which are currently
trapped above human barriers with no opportunity to express anadromy,
should be considered part of the listed steelhead ESUs. The BRT's
conclusions regarding the ESU status of Case 3 resident populations
(above human barriers) is described above.

Trout Unlimited (2003) argued that, based on substantial ecological and
life history differences, anadromous and resident *O. mykiss* should be
in separate ESUs, even in cases where there are no appreciable molecular
genetic differences between the two forms. They cited studies showing a)
little evidence that transplanted rainbow trout can give rise to
anadromous populations, and b) one study in the Deschutes River, in
which all anadromous fish examined were found to have an anadromous
female parent and all resident fish examined were found to have a
resident female parent, as evidence for a genetic basis for the
differences between the two forms. This argument is similar to the
arguments the BRT has considered in previous status reviews, that summer
and winter steelhead, or spring and fall chinook in coastal basins,
should be in different ESUs (Busby et al. 1996; Myers et al. 1998). As
in those status reviews, the BRT does not dispute that the two forms of
*O. mykiss* can exhibit some degree of reproductive isolation, even in
areas where they co-occur. However, the strong genetic similarity of the
two forms in sympatry in every case where they have been examined
indicates that, in general, the two forms are genetically linked on
evolutionary time frames. Furthermore, the Deschutes River study
(Zimmerman and Reeves 2000) also examined a population in British
Columbia, where the authors found that anadromous fish can give rise to
resident offspring, and vice versa---a result that has been found in
other areas as well. In general, genetic data show that resident and
anadromous *O. mykiss* below barriers in the same basin are genetically
more similar to each other than either is to the same form in another
basin. Therefore, lumping steelhead and resident populations into
separate ESUs would create artificial units in which each population had
its nearest relative in a different ESU. This problem could be resolved
only by considering every population (anadromous or resident) its own
ESU---a result that would lead to hundreds of ESUs of *O. mykiss* and
would be inconsistent with the approach NMFS has taken in all other
status reviews for Pacific salmon. Therefore, the BRT continued to
consider the evolutionary relationships between resident and anadromous
populations in a way that was consistent with the approach used in
evaluating alternative life history forms in previous status reviews.

Although resident *O. mykiss* may occasionally produce anadromous
offspring, and vice versa, there is (as noted by Trout Unlimited 2003)
little empirical evidence to indicate that a population of resident *O.
mykiss* can give rise to a self-sustaining anadromous *population*. This
issue is relevant to extinction risk analysis for ESUs containing both
forms and is discussed in Section B of this report.

Risk Assessments

ESA Definitions

After the composition of an ESA species is determined, the next question
to address is, "Is the species threatened or endangered?" Section 3 of
the ESA defines 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." Neither NMFS nor the USFWS
have developed formal policy guidance about how to interpret the ESA
definitions of threatened or endangered species.

The BRT considers a variety of information in evaluating the level of
risk faced by an ESU. According to Section 4 of the ESA, the
determination of whether a species is threatened or endangered should be
made "solely on the basis of the best scientific and commercial data
available" regarding the species' current status, after taking into
account efforts being made to protect the species. In its biological
status reviews, the BRT does not evaluate possible future effects of
protective efforts, except to the extent the effects are already
reflected in metrics of population or ESU viability. Protective efforts
are taken into account in a separate process by the NMFS regional
offices prior to making listing determinations. Therefore, the BRT does
not make recommendations as to whether identified ESUs should be listed
as threatened or endangered species because that determination requires
evaluation of factors not considered by the team. Rather, the BRT draws
scientific conclusions about the current risk of extinction faced by
ESUs, under the assumption that present conditions will continue into
the future (recognizing, of course, that natural demographic and
environmental variability are inherent features of "present
conditions").

Factors for Decline

According to Section 4 of the ESA, the Secretary (of Commerce or the
Interior) shall determine whether a species is threatened or endangered
as a result of any (or a combination) of the following factors:
destruction or modification of habitat; overutilization; disease or
predation; inadequacy of existing regulatory mechanisms; or other
natural or man-made factors. Collectively, these are often referred to
as "factors for decline." In the Federal Register notices announcing the
ESA listing decisions for West Coast salmon and steelhead, NMFS included
sections identifying what have come to be known as the 4H factors for
decline---habitat degradation and loss, hydropower development,
overharvest, and hatchery propagation---as well as other factors.
However, in the status reviews, the BRT did not attempt a rigorous
analysis of this subject, and the same is true for this report. There
are several reasons for this.

-   First, the BRT chose to focus primarily on the question of whether
    an ESU is at risk rather than how it came to be at risk. Although
    the latter question is important, a population or ESU that has been
    reduced to low abundance will continue to be at risk for demographic
    and genetic reasons until it reaches a larger size, regardless of
    the reasons for its initial decline. Furthermore, in some cases, a
    factor that was important in causing the original declines may no
    longer be an impediment to recovery.

-   Second, unlike many other ESA-listed species that face a single
    primary threat, salmon face a bewildering array of potential threats
    throughout every stage of their complex life cycle. It is relatively
    easy to simply enumerate current and past threats to salmon
    populations, but it is much more difficult to evaluate the relative
    importance of a wide range of interacting factors.

-   Third, evaluating the degree to which historic factors for decline
    will continue to pose a threat in the future generally requires
    consideration of issues that are more in the realm of social science
    than biological science---such as whether proposed changes will be
    funded, and, if funded, will be implemented effectively.

In it's listing determination for the updated status reviews, NMFS will
consider factors for decline and the extent to which they have been
alleviated by protective efforts. It is expected that these issues will
be addressed in detail in formal ESA recovery planning for ESUs that
remain listed. The agency has outlined a two-step process for recovery
planning; the first step is identifying biologically based delisting
criteria, and the second step is developing a suite of actions (the
Recovery Plan) that has a high probability of achieving the recovery
goals. (For more information about ESA recovery planning for West Coast
salmon and steelhead, visit
http://www.nwfsc.noaa.gov/cbd/trt/about.htm.) Delisting would occur only
after the ESU satisfied both the biological delisting criteria and
associated administrative delisting criteria, which typically involve
assurances that the threats to the continued existence of the ESU have
been satisfactorily resolved.

Although this report does not consider factors for decline in a
comprehensive way, the BRT did consider major risk factors that were
identified in previous status reviews. The sections in this report
focusing on specific ESUs summarize the previous BRT conclusions and
identify any major changes in risk factors that have occurred since the
time of listing.

Artificial Propagation

The 1993 NMFS ESA policy for artificial propagation of Pacific salmon
and steelhead recognizes that artificial propagation can be one of the
conservation tools used to help achieve recovery of ESA-listed species,
but it does not consider hatcheries to be a substitute for conservation
of the species in its natural habitat. Therefore, ESA risk analyses for
salmon and steelhead ESUs were conducted for "natural" fish (which are
defined as the progeny of naturally spawning fish), based on whether or
not the natural populations can be considered self-sustaining without
regular infusion of hatchery fish. This is the same provision
articulated in the joint USFWS-NMFS policy on artificial propagation of
all species under the ESA (Federal Register, Volume 65, Number 114, June
13, 2000, p. 37102) and is consistent with the approach the USFWS has
used to evaluate captive propagation programs for other species, such as
the condor (USFWS 1996) and the Bonytail chub (USFWS 2002).

The draft revised salmon hatchery policy outlines a three-step approach
for considering artificial propagation in listing determinations:

1.  Identify which hatchery populations are part of the ESU (see
    previous section).

2.  Review the status of the ESU.

3.  Evaluate existing protective efforts and make a listing
    determination.

4.  This document is concerned with step 2---the risk analysis for
    listed salmon and steelhead ESUs.

The draft revised hatchery policy interprets the purpose of the ESA is
to conserve threatened and endangered species in their natural habitats.
In its risk evaluations, the BRT therefore used the approach it has in
the past---focusing on whether populations and ESUs are self-sustaining
in their natural habitat. In this report, therefore, when we refer to
evaluations or conclusions of the BRT regarding the status of ESUs, we
are referring to analyses conducted using the criterion of
self-sustainability of natural populations.

Artificial propagation can be used as a conservation tool. Potential
benefits of artificial propagation for natural populations include
reducing the short-term risk of extinction, helping to maintain a
population until the factors limiting recovery can be addressed,
reseeding vacant habitat, and helping to speed recovery. Whether these
potential benefits will be realized in any particular case is difficult
to predict. To the extent that such benefits have already occurred, they
will be reflected in the population abundance and trend data considered
by the BRT. The draft revised hatchery policy also indicates that the
potential future conservation benefits of artificial propagation should
be considered before a listing determination is made. The potential
conservation benefits of artificial propagation, together with other
protective efforts, will be considered by NMFS regional office and
headquarters staff in determining whether to propose any changes to the
current ESA listing for West Coast salmon and steelhead.

Artificial propagation is important to consider in ESA evaluations of
anadromous Pacific salmonids for several other reasons. First, although
natural fish are the subject of risk assessments, possible positive or
negative effects of artificial propagation on natural populations must
also be evaluated. For example, artificial propagation can alter
life-history characteristics such as smolt age and migration and spawn
timing. Second, in addition to the potential to increase abundance of
fish, artificial propagation poses a number of risks to natural
populations that may affect their risk of extinction or endangerment. In
contrast to most other types of risk for salmon populations, those
arising from artificial propagation are often not reflected in
traditional indices of population abundance. For example, to the extent
that habitat degradation, overharvest, or hydropower development have
contributed to a population's decline, these factors will already be
reflected in population abundance data and accounted for in the risk
analysis. The same is not necessarily true of artificial propagation.
Hatchery production may mask declines in natural populations that will
be missed if only raw population abundance data are considered.
Therefore, a true assessment of the viability of natural populations
cannot be attained without information about the genetic and demographic
contribution of naturally spawning hatchery fish. Furthermore, even if
such data are available, they will not in themselves provide direct
information about possible deleterious effects of fish culture. Such an
evaluation requires consideration of the genetic and demographic risks
of artificial propagation for natural populations.

Resident Fish

As indicated above, the BRT concluded in previous status reviews that at
least some resident *O. mykiss* populations belonged to steelhead ESUs,
and these resident fish were considered in the overall risk analyses for
those ESUs. However, in most cases, little or no information was
available about the numbers and distribution of resident fish, as well
as about the extent and nature of their interactions with anadromous
populations. Given this situation, the previous risk analyses for
steelhead ESUs focused primarily on the status of anadromous
populations.

In these updated status reviews, increased efforts have been made to
gather biological information for resident *O. mykiss* populations to
assist in the risk analyses. (Although the two listed sockeye salmon
ESUs considered in this report \[Redfish Lake and Lake Ozette\] have
associated kokanee populations, in neither case are the kokanee
considered to be part of the sockeye salmon ESU, so the kokanee were not
formally considered in the risk analyses.) Information on resident fish
is summarized below in the report for steelhead (Section B), where
ESU-specific information is discussed in more detail. The steelhead
report also contains a more general discussion of how resident fish were
considered in the risk analyses for steelhead ESUs.

Factors Considered in Status Assessments

Salmonid ESUs are typically metapopulations; that is, they are usually
composed of multiple populations with some degree of interconnection, at
least over evolutionary time periods. This makes the assessment of
extinction risk difficult. The approach to this problem that NMFS
adopted for recovery planning is outlined in the viable salmonid
populations (VSP) report (McElhany et al. 2000). In this approach, risk
assessment is addressed at two levels: first, the population level, then
at the overall ESU level. We have modified previous BRT approaches to
ESU risk assessments to incorporate VSP considerations.

Individual populations are assessed according to the four VSP criteria:
abundance, growth rate/productivity, spatial structure, and diversity.
The condition of individual populations is then summarized on the ESU
level, and larger-scale issues are considered in evaluating the status
of the ESU as a whole. These larger-scale issues include total number of
viable populations, geographic distribution of these populations (to
ensure inclusion of major life-history types and to buffer the effects
of regional catastrophes), and connectivity among these populations (to
ensure appropriate levels of gene flow and recolonization potential in
case of local extirpations). These considerations are detailed in
McElhany et al. (2000).

In previous status reviews, the BRTs have used a simple "risk matrix"
for quantifying ESU-scale risks according to major risk factors. The
revised matrix (Table 1) integrates the four major VSP criteria
(abundance, productivity, spatial structure, and diversity) directly
into the risk assessment process. After reviewing all relevant
biological information for a particular ESU, each BRT member assigns a
risk score (see below) to each of the four VSP criteria. Use of the risk
matrix makes it easier to compare risk factors within and across ESUs.
The scores are tallied and reviewed by the BRT before making its overall
risk assessment (see FEMAT method, below). Although this process helps
to integrate and quantify a large amount of diverse information, there
is no simple way to translate the risk matrix scores directly into an
assessment of overall risk. For example, simply averaging the values of
the various risk factors would not be appropriate; an ESU at high risk
for low abundance would be at high risk even if there were no other risk
factors.

**Scoring VSP criteria.** Risks for each VSP factor are ranked on a
scale of 1 (very low risk) to 5 (very high risk):

1.  *Very Low Risk.* Unlikely that this factor contributes significantly
    to risk of extinction, either by itself or in combination with other
    factors.

2.  *Low Risk.* Unlikely that this factor contributes significantly to
    risk of extinction by itself, but some concern that it may, in
    combination with other factors.

3.  *Moderate Risk.* This factor contributes significantly to long-term
    risk of extinction, but does not in itself constitute a danger of
    extinction in the near future.

4.  *High Risk.* This factor contributes significantly to long-term risk
    of extinction and is likely to contribute to short-term risk of
    extinction in the foreseeable future.

5.  *Very High Risk.* This factor by itself indicates danger of
    extinction in the near future.

**Recent events.** The "recent events" category considers events that
have predictable consequences for ESU status in the future but have
occurred too recently to be reflected in the population data. Examples
include a flood that decimated most eggs or juveniles in a recent
broodyear, or large jack returns that generally anticipate strong adult
returns in subsequent year(s). This category is scored as follows:

++ --- expect a strong improvement in status of the ESU;

\+ --- expect some improvement in status;

0 --- neutral effect on status;

\- --- expect some decline in status;

\-- --- expect strong decline in status.

Table 1. Template for the risk matrix used in BRT deliberations. The
matrix is divided into five sections that correspond to the four VSP
"parameters" (McElhany et al. 2000) plus a "recent events" category.

**\[ESU Name\]**

+---------------------------------------------------------------+------+
| Risk Category                                                 | Sco  |
|                                                               | re\* |
+---------------------------------------------------------------+------+
| *[Abundance]{.underline}*                                     |      |
|                                                               |      |
| Comments:                                                     |      |
+---------------------------------------------------------------+------+
| *[Growth Rate/Productivity]{.underline}*                      |      |
|                                                               |      |
| Comments:                                                     |      |
+---------------------------------------------------------------+------+
| *[Spatial Structure and Connectivity]{.underline}*            |      |
|                                                               |      |
| Comments:                                                     |      |
+---------------------------------------------------------------+------+
| *[Diversity]{.underline}*                                     |      |
|                                                               |      |
| Comments:                                                     |      |
+---------------------------------------------------------------+------+
| *[Recent Events]{.underline}*                                 |      |
+---------------------------------------------------------------+------+

\* Rate overall risk of ESU on 5-point scale (1--very low risk; 2--low
risk; 3--moderate risk; 4--increasing risk; 5--high risk), except recent
events double plus (++, strong benefit) to double minus (\--, strong
detriment)

**Historical distribution and abundance.** The ESA has no provision that
requires a species to occupy its entire historic habitat or reach
historic levels of abundance before it can be considered no longer
threatened or endangered. Using the VSP criteria described above, it is
only necessary that an ESU contain enough viable populations and satisfy
concerns for spatial structure and diversity. However, developing
strictly quantitative viability criteria is extremely challenging, even
at the population level (see "Methods"). Therefore, other approaches
that provide insight into viability are also important to consider. If
our definitions of ESUs (groups of populations on independent
evolutionary trajectories) and populations (demographically independent
units over at least a 100-year time frame) are correct, then by
definition they were sustainable at historic levels. Therefore, we can
be confident that a population or ESU that approximates its historic
distribution and abundance will be viable into the future. This *a
priori* presumption of viability diminishes the further the current
status departs from the historical template. For a population or ESU
that is greatly reduced from its historic distribution and/or abundance,
there is little *a priori* reason to assume the current status is
viable. The viability of such a population or ESU is in considerable
doubt unless independent data can be developed to assess viability.

**Marine productivity**. In the last decade, evidence has accumulated to
demonstrate (1) recurring, decadal-scale patterns of ocean-atmosphere
climate variability in the North Pacific Ocean (Zang et al. 1997, Mantua
et al. 1997), and (2) correlations between these oceanic productivity
"regimes" and salmon population abundance in the Pacific Northwest and
Alaska (Hare et al. 1999, Mueter et al. 2002). There seems to be little
doubt that survival rates in the marine environment can be strong
determinants of population abundance for Pacific salmon and steelhead.
It is also generally accepted that for at least two decades, beginning
about 1977, marine productivity conditions were unfavorable for the
majority of salmon and steelhead populations in the Pacific Northwest
(in contrast, many populations in Alaska attained record abundances
during this period). Finally, there is evidence that an important shift
in ocean-atmosphere condition occurred around 1998. One indicator of the
ocean-atmosphere variation for the North Pacific is the Pacific Decadal
Oscillation index (PDO); Figure 2 shows that the PDO has taken mostly
negative values since 1999 (time period C on the graph), whereas the
values were positive in most of the previous two decades (time period B)
and generally negative again for a long period before that (period A).
Negative PDO values are associated with relatively cool ocean
temperatures (and generally high salmon productivity) off the Pacific
Northwest, and positive values are associated with warmer, less
productive conditions. As discussed in this report, increases in many
salmon populations in recent years may be largely a result of more
favorable ocean conditions.

Although these facts are relatively well established, much less
certainty can be attached to any predictions about what this means for
the viability of listed salmon and steelhead. For several reasons,
considerable caution is needed to project into the future. First,
empirical evidence for "cycles" in PDO, marine productivity, and salmon
abundance extends back only about a century, or about three periods of
two- to four-decades' duration. This is a very short data record for
inferring future behavior of a complex system. Thus, as with the stock
market, the past record is no guarantee of future performance. Second,
the past decade has seen particularly wide fluctuations not only in
climatic indices (e.g., the 1997--1998 El Niño was in many ways the most
extreme ever recorded, and the 2000 drought was one of the most severe
on record), but also in abundance of salmon populations. In general, as
the magnitude of fluctuations increases, the population extinction rate
also increases. Third, if there is anthropogenically caused climate
change in the future, it could affect ocean productivity. The range of
future climate change scenarios consistent with existing data is so wide
that future consequences cannot be predicted with any certainty;
however, many models suggest that northern latitudes are likely to
experience significant temperature increases (IPCC 2001). Finally,
changes in the pattern of ocean-atmosphere interactions do not affect
all species (or even all populations of a given species) in the same way
(Peterman et al. 1998).

![](media/image2.wmf)

Figure 2. Monthly values for the Pacific Decadal Oscillation Index,
which is based on sea surface temperatures in the North Pacific. Values
shown are deviations from the long-term (1900--1993) mean. See text for
discussion of time periods A, B, and C. (From
http://tao.atmos.washington.edu/pdo/)

Based on these considerations, the BRT identified a number of possible
future scenarios for impacts of ocean productivity on listed salmon and
steelhead populations:

1.  The PDO index could remain primarily negative for another decade or
    two (a typical duration for "regimes" observed in the past), leading
    to marine productivity conditions that are generally more favorable
    to Pacific Northwest salmon and steelhead than occurred from the
    mid-1970s to the late 1990s.

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6.  The last several years might be an anomaly, and the PDO index might
    revert back to the positive regime it has largely been in since the
    mid 1970s. It is worth noting in this regard that the PDO index has
    been positive in every month from August 2002 through March 2003
    (Figure 2).

7.  Marine and freshwater systems may continue to see wide fluctuations
    in environmental conditions.

8.  Anthropogenically caused climate change might be a significant
    factor in the future, with consequences that are difficult to
    predict.

Given all these uncertainties, the BRT was reluctant to make any
specific assumptions about the future behavior of the ocean-atmospheric
systems or their effects on the distribution and abundance of salmon and
steelhead. The BRT was concerned that even under the most optimistic
scenario (a), increases in abundance might be only temporary and could
mask a failure to address underlying factors for decline. The real
conservation concern for West Coast salmon and steelhead is not how they
perform during periods of high marine survival, but how prolonged
periods of poor marine survival affect the VSP parameters of abundance,
growth rate, spatial structure, and diversity. It is reasonable to
assume that salmon populations have persisted over time, under pristine
conditions through many such cycles in the past. Less certain is how the
populations will fare in periods of poor ocean survival when their
freshwater, estuary, and nearshore marine habitats are degraded.

Overall Risk Assessment

The BRT analysis of overall risk to the ESU uses categories that
correspond to definitions in the ESA: in danger of extinction, likely to
become endangered in the foreseeable future, or neither. (As discussed
above, these evaluations do not consider protective efforts and
therefore are not recommendations regarding listing status.) The overall
risk assessment reflects professional judgment by each BRT member. This
assessment is guided by the results of the risk matrix analysis as well
as expectations about likely interactions among factors. For example, a
single factor with a "high risk" score might be sufficient to result in
an overall score of "in danger of extinction," but a combination of
several factors with more moderate risk scores could also lead to the
same conclusion.

To allow for uncertainty in judging the actual risk facing an ESU, the
BRT has adopted a "likelihood point" method, often referred to as the
"FEMAT" method because it is a variation of a method used by scientific
teams evaluating options under President Clinton's Forest Plan (Forest
Ecosystem Management: An Ecological, Economic, and Social Assessment
Report of the Forest Ecosystem Management Assessment Team \[FEMAT;
http://www.or.blm.gov/ForestPlan/ NWFPTitl.htm\]). In this approach,
each BRT member distributes ten likelihood points among the three ESU
risk categories, reflecting their opinion of how likely that category
correctly reflects the true ESU status. Thus, if a reviewer were certain
that the ESU was in the "not at risk" category, he or she could assign
all ten points to that category. A reviewer with less certainty about
ESU status could split the points among two or even three categories.
This method has been used in all status review updates for anadromous
Pacific salmonids since 1999.

# METHODS

###### 

###### Primary contributors: Thomas P. Good and Sarah Sydor

###### (Northwest Fisheries Science Center)

# 

Data on abundance, the fraction of hatchery-origin spawners, harvest,
age structure, and hatchery releases were requested from state, federal
and tribal sources \[Federal Register, Vol. 67, No. 28, February 11,
2002, p. 6215\] and were compiled with previous data to conduct updated
risk analyses for each ESU. Data on adult returns were obtained from a
variety of sources, including time series of freshwater spawner surveys,
redd counts, and counts of adults migrating past dams/weirs. Time series
were assembled and analyzed at the scale of VSP populations where these
have been identified by Technical Recovery Teams (TRTs) or
"quasi-populations" where populations are in the process of being
identified by TRTs.

Preliminary data and analyses were reviewed by state, federal, and
tribal comanagers for accuracy and completeness. Where possible,
population or ESU-level estimates of the fraction of hatchery-origin
spawners were obtained or calculated using information from scale
analyses, fin clips, etc. Estimates of harvest were obtained for some
stocks directly; for others, harvest rates on nearby indicator stocks
were used to estimate the number of fish in the target population that
would have returned to spawn in the absence of harvest. See appendices
at the end of each species section for detailed information and
references for data sources.

####### Recent abundance

Recent abundance of natural spawners is reported as the geometric mean
(and range) of the most recent data to be consistent with previous
coast-wide status reviews of these species (Weitkamp et al. 1995, Busby
et al. 1996, Gustafson et al. 1997, Johnson et al. 1997, Myers et al.
1998). Geometric means were calculated to represent the recent abundance
of natural spawners for each population or quasi-population within an
ESU. Geometric means were calculated for the most recent five years
(chinook, steelhead), four years (chum, sockeye), or three years (coho);
these time frames were selected to correspond with modal age at maturity
for each species. Zero values in the data set were replaced with a value
of one, and missing data values within a multiple-year range were
excluded from geometric mean calculations. The geometric mean is the
*n*th root of the product of the *n* data:

${\overline{X}}_{G} = \sqrt[n]{N_{1}N_{2}N_{3}\text{.}\text{.}\text{.}N_{n}}$,
(Eq. 1)

where *N~t~* is the abundance of natural spawners in year *t.*

Arithmetic means (and ranges) were also calculated for the most recent
abundance data:

> ${\overline{X}}_{A} = \frac{\sum_{}^{}N_{i}}{n}$, (Eq. 2)

where *N~t~* is the abundance of natural spawners in year *t.*

####### 

####### Trends in abundance

Short-term and long-term trends were calculated from time series of the
total number of adult spawners. Short-term trends were calculated using
data from 1990 to the most recent year, with a minimum of 10 data points
in the 13-year span. Long-term trends were calculated using all data in
a time series.

Trend was calculated as the slope of the regression of the number of
natural spawners (log-transformed) over the time series; to mediate for
zero values, one was added to natural spawners before transforming the
data. Trend was reported in the original units as exponentiated slope,
such that a value \> 1 indicates a population trending upward, and a
value \< 1 indicates a population trending downward. The regression was
calculated as

> $\text{ln}(N + 1) = \beta_{0} + \beta_{1}X + \varepsilon$, (Eq. 3)

where *N* is the natural spawner abundance, *β*~0~ is the intercept,
*β*~1~ is the slope of the equation, and *ε* is the random error term.

Confidence intervals (95%) for the slope, in their original units of
abundance, were calculated as

> $\text{exp}(\text{ln}(b_{1}) - t_{0\text{.}\text{05}(2),\text{df}}s_{b_{1}}) \leq \beta_{1}\text{exp}(\text{ln}(b_{1}) + t_{0\text{.}\text{05}(2),\text{df}}s_{b_{1}})$,
> (Eq. 4)

where *b*~1~ is the estimate of the true slope *β*~1~, *t*~0.05(2)~,
*~df~* is the two-sided *t*-value for a confidence level of 0.95, *df*
is equal to *n*-2, *n* is the number of data points in the time series,
and *s~b1~* is the standard error of the estimate of the slope, *b*~1~.
The probability that the trend value was declining \[P(trend \< 1)\] was
also calculated.

####### Population growth rate

In addition to analyses of trends in natural spawners, we calculated the
median short-term population growth rate (λ) of natural-origin spawners
as a measure for comparative risk analysis. Lambda more accurately
reflects the biology of salmon and steelhead, as it incorporates
overlapping generations and calculates running sums of cohorts. It is an
essential parameter in viability assessment, as most population
extinctions are the result of steady declines, λ \< 1. It has been
developed for data sets with high sampling error and age-structure
cycles (Holmes 2001). These methods have been extensively tested using
simulations for both threatened and endangered populations as well as
for stocks widely believed to be at low risk (Holmes, in press), and
cross-validated with time series data (Holmes and Fagan 2002).

The λ of natural-origin spawners was calculated in two ways for each
population over the short-term time frame (1990-most recent year). The
first (λ) assumed that hatchery-origin spawners had zero reproductive
success, while the second (λ~h~) assumed that hatchery-origin spawners
had reproductive success equivalent to that of natural-origin spawners.
These extreme assumptions bracket the range likely to occur in nature.
Empirical studies indicate that hatchery-origin spawning fish generally
have lower (and perhaps much lower) reproductive success than
natural-origin spawners (reviewed by Reisenbichler and Rubin 1999).
However, this difference can vary considerably across species and
populations, and it is very rare that data are available for a
particular population of interest. Therefore, to be conservative, we
bracketed the scenarios that are likely to be occurring in nature.

A multi-step process based on methods developed by Holmes (2001), Holmes
and Fagan (2002) and described in McClure et al. (in press) was used to
calculate estimates for λ, its 95% confidence intervals, and its
probability of decline \[P(λ \< 1)\]. The first step was calculating
4-year running sums for natural-origin spawners as

$R_{t} = \sum_{i = 1}^{4}N_{t - i + 1}$. (Eq. 5)

where *N*~t~ is the number of natural-origin spawners in year *t.* A
4-year running sum window was used for all species, as analysis by
McClure et al. (in press) indicates this is an appropriate window for a
diverse range of species life histories.

Next, an estimate of μ, the rate at which the median of *R* increases
through time (Holmes 2001), was calculated as

$\hat{\mu} = \text{mean}\left( \text{ln}\left( \frac{R_{t + 1}}{R_{t}} \right) \right)$
(Eq. 6)

---the mean of the natural log-transformed running sums of
natural-origin spawners. The point estimate for λ was then calculated as
the median annual population growth rate,

$\hat{\lambda} = e^{\hat{\mu}}$ . (Eq. 7)

Confidence intervals (95%) were calculated for $\hat{\lambda}$ to
provide a measure of the uncertainty associated with the growth rate
point estimate. First, an estimate of variability for each population
was determined by calculating an estimate for $\sigma_{\text{pop}}^{2}$
using the slope method (Holmes 2001). The slope method formula is

> ${\hat{\sigma}}_{\text{pop}}^{2} = \text{slope  of var}\left( \text{ln}\left( \frac{R_{t + \tau}}{R_{t}} \right) \right)\text{ vs}\text{.}\tau\text{.}$,
> (Eq. 8)

where τ is a temporal lag in the time series of running sums.

Individual population variance estimates were highly uncertain, so a
more robust variance estimate, $\sigma_{\text{avg}}^{2}$, was obtained
by averaging the $\sigma_{\text{pop}}^{2}$estimates from all the
populations in an ESU. This average variance estimate was then applied
as the variance for every population in an ESU. The degrees of freedom
associated with the average variance estimate are obtained by summing
the degrees of freedom for each of the individual population variance
estimates. The degrees of freedom for the individual population
estimates were determined using the method of Holmes and Fagan (2002),
which identifies the adjusted degrees of freedom associated with slope
method variance estimates. The calculation for the adjusted degrees of
freedom is

> *df* = 0.212*n* -- *1.215*, (Eq. 9)

where *n* is the length of the time series. Using the average variance
estimate and the summed degrees of freedom, the 95% confidence intervals
for λ were calculated as

> $\text{exp}\left( \hat{\mu} \pm t_{\text{.}\text{05}(2),\text{df}}\sqrt{\frac{{\hat{\sigma}}_{\text{slp}^{2}}}{(n - 4)}} \right)$.
> (Eq. 10)

In addition, the probability that the population growth rate was
declining \[P(λ \< 1)\] was calculated utilizing the fact that ln(λ)
follows a *t*-distribution. This probability is calculated by finding
the probability that the natural log of the calculated lambda divided by
its standard error is less than zero.

The preceding treatment ignores contributions of hatchery-origin
spawners to the next generation, in effect assuming that they had zero
reproductive success. This assumption produces the most optimistic view
of viability of the natural population. The other extreme assumption
(that hatchery-origin spawners have reproductive success equivalent to
that of natural-origin spawners), produces the most pessimistic view of
viability of the natural population, given any particular time series of
data. To calculate the median growth rate under this assumption (λ~h~),
a modified approach to the method developed by Holmes (2001) was used to
calculate estimates for λ ~h~, 95% confidence intervals for λ~h~, and to
determine *P*(λ~h~ \< 1). The first step was calculating 4-year running
sums (*RN*) for natural-origin spawners as

#  $(\text{RN})_{t} = \sum_{i = 1}^{4}N_{t - i + 1}$. (Eq. 11)

Next, the 4-year running sum of hatchery-origin spawners was calculated
as

> $(\text{RH})_{t} = \sum_{i = 1}^{4}H_{t - i + 1}$, (Eq. 12)

where *H~t~* is the number of hatchery spawners in year *t.*

### The ratio of total spawners to natural origin spawners was calculated as 

> $\psi_{t} = \frac{(\text{RN})_{t} + (\text{RH})_{t}}{(\text{RN})_{t}}\text{.}$
> (Eq. 13)

The average age at reproduction, *T*, was calculated in three steps:

1.  Determine the total number of spawners for each age (*A*) by
    calculating

> $A_{j} = \sum_{j = 1}^{\text{max}\text{ age}}{\sum_{\text{all}t}^{}a_{j}(N + H)_{t}\text{.}}$
> (Eq. 14)

### 2. Calculate the total number of spawners (*G*)

> $G = \sum_{j = 1}^{\text{max}\text{age}}A_{j}$. (Eq. 15)

### 3. Determine the average age at reproduction (*T*) by calculating

> $T = \sum_{j = 1}^{\text{max}\text{age}}\frac{j \times A_{j}}{G}$.
> (Eq. 16)

Next, an estimate of *μ*, the rate at which the median increases through
time (Holmes 2001), was calculated as

> $\hat{\mu} = \text{mean}\left( \text{ln}\left( \frac{(\text{RN})_{t + 1}}{(\text{RN})_{t}} \right) - \frac{1}{T}\text{ln}\left( \psi_{t} \right) \right)\text{.}$
> (Eq. 17)

The point estimate for λ*~h~* was then calculated as the median annual
population growth rate (Eq. 7).

Confidence intervals (95%) for λ~h~ and its probability of decline
\[P(λ~h~ \< 1)\] were calculated as for λ, with modification to the
slope method for calculating the variance:

> ${\hat{\sigma}}^{2} = \text{slope  of var}\left( \text{ln}\left( \frac{(\text{RN})_{t + \tau}}{(\text{RN})_{t}} \right) - \frac{1}{T}\text{ln}\left( \prod_{i = 0}^{\tau - 1}\psi_{t + i} \right) \right)\text{ vs}\text{.}\tau\text{.}$
> (Eq. 18)

# Calculating recruits

Recruits, or spawners in the next generation, from a give brood year
were calculated as

> $C_{t} = \sum_{i = 1}^{\text{MaxAge}}N_{t + i}A(i)_{t + i}$ , (Eq. 19)

where *C~t~* is the number of recruits from brood year *t*, *N~t~* is
the number of natural origin spawners in year *t*, and *A(i)~t~* is the
fraction of age *i* spawners in year *t*. The estimate of preharvest
recruits is similarly

> $C\left( \text{preHarvest} \right)_{t} = \sum_{i = 1}^{\text{MaxAge}}P_{t + i}A(i)_{t + i}$,
> (Eq. 20)

where *C(preHarvest)~t~* is the number of preharvest recruits in year
*t*, *P~t~* is the number of natural origin spawners that would have
returned in year *t* if there had not been a harvest, and *A(i)~t~* is
the fraction of age *i* spawners in year *t* had there not been a
harvest. \[Because *P~t~* is in terms of the number of fish that would
have appeared on the spawning grounds had there not been a harvest, it
can be quite difficult to estimate and simplifying assumptions are often
made\].

# Population Viability Analysis

A variety of quantitative approaches to Population Viability Analysis
(PVA) have been used with Pacific salmonids. Because no consensus has
emerged on how best to model population viability in salmon, we did not
employ a standardized PVA model in this report. However, we considered
results of PVA analyses that had been conducted for specific
populations.

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