# Preliminary conclusions regarding the updated status of listed ESUs of West Coast salmon and steelhead 

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# West Coast Salmon Biological Review Team

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# Northwest Fisheries Science Center

**2725 Montlake Boulevard East**

## Seattle, WA 98112 {#seattle-wa-98112 .unnumbered}

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# Southwest Fisheries Science Center

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

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# February 2003

# Co-manager review draft 

**\[This is a draft document being provided to state, tribal, and
federal comanagers for technical review.\]**

# EXECUTIVE SUMMARY

This draft report summarizes preliminary scientific conclusions of the
NMFS Biological Review Team (BRT) regarding the updated status of 26
ESA-listed Evolutionarily Significant Units (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 decade of the 1990s. The status
review updates were undertaken to allow consideration of new data that
have 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. The
draft BRT conclusions in this report should be considered preliminary
for two reasons. First, the BRT will not finalize its conclusions until
state, tribal, and other federal comanagers have had an opportunity to
review and comment on the draft report. Second, some policy issues
regarding the treatment of hatchery fish and resident fish in ESU
determinations and risk analyses are not resolved at this time.

When finalized, this draft report would represent 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 final BRT report and after considering the
conservation benefits of such 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: 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 as
well as make comparisons of relative risk across ESUs and species. These
data and other information were considered by the BRT 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 risk analyses presented to the BRT focused on the
viability of populations sustained by natural production.

For the following ESUs, the majority BRT conclusion was "in danger of
extinction:" Upper Columbia spring-run chinook, Sacramento River
winter-run chinook, Upper Columbia 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, Middle
Columbia 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, S. Oregon/N. California Coast coho, Lake Ozette
sockeye, Hood Canal summer-run chum, and Lower Columbia River chum. In a
number of ESUs, adult returns over the last 1-3 years have been
significantly higher than have been observed in the recent past, at
least in some populations. The BRT found these results, which affected
the overall BRT conclusions for some ESUs, to be encouraging. For
example, the majority BRT conclusion for Snake River fall chinook salmon
was "likely to become endangered," whereas the BRT concluded at the time
of the original status review that this ESU was "in danger of
extinction." This change reflects the larger adult returns over the past
several years, which nevertheless remain well below preliminary targets
for ESA recovery. In the Upper Columbia River, the majority BRT
conclusions for spring chinook salmon and steelhead were still "in
danger of extinction," but a substantial minority of the votes fell in
the "likely to become endangered" category. The votes favoring the less
severe risk category reflect the fact that recent increases in
escapement have at least temporarily somewhat alleviated the immediate
concerns for persistence of individual populations, many of which fell
to critically low levels in the mid 1990s. Overall, although recent
increases in escapement were considered a favorable sign by the BRT, the
response was uneven across ESUs and, in some cases, across populations
within ESUs. Furthermore, in most instances in which recent increases
have occurred, they have not yet been sustained for even a full
salmon/steelhead generation. The causes for the increases are not well
understood, and in many (perhaps most) cases may be due primarily to
unusually favorable conditions in the marine environment rather than
more permanent alleviations in the factors that led to widespread
declines in abundance over the past century. In general, the BRT felt
that ESUs and populations would have to maintain themselves for a longer
period of time at levels considered viable before it could be concluded
that they are not at significant continuing risk.

Table of Contents

#  Title page 1

#  Executive Summary 2

#  Table of Contents 4

#  Introduction/Methods 6

References/Appendix 20

## Chinook

1.  Background & history of listings A1

2.  Chinook ESU summaries

### Snake River fall-run chinook A3

### Snake River spring/summer-run chinook A8

### Upper Columbia River spring-run chinook A17 

### Puget Sound chinook A27

### Lower Columbia River chinook A54

### Upper Willamette River chinook A83

### California Coastal chinook A93

### Sacramento River winter-run chinook A103

### Central Valley spring-run chinook A110

#### Chinook Preliminary BRT conclusions A119

#### References A124

> A.5 Appendices A131

## Steelhead

3.  Background & history of listings B1

4.  Steelhead ESU summaries

### Snake River Basin steelhead B6

### Upper Columbia River steelhead B18 

### Middle Columbia River steelhead B25

### Lower Columbia River steelhead B34

### Upper Willamette River steelhead B50

### Northern California steelhead B58

### Central California Coast steelhead B70

### South-Central California Coast steelhead B77

### Southern California steelhead B83

### California Central Valley steelhead B90

#### Steelhead Preliminary BRT conclusions B100

5.  References B107

6.  Appendices B117

## Coho

7.  Background & history of listings C1

8.  Coho ESU summaries

### Oregon Coast coho C3

### Southern Oregon/Northern California Coasts coho C25

### Central California coho C47

### Lower Columbia River coho C62

#### Coho Preliminary BRT conclusions C75

9.  References C78

10. Appendices C90

## Sockeye

11. Background & history of listings D1

12. Sockeye ESU summaries

### Snake River sockeye D3

### Ozette Lake sockeye D8

#### Sockeye Preliminary BRT conclusions D13

13. References D14

14. Appendices D16

## Chum 

15. Background & history of listings E1

16. Chum ESU summaries

### Hood Canal summer-run chum E3

### Lower Columbia River chum E17 

#### Chum Preliminary BRT conclusions E29

17. References E30

18. Appendices E32

# INTRODUCTION

During the 1990s, the National Marine Fisheries Service (NMFS) conducted
a series of reviews of the status of West Coast populations of Pacific
salmon and steelhead (*Oncorhynchus* spp.) with respect to the United
States 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 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 Northwest Fisheries
Science Center (http://www.nwfsc.noaa.gov/pubs/), Southwest Regional
Office (http://swr.nmfs.noaa.gov/salmon.htm), Santa Cruz Laboratory
(http://www.pfeg.noaa.gov/tib/esa/salmonids/esa_docs/index.html), and
Northwest Regional Office
(http://www.nwr.noaa.gov/1habcon/habweb/listnwr.htm) websites.

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, and regional planners will
use this information to help 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 ruling in a lawsuit 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). That 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 of the other listed ESUs of salmon and steelhead. Second,
another lawsuit currently pending that involves the Southern California
ESU of steelhead ([EDC v. Evans]{.underline}, SACV-00-1212-AHS (EEA),
United States District Court, C.D. California) 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 even for the most recently
listed ESUs, and up to a decade has passed since the first populations
were listed in the Sacramento and Snake Rivers. Furthermore, in some
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 preliminary conclusions of the Biological Review Team (BRT)
regarding their 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. The BRT membership is indicated in the sections
for each species.

## ESU determinations {#esu-determinations .unnumbered}

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, 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 evolutionarily significant unit (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
Biological Review Teams have used a comprehensive approach to defining
ESUs that utilized all available scientific information. A discussion of
how the NMFS policy was applied in a number of ESA status reviews can be
found in Waples (1995).

## Geographic boundaries {#geographic-boundaries .unnumbered}

The status review updates focused primarily on risk assessments, and 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 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 pending resolution
of this issue, the BRT has not attempted to revisit the ESU
determinations for hatchery populations in this draft report. However, a
working group has updated the stock histories and biological information
for every hatchery population associated with each listed ESU, and
comanagers and others are currently reviewing that information for
accuracy and completeness (SSHAG 2003). This draft report has also
provisionally assigned each hatchery population to one of four
categories: (listed below). It remains to be determined how these
categories relate to ESU membership.

**Category 1---**The hatchery population was derived from a native,
local population; is released within the range of the natural population
from which it was derived; and has experienced only relatively minor
genetic changes from causes such as founder effects, domestication or
non‑local introgression. Examples of populations that fall into this
category include:

a\) A hatchery population that has been recently founded (e.g., within
one or two generations) from a representative sample of a native,
natural population.

b\) A hatchery population that was founded some time in the past (e.g.,
more than two generations ago) as a representative sample from a native,
natural population, and has received regular, substantial, and
representative infusions of natural fish from the original founding
population into the broodstock since that time.

**Category 2---**The hatchery population was derived from a local
natural population, and is released within the range of the natural
population from which it was derived, but is known or suspected to have
experienced a moderate level of genetic change from causes such as
founder effects, domestication or non‑native introgression. Examples of
populations that fall into this category include:

a\) A hatchery population for which there is direct evidence (e.g., from
molecular genetic data or breeding studies) of moderate genetic
divergence between the hatchery population and the natural population
from which it was derived. In this context, "moderate divergence" would
be a level of divergence typical of that observed among natural
populations within the same ESU.

b\) A hatchery population that was founded from a native, natural
population, but 1) the sample was not representative; or 2) the
broodstock has received few or no reintroductions of native, natural
fish since the time of founding; or 3) the hatchery population is
believed to have experienced moderate genetic change (e.g., from
domestication or non‑local introgression) since the time of founding.

c\) A hatchery population that was founded predominantly from a local
natural population but has also had a greater level of introgression
from non-local stocks than would be expected from natural straying
rates.

**Category 3---**The hatchery population was derived predominantly from
other populations that are in the same ESU, but is substantially
diverged from the local, natural population(s) in the watershed in which
it is released. Examples include:

a\) A hatchery population that has been deliberately artificially
selected, has experienced substantial unintentional domestication, or
both.

b\) A hatchery population that was founded in a substantially
non-representative way or was founded long ago (many salmon generations)
and has received few or no infusions of wild fish into the broodstock
since the time of founding.

c\) A hatchery population that was founded from a mixture of several
natural or hatchery populations from within the ESU, or has experienced
substantial introgression from non-local populations (much higher than
would be expected from natural straying).

d\) A hatchery population that was founded from within the ESU, but is
released outside of the historical range of the natural population from
which it was founded (but still within the historical range of the ESU).

**Category 4---**The hatchery population was predominantly derived from
populations that are not part of the ESU in question; or there is
substantial uncertainty about the origin and history of the hatchery
population.

##### 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. As is
the case with hatchery fish, it is important to determine the
relationship 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
jurisdiction for resident fish. At the time this report was prepared,
the two agencies had not reached agreement on how to determine the
ESU/DPS status of resident fish or how to make the listing
determinations for the overall ESU/DPSs.

For the purposes of this status review update, the BRT adopted a
provisional working framework for determining the ESU/DPS status of
resident *O. mykiss* 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.
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 provisional 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 between resident
> and anadromous forms;
>
> Case 2: long-standing natural barriers (e.g., a waterfall) separate
> resident and anadromous forms;
>
> Case 3: relatively recent (e.g., within last 100 years) human actions
> (e.g., construction of a dam without provision for upstream fish
> passage) separate resident and anadromous forms.

As a provisional framework, NMFS has adopted the following working
assumptions about ESU membership of resident fish falling in each of
these categories:

> Case 1: Resident fish 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 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: resident fish assumed provisionally to be part of the ESU.
> Rationale: Case 3 populations were, most likely, Case 1 populations
> (and hence part of the ESU) prior to construction of the artificial
> barrier.

These default assumptions about ESU membership 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. In addition, some Case 3 populations that historically were
part of the ESU may no longer be, as a result of rapid divergence in a
novel environment, or displacement by or introgression from non-native
hatchery rainbow trout. The BRT reviewed available information about
individual resident populations of *O. mykiss* and *O. nerka* to
determine which Case each population fits into and whether any
information exists to override the default assumption about ESU
membership.

#### Risk Assessments {#risk-assessments .unnumbered}

### ESA definitions {#esa-definitions .unnumbered}

After the composition of an ESA species is determined, the next question
to address is, "Is the 'species' threatened or endangered?" 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." Neither
NMFS nor the FWS have developed any formal policy guidance about how to
interpret the definitions of threatened or endangered species in the
act.

A variety of information is considered in evaluating the level of risk
faced by an ESU. According to the ESA, the determination of 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. In its biological status reviews, the BRT does not
evaluate likely or possible effects of conservation measures except to
the extent they are reflected in metrics of population or ESU viability;
these measures 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 risk of
extinction faced by identified ESUs under the assumption that present
conditions will continue into the future (recognizing, of course, that
existing trends in factors affecting populations and natural demographic
and environmental variability are inherent features of "present
conditions").

###### 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 have focused on "natural" fish (which are
defined as the progeny of naturally spawning fish),and whether 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 USFWS has used in evaluating
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

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

The draft revised hatchery policy reaffirms the interpretation that 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. The draft policy also
indicates that the potential conservation benefits of artificial
propagation should be considered before a listing determination is made.
The potential conservation benefits of artificial propagation, together
with other conservation measures, will be considered by NMFS Regional
Office and Headquarters staff in developing a listing proposal.

Artificial propagation is also important to consider in ESA evaluations
of anadromous Pacific salmonids for several other reasons. First,
although natural fish are the focus of ESU determinations, 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
short-term abundance of fish in an ESU, 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 possibly 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, and 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. An approach to this problem has been adopted
by NMFS for recovery planning, and is outlined in the "Viable Salmonid
Populations" (VSP) report by McElhany et al. (2000). In this approach,
risk assessment is addressed at two levels: first, the simpler
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 status of
the ESU as a whole. These larger-scale issues include total number of
viable populations, geographic distribution of these populations (to
insure 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).

**The Risk Matrix**

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 (see Appendix 1) integrates the four major VSP criteria
(abundance, productivity, spatial structure, 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 not a 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 concerns
for any other risk factor.

**Scoring VSP criteria**. Risks for each of the four VSP factors are
ranked on a scale of 1 (very low risk) to 5 (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) Increasing Risk*. Present risk is Low or Moderate, but is likely
> to increase to high risk in the foreseeable future if present
> conditions continue.
>
> *5) 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.

## Overall risk assessment {#overall-risk-assessment .unnumbered}

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 conservation measures 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
BRTs have adopted a "likelihood point" method. This method, also
referred to as the FEMAT method because it was 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), allows each reviewer to
distribute 10 likelihood points among the three ESU risk categories,
reflecting their opinion of the likelihood that that category correctly
reflects the true ESU status. Thus, if a reviewer were certain that the
ESU was in the "not at risk" category; then s/he could assign all 10
points to that category. A reviewer with less certainty about ESU status
could split the points among two or even three categories. The FEMAT
method has been used in all status review updates for anadromous Pacific
salmonids since 1999.

# METHODS

# 

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 at the
scale of population where these have been identified by TRTs or
quasi-population where population identification is ongoing.

# Calculating recruits

Recruits from a give brood year are calculated as

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

where *R~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. 2)

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. \[Because *P~t~* is in terms of the number of fish that would
have appeared on the spawning grounds had there not been a harvest, it
can be quite difficult to estimate and simplifying assumptions are often
made\].

####### Mean abundance

Recent average abundance of natural-origin spawners is reported as the
geometric mean of the most recent data. Five-year geometric means were
calculated to represent the recent abundance of natural-origin spawners
for each population or quasi-population within an ESU. Five-year
geometric means for the most recent 5 years of available data were
calculated, as well as the minimum and maximum 5-year geometric means
for the entire time series. The equation for a 5-year geometric mean is

$\text{GM}_{N_{t}} = \sqrt[5]{N_{t}N_{t - 1}N_{t - 2}N_{t - 3}N_{t - 4}}$,
(Eq. 3)

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

Zero values in the data set were replaced with a value of one, and
missing data values within a 5-year range were excluded from geometric
mean calculations. For example, if data were available from 1997--2001,
with no data for 1998, the geometric mean was calculated as

> $\text{GM}_{N_{\text{1997}}} = \sqrt[4]{N_{\text{1997}}N_{\text{1999}}N_{\text{2000}}N_{\text{2001}}}$.
> (Eq. 4)

####### Trends in abundance

Short-term and long-term trends were calculated from time series of
adult spawners. Short-term was defined as that resulting from data from
1990 to the most recent year of data, with a minimum of 10 data points
in the 13-year span. Long-term trend was defined as that resulting from
all data in a time series.

Trend was calculated as the slope of the regression of natural-origin
spawners (log-transformed); one was added to natural-origin spawners
before transforming the data to mediate for zero values. 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. 5)

where *N* is the natural-origin 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. 6)

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~.
In addition, the probability that the trend value was declining
\[P(trend \< 1)\] was calculated.

**Lambda calculations**

The median growth rate (λ) of natural-origin spawners was calculated in
two ways for each population over both short-term and long-term time
frames as above (short-term = 1990-most recent year and long-term = all
data). 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. However, this
parameter can vary considerably across species and populations, and it
is very rare that data are available for a particular population of
interest.

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. 7)

where *N*~t~ is the number of natural-origin spawners in year *t.*

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. 8)

---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. 9)

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 was determined by
calculating an estimate for σ^2^ using the slope method (Holmes 2001).
An estimate for *σ*^2^, ${\hat{\sigma}}_{\text{slp}}^{2}$was calculated
for each population in an ESU, after which an arithmetic average of
populations was calculated. This average was used as the measurement of
variability for calculating confidence intervals for both short-term and
long-term time series for all populations in an ESU.

We determined the degrees of freedom for the appropriate *t*-value for
use in confidence interval calculations based on the method for
adjusting degrees of freedom when variance is calculated using the slope
method (Holmes and Fagan 2002). The adjusted degrees of freedom were
then summed over all populations in an ESU to obtain the *df* to
determine *t*. The degrees of freedom for each population was calculated
as

> *df* = 0.333 + 0.212*n* -- *L*, (Eq. 10)

where *n* is the length of the time series and *L* is the number of
counts summed to calculate *R~t~* (*L =* 4 in these analyses).
Confidence intervals were calculated as

> $\text{exp}\left( \hat{\mu} \pm t_{\text{.}\text{05}(2),\text{df}}\sqrt{\frac{{\hat{\sigma}}_{\text{slp}^{2}}}{\gamma}(n - 4)} \right)$,
> (Eq. 11)

where γ ≅ 1. In addition, the probability that trend was less than one
was calculated utilizing the fact that ln(λ) follows a *t*-distribution.
The probability that λ is less than one is calculated by finding the
probability that the natural log of the calculated lambda divided by its
standard error is less than one, given the degrees of freedom, which is
the number of data points used to calculate lambda minus two.

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
produces the most pessimistic view of viability of the natural
population. To calculate the median growth rate under this assumption,
that hatchery-origin spawners have reproductive success equivalent to
that of natural-origin spawners (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. 12)

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. 13)

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

###  {#section-25 .unnumbered}

### The ratio of total spawners to natural origin spawners was calculated as  {#the-ratio-of-total-spawners-to-natural-origin-spawners-was-calculated-as .unnumbered}

> $\psi_{t} = \frac{(\text{RN})_{t} + (\text{RH})_{t}}{(\text{RN})_{t}}\text{.}$
> (Eq. 14)

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. 15)

### 2. Calculate the total number of spawners (*G*) {#calculate-the-total-number-of-spawners-g .unnumbered}

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

### 3. Determine the average age at reproduction (*T*) by calculating {#determine-the-average-age-at-reproduction-t-by-calculating .unnumbered}

> $T = \sum_{j = 1}^{\text{max}\text{age}}\frac{j \times A_{j}}{G}$.
> (Eq. 17)

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. 18)

The point estimate for λ*~h~* was then calculated as the median annual
population growth rate,

> ${\hat{\lambda}}_{h} = e^{\hat{\mu}}$. (Eq. 19)

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. 20)

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Appendix 1. A template for the risk matrix used in BRT deliberations.
The matrix is divided into five sections: corresponding to the four VSP
\"parameters\" (McElhany et al. 2000) plus a \"recent events\" category.

**\[ESU Template\]**

+---------------------------------------------------------------+------+
| **Risk Category**                                             | **S  |
|                                                               | core |
|                                                               | \*** |
+---------------------------------------------------------------+------+
| *[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)