[Federal Register Volume 64, Number 179 (Thursday, September 16, 1999)]
[Rules and Regulations]
[Pages 50394-50415]
From the Federal Register Online via the Government Publishing Office [www.gpo.gov]
[FR Doc No: 99-24051]



[[Page 50393]]

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Part IV





Department of Commerce





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National Oceanic and Atmospheric Administration



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50 CFR Part 223



Endangered and Threatened Species; Threatened Status for Two Chinook 
Salmon Evolutionarily Significant Units (ESUs) in California; Final 
Rule

  Federal Register / Vol. 64, No. 179 / Thursday, September 16, 1999 / 
Rules and Regulations  

[[Page 50394]]



DEPARTMENT OF COMMERCE

National Oceanic and Atmospheric Administration

50 CFR Parts 223

[Docket No. 990303060-9231-03; I.D. 022398C]
RIN 0648-AM54


Endangered and Threatened Species; Threatened Status for Two 
Chinook Salmon Evolutionarily Significant Units (ESUs) in California

AGENCY: National Marine Fisheries Service (NMFS), National Oceanic and 
Atmospheric Administration (NOAA), Commerce.

ACTION: Final rule; notice of determination.

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SUMMARY: Previously, NMFS completed a comprehensive status review of 
west coast chinook salmon (Oncorhynchus tshawytscha) populations in 
Washington, Oregon, Idaho, and California and identified 15 ESUs within 
this range. After soliciting additional data to resolve scientific 
disagreements, NMFS now issues a final rule to list two ESUs as 
threatened under the Endangered Species Act (ESA). The Central Valley 
spring-run ESU was originally proposed as endangered, but new 
information indicates that the ESU should instead be considered a 
threatened species. The California Coastal ESU was originally proposed 
as threatened, as part of a larger Southern Oregon and California 
Coastal ESU, but new information supports a threatened listing for a 
revised ESU consisting of California coastal chinook salmon populations 
from Redwood Creek (Humboldt County) south through the Russian River. 
Other coastal populations to the north of this ESU (and originally 
proposed as threatened) are now considered part of a separate Southern 
Oregon and Northern California Coastal ESU that does not warrant 
listing at this time.
    NMFS is also making final listing determinations for two other 
chinook salmon ESUs originally proposed as threatened. It has 
considered new information about the Central Valley fall and late fall-
run ESU and has determined that listing is not warranted at this time, 
but it will consider it a candidate species. In the case of the 
proposed ESU expansion for threatened Snake River fall-run chinook 
salmon, NMFS has determined that the ESU does not include Deschutes 
River populations and that listing this latter population is not 
warranted at this time.
    In the two ESUs identified as threatened, only naturally spawned 
populations of chinook salmon are listed. At this time, no hatchery 
populations are deemed essential for recovery in either of the two 
listed ESUs, so no hatchery populations are part of this final listing 
determination.
    NMFS intends to issue protective regulations under section 4(d) of 
the ESA for these threatened ESUs. Even though NMFS is not now issuing 
protective regulations for the threatened ESUs, Federal agencies are 
required under section 7 to consult with NMFS if any activity they 
authorize, fund, or carry out may affect listed chinook salmon in these 
ESUs.

DATES: Effective November 15, 1999.

ADDRESSES: Branch Chief, NMFS, Northwest Region, Protected Resources 
Division, 525 NE. Oregon St., Suite 500, Portland, OR 97232-2737; 
Assistant Regional Administrator, Protected Resources Division, NMFS, 
Southwest Region, 501 West Ocean Blvd., Suite 4200, Long Beach, CA 
90802-4213; Salmon Coordinator, Office of Protected Resources, NMFS, 
1315 East-West Highway, Silver Spring, MD 20910.
    Reference materials regarding this listing determination can also 
be obtained from the internet at www.nwr.noaa.gov.

FOR FURTHER INFORMATION CONTACT: Garth Griffin at (503) 231-2005, Craig 
Wingert at (562) 980-4021, or Chris Mobley at (301) 713-1401.

SUPPLEMENTARY INFORMATION:

Species Background

    Chinook salmon are anadromous and semelparous, i.e., as adults they 
migrate from the marine environment into the freshwater rivers and 
streams of their birth (anadromous) where they spawn and die 
(semelparous). They are the largest of the Pacific salmon species and 
are distributed in freshwater and marine areas from California to Asia. 
The four ESUs considered in this determination spawn and rear in 
coastal and interior rivers in California and Oregon and forage in vast 
nearshore and marine zones of the North Pacific Ocean. More detailed 
biological information for west coast chinook salmon can be found in 
species' status assessments by NMFS (Matthews and Waples, 1991; Waples 
et al., 1991; NMFS, 1995; Waknitz et al., 1995; Myers et al., 1998; 
NMFS, 1998a; NMFS, 1999a), Oregon Department of Fish and Wildlife 
(ODFW, 1991; Nickelson et al., 1992; Kostow et al., 1995), California 
Department of Fish and Game (CDFG)(Clark, 1929; CDFG, 1965; Hallock and 
Fry, 1967; Reynolds et al., 1993; Yoshiyama et al., 1996), and for 
species life history summaries (Miller and Brannon, 1982; Healey, 
1991), and in previous Federal Register documents (56 FR 29542, June 
27, 1991; 63 FR 11482, March 9, 1998).

Previous Federal ESA Actions Related to West Coast Chinook Salmon

    Descriptions of previous Federal ESA actions pertaining to west 
coast chinook salmon are summarized in the proposed rule (63 FR 11482, 
March 9, 1998), and recent final rule (63 FR 14308, March 24, 1999) for 
several chinook salmon ESUs. NMFS initially announced its intention to 
conduct a coastwide review of chinook salmon status in response to a 
petition to list several Puget Sound chinook salmon stocks on September 
12, 1994 (59 FR 46808). Having received on February 1, 1995, a more 
comprehensive petition from the Oregon Natural Resources Council and 
from Dr. Richard Nawa, NMFS reconfirmed its intention to conduct a 
coastwide review (60 FR 30263, June 8, 1995). During that review, NMFS 
requested public comment and assessed the best available scientific and 
commercial data, including technical information from Pacific Salmon 
Biological Technical Committees (PSBTCs) and from other interested 
parties. The PSBTCs consisted primarily of scientists (from Federal, 
state, and local resource agencies, Indian tribes, industries, 
universities, professional societies, and public interest groups) 
possessing technical expertise relevant to chinook salmon and their 
habitats. The NMFS Biological Review Team (BRT), composed of staff from 
NMFS' Northwest, Southwest, and Auke Bay Fisheries Science Centers, 
Northwest and Southwest Regions, as well as staff from the National 
Biological Survey, reviewed and evaluated scientific information 
provided by the PSBTCs and other sources. Early drafts of the BRT 
review were distributed to state and tribal fisheries managers and peer 
reviewers who are experts in the field to ensure that NMFS' evaluation 
was as accurate and complete as possible. The BRT then incorporated all 
comments into the coastwide chinook salmon status review.
    Based on the results of the completed status report on west coast 
chinook salmon (Myers et al., 1998), NMFS identified 15 ESUs of chinook 
salmon from Washington, Oregon, Idaho, and California, including 11 new 
ESUs, and 1 redefined ESU (63 FR 11482, March 9, 1998). After assessing 
information concerning chinook salmon abundance, distribution, 
population trends, and risks and after considering efforts being made 
to protect chinook salmon, NMFS

[[Page 50395]]

determined that several chinook salmon ESUs did not warrant listing 
under the ESA. The chinook salmon ESUs not requiring ESA protection 
included the Upper Klamath and Trinity River ESU, Oregon Coast ESU, 
Washington Coast ESU, Middle Columbia River spring-run ESU, and Upper 
Columbia River summer- and fall-run ESU.
    Also based on this evaluation, and after considering efforts being 
made to protect chinook salmon, NMFS proposed that seven chinook salmon 
ESUs warranted listing as either endangered or threatened species under 
the ESA. The chinook salmon ESUs proposed as endangered species 
included California Central Valley spring-run and Washington's Upper 
Columbia River spring-run chinook salmon. The chinook salmon ESUs 
proposed as threatened species included California Central Valley fall 
and late fall-run, Southern Oregon and California Coastal, Puget Sound, 
Lower Columbia River, and Upper Willamette River spring-run chinook 
salmon. Additionally, NMFS found that fall-run chinook salmon from the 
Deschutes River in Oregon shared a strong genetic and life history 
affinity to currently listed Snake River fall-run chinook. Based on 
this affinity, NMFS proposed to revise the existing listed Snake River 
fall-run ESU to include fall-run chinook salmon in the Deschutes River. 
The resulting revised ESU would be listed as threatened.
    Following these proposed listings, NMFS conducted 21 public 
hearings within the range of the proposed chinook salmon ESUs in 
California, Oregon, Washington, and Idaho. NMFS accepted and reviewed 
public comments solicited during a 112-day public comment period. Also 
during the comment period, NMFS solicited peer and co-manager review of 
NMFS' proposal and received comments and new scientific information 
concerning the status of the chinook salmon ESUs proposed for listing. 
NMFS also received information regarding the relationship of existing 
hatchery stocks to native populations in each ESU. This new information 
was evaluated by NMFS' BRT and published in an updated status review 
for these chinook salmon entitled ``Status Review Update for West Coast 
Chinook Salmon (Oncorhynchus tshawytscha) from Puget Sound, Lower 
Columbia River, Upper Willamette River, and Upper Columbia River 
Spring-run ESUs.'' (NMFS, 1998a).
    Based on these public hearings, comments, and additional technical 
meetings with Indian tribes and the states, NMFS found that listing was 
warranted for four ESUs (Upper Columbia River spring-run, Puget Sound, 
Lower Columbia River, and Upper Willamette River spring-run ESUs) (63 
FR 14308, March 24, 1999). However, substantial scientific 
disagreements precluded the agency from making final determinations for 
California's Central Valley spring-run and Central Valley fall and late 
fall-run, Southern Oregon and California Coastal, and Snake River fall-
run ESUs. Therefore, in accordance with section 4(b)(6)(B)(i) of the 
ESA, NMFS extended the period for making final determinations for these 
ESUs by 6 additional months (63 FR 14329, March 24, 1999).
    During the 6 month period, NMFS received new scientific information 
concerning the boundaries, population structure, and status of the 
deferred ESUs and met with the affected states, Indian Tribes, and 
Federal co-managers. This new information was considered by NMFS' BRT, 
and NMFS has now completed an updated status review that analyzes this 
new information as well as the ESU status of existing hatchery stocks 
(NMFS, 1999a). Based on this updated status review and other 
information, NMFS now issues its final determinations for these four 
proposed ESUs. Copies of NMFS' updated status review reports and 
related documents are available upon request (see ADDRESSES).

Summary of Comments and Information Received in Response to the 
Proposed Rule

    NMFS held 21 public hearings in California, Oregon, Idaho, and 
Washington to solicit comments on this and other salmonid listing 
proposals (63 FR 16955, April 7, 1998; 63 FR 30455, June 4, 1998). 
During the 112-day public comment period, NMFS received nearly 300 
written comments regarding the west coast chinook salmon proposed rule. 
A number of comments addressed issues pertaining to the proposed 
critical habitat designation for west coast chinook salmon. NMFS will 
address these comments in a forthcoming Federal Register document 
announcing the agency's conclusions about critical habitat for all 
listed chinook salmon ESUs.
    NMFS also sought new data and analyses from tribal, state, and 
Federal co-managers and met with them to formally discuss technical 
issues associated with the deferred chinook salmon ESUs. This new 
information and analysis were considered by NMFS' BRT in its re-
evaluation of ESU boundaries and species' status; this information is 
discussed in an updated status review report for these chinook salmon 
ESUs (NMFS, 1999a).
    In addition to soliciting and reviewing public comments, NMFS 
sought peer review of its listing proposals. On July 1, 1994, NMFS, 
jointly with the U.S. Fish and Wildlife Service (FWS), published a 
series of policies regarding listings under the ESA, including a policy 
for peer review of scientific data (59 FR 34270). In accordance with 
this policy, NMFS solicited 13 individuals to take part in a peer 
review of its west coast chinook salmon proposed rule. All individuals 
solicited are recognized experts in the field of chinook salmon biology 
and represent a broad range of interests, including Federal, state, and 
tribal resource managers and academia. Four individuals took part in 
the peer review of this action; new information and comments provided 
by the public and comments from peer reviewers were considered by NMFS' 
BRT and are summarized in the updated status review documents (NMFS, 
1998a; NMFS, 1999a). Copies of these documents are available upon 
request (see ADDRESSES).
    A summary of comments received in response to the proposed rule 
follows.

Issue 1: Sufficiency and Accuracy of Scientific Information and 
Analysis

     Comment 1: Some commenters questioned the sufficiency and accuracy 
of data NMFS employed in the listing proposal. In contrast, peer 
reviewers commented that the agency's status review was both credible 
and comprehensive, even though they may not have concurred with all of 
NMFS' conclusions.
     Response: Section 4(b)(1)(A) of the ESA requires that NMFS make 
its listing determinations solely on the basis of the best available 
scientific and commercial data, after reviewing the status of the 
species and taking into account any efforts being made to protect such 
species. NMFS believes that information contained in the agency's 
status review (Myers et al., 1998), together with more recent 
information obtained in response to the proposed rule (NMFS, 1998a; 
NMFS, 1999a), represents the best scientific and commercial information 
presently available for the chinook salmon ESUs addressed in this final 
rule. NMFS has made every effort to conduct an exhaustive review of all 
available information and has solicited information and opinion from 
all interested parties, including peer reviewers as described 
previously. If new data become available to change these conclusions, 
NMFS will act accordingly.

[[Page 50396]]

    Comment 2: Several of the comments received suggested that the ESA 
does not provide for the creation of ESUs and that ESUs do not 
correspond to species, subspecies, or distinct population segments 
(DPSs) that are specifically identified in the ESA. Further, NMFS' use 
of genetic information (allozyme- or DNA-derived) to determine ESU 
boundaries was criticized by several commenters. It was argued that 
allozyme-based electrophoretic data cannot be used to imply either 
evolutionary significance or local adaptation. Other commenters 
indicated that NMFS used genetic distances inconsistently in 
determining the creation of ESUs. Several commenters argued that there 
was insufficient scientific information presented to justify the 
establishment of the chinook salmon ESUs discussed. Information was 
lacking concerning a number of ``key'' criteria for defining ESUs, such 
as phenotypic differences, evolutionary significance, or ecological 
significance of various chinook populations. Commenters contended that 
NMFS did not find any life history, habitat, or phenotypic 
characteristics that were unique to any of the ESUs discussed. 
Disagreement within the BRT regarding ESU delineations was also given 
as a reason for challenging the proposed listing decision.
     Response: General issues relating to ESUs, DPSs, and the ESA have 
been discussed extensively in past Federal Register documents as 
described in this paragraph. Regarding application of its ESU policy, 
NMFS relies on its policy describing how it will apply the ESA 
definition of ``species'' to anadromous salmonid species published in 
1991 (56 FR 58612, November 20, 1991). More recently, NMFS and FWS 
published a joint policy, that is consistent with NMFS' policy, 
regarding the definition of ``distinct population segments'' (DPSs)(61 
FR 4722, February 7, 1996). The earlier policy is more detailed and 
applies specifically to Pacific salmonids and, therefore, was used for 
this determination. This policy indicates that one or more naturally 
reproducing salmonid populations will be considered to be distinct and, 
hence, a species under the ESA, if they represent an ESU of the 
biological species. To be considered an ESU, a population must satisfy 
two criteria: (1) It must be reproductively isolated from other 
population units of the same species, and (2) it must represent an 
important component in the evolutionary legacy of the biological 
species. The first criterion, reproductive isolation, needs not be 
absolute but must have been strong enough to permit evolutionarily 
important differences to occur in different population units. The 
second criterion is met if the population contributes substantially to 
the ecological or genetic diversity of the species as a whole. Guidance 
on applying this policy is contained in a NOAA Technical Memorandum 
entitled ``Definition of 'Species' Under the Endangered Species Act: 
Application to Pacific Salmon'' (Waples, 1991) and in a more recent 
scientific paper by Waples (1995).
    The National Research Council (NRC) has recently addressed the 
issue of defining species under the ESA (NRC, 1995). Its report found 
that protecting DPSs is soundly based on scientific evidence, and 
recommends applying an ``Evolutionary Unit'' (EU) approach in 
describing these segments. The NRC report describes the high degree of 
similarity between the EU and ESU approaches (differences being largely 
a matter of application between salmon and other vertebrates), and 
concludes that either approach would lead to similar DPS descriptions 
most of the time.
    ESUs were identified using the best available scientific and 
commercial information. As discussed in the status review, genetic data 
were used primarily to evaluate the criterion regarding reproductive 
isolation, not evolutionary significance. In some cases, there was a 
considerable degree of confidence in the ESU determinations; in other 
cases, more uncertainty was associated with this process. Similarly, 
the risk analysis necessarily involved a mixture of quantitative and 
qualitative information and scientific judgement. NMFS' process for 
conducting its risk assessment has evolved over time as the amount and 
complexity of information has changed, and NMFS continues to seek and 
incorporate comments and suggestions to improve this process. NMFS 
believes that there is evidence to support the identification of DPSs 
for chinook salmon. The chinook salmon status reviews describe a 
variety of characteristics that support the ESU delineations for this 
species, including ecological and life history parameters. NMFS also 
assessed available genetic data for the proposed ESUs and concludes 
that sufficient genetic differences existed between these and adjacent 
ESUs to support separate delineations. As described later in this 
notice, new information has resulted in significant changes in the 
configurations of some proposed ESUs.

Issue 2: Status Assessments for Chinook Salmon ESUs

    Comment 3: Some comments suggested that risk assessments were made 
in an arbitrary manner and that NMFS did not rely on the best available 
science. Several commenters questioned NMFS' methodology for 
determining whether a given chinook salmon ESU warranted listing. In 
some cases, such commenters also expressed opinions regarding whether 
listing was warranted for a particular chinook salmon ESU.
    Response: Throughout the status review of west coast chinook 
salmon, NMFS has solicited and evaluated the best available scientific 
and commercial data for the species. The agency believes that this 
review, coupled with considerable input from the public, comanagers, 
peer reviewers, and other species experts, clearly demonstrates that 
the listing determinations are not arbitrary but instead are based on 
an open and rigorous scientific assessment. Section 3 of the ESA 
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.'' NMFS has 
identified a number of factors that should be considered in evaluating 
the level of risk faced by an ESU, including: (1) absolute numbers of 
fish and their spatial and temporal distribution; (2) current abundance 
in relation to historical abundance and current carrying capacity of 
the habitat; (3) trends in abundance; (4) natural and human-influenced 
factors that cause variability in survival and abundance; (5) possible 
threats to genetic integrity (e.g., from strays or outplants from 
hatchery programs); and (6) recent events (e.g., a drought or changes 
in harvest management) that have predictable short-term consequences 
for abundance of the ESU. A more detailed discussion of the status of 
individual ESUs is provided later in this document under Issues 5 
through 8.

Issue 3: Factors Contributing to the Decline of West Coast Chinook 
Salmon

     Comment 4: Some comments identified factors for decline that were 
either not identified in the status review or which they believed were 
not given sufficient weight in the risk analysis. Other commenters 
contended that recent declines in chinook salmon abundance were related 
to natural factors such as predation and changes in

[[Page 50397]]

ocean productivity. Furthermore, these commenters contend that NMFS did 
not show how the present declines were significantly different from 
natural variability in abundance, nor that abundances were below the 
current carrying capacity of the marine environment and freshwater 
habitat.
    Response: The status review did not attempt to exhaustively 
identify factors for decline, except insofar as they contributed 
directly to the risk analysis. Nevertheless, NMFS agrees that a 
multitude of factors, past and present, have contributed to the decline 
of west coast chinook salmon. Many of the identified factors were 
specifically cited as risk agents in NMFS's status review (Myers et 
al., 1998) and listing proposal (63 FR 11482, March 9, 1998). NMFS 
recognizes that natural environmental fluctuations have likely played a 
role in the species' recent declines. However, NMFS believes other 
human-induced impacts (e.g., harvest in certain fisheries, artificial 
propagation, and widespread habitat modification) have played an 
equally significant role in the decline of chinook salmon.
    NMFS' status review briefly addressed the impact of adverse marine 
conditions and climate change, but concluded that there is considerable 
uncertainty regarding the role of these factors in chinook salmon 
abundance. At this time, we do not know whether these climate 
conditions represent a long-term shift in conditions that will continue 
into the future or short-term environmental fluctuations that can be 
expected to reverse soon. A recent review by Hare et al. (1999) 
suggests that these conditions could be part of an alternating 20- to 
30-year long regime pattern. These authors concluded that, while at-
risk salmon stocks may benefit from a reversal in the current climate/
ocean regime, fisheries management should continue to focus on reducing 
impacts from harvest and artificial propagation and improving 
freshwater and estuarine habitats.
    NMFS believes there is ample evidence to suggest that the 
elimination and degradation of freshwater habitats have contributed to 
the decline of these chinook salmon ESUs. The past destruction, 
modification, and curtailment of freshwater habitat was reviewed in a 
recent NMFS coastwide assessment for steelhead (NMFS, 1996), and, more 
recently, for chinook salmon (NMFS, 1998b). Many of the identified 
risks and conclusions apply specifically to these chinook salmon. 
Examples of habitat alterations affecting chinook salmon include: water 
withdrawal, conveyance, storage, and flood control (resulting in 
insufficient flows, stranding, juvenile entrainment, and increased 
stream temperatures); and logging and agriculture (resulting in loss of 
large woody debris, sedimentation, loss of riparian vegetation, and 
habitat simplification)(NMFS, 1996; Spence et al., 1996; Myers et al., 
1998; NMFS, 1998b). These human-induced impacts in freshwater 
ecosystems have likely reduced the species' resiliency to natural 
factors for decline such as drought and poor ocean conditions. A 
critical next step in restoring listed chinook salmon will be 
identifying and ameliorating specific factors for decline at both the 
ESU and population level.
    With respect to predation issues raised by some commenters, NMFS 
has recently published reports describing the impacts of California sea 
lions and Pacific harbor seals upon salmonids and on the coastal 
ecosystems of Washington, Oregon, and California (NMFS, 1997 and 
1999b). These reports conclude that in certain cases where pinniped 
populations co-occur with depressed salmonid populations, salmon 
populations may experience severe impacts due to predation. An example 
of such a situation is at the Ballard Locks, Washington, where sea 
lions are known to consume significant numbers of adult winter 
steelhead. These reports further conclude that data regarding pinniped 
predation are quite limited and that substantial additional research is 
needed to fully address this issue. Existing information on the 
seriously depressed status of many salmonid stocks is sufficient to 
warrant actions to remove pinnipeds in areas of co-occurrence where 
pinnipeds prey on depressed salmonid populations (NMFS, 1997 and 
1999b).

Issue 4: Consideration of Existing Conservation Measures

    Comment 5: Several comments expressed concerns about NMFS' reliance 
and characterization of the efficacy of the Northwest Forest Plan 
(NFP), citing significant differences in management practices between 
various Federal land management agencies. Numerous commenters noted 
that an array of state and Federal conservation measures were underway 
for this and other species (particularly in California) and asked that 
NMFS give them more consideration in its listing determination.
    Response: In the listing proposal, NMFS noted that the NFP requires 
specific management actions on Federal lands, including actions in key 
watersheds in southern Oregon and northern California that comply with 
special standards and guidelines designed to preserve their refugia 
functions for at-risk salmonids (i.e., watershed analysis must be 
completed prior to timber harvests and other management actions, road 
miles should be reduced, no new roads can be built in roadless areas, 
and restoration activities are prioritized). In addition, the most 
significant element of the NFP for anadromous fish is its Aquatic 
Conservation Strategy (ACS), a regional-scale aquatic ecosystem 
conservation strategy that includes: (1) Special land allocations (such 
as key watersheds, riparian reserves, and late-successional reserves) 
to provide aquatic habitat refugia; (2) special requirements for 
project planning and design in the form of standards and guidelines; 
and (3) new watershed analysis, watershed restoration, and monitoring 
processes. These ACS components collectively ensure that Federal land 
management actions achieve a set of nine ACS objectives that strive to 
maintain and restore ecosystem health at watershed and landscape scales 
to protect habitat for fish and other riparian-dependent species and 
resources and to restore currently degraded habitats. NMFS will 
continue to support the NFP strategy and address Federal land 
management issues via ESA section 7 consultations in concert with this 
strategy.
    Additional consideration was given to various conservation efforts 
in California and elsewhere within the range of proposed chinook ESUs 
that have been implemented or are expected to be initiated. See 
``Efforts Being Made to Protect West Coast Chinook Salmon'' later in 
this document.
     Comment 6: Several comments expressed concern over the need to 
list these chinook salmon ESUs and the effects of these listings on 
Indian resources, programs, land management, and associated Trust 
responsibilities. Particular concern was expressed about the effects of 
listing Deschutes River chinook salmon on tribal fishing for this and 
other species.
     Response: NMFS acknowledges that ESA listings may impact Indian 
resources, programs, land management and associated Trust 
responsibilities. NMFS will continue to work closely with affected 
Indian tribes through government to government consultation as harvest 
and other management issues arise and will continue to support the 
development of sound, strong tribal and state conservation efforts to 
restore listed chinook salmon and other west coast salmon populations.

[[Page 50398]]

Issue 5: ESU Delineation and Status of Central Valley Spring-run 
Chinook Salmon

     Comment 7: Some commenters questioned this ESU's configuration and 
felt that NMFS was inconsistent in separating spring and fall runs in 
the Central Valley. A peer reviewer stated that the genetic information 
presented was not sufficient to justify the creation of a separate 
spring-run chinook salmon ESU. The majority of commenters agreed that 
this ESU is currently at risk, but there were disparate views as to 
whether the risks warranted an endangered listing under the ESA. For 
example, one commenter believed that Central Valley spring-run 
populations have remained stable (although at low levels of abundance) 
and that current fluctuations are consistent with natural terrestrial 
and ocean productivity cycles. This commenter suggested that 
information on cohort replacement rates, the level of interaction 
between fall and spring runs, and the impact of various factors 
relating to the survival of emigrating juveniles and returning adults 
need to be further investigated before a listing determination can be 
made. Another commenter felt that listing was warranted, but that a 
threatened status was more appropriate, given the relatively stable 
population sizes for most spring-run fish over the last 20 years and 
the increasing abundance found in Butte Creek.
    Recent large returns to Butte Creek prompted a number of comments 
specific to spring-run chinook salmon in this Sacramento River 
tributary. One commenter suggested that the recent increases were due 
to high flows through the Sutter Bypass during the recent wet years. 
Spring-run adults returning to the upper Sacramento River would be 
attracted to the Bypass and routed up into Butte Creek. Therefore, the 
commenters contend that spring-run fish currently spawning in Butte 
Creek represent an amalgamation of fish from the upper Sacramento River 
and its tributaries. Another commenter believed that NMFS incorrectly 
suggested that the Butte Creek populations were the product of hatchery 
releases. Similarly, two commenters presented genetic information that 
indicates that the spring-run chinook salmon population in Butte Creek 
is not the result of strays from the Feather River Hatchery as was 
speculated by NMFS. They also noted that the 1998 abundance estimate 
for the Butte Creek spring run is approximately 19,000 spawners and 
that, if these fish are included in the total abundance estimate for 
the Central Valley spring-run chinook salmon ESU, there is a several 
fold increase in abundance.
    Several commenters cited specific factors for decline that impact 
the fall run: predation by non-native species, dam and reservoir 
operations, catastrophic stranding, incorporation of naturally produced 
salmon into hatchery broodstocks, and competition and predation by 
hatchery chinook salmon and steelhead on naturally produced chinook 
salmon. Some contended that a variety of existing conservation efforts 
aimed at addressing factors for decline (e.g., the Bay-Delta Accord, 
CALFED, and harvest and hatchery reforms) were sufficient to prevent 
this ESU from becoming extinct. In addition, some commenters believed 
that significant benefits would accrue to spring-run chinook salmon as 
a result of the State of California's ESA listing for the species, as 
well as actions by NMFS and the Pacific Fishery Management Council 
(PFMC) to protect winter-run chinook salmon. Others disagreed with 
these contentions and asserted that efforts had clearly failed to 
adequately protect chinook salmon in the Central Valley.
    Since the initial status review, NMFS has received new data and 
information which have helped resolve the scientific uncertainties 
associated with the proposed listing for this ESU (NMFS, 1999a), and 
are summarized as follows.
    Response - ESU Delineation:  NMFS recently analyzed new genetic 
data collected for California chinook salmon. In 1998 and 1999, NMFS, 
CDFG, FWS, and the U.S. Forest Service (USFS) collected samples of 
spawned adult chinook salmon from 13 rivers and hatcheries in the 
Central Valley and Klamath River Basin. The new samples were analyzed 
along with allozyme data for California and southern Oregon chinook 
salmon that were previously used in the NMFS coastwide status review 
(Myers et al., 1998). The population structure revealed by the new 
analysis of allozyme data was consistent with the delineations of major 
genetic groups described in previous genetic studies of California and 
southern Oregon chinook salmon (Utter et al., 1989; Bartley et al., 
1992; Myers et al., 1998). The most genetically divergent group of 
samples was from the Central Valley. Within the Central Valley, the 
most genetically divergent sample was from the Coleman National Fish 
Hatchery (CNFH) winter-run population. Spring-run chinook salmon 
sampled from Deer and Butte Creeks were distinct from the winter-run 
fish sample and also from samples of fall- and late fall-run chinook 
salmon from the Central Valley. The Deer Creek and Butte Creek samples 
were genetically distinct from each other. The sample of spring-run 
chinook salmon from the Feather River Hatchery was genetically 
intermediate between spring- and fall-run samples and most similar to 
the sample of Feather River Hatchery fall-run chinook salmon. Samples 
of fall-run and late fall-run populations formed a diverse subcluster 
that included samples from both Sacramento and San Joaquin populations.
    Banks et al. (1999) studied 5 to 11 microsatellite loci in 41 
samples to assess genetic diversity among winter-, spring-, fall-, and 
late fall-run chinook salmon in California's Central Valley. Five 
homogeneous subpopulations were found: (1) wild and hatchery broodstock 
winter run, (2) wild spring run from Deer and Mill Creeks, (3) wild 
spring run from Butte Creek, (4) wild and hatchery fall run, and (5) 
wild and hatchery late-fall run. Winter-run samples were the most 
genetically divergent. Butte Creek spring-run chinook salmon were the 
next most divergent, followed by spring-run samples from Deer and Mill 
Creeks. Fall and late-fall runs were separated by a very small genetic 
distance. It is noteworthy that the sample of Butte Creek spring-run 
fish did not show evidence of introgression from Feather River hatchery 
fall-run stock. However, fewer alleles and lower heterozygosities in 
both winter-run and Butte Creek spring-run samples indicate that these 
populations may have experienced past reductions in population size.
    Banks et al. (1999) used five microsatellite loci to investigate 
genetic relationships among 11 fall- and spring-run chinook salmon 
populations in the Klamath River and to compare these populations to 
chinook salmon from the Central Valley. Despite extensive sampling and 
analysis, no homogeneous population pools were found. Overall, Klamath 
River Basin populations were differentiated from Central Valley 
populations, and winter-run chinook salmon were genetically distinct 
and did not cluster with other populations.
    Nielsen et al. (1994) and Nielsen (1995) examined mitochondrial DNA 
(mtDNA) variation in 14 samples of chinook salmon from Central Valley 
rivers and hatcheries and one sample from Guadalupe River, a southern 
tributary of San Francisco Bay. Nielsen et al. (1999) concluded that 
their data support their earlier conclusions (Nielsen et al., 1994) 
that fall, late fall, spring, and winter runs of Central Valley chinook 
salmon show consistently significant differences for the mtDNA locus, 
indicating infrequent

[[Page 50399]]

straying and limited gene flow among the temporal spawning runs.
    Kim et al. (1999) examined genetic variation in winter-, spring-, 
fall-, and late fall-run adult chinook salmon taken from the upper 
Sacramento River between 1991 and 1995. An analysis of population 
structure indicated that winter-run chinook salmon were the most 
genetically distinct, while fall- and late fall-run samples were 
closely related to each other. Spring-run samples were genetically 
intermediate between the winter and fall and late-fall runs. A sample 
of Butte Creek spring-run chinook salmon was genetically similar to 
Sacramento River mainstem spring-run samples.
    Ecological and life history information for this ESU was also re-
evaluated, particularly historical and current information concerning 
Butte Creek populations. Yoshiyama et al. (1996) reported that spring, 
fall, and probably late-fall runs of chinook salmon historically 
utilized Butte Creek. Gold mining, logging activities, and irrigation 
withdrawals have all had a considerable impact on habitat quality 
(Clark, 1929; Hanson et al., 1940). In 1917, two diversion dams were 
constructed by Pacific Gas and Electric. The Centerville Diversion Dam 
eliminated access to the upper watershed (Mills and Ward, 1996). Clark 
(1929) reported that the fall-run fish had declined dramatically and 
that summer flows in the lower river had been reduced by irrigation 
withdrawals. There was no mention of the status of a spring run. A 
survey by Hanson et al. (1940) reported that much of the upper 
watershed had been logged, and that mining operations continued to 
impact the river flow, and that ``none of the flow of Butte Creek 
except perhaps a little seepage reaches the Sacramento River during 
this summer.
    Yoshiyama et al. (1996) reported that Butte Creek spring-run 
chinook salmon enter the creek in February through April (compared with 
May or June for Feather River spring-run chinook salmon). USFS 
monitoring (which began in 1930) indicated that flows in Butte Creek 
peak during the February to June period (peaks vary from 1,000 to over 
10,000 cubic feet per second (cfs), with a maximum of 25,000 cfs in 
1997), but are below 100 cfs during much of the remainder of the year 
(U.S. Geological Survey, 1999). Although Butte Creek originates in the 
Sierra Nevada Mountains (2000 m), spring-run adults spawn at a 
relatively low altitude (300 m), in part because of the absence of 
passage at the Centerville Dam. Yoshiyama et al. (1996) were uncertain 
if spring-run chinook salmon historically migrated above a 7.6 m 
waterfall located near the Centerville Dam. Spring-run chinook salmon 
spawn in September. Juveniles emigrate primarily as fry (December to 
March) and may rear in the Sacramento River Delta for extended periods 
(Baracco, 1996). Fall-run chinook salmon are reported to spawn further 
downstream, below the Parrot-Phelam Dam (Yoshiyama et al., 1996).
    Based on a re-assessment of information relevant to the 
configuration of this ESU, NMFS reiterates its previous decisions that 
the spring-run populations in the Central Valley constitute a distinct 
ESU and that the extirpated spring-run populations in the southern 
portion of this ESU may have constituted their own ESU (based on 
ecological and biogeographical data). NMFS considered several issues 
related to the configuration of the Central Valley spring-run chinook 
salmon ESU. The genetic data indicate that spring-run fish spawning in 
Butte Creek are not the progeny of Feather River Hatchery spring-run 
releases, but represent a naturally spawning population distinct from 
both Feather River fish and spring-run chinook salmon in Deer and Mill 
Creeks. Further sampling and analysis of mainstem Sacramento River 
spring-run fish (the only remaining known population that is not 
presently genetically described) are potentially important to 
understanding the relationship among Central Valley spring-run chinook 
salmon populations. Furthermore, NMFS is concerned that hatchery 
operations at the Feather River Hatchery may have resulted in the 
hybridization of spring- and fall-run fish. However, NMFS concludes 
that the Feather River spring run may retain ``spring-run'' life 
history characteristics and concludes it is still part of this ESU.
    Response - ESU Status: NMFS also examined updated risk information 
for this ESU. Abundance of spring-run chinook salmon has increased in 
several streams since 1996, the most recent year considered in the 
previous risk evaluation by NMFS. The Feather River population 
abundance has been fairly constant at 3,000 to 7,000 fish per year 
spawning naturally. The 5-year geometric mean abundance of spring-run 
chinook salmon in the Feather River increased from 4,260 fish through 
1996 to 5,013 through 1998. CDFG and other fisheries biologists 
familiar with Central Valley runs believe that the so-called spring-run 
fish in the Feather River are not likely to be representative of the 
historically wild spring-run fish because of the introgression between 
wild spring-run populations and hatchery spring- and fall-run chinook 
salmon (CDFG, 1998a). Three streams, Deer, Mill, and Butte Creeks, 
which contain naturally spawning populations of spring-run chinook 
salmon in this ESU, have also shown increases in mean abundance. The 5-
year geometric mean abundance in Deer Creek increased from 564 through 
1997 to 805 through 1998, and, in Mill Creek, the mean abundance 
increased from 252 through 1996 to 346 through 1998.
    The most impressive change in status since the previous NMFS risk 
evaluation for this ESU was the continuing strong return of spring 
chinook to Butte Creek. In 1998, 20,259 spring-run chinook salmon 
returned to the creek, 2.7 times greater than the 1995 parental cohort 
of 7,500 fish resulting in a 5-year geometric mean abundance of 2,302 
fish. The dissimilarity in genetic composition (Banks et al., 1999; Kim 
et al., 1999) and lack of concordance of trends in abundance (CDFG, 
1998b) of Butte Creek and Feather River spring chinook suggest that the 
recent large escapements of spring chinook to Butte Creek are not the 
result of fish straying from the Feather River.
    The spawning population of spring-run chinook salmon in the 
mainstem Sacramento River above Red Bluff Diversion Dam has continued 
to decline in abundance since the previous risk evaluation. The 5-year 
geometric mean abundance through 1998 is estimated to be around 300 
fish, down from a mean of 435 through 1996. CDFG discussed sporadic 
reports of spring-run chinook salmon in Antelope, Cottonwood, and Big 
Chico Creeks, but the infrequent occurrence of these fish indicates 
that they do not represent self-sustaining populations (CDFG, 1998a).
    After reviewing additional scientific information regarding the 
status of this ESU, NMFS concludes that the Central Valley spring-run 
chinook salmon ESU is not currently at risk of extinction but is likely 
to become endangered in the foreseeable future. NMFS is encouraged by 
the increase in abundance in Deer and Butte Creeks. Next to Butte 
Creek, the largest population of spring-run chinook salmon in the ESU 
is in the Feather River, and NMFS has concerns regarding the extensive 
introgression with fall-run fish in the hatchery population. The 
prospects for using the Feather River stock for conservation purposes 
in this ESU are unclear. The complete extirpation of the spring run 
from the San Joaquin River and the loss of historical spawning habitat 
above the dams in the Sacramento River Basin have resulted in a greatly 
reduced distribution of spring-run fish in the Central Valley. The 
primary reasons for

[[Page 50400]]

the change in the risk evaluation from ``presently in danger of 
extinction'' previously proposed by NMFS were the increase in abundance 
of Butte Creek fish in recent years and the genetic evidence that the 
spring chinook salmon in Butte Creek are not of hatchery origin.
    NMFS also notes a number of recent events that may have improved 
conditions for the Central Valley spring-run chinook salmon ESU, 
including reduced ocean and in-river harvest levels, the Federal 
listing of winter-run chinook salmon and Central Valley steelhead, the 
state listing of spring-run chinook salmon, and the habitat 
improvements occurring under the CALFED program. NMFS has considered 
the impacts of various conservation efforts affecting this ESU under 
the section ``Efforts Being Made to Protect West Coast Chinook Salmon'' 
of this document.

Issue 6: ESU Delineation and Status of Central Valley Fall and Late 
Fall-run Chinook Salmon

     Comment 8: The vast majority of public comments on these four 
chinook salmon listing proposals involved NMFS' assessment of the 
Central Valley fall and late fall-run ESU. While some commenters agreed 
with NMFS' listing proposal, most did not agree that this ESU warranted 
listing as a threatened species. Others believed that NMFS' risk 
assessment may have been significantly influenced by six recent drought 
years. One commenter asserted that Central Valley chinook salmon 
populations have historically undergone extreme fluctuations in 
abundance due to environmental fluctuations and that NMFS did not 
adequately take these fluctuations (and the ability of the natural 
populations to recover) into account when assessing the risk of 
extinction. Several commenters also highlighted the high overall 
escapement level for this ESU and felt that there was not sufficient 
evidence to justify a listing. One commenter asserted that the small 
river systems that flow into San Francisco Bay did not historically 
support chinook salmon. Another did not agree that the San Joaquin 
River Basin constituted a significant portion of the ESU and felt that 
the depressed nature of San Joaquin fall-run stocks was not an adequate 
basis for a listing. Others believed that the ESU should be split into 
two ESUs. Several commenters cited specific factors for decline that 
impact the fall run: predation by non-native species, dam and reservoir 
operations, catastrophic stranding, incorporation of naturally produced 
salmon into hatchery broodstocks, and competition and predation by 
hatchery chinook salmon and steelhead on naturally produced chinook 
salmon.
    Issues related to hatchery-produced chinook salmon in this ESU were 
particularly common. Many commenters felt that NMFS did not 
conclusively show that hatchery-produced fish were a risk to naturally-
produced fish. Some felt that NMFS needed to provide a method for 
distinguishing hatchery and natural production, and justify the 
exclusion of hatchery fish from the risk determination (given that the 
majority of the broodstock originated from within the ESU). One 
commenter argued that, in many instances, hatchery and naturally 
spawning fish have co-mingled for generations, hence the fish are 
genetically indistinguishable and effectively represent one population. 
In many cases the persistence of naturally spawning fish has been 
dependent on the continued operation of the hatchery program. Under 
these conditions, the commenter contended, hatchery abundances should 
be included in the assessment of the risk of extinction for an ESU. 
Another suggested that, if hatchery impacts were great, NMFS should 
conclude that the Central Valley fall and late fall-run chinook salmon 
ESU was similar to the Lower Columbia River coho salmon ESU and exclude 
the Central Valley chinook salmon ESU from consideration for listing. 
One commenter argued that NMFS needed to identify which hatchery 
populations are in the ESU and which are not before making any 
conclusions on the status of this ESU. Another included data that 
indicated a rising proportion of coded-wire tag (CWT) fish being 
recovered in tributaries to the San Joaquin River; these CWT estimates 
did not take into account the contribution of unmarked hatchery-reared 
fish. In determining the risks facing this ESU, one commenter suggested 
that NMFS use the San Joaquin Basin populations as a benchmark. Still 
another called for more genetic sampling to determine whether the San 
Joaquin River Basin should be established as a separate ESU.
    Finally, numerous commenters highlighted the importance of taking 
into account habitat restoration programs that are underway throughout 
the Central Valley and asserted that recent run sizes for the San 
Joaquin Basin have been increasing partly because of improvements in 
habitat conditions (e.g., gravel, temperature, and flows). Some 
believed that demonstrable habitat improvements had and would result 
from the CALFED program and that these results were predictable given 
the definitive nature of the program and the guaranteed nature of the 
funding. However, other commenters were skeptical that these efforts 
would be sufficient to reduce the risks facing this ESU. Key elements 
of the programs cited by commenters involved modified flow regimes, 
improved passage facilities, improved hatchery and harvest practices, 
and improved monitoring. In addition, some commenters believed that 
significant benefits would accrue to fall- and late fall-run chinook 
salmon as a result of the State of California's ESA listing for the 
spring run, as well as of actions by NMFS and the PFMC to protect 
winter-run chinook salmon.
    Since the initial status review, NMFS has received new data and 
information which have helped resolve the scientific uncertainties 
associated with the proposed listing for this ESU (NMFS, 1999a), and 
are summarized as follows.
    Response - ESU Delineation:  NMFS recently analyzed new genetic 
data collected for California chinook salmon. In 1998 and 1999, NMFS, 
CDFG, FWS, and USFS collected samples of spawned adult chinook salmon 
from 13 rivers and hatcheries in the Central Valley and Klamath River 
Basin. The new samples were analyzed along with allozyme data for 
California and southern Oregon chinook salmon that were previously used 
in the NMFS coastwide status review (Myers et al., 1998). The 
population structure revealed by the new analysis of allozyme data was 
consistent with the delineations of major genetic groups described in 
previous genetic studies of California and southern Oregon chinook 
salmon (Utter et al., 1989; Bartley et al., 1992; Myers et al., 1998). 
The most genetically divergent group of samples was from the Central 
Valley. Within the Central Valley, the most genetically divergent 
sample was from the CNFH winter-run population. Spring-run chinook 
salmon sampled from Deer and Butte Creeks were distinct from the 
winter-run fish sample and also from samples of fall- and late fall-run 
chinook salmon from the Central Valley. The Deer Creek and Butte Creek 
samples were genetically distinct from each other. The sample of 
spring-run chinook salmon from the Feather River Hatchery was 
genetically intermediate between spring- and fall-run samples and most 
similar to the sample of Feather River Hatchery fall-run chinook 
salmon. Samples of fall- and late fall-run populations formed a diverse 
subcluster that included samples from both Sacramento and San Joaquin 
populations.
    Microsatellite DNA variation has also been used in recent studies 
to examine

[[Page 50401]]

genetic relationships among populations of chinook salmon in 
California. Nielsen et al. (1994) found significant heterogeneity among 
fall-run hatchery stocks and also among naturally spawning fall-run 
populations but there was no significant geographic structure at the 
basin level for wild fall-run chinook salmon. However, comparisons of 
wild fall-run carcasses and hatchery stocks suggest that naturally 
spawning fall-run fish in several basins retain some degree of genetic 
distinctiveness not found in hatcheries. Allele-frequencies for carcass 
collections made on the American, Tuolumne, Merced, and Feather Rivers 
were significantly different from samples of hatchery populations found 
within the same drainage. The Merced and Mokelumne Rivers were found to 
be most similar to hatchery populations on their respective rivers. The 
heterogeneity comparisons for some wild fall-run carcass collections 
may have been biased by small sample sizes. Fall-run hatchery 
populations were differentiated from populations of other run times but 
samples of wild fall-run populations were not compared to populations 
of winter, spring, or late-fall runs. Naturally spawning late fall-run 
fish were differentiated in allozyme analysis from all other 
populations including CNFH late fall-run salmon. The naturally spawning 
late fall-run population was most genetically similar to either winter-
run fish or the CNFH late fall-run population, depending on the genetic 
distance measure used. Nei's measure of genetic distance indicated that 
late fall-run populations were most similar to hatchery fall-run 
populations.
    Banks et al. (1999) used five microsatellite loci to investigate 
genetic relationships among 11 fall- and spring-run chinook salmon 
populations in the Klamath River and to compare these populations to 
chinook salmon from the Central Valley. Despite extensive sampling and 
analysis, no homogeneous population pools were found. Klamath River 
Basin populations were differentiated from Central Valley populations, 
and winter-run chinook salmon were genetically distinct and did not 
cluster with other populations.
    Nielsen et al. (1994) and Nielsen (1995) examined mtDNA variation 
in 14 samples of chinook salmon from Central Valley rivers and 
hatcheries and 1 sample from the Guadalupe River, a southern tributary 
of San Francisco Bay. Nielsen et al. (1999) concluded that their data 
support their earlier conclusions (Nielsen et al., 1994) that fall, 
late-fall, spring, and winter runs of Central Valley chinook salmon 
show consistently significant differences for the mtDNA locus, 
indicating infrequent straying and limited gene flow among the temporal 
spawning runs. Nielsen et al. (1999) concluded that additional sampling 
is needed to test for significant genetic differences among natural 
spawning and hatchery populations of fall-run chinook salmon. A sample 
of chinook salmon from Guadalupe River showed significant haplotype 
frequency differences from samples of the four spawning runs in the 
Central Valley, primarily due to a haplotype (CH9) found in 2 fish in 
the Guadalupe River. This haplotype has not been observed in fish from 
the Central Valley but has been found in samples of Russian River 
chinook salmon. The remaining 27 samples from the Guadalupe River could 
not be differentiated from the chinook salmon in the Merced and Feather 
River hatcheries through the use of mtDNA.
    Kim et al. (1999) examined genetic variation in winter-, spring-, 
fall-, and late fall-run adult chinook salmon taken from the upper 
Sacramento River between 1991 and 1995. An analysis of population 
structure indicated that winter-run chinook salmon were the most 
genetically distinct, while fall- and late fall-run samples were 
closely related to each other. Spring-run samples were genetically 
intermediate between the winter and fall/late- fall runs. A sample of 
Butte Creek spring-run chinook salmon was genetically similar to 
Sacramento River mainstem spring-run samples.
    NMFS also re-examined ecological and life history information for 
this ESU. The San Joaquin River Basin includes the Mokelumne, 
Consumnes, Calaveras, Stanislaus, Tuolumne, and Merced Rivers. 
Historically, salmon also utilized the Kings River during years of high 
precipitation (Yoshiyama et al., 1996). Ecologically, the Consumnes and 
Calaveras are distinct from the other San Joaquin River Basin 
tributaries in that their flows are influenced by rainfall rather than 
snow melt. Historically, fall-run chinook salmon were present in all of 
the basins, and there is some evidence that a late-fall run may have 
existed in the Mokelumne River (Yoshiyama et al., 1993). Furthermore, 
Reynolds et al. (1993) described a ``winter-run'' population that 
spawned in the Calaveras River from 1972 to 1984; however, this 
population appears to have been extirpated, and its relationship with 
other temporal runs in the Central Valley was never established. 
Impassible dams and water withdrawals have severely reduced the 
quantity and quality of salmon habitat. Presently, only 45 percent of 
the total historical chinook salmon habitat is accessible (not 
including habitat in the Kings River Basin). Much of the habitat lost 
would have been utilized by spring-run chinook salmon; however, water 
conditions in the remaining habitat have degraded. Ecologically, rivers 
in the San Joaquin (including the Mokelumne River) and American River 
Basins experience peak flows in May, fed primarily by snow melt from 
the Sierra Nevada Range. Geologically, the Sierra Nevada Range is very 
different from the volcanic structure of the Cascades that constitute 
the headwaters for most rivers in the northern portion of the Central 
Valley.
    There is little historical information concerning the life history 
characteristics of fall-run chinook salmon in the San Joaquin River 
Basin. Fall-run chinook salmon in the San Joaquin River Basin enter 
fresh water in late September or October (depending on water 
conditions) and spawn in November and December, with some spawning 
continuing into January. The mean date of entry (for the years 1974 to 
1995) into the trap at the Merced River Fish Facility is October 21. In 
1939, Hatton (1940) reported that the date of river entry for the fall 
run varied from early and mid-October for the Tuolumne and Merced 
Rivers, early November for the Mokelumne River, and early December for 
the Consumnes River. The majority of juveniles emigrate during their 
first winter (January to March). The run and spawn timing currently 
exhibited by fall-run fish in the San Joaquin River Basin may not 
reflect historical timing due, in part, to changes in river flow and 
temperature conditions over the last century. However, it is clear that 
the environmental conditions in the San Joaquin River represent the 
extreme of chinook salmon temperature tolerance. In the 1870s, salmon 
were observed migrating through the San Joaquin River in July and 
August (which were probably the historical spring-run chinook salmon) 
when water temperatures were in excess of 26 degrees Centigrade (U.S. 
Fish Commission, 1876). Despite an apparent tolerance to high water 
temperature conditions, San Joaquin River Basin chinook salmon 
populations continued to deteriorate until only the late portion of the 
fall run was able to ascend the tributaries (Clark, 1929).
    The age at maturation for fall-run chinook salmon varies 
considerably from year to year due to differential survival of 
emigrating juveniles and returning adults related to water conditions. 
Most notably, a number of female San Joaquin River fall-run

[[Page 50402]]

chinook salmon mature after only 2 years (Myers et al., 1998).
    Based on a re-assessment of information relevant to the 
configuration of this ESU, NMFS maintains that the original description 
proposed for the Central Valley fall and late fall-run chinook salmon 
ESU is valid. NMFS believes that the new genetic information on spring-
run and winter-run populations in the Central Valley further reinforces 
the previous decision to establish ESUs for the winter and spring runs 
distinct from the fall- and late-fall run (Myers et al., 1998). NMFS 
also maintains the agency's previous conclusion that Central Valley 
fall and late- fall runs are in the same ESU.
    NMFS considered the possible existence of a distinct fall/late 
fall-run ESU in the southern portion of the existing ESU (i.e., San 
Joaquin River and tributaries). The agency believes that ecological 
differences in the northern and southern Central Valley were large 
enough to have historically supported two ESUs of fall- and late fall-
run chinook salmon, with fish from the American, Mokelumne, Stanislaus, 
Tuolumne, Merced, and San Joaquin River Basins in the southern ESU and 
fish from areas north of the American River in a northern ESU. Allozyme 
analysis indicated that samples of hatchery and naturally spawning 
fall-run chinook salmon from the American River and San Joaquin River 
Basin formed a cluster within the general grouping of Central Valley 
chinook salmon populations.
    The status of chinook salmon spawning in tributaries to San 
Francisco Bay was also considered. The presence of chinook salmon 
adults and juveniles (including observed spawning activities) has been 
recorded in a number of rivers and creeks draining into San Francisco 
Bay (Leidy, 1984; Myers et al., 1998; San Francisco Estuary Project, 
1998; Jones, 1999, unpubl. data). However, NMFS was unable to establish 
if any of these populations were self-sustaining. Although the 
historical relationship between chinook salmon spawning in San 
Francisco Bay tributaries and the coastal and Central Valley ESUs is 
not known, present day adults may have originated from the numerous 
off-site releases of Central Valley hatchery fall-run chinook salmon 
into the delta or San Francisco Bay. Additional information on genetic 
and life history traits for San Francisco Bay chinook salmon and their 
relationships with Central Valley and coastal chinook salmon 
populations is necessary to resolve this issue.
    Response - ESU Status: NMFS also examined updated risk information 
for this ESU. Trends in abundance of fall- and late fall-run chinook 
salmon in this ESU continue to be mixed, but natural spawning abundance 
is quite high (5-year geometric mean was 190,000 natural spawners for 
the Sacramento River Basin). The number of mainstem fall-run spawners 
continues to decline in the upper Sacramento River, as indicated by 
counts at Red Bluff Diversion Dam (5-year geometric mean abundance 
through 1996 was 78,996 fish, and mean abundance through 1998 was 
26,092 fish). The dam counts represent the total number of fall-run 
chinook salmon returning to that portion of the river, including 
hatchery fish. Available evidence suggests that at least 20 to 40 
percent of these natural spawners are of hatchery origin (Heberer, 
1999). The other Sacramento River Basin streams showing continued 
declines in abundance of fall-run chinook salmon are Deer and Mill 
Creeks (short-term trend in abundance through 1998 was -10 percent per 
year for Mill Creek, long-term trend in abundance through 1998 was -2.8 
percent per year for Deer Creek). All other streams for which there are 
abundance data show increases in abundance over the past 10 years. As 
discussed in the BRT report (Myers et al., 1998), many of the streams 
with high abundance of fall-run chinook salmon in this ESU are 
influenced by hatchery programs (especially the Feather and American 
Rivers and Battle Creek), so the contribution of those populations to 
the overall persistence of the wild component of the ESU is not clear.
    The late-fall component of the Sacramento River run continues to 
have low, but perhaps stable abundances. Recent estimates up to 1992, 
when Red Bluff Diversion Dam counts were still accurate, ranged from 
6,700 to 9,700. Estimates from 1993 to 1997 were essentially incomplete 
due to the inability to monitor fish at the Red Bluff Diversion Dam. 
Beginning in 1998, carcass surveys again allowed a reasonable estimate 
to be made, and the 1998 abundance estimate (9,717 fish) seems 
comparable to the early 1990s. Nevertheless, there is considerable 
uncertainty in estimating the recent trend in abundance due to changes 
in estimation methods.
    Populations of fall-run chinook salmon in the San Joaquin River 
Basin have exhibited synchronous population booms and busts and 
currently appear to be on an upward trend in abundance. Aside from a 
negative short-term trend in abundance in the Stanislaus River (-6.2 
percent per year through 1998), the other tributaries to the San 
Joaquin River are exhibiting increases in abundance over the most 
recent 10 years. Lindley (NMFS, unpubl. data) developed a series of 
models relating recruitment of fall chinook in the Tuolomne and 
Stanislaus Rivers to various factors to see if there was a simple 
explanation for the high variability in recruitment. Explanatory 
variables examined included spring river flow, ocean harvest, hatchery 
releases, sea surface temperature, and spawning stock. The model 
providing the best fit to empirical data was a logistic growth (stock-
recruit) model with the carrying capacity parameter a linear function 
of river flow during the downstream juvenile migration period (Lindley, 
NMFS, unpubl. data). The apparent dependency of stock-recruitment 
relationships on flow does not rule out the potential influences of 
other factors (e.g., hatchery production) on variability in recruitment 
(Lindley, NMFS, unpubl. data).
    The influence of hatchery fish on natural production in the San 
Joaquin River Basin is not clear. As in the rest of the Central Valley, 
the nature of CWT applications and insufficient sampling of natural 
spawners make quantitative estimation of hatchery influence difficult.
    After reviewing additional scientific and commercial information 
regarding the status of this ESU, NMFS concludes that the Central 
Valley fall and late fall-run chinook salmon ESU is not presently in 
danger of extinction, nor is it likely to become so in the foreseeable 
future. The change in the risk evaluation was due primarily to the 
increases in abundance in Central Valley streams. The number of natural 
spawners is quite high (190,000 fish) and numerous streams have seen 
increases during the past 10 years, with some exceptions. The recent 
upward trends in fall-run chinook salmon populations in the San Joaquin 
tributaries are also encouraging, but NMFS is concerned about the high 
variation in abundance and its strong correspondence with human and 
naturally impacted flow regimes. The late fall-run chinook salmon 
escapement appears to be higher than it has been in recent years, but 
NMFS is concerned about the uncertainty in the escapement estimates.
    The major sources of continued threats to the chinook salmon in 
this ESU are habitat degradation (primarily water withdrawals and 
stream shifts), water quality, loss of riparian and estuarine habitat, 
and the influence of hatchery fish. NMFS believes that several recent 
actions are likely to

[[Page 50403]]

mitigate the threats facing chinook salmon in the Central Valley fall 
and late fall-run chinook salmon ESU, including harvest reductions, the 
listing of winter-run chinook salmon and steelhead under the Federal 
ESA, the listing of spring-run chinook salmon under the California ESA 
(CESA), improvements in water flow and habitat conditions resulting 
from development and implementation of restoration projects as part of 
the CALFED and Central Valley Project Improvement Act (CVPIA) programs, 
implementation of the Vernalis Adaptive Management Plan (VAMP) in the 
San Joaquin River Basin, and the recently initiated comprehensive 
review of hatchery programs in the Central Valley by CDFG and FWS. NMFS 
has considered the impacts of various conservation efforts affecting 
this ESU under the section ``Efforts Being Made to Protect West Coast 
Chinook Salmon'' of this document.

Issue 7: ESU Delineation and Status of Southern Oregon and California 
Coastal Chinook Salmon

     Comment 9: Many commenters, disputing the proposed boundaries for 
this ESU, questioned NMFS' rationale for a separate Upper Klamath and 
Trinity River chinook salmon ESU within the range of the larger 
Southern Oregon and California Coastal ESU. For example, one commenter 
disputed the southern border of the ESU and asserted that there is no 
definitive proof that chinook salmon populations existed in any of the 
San Francisco Bay tributaries. Furthermore, they stated that native 
chinook salmon were now extinct in the Russian River and that the ESU's 
boundary should extend no farther south than to the limit of extant 
chinook salmon populations. Another commenter believed that the chinook 
salmon population in the Russian River was never historically abundant. 
Several commenters suggested that this ESU be divided into two ESUs, 
but the suggested configurations varied. Some believed that the 
existing ESU should be split south of the Klamath River while others 
believed that the split should be north of the Klamath River. Still 
another believed that the ESU should be split north of the Eel River. 
Finally, some commenters believed that NMFS should adopt ESU 
configurations more similar to those for coho salmon or steelhead, both 
of which have multiple ESUs within the range of the Southern Oregon and 
California Coastal chinook salmon ESU. Most commenters suggesting 
alternative ESU configurations believed that chinook salmon in the 
``transboundary'' region of Oregon and California would not require 
protection under the ESA.
    Some commenters and peer-reviewers felt that, in a number of cases 
where spring- and fall-run chinook salmon were included in the same 
ESU, separate ESUs should have been established. These recommendations 
were substantiated with information on ecological differences in 
spring- and fall-run spawning and juvenile rearing habitat. 
Furthermore, it was argued that separation in spawning time and 
location provided a significant amount of reproductive isolation, even 
in those systems where dams had restricted access to historical spring-
run spawning habitat. Several of the commenters highlighted these 
ecological and life history differences in those ESUs where genetic 
data were limited or lacking. Furthermore, the commenters stated that 
the lumping of different runs was inconsistent, given the creation of 
distinct fall- and spring-run ESUs in the Central Valley of California.
    Several commenters highlighted the benefits from various 
restoration programs underway in the range of the proposed ESU (e.g., 
the NFP and Oregon Coastal Salmon Restoration Initiative), while others 
expressed little confidence in the adequacy of existing conservation 
efforts. One commenter described risks to chinook salmon in the Eel 
River Basin by the introduction of the Sacramento pikeminnow 
(Ptychocheilus grandis) in the late 1970s, noting increases in the 
number of pikeminnow in the Eel River Basin which corresponded with 
declines in chinook salmon during the 1980s and 1990s. Another 
commenter suggested that NMFS had underestimated the impact of 
predators (such as cormorants) on chinook salmon populations in the 
range of the proposed ESU.
    Since the initial status review, NMFS has received new data and 
information which have helped resolve the scientific uncertainties 
associated with the proposed listing for this ESU (NMFS, 1999a), and 
are summarized as follows.
     Response - ESU Delineation: NMFS recently analyzed new genetic 
data for California chinook salmon. In 1998 and 1999, NMFS, CDFG, FWS, 
and USFS collected samples of spawned adult chinook salmon from 13 
rivers and hatcheries in the Central Valley and Klamath River Basin. 
The new samples were analyzed along with allozyme data for California 
and southern Oregon chinook salmon that were previously used in the 
NMFS coastwide status review (Myers et al., 1998). The population 
structure revealed by the new analysis of allozyme data was consistent 
with the delineations of major genetic groups described in previous 
genetic studies of California and southern Oregon chinook salmon (Utter 
et al., 1989; Bartley et al., 1992; Myers et al., 1998). The most 
genetically divergent group of samples was from the Central Valley. The 
remaining samples formed two large genetic groups composed of samples 
from the Klamath River Basin and those from coastal rivers. The single 
sample from the lower Klamath River, Blue Creek, was included in the 
cluster of coastal samples. The samples from coastal rivers were 
further differentiated into two subclusters of samples from rivers 
south of the Klamath River and from those to the north (including Blue 
Creek).
    Several subclusters appeared within the samples of chinook salmon 
from the Klamath River Basin. The sample from Blue Creek in the lower 
Klamath River was the most genetically distinct of all the samples from 
the Klamath River Basin. Samples from the Trinity and Salmon Rivers 
(both fall- and spring-run populations) clustered separately from 
samples from rivers farther upstream.
    Nielsen et al. (1994) reported that mtDNA haplotypes from some of 
the fall-run chinook salmon smolts captured in 1993 and 1994 from the 
Russian River did not match haplotypes from the Russian River hatchery 
(Warm Springs Hatchery) population; in fact, there was a rare haplotype 
that was found only in chinook salmon from the Russian and Guadalupe 
(San Francisco Bay) Rivers. In 1999, several naturally produced chinook 
salmon juveniles were collected in the Russian River Basin by the 
Sonoma County Water Agency, and a subset of these were genetically 
analyzed by the Bodega Bay Marine Laboratory (Banks, 1999, unpubl. 
data).
    Banks et al. (1999) used five microsatellite loci to investigate 
genetic relationships among 11 fall- and spring-run chinook salmon 
populations in the Klamath River and to compare these populations to 
chinook salmon from the Central Valley. Results revealed two large 
clusters with Klamath River Basin populations differentiated from 
Central Valley populations. Within the Klamath River Basin, Blue Creek 
from the lower Klamath River was the most genetically divergent 
population and was found to be more similar to southern Oregon and 
California coastal chinook populations than to upper Klamath/Trinity 
River populations. The most upstream populations from the Klamath River 
(Scott River, Shasta River, and Iron Gate Hatchery) were differentiated 
from subclusters of fall- and spring-run populations in the Trinity and 
Salmon Rivers.

[[Page 50404]]

    Little new information on life history traits is available for this 
ESU. Comparisons of the timing of adult chinook salmon passage over 
dams on the Mad River (Sweasey Dam) and South Fork Eel River (Benbow 
Dam) in 1948 to 1949 (Murphy and Shapovalov, 1950) does not reveal a 
shift in run timing when compared with recent information presented in 
Myers et al. (1998), indicating that introductions of out-of-basin 
stocks have had little observable impact. A review of ocean 
distribution information collected from 1986 to 1989 (Gall et al., 
1989) suggests that there may be geographic and timing differences in 
the ocean distribution of chinook salmon from the Smith River and 
southern Oregon relative to Eel River and other coastal stocks.
    There was little information available on the southern limit of 
self-sustaining chinook populations in this ESU. Cobb (1930) discussed 
the existence of fall-run populations in the Noyo and Mattole Rivers; 
furthermore, the Noyo River fall-run population was large enough to 
sustain a small fishery early in this century. Clark (1940) estimated 
that the salmon catch in the Eel River during 1916 was nearly 450,000 
kg, and 32,000 kg in the Mad River during 1918. Snyder (1908) described 
the presence of chinook salmon in the Russian River; however, 
Shapavalov (1944) made no mention of the presence of chinook salmon in 
the Russian River. In October of 1972, a number of salmon (no 
identification of the species was possible) were observed spawning in 
the Russian River below Dry Creek (Holman, 1972).
    Within San Francisco Bay there are a number of streams where 
chinook salmon have been observed (Jones, 1999). Spawning chinook 
salmon or redds have been observed in the Guadalupe River, Napa River, 
Petaluma River, Walnut Creek, and Green Valley Creek (Jones, 1999). 
There is very little information on the origin or sustainability of 
chinook salmon ``populations'' in these systems. South of San Francisco 
Bay, chinook salmon have historically been documented in the San 
Lorenzo and Pajaro Rivers (Snyder, 1913) and in the Ventura River 
(Jordan and Gilbert, 1881). However, it is unclear if coastal 
populations south of the Russian River were historically persistent or 
if they were merely colonized by more northerly populations on an 
intermittent basis during favorable climatic periods (Myers et al., 
1998). Recently, adult chinook salmon have also been observed in Scott 
Creek, but in low numbers and only on an intermittent basis (Streig, 
Monterey Bay Salmon & Trout Project, pers. comm.). Currently, there are 
no known persistent populations of chinook salmon on the coast south of 
San Francisco Bay.
    Based on a re-assessment of information relevant to the 
configuration of this ESU, NMFS concludes that the proposed Southern 
Oregon and California Coastal chinook salmon ESU should be split into 
two ESUs: a Southern Oregon and Northern California Coastal chinook 
salmon ESU, extending from Euchre Creek through the Lower Klamath River 
(inclusive), and a California Coastal chinook salmon ESU, extending 
from Redwood Creek south through the Russian River (inclusive). This 
new ESU boundary is similar to that designated between Klamath 
Mountains Province and Northern California steelhead ESUs. At this 
time, NMFS concludes that the Russian River Basin presently contains 
the most southern persistent population of chinook salmon on the 
California coast.
    NMFS reconsidered the reconfiguration of this proposed ESU based on 
a number of issues. The acquisition of new genetic samples from the 
Central Valley, California coastal streams, and Upper Klamath and 
Trinity Rivers made possible a new analysis indicating distinct 
clusters of coastal populations north and south of the Klamath River. 
The genetic distances between these clusters correspond roughly to the 
differences observed between Central Valley spring- and fall and late 
fall-run chinook salmon ESUs, and the Washington and Oregon coast 
chinook salmon ESUs.
    Ecological differences between the northern and southern portions 
of the Southern Oregon and California Coastal chinook salmon ESU were 
also discussed. Rivers to the north (especially the Rogue River) tended 
to be larger than those to the south. River flows in the northern 
portion tend to peak in January, while those to the south peak in 
February (Myers et al., 1998). Annual precipitation is considerably 
higher in the northern portion than in the south. These geographic and 
ecological differences may be responsible for the presence of a limited 
proportion of yearling outmigrants (less than 10 percent) in the 
northern portion of the ESU compared with the apparent absence of 
yearling outmigrants in the southern portion. Furthermore, soils in the 
southern portion are highly erodible, causing high silt loads that 
result in berms which close off the mouths of many of the rivers during 
summer low flows. River conditions in most of these coastal basins, 
especially in the south, have very limited temporal windows for adult 
access and juvenile emigration. Given these conditions, it is unlikely 
that substantial differences in the life history traits normally 
measured (e.g., run timing, spawn timing, juvenile emigration) could 
evolve among most rivers in the northern and southern portions of the 
proposed ESU. However, NMFS did consider the presence of spring-run 
chinook salmon in the northern portion of the ESU, Rogue and Smith 
Rivers, as a further indicator of geographic and life history 
differences (although there may have historically been a spring run in 
the Eel River). Finally, there was some ocean harvest information that 
indicated differences in the migration pattern of populations from the 
northern (Rogue and Smith Rivers) and southern (Eel River) portions of 
the proposed ESU (Gall et al., 1989).
    Response - ESU Status:  New abundance information was provided by 
several commenters and co-managers for a number of streams in the 
Southern Oregon and Northern California Coastal chinook salmon ESU 
(Howard and Albro, 1997; Howard, 1998 and 1999; USFS, 1997 and 1999; 
Waldvogel, 1997 and 1999; Yurok Tribal Fisheries Program, 1997 and 
1999; ODFW, 1999). Recent total estimated escapement of fall- and 
spring-run chinook salmon in Oregon streams is close to 100,000 fish. 
The largest run of fall chinook salmon in the ESU occurs in the Rogue 
River, and ODFW recently has revised its estimates of abundance to 
average over 51,000 fish in the run during the most recent 5 years. In 
addition, ODFW estimated that the escapement of fall chinook to the 
Chetco River in 1995 and 1996 was 8,500 and 3,500 fish, respectively. 
In spite of the high estimated abundances in the Chetco River, between 
31 and 58 percent of those naturally spawning fish were estimated to be 
of hatchery origin.
    Although trends in abundance are mixed over the long term, most 
short-term trends in abundance of fall chinook salmon are positive in 
the smaller coastal streams in the ESU. Spawning ground surveys from a 
number of smaller coastal and tributary streams from Euchre Creek to 
the Smith River show declines in abundance from the late 1970s through 
the early 1990s, but recently, the peak counts predominantly show 
increases. In addition to adult counts, downstream migrant trapping 
generally shows increases in production in fall chinook juveniles over 
the last 4 years in the Pistol and Winchuck Rivers and in Lobster 
Creek, a tributary to the lower Rogue River. Short- and long-term

[[Page 50405]]

trends in abundance for the Rogue River fall chinook are declining, but 
as mentioned above, the overall run size is still large.
    Northern coastal California streams support small, sporadically 
monitored populations of fall-run chinook salmon. Trends in fall 
chinook salmon abundance in those California streams that are monitored 
are mixed; in general, the trends tend to be more negative in streams 
that are farther south along the coast (i.e., populations in the Eel, 
Mattole, and Russian Rivers). Estimates of absolute population 
abundance are not available for most populations in the California 
portion of the region encompassing this ESU.
    The release of hatchery fall chinook salmon into some southern 
Oregon coastal streams recently has been reduced or discontinued. 
Releases of fall chinook salmon into the lower Rogue River were reduced 
to 75,000 smolts and 75,000 unfed fry, and the Chetco River program 
recently was reduced to 150,000 smolts. ODFW also has provided NMFS 
with new estimates of the percentage of hatchery fall chinook salmon 
spawning naturally in the Chetco River. In 1995 and 1996, the 
percentage of naturally spawning hatchery fish was 31 and 58 percent, 
respectively. During those same years, the estimated numbers of 
naturally spawning adults returning to the Chetco River were 8,530 and 
3,561 fall chinook salmon, respectively.
    Most spring-run chinook salmon in this ESU continue to be 
distributed in a few populations that are declining in abundance. The 
run size of spring-run chinook salmon in the Rogue River above Gold Ray 
Dam has averaged 7,709 over the last 5 years, and the estimated 
percentage of hatchery fish in the run has ranged from 25 to 30 percent 
over that time period. The Smith River contains the only known 
populations of spring-run chinook salmon on the California coast, and 
those runs continue to decline in the Middle Fork, but are increasing 
in the South Fork. ODFW believes that spring-run chinook populations in 
the Smith River probably have always been small, based on in-river 
fishery landings, historical cannery records, and the judgement of 
local biologists.
    In the California Coastal chinook salmon ESU, fall chinook salmon 
occur in relatively low numbers in northern streams and, only 
sporadically, in streams in the southern portion of the ESU's range. 
Estimates of absolute population abundance are not available for most 
populations in this ESU. The 5-year geometric mean abundance of fall 
chinook passing Cape Horn Dam on the upper Eel River is 36 fish, but 
those counts are considered to be a small and variable fraction of the 
run in the Eel River.
    Trends in fall chinook salmon abundance in those California streams 
that are monitored are mixed; in general, the trends tend to be more 
negative in streams that are farther south along the coast (i.e., 
populations in the Eel, Mattole, and Russian Rivers). Trends in 
abundance in several tributaries in the Redwood Creek drainage have 
been monitored since 1995; these numbers will be useful in assessing 
the status of chinook salmon in those streams in the future. Trends in 
abundance in the Mad River Basin have been declining over the long 
term, but they are showing signs of increase in recent years. Peak 
index counts and carcass surveys have been conducted since the mid-
1960s in Sprowl and Tomki Creeks, both tributaries to the Eel River. 
The long-term trend in abundance in Sprowl Creek is -4.4 percent per 
year, but recent years show increases. In contrast, both the long- and 
short-term trends in abundance in Tomki Creek are severely declining. 
Shorter-term monitoring has occurred in other Eel River tributaries 
since the late 1980s; abundance in Hollow Tree and Redwood Creeks has 
been declining precipitously. Recent monitoring of index areas in the 
Mattole and Russian River Basins indicates declining trends in 
abundance, with the exception of the increasing abundance at the Coyote 
Valley Fish Facility on the Russian River from 1992 to 1998. Hatchery 
chinook salmon occur in the Russian and North Fork Mad Rivers, but the 
contribution of hatchery fish to natural spawning escapements is not 
known.
    After reviewing additional scientific and commercial information 
regarding the status of these revised ESUs, NMFS concludes that the 
revised California Coastal chinook salmon ESU is likely to become 
endangered in the foreseeable future. Most of NMFS' concerns regarding 
the status of this ESU are related to abundance and trends/productivity 
risks. NMFS believes that widespread declines in abundance of chinook 
salmon relative to historical levels and the present distribution of 
small populations with sometimes sporadic occurrences contribute to the 
risks faced by this ESU. Overall, NMFS is concerned about the paucity 
of information on the presence or abundance of chinook salmon in the 
geographic area encompassing this ESU. The abundance data series are 
short-term for most of the streams in this ESU, and there are no 
current data for the long time series at Benbow Dam for the population 
that may have been historically the largest (South Fork Eel River).
    NMFS believes that habitat degradation and water withdrawals in the 
river drainages in coastal California have contributed to the continued 
reduction in abundance and distribution of chinook salmon in this ESU. 
Smaller coastal drainages, such as the Noyo, Navarro, Garcia, and 
Gualala Rivers, likely supported chinook salmon runs historically, but 
they contain few or no fish today. The Russian River probably contains 
some natural production, but the origin of those fish is not clear 
because of a number of non-native introductions of hatchery fish over 
the last century. NMFS is concerned about the possible extinction of 
the spring run in the upper Eel River, which represents an important 
loss of life history diversity in this ESU.
    NMFS believes that the following factors are likely to have 
improved the conditions for chinook salmon in the California Coastal 
chinook salmon ESU: Reductions in the Klamath Management Zone (KMZ) and 
Central Valley harvest index, the listing of coho salmon and steelhead 
under the Federal ESA, changes in harvest regulations by the States of 
Oregon and California to protect coho salmon and steelhead, 
improvements in stream water quality due to enhanced enforcement of 
Clean Water Act standards, and changes in timber and land-use practices 
resulting from completed Habitat Conservation Plans (HCPs).
    In contrast, NMFS concludes that chinook salmon in the revised 
Southern Oregon and Northern California Coastal chinook salmon ESU are 
not presently in danger of extinction, nor are they likely to become so 
in the foreseeable future. NMFS is encouraged by the overall numbers of 
chinook salmon in this ESU and by the recent increases in abundance in 
many of the smaller coastal streams. In addition to the large runs 
returning to the Rogue River, chinook salmon appear to be well 
distributed in a number of coastal streams throughout the geographic 
region encompassing this ESU. Although many of the new data sets 
received by NMFS are of short duration, NMFS is encouraged by recent 
efforts by the co-managers to improve monitoring of chinook salmon in 
this region. Risks associated with the presence of hatchery fish in 
this ESU are relatively low; nevertheless, NMFS is concerned about the 
high percentages of naturally spawning hatchery fish in the Chetco 
River and in the spring-run chinook salmon population in the Rogue 
River. In addition, the restricted distribution of

[[Page 50406]]

spring-run chinook salmon to the Rogue and Smith River Basins and their 
significant decline in the Rogue River could represent an important 
threat to the total diversity of fish in this ESU.
    NMFS believes several factors are likely to have improved the 
conditions for chinook salmon in the Southern Oregon and Northern 
California Coastal chinook salmon ESU, including reductions in the KMZ 
troll fishery, the ESA listing of coho salmon, changes in harvest 
regulations by the States of Oregon and California to protect naturally 
produced coho salmon and steelhead, and changes in timber and land-use 
practices on Federal public lands resulting from the NFP. NMFS has 
considered the impacts of various conservation efforts affecting this 
ESU under the section ``Efforts Being Made to Protect West Coast 
Chinook Salmon'' of this document.

Issue 8: ESU Delineation and Status of Snake River Fall Chinook Salmon

     Comment 10: Several commenters, including state and tribal co-
managers, disagreed with the inclusion of the Deschutes River fall-run 
chinook salmon in this ESU. They argued that the Deschutes River and 
Snake River Basins are ecologically distinct. Furthermore, the 
geographic distance between these basins would preclude any significant 
genetic exchange, especially if one considers the historical spawning 
distribution of Snake River chinook salmon. There were a number of 
scenarios given to explain the genetic similarity between the Deschutes 
River and Snake River fall-run populations. One scenario suggested 
that, with the loss of the majority of their historical spawning 
habitat, the existing Snake River fall-run chinook salmon ESU no longer 
represented the historical population. An alternative view was that the 
genetic differences among all ocean-type chinook salmon above the 
Dalles Dam were relatively small and that the clustering of populations 
was subject to possible bias depending on the procedures used. It was 
also stressed that the existing allozyme information was acquired after 
the Columbia River Basin had undergone considerable alterations 
(mainstem dam construction) and many of the native populations had been 
extirpated. It was also suggested that the marine CWT recovery 
information for the Deschutes River fall run was potentially biased due 
to the limited number of tags recovered and the limited number of 
broodyears that were tagged. Two commenters asserted that an ocean-type 
summer run existed (and may still exist) in the Deschutes River, and 
this would evolutionarily link the Deschutes River ocean-type fish more 
closely with ocean-type fish in the Upper Columbia River summer- and 
fall-run chinook salmon ESU. Some reviewers suggested that all ocean-
type chinook salmon above the historical location of Celilo Falls 
should be considered one ESU. The most commonly suggested alternative 
ESU configuration included the Deschutes River and the now extinct 
populations that were in the John Day, Umatilla, and Walla Walla Rivers 
as a separate ESU.
    Several other commenters challenged the NMFS exclusion of hatchery 
fish abundances from the risk assessment. They argued that, in many 
instances, hatchery and naturally spawning fish have co-mingled for 
generations. These fish are genetically indistinguishable and 
effectively represent one population. In many cases, the persistence of 
naturally spawning fish has been dependent on the continued operation 
of the hatchery program. Under these conditions, they contend, hatchery 
abundances should be included in the risk assessment for an ESU.
    Since the initial status review, NMFS has received new data and 
information which have helped resolve the scientific uncertainties 
associated with the proposed listing for this ESU (NMFS, 1999a), and 
are summarized as follows.
    Response - ESU Delineation: The Confederated tribes of the Warm 
Springs Reservation (CTWSRO) provided NMFS with a preliminary report of 
genetic studies of fall-run chinook salmon in the Deschutes River 
(CTWSRO, 1999). Both allozyme and mtDNA loci were used to determine if 
the Deschutes fall chinook population is more genetically and 
demographically related to the Snake River fall chinook populations 
than to any other population in the Columbia Basin. The authors 
concluded from the mtDNA and allozyme data that there is little or no 
geographic organization of the fall-run genetic data and no compelling 
evidence to support adding the Deschutes River to the Snake River fall-
run chinook salmon ESU.
    The similarity in life history traits between the Deschutes and 
Snake River fall-run populations was an important factor in the 
proposed ESU designation incorporating these two geographically 
separated basins into one ESU. Since the time of the proposed rule, 
NMFS has reviewed additional information on ecological and life history 
traits for this ESU and a CTWSRO analysis of information previously 
reviewed by the BRT (CTWSRO, 1999). Similarities in ocean distribution, 
as reflected by CWT recoveries, were observed for wild Deschutes River 
fall-run and Snake River fall-run chinook salmon. Analysis by CTWSRO 
(1999) indicates that there was a strong correlation (0.95) in the 
ocean distributions of Deschutes River and Snake River fish; however, 
there were equally strong similarities between Deschutes River fish and 
fall-run fish from a number of lower Columbia River basins. The 
correlation between the distribution of ocean recoveries for the 
Deschutes River fall-run and that for upriver ``bright'' fall-run 
chinook salmon (i.e. Hanford Reach, Priest Rapids) was much weaker 
(0.61). Because only 35,000 Deschutes River fall-run fish were tagged 
during each of 3 broodyears (1977 to 1979), and of these only 79 tags 
were recovered in the ocean fishery, CTWSRO (Patt, 1999) cautioned the 
use of this information to establish the ESU configuration.
    Age structure information was also used in the initial NMFS 
decision to group fall-run chinook salmon in the same ESU. In the 
Coastwide Status Review (Myers et al., 1998) similarities were observed 
between the Deschutes River and Snake River fall-run populations, 
relative to Hanford Reach and other upper Columbia River fall-run 
populations. Age structure for the Deschutes River, Snake River (using 
Lyons Ferry return data), and Hanford Reach fall-run fish was 
determined using scale data from several broodyears in the late 1970s 
and 1980s. CTWSRO (Patt, 1999) also presented run reconstructions 
provided by Howard Schaller (ODFW). For the Deschutes and Hanford Reach 
data series, this information, based on scales recovered from returning 
adults, age-length indices, and CWT recoveries, represented a more 
complete description of the populations concerned than was presented in 
Myers et al. (1998). However, the Snake River age structure data were 
not based on the direct measurement of Snake River fish, but rather 
derived from an index of upriver bright stocks. It was advised that 
considerable caution be used in employing the Snake River age structure 
data in any comparisons (Schaller, ODFW, pers. comm.).
    Spawn timing differences presented by CTWSRO (1999) indicated that 
Deschutes River fish spawn primarily in October (in contrast to the 
November peak spawning cited in Myers et al., 1998), rather than in 
early and mid-November for fall-run chinook salmon in the Snake River 
and Hanford Reach of the Columbia River (Myers et al., 1998). This 
earlier timing may be related to water conditions in the Deschutes 
River or may be an indicator of the integration of a historical summer 
run into the fall run. A review of historical

[[Page 50407]]

information indicated that fall-run chinook in the Snake River near 
Salmon Falls (Rkm 922) arrived on the spawning grounds in late August 
and September and that ripe fish were caught in the fishery in early 
October (Evermann, 1896). Spawning was nearly complete by the end of 
October. Differences in the spawning time of present day and historical 
Snake River fall-run chinook salmon populations may be a response to 
different temperature and flow regimes in the lower river (the current 
accessible habitat) or may indicate the extirpation of the earlier, 
upriver, spawning populations from the ESU.
    Fecundity estimates provided an additional life history trait for 
comparison. Myers et al. (1998) cited average fecundity values for 
Deschutes River fall-run chinook salmon of 4,439 eggs per female, and 
for Lyons Ferry Hatchery fish (Snake River) 3,102 eggs per female 
(adjusted to 4,011 eggs per female at a standard length of 740 mm). 
Fecundity estimates (Howell et al., 1985) for wild Snake River fall-run 
chinook salmon (trapped at Oxbow Dam) of 4,276 (1961 to 1969) and 4,185 
eggs per female (1977 to 1983) were similar to Deschutes River fish, 
but do not include spawner sizes and are difficult to compare.
    Meristic data were also reviewed to assess the similarities of the 
fall-run stocks under consideration. Of the traits analyzed by Schreck 
et al. (1986), only lateral line scale counts were potentially useful 
in discriminating among the Deschutes, Snake, and mainstem Columbia 
River (Hanford Reach) populations. Deschutes River fall-run chinook 
salmon exhibited a lower mean lateral scale count (136.6) compared with 
the fall-run fish from Hanford Reach (140.6) and the Snake River (Lyons 
Ferry Hatchery) (143.3). The Deschutes River lateral line scale counts 
most closely resembled those from several fall-run populations in the 
Lower Columbia River (below the location of Celilo Falls); however, 
these differences may not be statistically significant.
    Little documentation is available on the existence of a summer run 
in the Deschutes River Basin. This issue is relevant to the discussion 
on ESU configuration due to the ocean-type life history expressed by 
summer-run fish in the Upper Columbia River and the stream-type life 
history expressed by summer-run fish in the Snake River Basin. If, as 
has been asserted by Patt (1999), the summer run in the Deschutes River 
Basin exhibited an ocean-type life history, it would provide an 
evolutionary link with the upper Columbia River ocean-type stocks. 
Information presented by CTWSRO (1999) indicates that there was a 
significant temporal separation in the arrival of spring-run and 
summer/fall-run adults at the Pelton Dam Trap (River kilometer (Rkm) 
161). Jonasson and Lindsay (1988), Beaty (1996), and Lichatowich (1998) 
have suggested that summer-run fish existed in the Deschutes River. 
Whether these summer-run fish historically spawned above the present 
site of Pelton Dam or above Sherars Falls, which reportedly was 
impassable during low summer flows early in this century, is not known 
although both scenarios would have provided for the geographic 
separation of summer and fall runs. In the 1960s, three returning 
adults that were tagged while passing Bonneville Dam during July were 
later recovered in the Metolius River, tributary to the Deschutes River 
at Rkm 178 (Galbreath, 1966). However, Nehlsen (1995) cited several 
personal communications which indicate that fall spawning fish were not 
observed in the Deschutes River Basin above the site of Pelton Dam. 
Analysis of downstream juvenile migrants (1959 to 1962) through the 
Pelton project did not detect any subyearling migrants (which would be 
consistent with the presence of ocean-type fish). Analysis of mtDNA 
variability from fish sampled at Sherars Falls and the Pelton Dam Trap 
suggests that genetic differences exist among adults collected at the 
two sampling locations (CTWSRO, 1999). It has been suggested that the 
genetic differences are indicative of a vestigial run of summer-run 
fish that have retained the propensity to migrate farther upstream than 
do fall-run fish. However, Jonasson and Lindsey (1988) state that there 
is no correlation between the date of ascending Sherars Falls and the 
date or location of subsequent spawning. Furthermore, analysis of 
scales from adults sampled at Sherars Falls in 1978 indicated that 
stream-type fish constituted 31.2, 25, 4.4, and 2.2 percent of the run 
passing the Falls in July, August, September, and October, respectively 
(Aho et al., 1979). During 1979, the percentage of stream-type fish 
sampled at Pelton Trap during this same period dropped to 14 and 5.5 
percent for July and August, respectively. The possibility exists that 
many of the fish sampled in the mtDNA study (especially at the Pelton 
Trap) were stream-type fish; further analysis of allozyme variation may 
resolve this issue.
    Ecological differences among the Deschutes River Basin, the upper 
Columbia River Basin, and the Snake River Basin (especially historical 
fall-run spawning areas in the upper mainstem Snake River) were 
reviewed previously (Waples et al., 1991; Myers et al., 1998). Although 
the mainstem Columbia River and the lower reaches of its tributaries 
(including the Snake River) are all in the Columbia River Basin 
Ecoregion (Omernick and Gallant, 1986), the upper Snake River (above 
the Hells Canyon Dam complex) flows through three different ecoregions. 
Irving and Bjornn (1981) indicated that prior to 1958 the major 
spawning area for Snake River fall-run chinook salmon was in a 30-mile 
section between Swan Falls Dam and Marsing, Idaho, and historically, 
fall-run chinook salmon spawning extended as far upstream as Shoshone 
Falls (Howell et al., 1985). Historically, most of the fall-run chinook 
spawning would have taken place in the Snake River Basin/High Desert 
Ecoregion.
    Fall-run chinook salmon populations in the John Day, Umatilla, and 
Walla Walla Rivers were thought to have been extirpated (Kostow, 1995). 
However, there have been recent reports of chinook salmon spawning in 
the lower mainstem John Day River, but there is no information to 
establish the source of these fish or whether they were reproductively 
successful.
    Based on its re-assessment of information relevant to the 
configuration of this ESU, NMFS believes that the proposed ESU 
configuration, combining ocean-type fish in the Snake and Deschutes 
River Basins into one ESU, was not supported by the information 
available. The agency concludes that the Deschutes River summer- and 
fall-run fish should be considered in a separate ESU, rather than be 
grouped with either the Snake River fall-run or Upper Columbia River 
summer- and fall-run chinook salmon ESUs. There is considerable 
uncertainty on the historical configuration of this new ESU, 
specifically whether it included fall-run populations in the John Day, 
Umatilla, and Walla Walla Rivers.
    In reaching this conclusion, NMFS considered several scenarios for 
the configuration of the Snake River fall-run chinook salmon ESU and 
the potential reconfiguration of the Upper Columbia River summer- and 
fall-run chinook salmon ESU. NMFS identified four potential 
configurations: (1) The grouping of all ocean-type chinook salmon above 
the historical site of Celilo Falls into one ESU, (2) the configuration 
in the proposed rule, with Deschutes River summer- and fall-run chinook 
salmon being grouped with the existing Snake River fall-run chinook 
salmon ESU and a separate Upper Columbia River summer- and fall-run 
chinook

[[Page 50408]]

salmon ESU, (3) the grouping of Deschutes River summer- and fall-run 
chinook salmon with other ocean-type mainstem and tributary spawners in 
the Upper Columbia River summer- and fall-run chinook salmon ESU and a 
separate Snake River fall-run chinook salmon ESU, and (4) the creation 
of a new Deschutes River chinook salmon ESU, which may or may not have 
included the extirpated populations that existed in the John Day, 
Umatilla, and Walla Walla Rivers, along with the existing Snake River 
fall-run and Upper Columbia River summer- and fall-run chinook salmon 
ESUs.
    There is considerable uncertainty regarding the importance of 
ecological and geographic factors in providing the basis for 
reproductive isolation and local adaptation. For example, because the 
mainstem Columbia River (above Celilo Falls) and the lower reaches of 
its tributaries are all in the Columbia River Basin Ecoregion, there is 
an ecological link for the majority of the existing spawning 
populations of ocean-type fish. Historically, mainstem and tributary 
spawners may have formed a continuum of populations throughout the 
upper Columbia River and, to a lesser extent, the Snake River. 
Furthermore, genetic and life history differences are modest (or the 
interpretations of the existing data are ambiguous) among ocean-type 
chinook salmon populations above Celilo Falls, suggesting that perhaps 
all of the populations are part of a single ESU. Another viewpoint is 
that the three lines of evidence (genetics, ecology, life history) used 
in the 1991 status review (Waples et al., 1991) to determine that Snake 
and Upper Columbia fall chinook salmon are in separate ESUs are still 
valid. In addition, the historical spawning distribution of most of the 
Snake River fall-run populations was well separated from Columbia River 
fall-run chinook salmon (Irving and Bjornn, 1981). NMFS considered all 
of these factors and believes that none of the new information gives 
sufficient cause to group all upriver bright fall-run chinook salmon 
into one ESU.
    NMFS reviewed the evidence for including Deschutes River fall-run 
chinook salmon in the Snake River fall-run chinook salmon ESU. Data 
provided by co-managers on genetics and ocean recoveries of CWTs were 
important elements of this review. NMFS is uncertain of the assertion 
made by CTWSRO (1999) that genetic samples from the Grande Ronde and 
Clearwater Rivers were representative of Snake River populations. 
Spawning surveys indicated that prior to 1990, redd counts in the 
Grande Ronde River were at or near zero, with counts in the Clearwater 
River numbering in the low tens of redds (Irving and Bjornn, 1981; 
Howell et al., 1985; Garcia et al., 1999). Recent increases in redd 
counts in the Snake River Basin, above Lower Granite Dam, have 
coincided with a large influx of non-Snake River fish (Production 
Advisory Committee, 1998). NMFS believes that the weight of the genetic 
evidence, from a number of different sources, indicates a closer 
relationship of Deschutes River fish with Snake River fish than with 
Columbia River fish. Data from CWT studies also show Deschutes River 
fall-run chinook salmon have an ocean distribution and age at capture 
more similar to Snake River (both Lyons Ferry Hatchery fish and wild 
Snake River fish) than to Columbia River upriver bright fall-run 
populations. Additionally, if (as has been suggested by ODFW) the 
Deschutes River fall-run population was part of a larger historical ESU 
that included the John Day, Umatilla, and Walla Walla Rivers, these 
intermediate populations could have provided a link between the 
Deschutes and Snake River Basins. However, the ecological 
distinctiveness of the historical Snake River, Umatilla and Walla Walla 
Rivers, and Deschutes River spawning habitats argues against their 
being included in the same ESU; for example, the Deschutes River is a 
spring-fed stream with relatively stable water temperature, which is 
very different from the mainstem Snake River.
    NMFS' re-consideration on the grouping of Deschutes River and Upper 
Columbia River summer- and fall-run populations focused on the 
historical distribution of mainstem spawners in the Columbia River, 
which extended more or less continuously from Celilo Falls to Kettle 
Falls, thus providing a link between different tributary populations, 
including the Deschutes River. In contrast, the center of fall-run 
spawning activity in the Snake River Basin was far removed from the 
confluence of the Snake and Columbia Rivers. Environmental features of 
the Deschutes and upper Columbia Rivers are more similar over this 
entire area than either is to the upper Snake River Basin. Tributary 
spawners in the Yakima, Wenatchee, and Okanogan Rivers are already 
included in the Upper Columbia River summer- and fall-run chinook 
salmon ESU, so it is possible to include Deschutes River ocean-type 
chinook salmon with the other upper river tributaries as well. NMFS 
also considered the possible ocean-type life history of the Deschutes 
River summer run. If that is the case, then the relationship between 
summer- and fall-run fish in the Deschutes River would resemble the 
Upper Columbia River, where summer- and fall-run fish are in the same 
ESU, rather than that in the Snake River, where the summer- and fall-
run fish are from different evolutionary lineages.
    After weighing the best available information, NMFS reaffirms the 
conclusion of previous status reviews that found that Snake River and 
Upper Columbia River ocean-type fish are in separate ESUs. There is 
remaining uncertainty about the ESU affinities of the Deschutes River 
population. The scenario with the Deschutes River population in a 
separate ESU from the Snake River fall-run and Upper Columbia River 
summer- and fall-run chinook salmon ESUs is probably the most 
compelling, but arguments can also be made for including the Deschutes 
River in the Upper Columbia or Snake River chinook salmon ESUs. One of 
the factors that influenced NMFS to identify three separate ESUs was 
the lack of conclusive evidence for including the Deschutes River in 
either of the existing ESUs.
    Under the assumption that the Deschutes River population is in a 
separate ESU from Upper Columbia or Snake River fish, NMFS was unable 
to resolve the historical extent of that ESU. The major uncertainty 
centers on the ESU status of historical populations from the John Day, 
Umatilla, and Walla Walla Rivers, which have been extirpated. The lack 
of biological information for these historical populations makes a 
determination of their ESU status difficult. The Deschutes River is 
distinctive enough ecologically to have supported its own ESU; however, 
it is reasonable to believe that the historical ESU also included 
ocean-type populations in tributaries at least as far upstream as the 
confluence with the Snake River. NMFS believes it is highly likely that 
all mainstem Columbia River spawners above Celilo Falls historically 
were part of what is now termed the Upper Columbia River summer- and 
fall-run chinook salmon ESU. The agency also believes that all ocean-
type chinook salmon in the Deschutes River (in particular, any 
vestigial summer-run fish that may exist) are part of the same ESU as 
the Deschutes River fall-run population.
    Response - ESU Status: As discussed previously, NMFS concludes that 
the Snake River fall-run chinook salmon ESU should remain unchanged, 
but is unable to conclude with certainty the ESU affinity of the 
Deschutes River population. Updated information on the abundance of 
fall-run chinook salmon

[[Page 50409]]

in the Deschutes River indicates that the run continues to increase in 
number--the most recently estimated 5-year geometric mean abundance is 
over 16,000 fish, and the short-term trend in abundance has been 
increasing by 18 percent per year (Pacific States Marine Fisheries 
Commission, 1999). However, there is considerable uncertainty 
associated with the run-size estimates of chinook salmon in the 
Deschutes River (Beaty, 1996). The population estimate is based on 
aerial redd surveys above and below Sherars Falls and on a mark-
recapture survey for fish passing above Sherars Falls. The expansion 
estimate is based on an estimate of the number of adults per redd for 
the entire river, calculated using the mark-recapture data for fish 
above the falls. Since the late 1970s, the distribution of spawners has 
shifted from the bulk of the spawning occurring from above to below 
Sherars Falls. The total number of redds below the falls has not 
significantly declined since 1972, but the redd counts above the falls 
have declined dramatically over that time period (Beaty, 1996). The 
shift in relative abundance of spawning adults above and below Sherars 
Falls has resulted in an expansion estimate based on mark-recapture 
studies on an increasingly small proportion of the total population in 
the river. The errors in run-size estimation for the Deschutes River 
have become so high that the overall estimate of run size is not 
reliable. Because of the problems associated with the run-size 
estimates, NMFS considered the trends in redd counts to be a relatively 
more reliable indicator of the status of the Deschutes River chinook 
salmon population. Nevertheless, there is reportedly high inter-annual 
variation in the quality of redd counts due to visibility problems 
during aerial surveys (Beaty, 1996), so even the redd count data are 
not completely reliable.
    Counts of chinook salmon at Pelton trap on the Deschutes River have 
declined since the late 1950s. The 5-year geometric mean abundance of 
fish at the trap is 81, and the short term trend in abundance is 
declining by over 6 percent per year. These fish may be representative 
of a remnant summer run of chinook salmon (CTWSRO, 1999). The 
percentage of hatchery chinook salmon in the Deschutes River continues 
to be very low, as reported in more detail in the historical 
information obtained at the time of the original NMFS status review 
(Myers et al., 1998).
    The estimated abundance of fall-run chinook salmon in the Snake 
River has been increasing over the most recent 10 years (5-year 
geometric mean abundance was 565 naturally produced fish, increasing by 
13.7 percent per year.) Redd counts from streams in the Snake River 
Basin starting in the mid 1980s to 1990s show mostly increasing trends 
in abundance, although the estimated population sizes continue to be 
very small.
    NMFS believes that the new information does not substantially 
change the risk assessments for the Snake River and Upper Columbia 
River chinook salmon ESUs, and the status of these ESUs was not 
reconsidered. Evaluation of the status of the ESU that includes the 
Deschutes River is difficult because the historical and current extent 
of the ESU is not well characterized. For this reason, NMFS did not 
attempt a formal extinction risk analysis for this ESU. However, the 
agency did review abundance, trend, and other information for the 
Deschutes River population and concludes that ocean-type chinook salmon 
in the Deschutes River do not appear to be in danger of extinction, nor 
are they likely to become so in the foreseeable future.
    NMFS remains concerned about the uncertainty in the abundance 
estimates for fall- and summer-run chinook salmon in the Deschutes 
River. Uncertainty about the true population status centers primarily 
around different indicators of status emerging from the analysis of 
redd counts (declining sharply in the upper basin; stable in the lower 
basin) and run size estimates based on expansion of mark-recapture 
studies (which indicate a relatively large and increasing population). 
The only conclusion NMFS can make from the data is that the numbers of 
chinook salmon above Sherars Falls have been severely declining since 
the mid-1970s, while the population below the falls appears to be 
stable. The shift in the proportion of the total Deschutes River fall-
run chinook salmon run spawning above and below Sherars Falls has 
resulted in unreliable expansion estimates for escapement both above 
and below the falls. In addition, the change in the estimated ratio of 
the number of adults per redd over time represents a significant 
problem for interpreting the expansion procedure used to generate the 
abundance estimates. NMFS is hopeful that recent efforts by the CTWSRO 
and ODFW to conduct more extensive mark-recapture studies in the lower 
river will improve escapement estimates.
    NMFS also was concerned about the severe decline and possible 
extinction of the summer-run chinook salmon in the Deschutes River. The 
significant reduction in this life history form would represent an 
important loss to the historical diversity in this ESU. The uncertainty 
associated with the geographic boundaries containing the historical ESU 
added to the overall uncertainty in the risk evaluation. The historical 
run sizes of fall-run chinook salmon in the Umatilla, John Day, and 
Walla Walla Rivers are not well known, and the numbers of fall-run 
chinook salmon present today are very low and do not represent 
naturally self-sustaining runs. If fall-run chinook salmon that 
historically occurred in those streams are considered to be part of the 
Deschutes River chinook salmon ESU, a higher extinction risk may be 
appropriate for the current ESU because extinction of the ESU would 
have occurred over a significant portion of its range.

Summary of Factors Affecting Chinook Salmon

    Section 4(a)(1) of the ESA and NMFS' listing regulations (50 CFR 
part 424) set forth procedures for listing species. The Secretary of 
Commerce (Secretary) must determine, through the regulatory process, if 
a species is endangered or threatened based upon any one or a 
combination of the following factors: (1) The present or threatened 
destruction, modification, or curtailment of its habitat or range; (2) 
overutilization for commercial, recreational, scientific, or 
educational purposes; (3) disease or predation; (4) inadequacy of 
existing regulatory mechanisms; or (5) other natural or human-made 
factors affecting its continued existence.
    The factors threatening naturally spawned chinook salmon throughout 
its range are numerous and varied. The present depressed condition is 
the result of several long-standing, human-induced factors (e.g., 
habitat degradation, water diversions, harvest, and artificial 
propagation) that serve to exacerbate the adverse effects of natural 
environmental variability from such factors as drought, floods, and 
poor ocean conditions.
    As noted earlier, NMFS received numerous comments regarding the 
relative importance of various factors contributing to the decline of 
chinook salmon. A summary of various risk factors and their roles in 
the decline of west coast chinook salmon was presented in NMFS' March 
9, 1998, proposed rule (63 FR 11482), as well as in several ``Factors 
for Decline'' reports published in conjunction with proposed rules for 
steelhead and for chinook salmon (NMFS, 1996 and 1998b).

[[Page 50410]]

Efforts Being Made to Protect West Coast Chinook Salmon

    Under section 4(b)(1)(A) of the ESA, the Secretary is required to 
make listing determinations solely on the basis of the best scientific 
and commercial data available and after taking into account efforts 
being made to protect a species. During the status review for west 
coast chinook salmon and for other salmonids, NMFS reviewed protective 
efforts ranging in scope from regional strategies to local watershed 
initiatives; some of the major efforts are summarized in the March 9, 
1998, proposed rule (63 FR 11482). Since then, NMFS has received some 
new information regarding these and other efforts being made to protect 
chinook salmon. Notable efforts within the range of the chinook ESUs to 
be listed continue to be the NFP, PACFISH, Oregon Plan for Salmon and 
Watersheds (OPSW), CVPIA, CALFED Bay-Delta Program implementation and 
development, development and implementation of VAMP, Klamath and 
Trinity Basin restoration programs and flow re-evaluations, CDFG's 
Salmonid Restoration Program for coastal watersheds, NMFS and state 
funded multi-county conservation planning efforts in California, and 
the ongoing ESA section 7 and habitat conservation planning efforts 
within the range of currently listed species.
    In California's Central Valley and coastal watersheds within the 
range of the chinook ESUs to be listed, several important conservation 
efforts have recently been implemented or initiated. In the Central 
Valley, the CALFED Bay-Delta Program and Ecosystem Restoration Plan are 
continuing to be implemented while a long-term implementation plan 
continues to be developed. The CALFED program and its implementation 
through 1997 is described in detail in previous Federal Register 
notices (63 FR 11482, March 9, 1998; 63 FR 13347, March 19, 1998). In 
1998, CALFED funded 71 restoration projects totaling $27.5 million 
throughout the Central Valley dealing with fish passage assessment, 
fish passage and/or screening projects, floodplain management/habitat 
restoration, watershed planning, and other activities. In 1999, CALFED 
funded 13 projects totaling $52.5 million in the Central Valley. Nearly 
$40 million of these funds were directed at major salmon and steelhead 
habitat restoration activities on Battle Creek in the upper Sacramento 
River and fish passage improvements at the Anderson-Cottonwood 
Irrigation District in the upper Sacramento River. Substantial new 
funding is anticipated in 2000.
    Several important projects have been initiated or implemented in 
the Central Valley since 1998 as a result of CALFED and/or CVPIA 
funding. In the Sacramento River Basin, significant efforts are 
underway to restore habitat in the Battle Creek drainage in the upper 
Sacramento River. NMFS, FWS, and CDFG have reached agreement with the 
Pacific Gas and Electric Company to restore access to nearly 42 miles 
of high quality spawning and rearing habitat. Water acquisitions are 
ongoing, and most restoration actions should be completed by 2002. This 
effort in Battle Creek will primarily benefit spring-run chinook 
salmon. Significant habitat restoration efforts are also underway in 
Butte, Deer, Mill and Clear Creeks which are tributaries to the upper 
Sacramento River to remove barriers, improve stream flows, and improve 
riparian habitat conditions which are expected to benefit both spring 
and fall chinook salmon. Major new fish screen projects have also 
recently been initiated or completed. Construction on the Glenn-Colusa 
Irrigation District fish screen was implemented and is scheduled for 
completion in late 1999. This is the single largest diversion on the 
upper Sacramento River (3,000 cfs) and will include a $1.0 million 
evaluation and monitoring program. New screens have been installed on 
four additional major diversions in the Sacramento River which total a 
combined diversion of nearly 2,000 cfs. In the San Joaquin River Basin, 
important habitat restoration projects have been implemented in the 
Tuolumne and Stanislaus Rivers to improve instream and riparian habitat 
and flow conditions. These efforts will benefit San Joaquin fall-run 
chinook salmon. Additional habitat restoration efforts were funded in 
the Delta region which should benefit all anadromous salmonids in the 
Central Valley.
    In the San Joaquin Basin, collaboration between water interests and 
state and Federal resource agencies has also led to the development of 
a scientifically based adaptive fisheries management effort known as 
VAMP. The VAMP is intended to (1) improve protection of fall-run 
chinook salmon smolt passage from the San Joquin River Basin, (2) 
gather scientific information on the effects of various flows and Delta 
facilities operations on the survival of salmon smolts through the 
Delta, and (3) provide environmental benefits in the San Joaquin River 
tributaries, the lower San Joaquin River, and the Delta. The 12-year 
plan will be implemented in 1999 through a combination of increasing 
experimental flow releases from tributary streams in the San Joaquin 
Basin and through such operational changes as the reduction of exports 
at the Delta export pumping plants during the peak smolt outmigration 
period (approximately April 15 to May 15). Additional attraction flows 
are targeted for adult fall-run chinook upstream passage in October. In 
coordination with VAMP, the California Department of Water Resources 
(CDWR) will install and operate a barrier at the head of Old River to 
improve the survival of juvenile fall chinook emigrating from the lower 
San Joaquin River. By selecting a combination of flows and export 
rates, VAMP represents a long-term commitment to evaluate the effects 
of San Joaquin River flows and Delta export rates on San Joaquin Basin 
fall-run chinook salmon and to provide improved interim protections.
    In June 1998, the State of California listed Sacramento River 
(Central Valley) spring-run chinook salmon as a threatened species 
under the CESA based on a status review conducted by CDFG. Since the 
state listing of Central Valley spring-run chinook, CDFG and NMFS have 
engaged in a joint ESA/CESA consultation/conference with the CDWR and 
the U.S. Bureau of Reclamation (BOR) to assess the effects the State 
Water Project's and the Central Valley Project's operations are having 
on Sacramento River spring-run chinook salmon. This consultation/
conference focuses on a 1-year operation period through the spring of 
2000, at which time it is anticipated that a plan for implementation of 
Stage 1 for the CALFED Bay-Delta Program and a Federal Record of 
Decision (ROD) will be completed. Pursuant to CDFG's 1994 Fish 
Screening Policy, all diversions that are located within the essential 
habitat of a CESA-listed species require screening. Accordingly, many 
unscreened diversions in the principal spring-run chinook salmon 
tributaries, particularly Butte Creek, have been identified and 
assigned a high priority for implementing corrective actions and 
receiving restoration funding.
    NMFS identified state and Federal hatchery practices within the 
Central Valley as a serious risk factor to fall- and spring-run chinook 
populations at the time of the listing proposal. In an effort to 
address these concerns, both the State of California and FWS have 
recently initiated several actions to address hatchery practice 
concerns. First, CDFG has obtained funding from CALFED to develop a 
statistically designed marking/tagging and recovery program for Central 
Valley hatchery-produced

[[Page 50411]]

chinook salmon to address questions about the relative contribution of 
hatchery and natural production in naturally-spawning adult 
populations, fisheries, and at Central Valley salmon hatcheries, and to 
develop a methodology for evaluating the desirability of selective 
fisheries. Second, CDFG, in conjunction with NMFS, has initiated a 
comprehensive review of anadromous salmonid hatchery practices in 
California. As part of this effort, CDFG has completed an internal 
review of its hatchery operating criteria at Iron Gate, Trinity River, 
Feather River, Nimbus, Mokelumne, and Merced hatcheries and, in some 
instances, modified operations. A major objective of this joint 
evaluation is to review these hatchery operating criteria and identify 
further modifications that are appropriate for natural stock integrity, 
while maintaining the mitigation and/or supplementation objectives of 
individual facilities. Finally, FWS, in conjunction with NMFS, has 
undertaken a reassessment of the mitigation goals and operational 
criteria for the CNFH, which is the only Federal hatchery in 
California. This assessment was initiated in early 1999 and may be 
integrated with the CDFG/NMFS review of state hatchery practices. In 
conjunction with its ongoing re-evaluation of CNFH hatchery programs, 
FWS has substantially reduced its future target for the production and 
release of fall-run chinook salmon fry in order to reduce the potential 
impacts on naturally spawning fall-run populations.
    In the 1998 fiscal year, CDFG's Salmonid Restoration Program 
established a Watershed Initiative element aimed at supporting local, 
community-based watershed planning and landowner-based timber harvest 
planning for coastal regions of California. That same fiscal year, CDFG 
funded $2.65 million in projects for the restoration of coastal salmon 
and anadromous trout habitat through its Salmon and Steelhead Trout 
Restoration Account. CDFG entered into 102 contracts, through the 
Fishery Restoration Grants Program, with public agencies, nonprofit 
groups, recognized Native American Tribes, and individuals to restore 
habitats lost or degraded as a result of past land use practices. 
During the 1999 and 2000 fiscal years, CDFG's Fishery Restoration 
Grants Program has increased funding for this program for coastal 
restoration project grants to approximately $7 million annually. In 
addition to funding these restoration programs, CDFG has substantially 
increased its program staff (36.2 additional personnel-years) to 
improve anadromous salmonid management efforts in coastal watersheds.
    Pursuant to a March 1998 Memorandum of Agreement between NMFS and 
the State of California, NMFS and the State committed to an expedited 
review of California's forest practice rules, their implementation, and 
enforcement. This effort has been ongoing over the past year and has 
resulted in proposals to improve forestry practices in California. 
These proposals are currently undergoing further review prior to being 
submitted to the Board of Forestry for action. The current schedule 
calls for implementing measures adopted by the Board in January 2000. 
NMFS believes this effort is critically important for improving habitat 
conditions in coastal watersheds for anadromous salmonids, including 
chinook salmon.
    An additional Federal effort affecting the Snake River fall-run 
chinook salmon ESU, the Interior Columbia Basin Ecosystem Management 
Project (ICBEMP), was not addressed in the proposed rule. ICBEMP 
addresses Federal lands in this region that are managed under USFS and 
Bureau of Land Management (BLM) Land and Resource Management Plans or 
Land Use Plans amended by PACFISH. PACFISH provides objectives, 
standards, and guidelines that are applied to all Federal land 
management activities, such as timber harvest, road construction, 
mining, grazing, and recreation. USFS and BLM implemented PACFISH in 
1995 intending to provide interim protection to anadromous fish habitat 
while a longer term, basin scale aquatic conservation strategy was 
developed by ICBEMP. It is intended that ICBEMP will have a Final 
Environmental Impact Statement and ROD by early 2000.
    For other ESUs already listed in the Interior Columbia Basin (e.g., 
Snake River chinook salmon, Snake River steelhead, Upper Columbia River 
steelhead, and Upper Columbia River spring-run chinook salmon), NMFS' 
ESA section 7 consultations have required several components that are 
in addition to the PACFISH strategy (NMFS, 1995; NMFS, 1998c). NMFS, 
USFS, and BLM intend these additional components to bridge the gap 
between interim PACFISH direction and the long-term strategy envisioned 
for ICBEMP. NMFS anticipates that these components will also be carried 
forward in the ICBEMP direction. These components include, but are not 
limited to, implementation monitoring and accountability, a system of 
watersheds that are prioritized for protection and restoration, 
improved and monitored grazing systems, road system evaluation and 
planning requirements, mapping and analysis of unroaded areas, multi-
year restoration strategies, and batching and analyzing projects at the 
watershed scale.
    In the range of these chinook salmon ESUs, several notable efforts 
have recently been initiated. Harvest, hatchery, and habitat 
protections under state control are evolving under OPSW. The OPSW is a 
long-term effort to protect all at-risk wild salmonids through 
cooperation between state, local, and Federal agencies, tribal 
governments, industry, private organizations, and individuals. Parts of 
the OPSW are already providing benefits including an aggressive program 
by the Oregon Department of Transportation to inventory, repair, and 
replace road culverts that block fish from reaching important spawning 
and rearing areas. The OPSW also encourages efforts to improve 
conditions for salmon through non-regulatory means, including 
significant efforts by local watershed councils. An Independent Multi 
disciplinary Science Team provides scientific oversight to OPSW 
components and outcomes. A recent Executive Order from Governor 
Kitzhaber reinforced his expectation that all state agencies will make 
environmental health improvement and salmon recovery part of their 
mission.
    NMFS and FWS are also engaged in an ongoing effort to assist in the 
development of multiple species HCPs for state and privately owned 
lands in Oregon, Washington, and California. While section 7 of the ESA 
addresses species protection associated with Federal actions and lands, 
Habitat Conservation Planning under section 10 of the ESA addresses 
species protection on private (non-Federal) lands. HCPs are 
particularly important since more than 85 percent of the habitat in the 
range of the Central Valley spring-run and California Coastal ESUs is 
in non-Federal ownership. The intent of the HCP process is to ensure 
that any incidental taking of listed species will not appreciably 
reduce the likelihood of survival of the species, will reduce conflicts 
between listed species and economic development activities, and will 
provide a framework that would encourage ``creative partnerships'' 
between the public and private sectors and state, municipal, and 
Federal agencies in the interests of endangered and threatened species 
and habitat conservation. Implementation of the recently approved 
Pacific Lumber HCP, which covers 210,000 acres in

[[Page 50412]]

California's coastal watersheds, has begun in earnest with review of 
timber harvest plans and formalization of watershed analysis and 
monitoring programs. The foundation of this HCP rests on watershed 
analysis which is used to tailor site-specific prescriptions for salmon 
conservation on a watershed-specific basis. The initial watershed 
analysis is proceeding and is expected to establish a framework for 
similar analyses in the Pacific Lumber HCP and other HCP efforts which 
are under development in California.
    NMFS will continue to evaluate state, tribal, and non-Federal 
efforts to develop and implement measures to protect and begin the 
recovery of chinook salmon populations within these ESUs. Because a 
substantial portion of land in these ESUs is in state or private 
ownership, conservation measures on these lands will be key to 
protecting and recovering chinook salmon populations in these ESUs. 
NMFS recognizes that strong conservation benefits will accrue from 
specific components of many non-Federal conservation efforts.
    While NMFS acknowledges that many of the ongoing protective efforts 
are likely to promote the conservation of chinook salmon and other 
salmonids, some are very recent and few address salmon conservation at 
a scale that is adequate to protect and conserve entire ESUs. NMFS 
concludes that existing protective efforts are inadequate to preclude a 
listing for the Central Valley spring-run and California Coastal 
chinook salmon ESUs. However, NMFS will continue to encourage these and 
future protective efforts and will work with Federal, state, and tribal 
fisheries managers to evaluate, promote, and improve efforts to 
conserve chinook salmon populations.

Determinations

    Section 3 of the ESA defines the term ``endangered species'' as any 
species that is in danger of extinction throughout all or a significant 
portion of its range. The term ``threatened species'' is defined as any 
species that is likely to become an endangered species within the 
foreseeable future throughout all or a significant portion of its 
range.
    After reviewing the best available information, including public 
and peer review comments, biological data on the species' status, and 
an assessment of protective efforts directed at the four chinook ESUs 
proposed for listing, NMFS has concluded that only two ESUs--the 
Central Valley spring-run ESU and California Coastal ESU--warrant 
protection under the ESA. NMFS has determined that both ESUs are at 
risk of becoming endangered in the foreseeable future throughout all or 
a significant portion of their range. While NMFS has determined that 
the Central Valley fall and late fall-run ESU does not warrant listing 
at this time, the agency remains concerned about the status of this ESU 
and will consider it a candidate species. The agency will reevaluate 
the status of the Central Valley fall and late fall-run ESU as new 
information becomes available to determine whether listing may be 
warranted.
    In the listed ESUs, only ``naturally spawned'' populations of 
chinook salmon are listed. NMFS' intent in listing only these 
populations is to protect chinook salmon stocks that are indigenous to 
(i.e., part of) the ESUs. In this listing determination, NMFS has 
identified various non-indigenous populations that co-occur with fish 
in the California Coastal ESU. NMFS recognizes the difficulty of 
differentiating between indigenous and non-indigenous fish, especially 
when the latter are not readily distinguishable with a mark (e.g., fin 
clip). Also, matings in the wild of either type would generally result 
in progeny that would be treated as listed fish (i.e., they would have 
been naturally spawned in the geographic range of the listed ESUs and 
have no distinguishing mark). Therefore, to reduce confusion regarding 
which chinook salmon are considered listed within the ESUs, NMFS will 
treat all naturally spawned fish as listed for purposes of the ESA. 
Efforts to determine the conservation status of an ESU would focus on 
the contribution of indigenous fish to the listed ESU. It should be 
noted that NMFS will take actions necessary to minimize or prevent non-
indigenous chinook salmon from spawning in the wild unless the fish are 
specifically part of a recovery effort.
    NMFS has evaluated the relationship between hatchery and natural 
populations of chinook salmon in the listed ESUs (NMFS, 1999a). In the 
Central Valley spring-run ESU, spring-run chinook salmon (and their 
progeny) from the Feather River Hatchery stock are considered part of 
the ESU. However, they are not considered to be essential for its 
recovery and are not listed at this time. In the California Coastal 
ESU, chinook salmon (and their progeny) from the following hatchery 
stocks are considered part of the ESU: Redwood Creek, Hollow Tree 
Creek, Freshwater Creek, Mad River Hatchery, Van Arsdale Station, Yager 
Creek, and Mattole River fall-run stock. However, they too, are not 
considered to be essential for the ESU's recovery and are not listed at 
this time. In addition, NMFS concludes that fall-run chinook salmon 
from the following stocks are not part of the California Coastal ESU 
(thus, not listed): Warm Springs Hatchery stock and fall-run fish of 
Feather River or Nimbus Hatchery origin that are released in this ESU.
    The determination that a hatchery stock is not ``essential'' for 
recovery does not preclude it from playing a role in recovery. Any 
hatchery population that is part of the ESU is available for use in 
recovery if conditions warrant. In this context, an ``essential'' 
hatchery population is one that is vital to incorporate into recovery 
efforts (for example, if the associated natural populations were 
extinct or at high risk of extinction). Under such circumstances, NMFS 
would consider taking the administrative action of listing existing 
hatchery fish.
    NMFS' ``Interim Policy on Artificial Propagation of Pacific Salmon 
Under the Endangered Species Act'' (58 FR 17573, April 5, 1993) 
provides guidance on the treatment of hatchery stocks in the event of a 
listing. Under this policy, ``progeny of fish from the listed species 
that are propagated artificially are considered part of the listed 
species and are protected under the ESA.'' In the case of hatchery 
chinook populations considered to be part of the Central Valley spring-
run ESU or California Coastal ESU, NMFS' protective regulations may not 
apply the take prohibitions to naturally spawned listed fish used as 
broodstock as part of an overall conservation program. According to the 
interim policy, the progeny of these hatchery-wild or wild-wild crosses 
would also be listed. Given the requirement for an acceptable 
conservation plan as a prerequisite for collecting broodstock, NMFS 
determines that it is not necessary to consider the progeny of 
intentional hatchery-wild or wild-wild crosses as listed (except in 
cases where NMFS has listed the hatchery population as well).
    In addition, NMFS believes it may be desirable to incorporate 
naturally spawned fish into these unlisted hatchery populations to 
ensure that their genetic and life history characteristics do not 
diverge significantly from the natural populations. NMFS, therefore, 
concludes that it is not inconsistent with NMFS' interim policy, nor 
with the policy and purposes of the ESA, to consider these progeny as 
part of the ESU but not listed.
    NMFS is not now issuing protective regulations under section 4(d) 
of the ESA for these ESUs. NMFS will propose such protective measures 
it considers

[[Page 50413]]

necessary for the conservation of chinook salmon ESUs listed as 
threatened in a forthcoming Federal Register document. Even though NMFS 
is not now issuing protective regulations for these ESUs, Federal 
agencies possess a duty under section 7 of the ESA to consult with NMFS 
if any activity they authorize, fund, or carry out may affect listed 
chinook salmon ESUs. The effective date for this requirement is 
November 15, 1999.

Prohibitions and Protective Measures

    Section 9 of the ESA prohibits certain activities that directly or 
indirectly affect endangered species. These prohibitions apply to all 
individuals, organizations, and agencies subject to U.S. jurisdiction. 
Section 4(d) of the ESA directs the Secretary to implement regulations 
``to provide for the conservation of [threatened] species,'' that may 
include extending any or all of the prohibitions of section 9 to 
threatened species. Section 9(a)(1)(g) also prohibits violations of 
protective regulations for threatened species implemented under section 
4(d). NMFS intends to issue protective regulations pursuant to section 
4(d) for the Central Valley spring-run and California Coastal ESUs, as 
well as for other threatened chinook salmon ESUs.
    In the case of threatened species, NMFS also has flexibility under 
section 4(d) of the ESA to tailor the protective regulations based on 
the adequacy of available conservation measures. Even though existing 
conservation efforts and plans are not sufficient to preclude the need 
for listings at this time, they are, nevertheless, valuable for 
improving watershed health and restoring salmon populations. In those 
cases where well-developed and reliable conservation measures or plans 
exist, NMFS may choose to incorporate them into the recovery planning 
process starting with protective regulations. NMFS has already adopted 
ESA section 4(d) protective regulations that ``except'' a limited range 
of activities from section 9 take prohibitions. For example, the 
interim rule for Southern Oregon/Northern California Coast coho salmon 
(62 FR 38479, July 18, 1997) does not apply the take prohibitions to 
habitat restoration activities conducted in accordance with approved 
plans and fisheries conducted in accordance with an approved state 
management plan. In the future, such rules may contain limits on take 
prohibitions applicable to such activities as forestry, agriculture, 
and road construction when such activities are conducted in accordance 
with approved conservation plans.
    These are all examples where NMFS may apply the modified ESA 
section 9 prohibitions in light of the protections provided in a 
conservation plan that is adequately protective. There may be other 
circumstances as well in which NMFS would use the flexibility of 
section 4(d) of the ESA. For example, if a healthy population exists 
within an overall ESU that is listed, it may not be necessary to apply 
the full range of prohibitions available in section 9. NMFS intends to 
use the flexibility of the ESA to respond appropriately to the 
biological condition of each ESU and to the strength of the efforts to 
protect them.
    Section 7(a)(4) of the ESA requires that Federal agencies consult 
with NMFS on any actions likely to jeopardize the continued existence 
of a species proposed for listing and on actions likely to result in 
the destruction or adverse modification of proposed critical habitat. 
For listed species, section 7(a)(2) requires Federal agencies to ensure 
that activities they authorize, fund, or conduct are not likely to 
jeopardize the continued existence of a listed species or to destroy or 
adversely modify its critical habitat. If a Federal action may affect a 
listed species or its critical habitat, the responsible Federal agency 
must enter into consultation with NMFS.
    Examples of Federal actions likely to affect chinook salmon in the 
listed ESUs include authorized land management activities of the USFS, 
BLM, and National Park Service, as well as operation of hydroelectric 
and storage projects of the BOR and U.S. Army Corps of Engineers (COE). 
Such activities include timber sales and harvest, hydroelectric power 
generation, and flood control. Federal actions, including the COE 
section 404 permitting activities under the Clean Water Act, COE 
permitting activities under the River and Harbors Act, National 
Pollution Discharge Elimination System permits issued by the 
Environmental Protection Agency, highway projects authorized by the 
Federal Highway Administration, Federal Energy Regulatory Commission 
(FERC) licenses for non-Federal development and operation of 
hydropower, and Federal salmon hatcheries, may also require 
consultation. These actions will likely be subject to ESA section 7 
consultation requirements that may result in conditions designed to 
achieve the intended purpose of the project while avoiding or reducing 
impacts to chinook salmon and their habitat within the range of the 
listed ESU.
    There are likely to be Federal actions ongoing in the range of the 
listed ESUs at the time the listing becomes effective. Therefore, NMFS 
will review all ongoing actions that may affect the listed species with 
Federal agencies and will complete formal or informal consultations, 
when necessary, for such actions pursuant to ESA section 7(a)(2).
    Sections 10(a)(1)(A) and 10(a)(1)(B) of the ESA provide NMFS with 
authority to grant exceptions to the ESA's ``taking'' prohibitions. 
Section 10(a)(1)(A) scientific research and enhancement permits may be 
issued to entities (Federal and non-Federal) conducting research that 
involves a directed take of listed species.
    NMFS has issued section 10(a)(1)(A) research or enhancement permits 
for other listed species (e.g., Snake River chinook salmon and 
Sacramento River winter-run chinook salmon) for a number of activities, 
including trapping and tagging to determine population distribution and 
abundance, and for collection of adult fish for artificial propagation 
programs. NMFS is aware of sampling efforts for chinook salmon within 
the listed chinook salmon ESUs, including efforts by Federal and state 
fisheries agencies and by private landowners. These and other research 
efforts could provide critical information regarding chinook salmon 
distribution and population abundance.
    ESA section 10(a)(1)(B) incidental take permits may be issued to 
non-Federal entities performing activities that may incidentally take 
listed species. The types of activities potentially requiring a section 
10(a)(1)(B) incidental take permit include the release of artificially 
propagated fish by state or privately operated and funded hatcheries, 
state or university research on other species not receiving Federal 
authorization or funding, the implementation of state fishing 
regulations, and timber harvest activities on non-Federal lands.

Take Guidance

    On July 1, 1994, (59 FR 34272) NMFS and FWS published a policy 
committing the Services to identify, to the maximum extent practicable 
at the time a species is listed, those activities that would or would 
not constitute a violation of section 9 of the ESA. The intent of this 
policy is to increase public awareness of the effect of a listing on 
proposed and ongoing activities within the species' range. NMFS 
believes that, based on the best available information, the following 
actions will not result in a violation of section 9: (1) Possession of 
chinook salmon from the listed ESUs acquired lawfully by permit issued 
by

[[Page 50414]]

NMFS pursuant to section 10 of the ESA, or by the terms of an 
incidental take statement pursuant to section 7 of the ESA; and (2) 
federally funded or approved projects that involve such activities as 
silviculture, grazing, mining, road construction, dam construction and 
operation, discharge of fill material, stream channelization or 
diversion for which a section 7 consultation has been completed, and 
when such an activity is conducted in accordance with any terms and 
conditions provided by NMFS in an incidental take statement accompanied 
by a biological opinion pursuant to section 7 of the ESA. As described 
previously in this notice, NMFS may adopt ESA section 4(d) protective 
regulations that ``except'' other activities from section 9 take 
prohibitions for threatened species.
    Activities that NMFS believes could potentially harm, injure, or 
kill chinook salmon in the listed ESUs and result in a violation of 
section 9 of the ESA include, but are not limited, to the following: 
(1) Land-use activities in riparian areas and areas susceptible to mass 
wasting and surface erosion, which may disturb soil and increase 
sediment delivered to streams, such as logging, grazing, farming, and 
road construction; (2) destruction or alteration of chinook salmon 
habitat in these listed ESUs, such as removal of large woody debris and 
``sinker logs'' or riparian shade canopy, dredging, discharge of fill 
material, draining, ditching, diverting, blocking, or altering stream 
channels or surface or ground water flow; (3) construction or operation 
of dams or water diversion structures with inadequate fish screens or 
fish passage facilities in a listed species' habitat; (4) construction 
or maintenance of inadequate bridges, roads, or trails on stream banks 
or unstable hill slopes adjacent to or above a listed species' habitat; 
(5) discharges or dumping of toxic chemicals or other pollutants (e.g., 
sewage, oil, gasoline) into waters or riparian areas supporting listed 
chinook salmon; (6) violation of discharge permits; (7) pesticide and 
herbicide applications; (8) interstate and foreign commerce of chinook 
salmon from the listed ESUs without an ESA permit, unless the fish were 
harvested pursuant to legal exception; (9) collecting or handling of 
chinook salmon from listed ESUs (permits to conduct these activities 
are available for purposes of scientific research or to enhance the 
propagation or survival of the species); and (10) release of non-
indigenous or artificially propagated species into a listed species' 
habitat or where they may access the habitat of listed species. This 
list is not exhaustive. It is intended to provide some examples of the 
types of activities that might or might not be considered by NMFS as 
constituting a take of listed chinook salmon under the ESA and its 
regulations. Questions regarding whether specific activities will 
constitute a violation of this rule and general inquiries regarding 
prohibitions and permits should be directed to NMFS (see ADDRESSES).

Effective Date of Final Listing

    Given the cultural, scientific, and recreational importance of 
chinook salmon and the broad geographic range of these chinook salmon 
ESUs, NMFS recognizes that numerous parties may be affected by the 
listings. Therefore, to permit an orderly implementation of the 
consultation requirements and take prohibitions associated with this 
action, the final listings will take effect on November 15, 1999.

Conservation Measures

    Conservation benefits are provided to species listed as endangered 
or threatened under the ESA through increased recognition, recovery 
actions, Federal agency consultation requirements, and prohibitions on 
taking. Increased recognition through listing promotes public awareness 
and conservation actions by Federal, state, and local agencies, private 
organizations, and individuals.
    Several conservation efforts are underway that may reverse the 
decline of west coast chinook salmon and other salmonids. NMFS is 
encouraged by these significant efforts, which could provide all 
stakeholders with a less regulatory approach to achieving the purposes 
of the ESA--protecting and restoring native fish populations and the 
ecosystems upon which they depend. NMFS will continue to encourage and 
support these initiatives as important components of recovery planning 
for chinook salmon and other salmonids.
    To succeed, protective regulations and recovery programs for 
chinook salmon will need to focus on conserving aquatic ecosystem 
health. NMFS intends that Federal lands and Federal activities play a 
primary role in preserving listed populations and the ecosystems upon 
which they depend. However, throughout the range of the listed ESUs, 
chinook salmon habitat occurs and can be affected by activities on 
state, tribal, or private land.
    Conservation measures that could be implemented to help conserve 
the species are listed here (the list is generalized and does not 
constitute NMFS' interpretation of a recovery plan under section 4(f) 
of the ESA). Progress on some of these is being made to different 
degrees in specific areas.
    1. Measures could be taken to promote practices that are more 
protective of (or restore) chinook salmon habitat across a variety of 
land and water management activities. Activities affecting this habitat 
include timber harvest; agriculture; livestock grazing and operations; 
pesticide and herbicide applications; construction and urban 
development; road building and maintenance; sand and gravel mining; 
stream channelization; dredging and dredged spoil disposal; dock and 
marina construction; diking and bank stabilization; dam construction/
operation; irrigation withdrawal, returns, storage, and management; 
mineral mining; wastewater/pollutant discharge; wetland and floodplain 
alteration; habitat restoration projects; and woody debris/structure 
removal from rivers and estuaries. Each of these activities could be 
modified to ensure that watersheds and specific river reaches are 
adequately protected in the short- and long-terms.
    2. Fish passage could be restored at barriers to migration through 
the installation or modification of fish ladders, upgrade of culverts, 
or removal of barriers.
    3. Harvest regulations could be modified to protect listed chinook 
salmon populations affected by both directed harvest and incidental 
take in other fisheries.
    4. Artificial propagation programs could be modified to minimize 
negative impacts (e.g., genetic introgression, competition, disease, 
etc.) upon native populations of chinook salmon.
    5. Predator control/relocation programs could be implemented in 
areas where predators pose a significant threat to chinook salmon.
    6. Measures could be taken to improve monitoring of chinook salmon 
populations and their habitat.
    7. Federal agencies such as the USFS, BLM, NPS, FERC, COE, U.S. 
Department of Transportation, and BOR could review their management 
programs and use their discretionary authorities to formulate 
conservation plans pursuant to section 7(a)(1) of the ESA.
    NMFS encourages non-Federal landowners to assess the impacts of 
their actions on threatened or endangered salmonids. In particular, 
NMFS encourages state and local governments to use their existing 
authorities and programs and encourages the formation of watershed 
partnerships to promote conservation in accordance with ecosystem 
principles. These partnerships will be successful

[[Page 50415]]

only if state, tribal, and local governments, landowner 
representatives, and Federal and non-Federal biologists all participate 
and share the goal of restoring salmon to the watersheds.

Critical Habitat

    Section 4(a)(3)(A) of the ESA requires that, to the extent prudent 
and determinable, critical habitat be designated concurrently with the 
listing of a species. Section 4(b)(6)(C)(ii) provides that, where 
critical habitat is not determinable at the time of final listing, NMFS 
may extend the period for designating critical habitat by no more than 
one additional year.
    In the proposed rule (63 FR 11482, March 9, 1998), NMFS described 
the areas that may constitute critical habitat for these chinook salmon 
ESUs. Since then, NMFS has received numerous comments from the public 
concerning the process and definition of critical habitat for these and 
other listed salmonids. The agency needs additional time to complete 
the needed biological assessments and evaluate special management 
considerations affecting critical habitat. Therefore, critical habitat 
is not yet determinable for these ESUs, and NMFS extends the deadline 
for designating critical habitat for no more than 1 year until the 
required assessments can be made.

Classification

    The 1982 amendments to the ESA, in section 4(b)(1)(A), restrict the 
information that may be considered when assessing species for listing. 
Based on this limitation of criteria for a listing decision and the 
opinion in Pacific Legal Foundation v. Andrus, 675 F.2d 825 (6th Cir., 
1981), NMFS has categorically excluded all ESA listing actions from the 
environmental assessment requirements of the National Environmental 
Policy Act (NEPA) under NOAA Administrative Order 216-6.
    As noted in the Conference Report on the 1982 amendments to the 
ESA, economic impacts cannot be considered when assessing the status of 
a species. Therefore, the economic analysis requirements of the 
Regulatory Flexibility Act (RFA) are not applicable to the listing 
process. In addition, this final rule is exempt from review under E.O. 
12866.
    This rule has been determined to be major under the Congressional 
Review Act (5 U.S.C. 801 et seq.)
    At this time NMFS is not promulgating protective regulations 
pursuant to ESA section 4(d). In the future, prior to finalizing its 
4(d) regulations for the threatened chinook salmon ESUs, NMFS will 
comply with all relevant NEPA and RFA requirements.

References

    A complete list of all references cited herein is available upon 
request (see ADDRESSES) and can also be obtained from the internet at 
www.nwr.noaa.gov.

Change in Enumeration of Threatened and Endangered Species

    In the proposed rule issued on March 9, 1998 (63 FR 11482), the 
Central Valley spring-run chinook salmon was added as an endangered 
species to paragraph (a) in Sec. 222.23, while several threatened 
chinook salmon ESUs (including populations in the California Coastal 
chinook salmon ESU) were enumerated under Sec. 227.4. Since that time 
NMFS has issued a final rule consolidating and reorganizing existing 
regulations regarding implementation of the ESA (64 FR 14052, March 23, 
1999). In this reorganization, Sec. 222.23 has been redesignated as 
Sec. 224.101, and Sec. 227.4 has been redesignated as Sec. 223.102. 
Given these reorganized regulations, as well as the Central Valley 
spring-run ESU's revised status as threatened, both the Central Valley 
spring-run and the California Coastal chinook salmon ESUs are now 
designated in this final rule as paragraphs (a)(20) and (a)(21) and 
added under Sec. 223.102, respectively.

List of Subjects in 50 CFR Part 223

    Endangered and threatened species, Exports, Imports, Marine 
mammals, Transportation.

    Dated: September 9, 1999.
Andrew A. Rosenberg,
Deputy Assistant Administrator for Fisheries, National Marine Fisheries 
Service.
    For the reasons set out in the preamble, 50 CFR part 223 is amended 
as follows:

PART 223--THREATENED MARINE AND ANADROMOUS SPECIES

    1. The authority citation for part 223 is revised to read as 
follows:

    Authority: 16 U.S.C. 1531 et seq.; 16 U.S.C. 742a et seq.; 31 
U.S.C. 9701.

    2. In Sec. 223.102, paragraphs (a)(20) and (a)(21) are added to 
read as follows:


Sec. 223.102  Enumeration of threatened marine and anadromous species.

* * * * *
    (a) * * *
    (20) Central Valley spring-run chinook salmon (Oncorhynchus 
tshawytscha). Includes all naturally spawned populations of spring-run 
chinook salmon in the Sacramento River Basin, and its tributaries, 
California.
    (21) California coastal chinook salmon (Oncorhynchus tshawytscha). 
Includes all naturally spawned populations of chinook salmon from 
Redwood Creek (Humboldt County, California) through the Russian River 
(Sonoma County, California).
* * * * *
[FR Doc. 99-24051 Filed 9-15-99; 8:45 am]
BILLING CODE 3510-22-F