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

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

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