U.S. Dept Commerce/NOAA/NMFS/NWFSC/PublicationsNOAA Technical Memorandum NMFS-NWFSC-10Status Review for Oregon's Illinois River Winter SteelheadPeggy J. Busby, Orlay W. Johnson, Thomas C. Wainwright, F. William       Waknitz, and Robin S. Waples
National Marine Fisheries ServiceNorthwest Fisheries       Science CenterCoastal Zone and Estuarine Studies Division2725       Montlake Blvd. E.Seattle WA 98112

May 1993 
U.S. DEPARTMENT OF COMMERCERonald H.       Brown, Secretary       
National Oceanic and Atmospheric       AdministrationJohn A. Knauss, Administrator

National Marine Fisheries ServiceWilliam W. Fox,       Jr., Assistant Administrator for Fisheries 
CONTENTSSummary
Acknowledgments
Introduction
Key   Questions in ESA Evaluations
The     "Species" QuestionThresholds     for Threatened or Endangered StatusHatchery     Fish and Natural Fish
Petition   to List Illinois River Winter Steelhead
Reproductive     IsolationGeographic       Isolation
North-south         genetic differencesDistance         to Illinois River spawning groundsIllinois         River Falls
Distinctive       Life History and Body Size Characteristics
Absence         of half-poundersTiming         of peak spawningSmolt         ageAge         and body size at first spawning
Effects       of Hatchery Fish
Evolutionary     SignificanceGeographic       Location
Thermal       Adaptation
Spawning       Distribution
Anadromous       Life History
Population     Trends
Summary   of Biological and Environmental Information
Environmental     FeaturesKlamath       Mountain Geological Province
Water       temperature
Illinois       River Falls
Life     HistoryFreshwater       Life History and Smoltification 
Half-Pounders
Saltwater       Life History
Spawning
Summer-         and winter-run steelheadAge         and body size at first spawningRepeat         spawningDistribution         of spawning in Illinois River
Resident       Fish
History     of Hatchery Stocks and OutplantingsSteelhead       Hatcheries
Releases       in the Illinois River
GeneticsPrevious       Studies
Protein         electrophoresisChromosomal         studiesDNA         analysis
New       Data
Population     TrendsRegional       Overview of Steelhead Abundance
Historical       Abundance in Southern Oregon
Abundance       of Illinois River Winter Steelhead
Variation         in fishing effort and effectivenessNonreporting         biasLocal         variation in fishing effort
Abundance       of Steelhead in Southern Oregon
Rogue,         Applegate, and Chetco RiversElk,         Pistol, and Winchuck Rivers
Discussion     and ConclusionsReproductive       Isolation
Straying         RatesBarriers         to MigrationGenetic         DataLife         History TraitsSummary
Evolutionary       Significance
Habitat         CharacteristicsPhenotypic         and Life History TraitsGenetic         DataEffects         of Artificial PropagationSummary
Conclusions

Citations
Appendix   - Glossary
SUMMARYThis report summarizes biological information gathered in conjunction with an Endangered Species Act (ESA) status review for winter steelhead (Oncorhynchus mykiss) from the Illinois River, a tributary of the Rogue River in southern Oregon. The National Marine Fisheries Service (NMFS) received a petition in May 1992 asking that this population be listed as a threatened or endangered species under the ESA. In evaluating the petition, two key questions had to be addressed: Do Illinois River winter steelhead represent a species as defined by the ESA? and, if so, is the species threatened or endangered? With respect to the first question, the ESA allows listing of "distinct population segments" of vertebrates as well as named species and subspecies. NMFS policy on this issue for Pacific salmon and steelhead is that a population will be considered "distinct" for purposes of the ESA if it represents an evolutionarily significant unit (ESU) of the species as a whole. To be considered an ESU, a population or group of populations must 1) be substantially reproductively isolated from other populations, and 2) contribute substantially to ecological/genetic diversity of the biological species. Once an ESU is identified, a variety of factors related to population abundance are considered in determining whether a listing is warranted. 
The petitioners argued that geographic isolation of the Illinois River spawning grounds, the partial barrier of Illinois River Falls, life history differences between steelhead from the Illinois and Rogue Rivers, and evidence for genetic differences between steelhead from southern and northern Oregon demonstrate reproductive isolation of Illinois River winter steelhead. Distinctive life history and habitat characteristics were the primary factors identified by the petitioners as evidence that Illinois River winter steelhead contribute substantially to the species' ecological/genetic diversity. A tenfold decline in angler catch of Illinois River winter steelhead since 1971 was cited as evidence that the population qualifies for listing under the ESA.

In evaluating the status of Illinois River winter steelhead, NMFS focused on information for coastal steelhead populations from southern Oregon and northern California. The National Marine Fisheries Service concluded that available information does not make a strong case for reproductive isolation of Illinois River winter steelhead. Genetic data, including new data gathered for this status review, fail to show that Illinois River winter steelhead as a group are distinct from other coastal steelhead populations. Although this does not prove that Illinois River winter steelhead are not reproductively isolated, it does mean that evidence to support reproductive isolation must be found elsewhere. Other lines of information are largely inconclusive in this regard. Straying data for naturally spawning steelhead in the region are largely nonexistent. Geographic features such as the Illinois River Falls are potential isolating mechanisms, but evidence that they operate in this way is lacking. Although other explanations are possible, life history characteristics suggest some degree of reproductive isolation from Rogue River steelhead. However, these same characteristics fail to show differences between Illinois River winter steelhead and most other coastal steelhead populations.

With respect to the second criterion for defining an ESU, several phenotypic and life history characteristics show modest differences between Illinois River winter steelhead and steelhead from the Rogue River. These differences suggest that either a) there are some genetic differences between steelhead from the two rivers, b) the natural environments of the two rivers differ in at least some respects, or c) artificial propagation has affected life history characteristics of Rogue River steelhead, thus causing them to differ from Illinois River winter steelhead. In any case, in the larger context of coastal steelhead from southern Oregon and northern California, it is the Rogue River fish, rather than the Illinois River winter steelhead, that appear to be somewhat anomalous. That is, steelhead from the Illinois River appear to be somewhat distinctive in comparison to Rogue River steelhead, but not in comparison to other coastal steelhead populations.

We therefore conclude that although Illinois River winter steelhead may be locally distinctive within the Rogue River basin, they do not by themselves represent an evolutionarily significant unit of the biological species Oncorhynchus mykiss.

Because Illinois River winter steelhead are therefore not a "species" as defined by the ESA, the question of whether they should be listed as threatened or endangered under the Act need not be addressed. Nevertheless, steelhead from the Illinois River are undoubtedly part of a larger ESU whose boundaries remain to be determined. Whether the larger ESU that contains Illinois River winter steelhead would merit protection under the ESA cannot be determined until the nature and extent of the ESU are identified and additional information about patterns of abundance in coastal steelhead is compiled. This status review, therefore, should be viewed as the first step in a process to define the larger ESU and determine whether it qualifies for protection under the ESA.
ACKNOWLEDGMENTS
The status review for the Illinois River winter steelhead was conducted by a team of scientists from the Northwest Fisheries Science Center (NWFSC). The biological review team relied on an extensive ESA public record developed pursuant to this review and comprised of public comments and research reports submitted by dedicated citizens and by state and federal agencies. Special acknowledgment should be extended to the Oregon Department of Fish and Wildlife (ODFW) and the U.S. Forest Service, who bore the burden of supplying the review team with a large number of publications required for this review.

The review team would also like to acknowledge the assistance of personnel from ODFW's Rogue River and Gold Beach District Offices, California Department of Fish and Game (CDFG) Region 1, Redwood National Park, and Six Rivers and Rogue River National Forests in the collections of steelhead for genetic analysis. Norman Buroker generously shared with us his unpublished data on steelhead mitochondrial DNA. We also would like to acknowledge personnel from the Genetics Project at the NWFSC for assistance with field collection and electrophoresis of collected samples: Paul Aebersold, Mary Ann Brainard, Jeffrey Hard, Kathleen Neely, Cynthia Shiflett, Frederick "Bud" Welch, and Stephanie Woods. Garth Griffin of the NMFS Northwest Region in Portland provided invaluable assistance in facilitating information exchange. Paul Moran and Linda Park assisted with reviewing DNA data.

Members of the biological review team were Peggy Busby, David Damkaer, Robert Emmett, Steve Grabowski, Orlay Johnson, Conrad Mahnken, Gene Matthews, Michael Schiewe, Thomas Wainwright, William Waknitz, Robin Waples, John Williams, and Gary Winans.
INTRODUCTION
The name steelhead refers to the anadromous form of Oncorhynchus mykiss. Endemic distribution of steelhead extends from the Kamchatka Peninsula in Asia, east to Alaska, and south along the Pacific coast of North America to northern Baja California (Barnhart 1986, Burgner et al. 1992).

Steelhead are commonly described as either summer-run (summer steelhead) or winter-run (winter steelhead), based on time and duration of spawning migration and state of sexual maturity at the time of river entry. Summer steelhead enter fresh water between May and October, in a sexually immature condition. After several months in fresh water, summer steelhead mature and spawn. Winter steelhead enter fresh water between November and April with well developed gonads and spawn shortly thereafter. Both summer and winter steelhead are found in some drainages, including the Rogue River basin of southwest Oregon. The Illinois River, a tributary to the Rogue River (Fig. 1), is generally considered to have only winter-run steelhead.

Illinois River winter steelhead were identified as being "at moderate risk of extinction" in a report on Pacific salmon stocks at risk (Nehlsen et al. 1991). Declining catch of winter steelhead from the Illinois River and public comment resulted in the imposition of no-take fishing regulations for Illinois River steelhead by the Oregon Department of Fish and Wildlife (ODFW) in 1992 (M. Jennings). In response to indications that the population is declining, Oregon Natural Resources Council, Siskiyou Regional Education Project, Federation of Fly Fishers, Kalmiopsis Audubon Society, Siskiyou Audubon Society, Klamath/Siskiyou Coalition, Headwaters, The Wilderness Society, North Coast Environmental Center, Oregon Chapter of The Sierra Club, and The National Wildlife Federation petitioned the National Marine Fisheries Service (NMFS) to list the Illinois River winter steelhead as a threatened or endangered "species" (ONRC et al. 1992) under the U.S. Endangered Species Act (ESA or Act) of 1973 as amended (U.S.C. 1531 et seq.). This report summarizes a review of the status of Illinois River winter steelhead conducted by the NMFS Northwest Region biological review team.
KEY QUESTIONS IN ESA EVALUATIONS
Two key questions must be addressed in determining whether a listing under the ESA is warranted:
- Is the entity in question a "species" as defined by the ESA?   
- If so, is the "species" threatened or endangered? 
The "Species" Question
As amended in 1978, the ESA allows listing of "distinct population segments" of vertebrates as well as named species and subspecies. However, the Act provides no specific guidance for determining what constitutes a distinct population, and the resulting ambiguity has led to the use of a variety of criteria in listing decisions over the past decade. To clarify the issue for Pacific salmon, NMFS published a policy describing how the agency will apply the definition of "species" in the Act to anadromous salmonid species, including steelhead (NMFS 1991). A more detailed description of this topic appears in the NMFS "Definition of Species" paper (Waples 1991). The NMFS policy stipulates that a salmon population (or group of populations) will be considered "distinct" for purposes of the Act if it represents an.evolutionarily significant unit (ESU) of the biological species. An ESU is defined as a population that (a) is reproductively isolated from conspecific populations and (b) represents an important component in the evolutionary legacy of the species. Types of information that can be useful in determining the degree of reproductive isolation include incidence of straying, rates of recolonization, degree of genetic differentiation, and the existence of barriers to migration. Insight into evolutionary significance can be provided by data on phenotypic and protein or DNA characters; life-history characteristics; habitat differences; and the effects of stock transfers or supplementation efforts.
Thresholds for Threatened or Endangered Status
Neither NMFS nor the U.S. Fish and Wildlife Service (USFWS), which share authority for administering the ESA, has an official policy regarding thresholds for considering ESA "species" as threatened or endangered. The National Marine Fisheries Service has published a nonpolicy document on this topic (Thompson 1991). There is considerable interest in incorporating the concepts of Population Viability Analysis (PVA) into ESA threshold considerations for Pacific salmon. However, most of the PVA models require substantial life-history information that often will not be available for Pacific salmon populations.

Therefore, NMFS considers a variety of information in evaluating the level of risk faced by an ESU. Important factors include 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, based on indices such as dam or redd counts or on estimates of spawner-recruit ratios; 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 improvements in mainstem passage) that have predictable short-term consequences for abundance of the ESU.
Hatchery Fish and Natural Fish
Because artificial propagation of Pacific salmonids has been widespread for many years, the influence of hatchery fish needs to be considered in most ESA status reviews. NMFS policy stipulates that in determining whether a population is "distinct" for purposes of the ESA, attention should focus on "natural" fish, which are progeny of naturally spawning fish (Waples 1991). This approach directs attention to fish that spend their entire life cycle in natural habitat and is consistent with the mandate of the Act to conserve threatened and endangered species in their native ecosystems. Implicit in this approach is the recognition that fish hatcheries are not a substitute for natural ecosystems.

The decision to focus on natural fish is based entirely on ecosystem considerations; the question of the relative merits of hatchery vs. natural fish is a separate issue. Fish are not excluded from ESA consideration simply because some of their direct ancestors may have spent time in a fish hatchery, nor does identifying a group of fish as "natural" as defined here automatically mean that they are part of an ESU.

Once the natural component of a population has been identified, the next step is to determine whether this population component is "distinct" for purposes of the ESA. In making this determination, we used guidelines in the NMFS "Definition of Species" paper (Waples 1991). We considered factors outlined in the section entitled "Effects of artificial propagation and other human activities" to determine the extent to which artificial propagation may have affected the natural fish, through either direct supplementation or straying of hatchery fish. Thus, fish meeting the definition of "natural" adopted here could be excluded from ESA considerations.

Threshold determinations also will focus on natural fish, on the premise that an ESU is not healthy unless a viable population exists in the natural habitat.
PETITION TO LIST ILLINOIS RIVER WINTER STEELHEAD
This section summarizes claims made by the petitioners (ONRC et al. 1992) to support the designation of the Illinois River winter steelhead as an ESU. Organization of this section, and references to the criteria of Reproductive Isolation and Evolutionary Significance, follows that of the petition. After discussing information relevant to each of these issues in the next section of this status review, we evaluate the merits of the petitioners' arguments in the Discussion and Conclusions section.
Reproductive Isolation
Geographic Isolation

North-south genetic differences--The petition cited Hatch (1990), who conducted electrophoretic analyses on steelhead from several Oregon streams and found evidence for a genetic difference between steelhead populations from northern vs. southern Oregon coastal drainages. The petitioners argued that these genetic differences presumably reflect reproductive isolation. Hatch identified Cape Blanco as a genetic break point and suggested that "there is a less than average amount of straying between the populations north and south of this feature" (Hatch 1990, p. 33-34). The petitioners pointed out that the mouth of the Rogue River is 43 km south of Cape Blanco.

Distance to Illinois River spawning grounds--The petitioners stated that steelhead migrate up to 121 km up the Illinois River to spawn, which isolates them from other Rogue River basin steelhead stocks.

Illinois River Falls--The petitioners proposed that navigating the natural falls at River Kilometer (RKm) 64 may have been a selective factor in the evolution of the Illinois River winter steelhead. They stated that prior to modification and ladder construction, stray steelhead "would not arrive at the proper time nor have the persistence to get over the barrier" (ONRC et al. 1992, p. 4).

Distinctive Life History and Body Size Characteristics

Absence of half-pounders--The petitioners described half-pounders as "a common life history type found in winter and summer steelhead that spawn in tributaries to the middle and upper Rogue River" (ONRC et al. 1992, p. 4). They contended that the absence of half-pounders in the Illinois River supports the theory of genetic isolation of Illinois River winter steelhead.

Timing of peak spawning--The petitioners referenced Rivers (1964), who indicated that peak spawning for Illinois River winter steelhead occurs 1 April, which he said was 2 weeks earlier than the peak for the middle Rogue River and 2 weeks later than the peak for the Applegate River. The petitioners cited timing of spawning as a heritable trait (Ricker.1972) and the importance of "run timing, emergence, and rearing patterns to streams that go dry or become uninhabitable by mid-summer" (ONRC et al. 1992, p. 4).

Smolt age--Rivers (1964) was cited for describing the Illinois River winter steelhead as having the longest freshwater phase of Rogue River basin steelhead stocks.

Age and body size at first spawning--The petitioners cited Rivers (1964), who concluded that "at the time of first spawning, winter steelhead in the Illinois River were older and were heavier at a given length than counterparts captured in the middle Rogue and in the Applegate River" (ODFW 1990, p. 34). The petition stated that "the larger body size of Illinois River adult steelhead may help them jump the Illinois River Falls" (ONRC et al. 1992, p. 5).

Effects of Hatchery Fish

The petitioners referred to ODFW records to document a low incidence of straying of hatchery steelhead into the Illinois River. The petition (ONRC et al. 1992, p. 5) stated that 
Scale samples from 52 Illinois River steelhead caught during   1984-85 were all interpreted as wild fish by ODFW....The Illinois River winter   steelhead is the only winter steelhead population known to be in compliance   with the Wild Fish Policy because of low straying rates of hatchery fish into   the Illinois River.Evolutionary Significance
Geographic Location

The petitioners described the Illinois River as "an interior valley in the southern fourth of the steelhead species' range" (ONRC et al. 1992, p. 5). They reiterated Hatch's (1990) findings of "phenotypic differences supporting a separation of steelhead south of Cape Blanco, Oregon" (ONRC et al. 1992, p. 5).

Thermal Adaptation

The petitioners calculated population size for Illinois River winter steelhead from 1966 to 1990 using ODFW catch data. They contended that the population "historically demonstrated a high level of productivity in an environment that appears extremely hostile to a cold water fish" (ONRC et al. 1992, p. 5). They cited ODFW (1990, p. 34) who reported that "adaptations to survive warm water in the Illinois River basin may be quite different than adaptations to survive in small tributaries of the Rogue River close to the coast."

Spawning Distribution

"Widely distributed spawning populations located throughout the Illinois Basin ensure genetic continuity and continued high productivity during natural environmental catastrophes" (ONRC et al. 1992, p. 5).

Anadromous Life History

"The anadromous life history is crucial to the steelhead's high degree of life history diversity. Anadromy allows Illinois River winter steelhead to colonize streams where local extinctions have occurred and also confers a competitive advantage through large body size and increased fecundity" (ONRC et al. 1992, p. 5-6).
Population Trends
The petitioners cited a tenfold decline in angler catch of Illinois River winter steelhead since 1971. They recognized that trends in catch may be affected by trends in angler effort but believed that such a dramatic decline in effort was unlikely. They also estimated that Illinois River winter steelhead survival has been below replacement level in 13 of 16 years (1971-86), with no prospect for improvement in the near future. The petitioners interpreted this consistent inability of the population to replace itself as evidence it is endangered according to the framework of a draft policy statement by NMFS and USFWS (1980).
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