Aquatic Management Indicator Species Analysis. Steelhead Trout. Ochoco National Forest. And. Crooked River National Grassland.

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1 Aquatic Management Indicator Species Analysis Steelhead Trout Ochoco National Forest And Crooked River National Grassland July 20, 2011 Prepared by: Mark Lehner Paulina RD Fisheries Biologist Reviewed by: Daniel Rife - Forest Fisheries Program Manager 1

2 Table of Contents I. INTRODUCTION... 3 Forest MIS discussion... 3 II. CONSERVATION STATUS... 5 III. BROADVIEW DESCRIPTION OF ANALYSIS AREA Deschutes Basin John Day Basin IV. SPECIES DISTRIBUTION MID COLUMBIA ESU STEELHEAD TROUT, Deschutes River Basin DPS MID COLUMBIA ESU STEELHEAD TROUT, John Day River Basin DPS Critical Habitat V. LIFE HISTORY Habitat requirements VI. POPULATION STATUS AND TREND Ochoco National Forest Deschutes Basin Steelhead Ochoco National Forest John Day Basin Steelhead VII. HABITAT AND TREND VIII. VIABILITY DETERMINATION Literature Cited Appendix A

3 Ochoco National Forest Aquatics Management Indicator Species Viability Analysis for Steelhead Trout (Oncorhynchus mykiss) I. INTRODUCTION Forest MIS discussion In the Ochoco National Forest Land and Resource Management Plan and the Crooked River National Grassland Land and Resource Management Plan (LRMP), three aquatic management indicator species (MIS) have been identified. They are rainbow trout, brook trout, and steelhead trout. Subsequent to the signing of these LRMP s rainbow trout on the east side of Cascade mountain crest in the Columbia basin and elsewhere were described as redband trout by Behnke (1992). Brook trout are a non-native trout that was planted for fishing opportunities in the 1920 s and 1930 s. They are known to exist in only a few streams on the Forest including Allen Creek, Lookout Creek, and Brush Creek. The Final Environmental Impact Statement (FEIS) for the Ochoco National Forest and Crooked River National Grassland states that management indicator species, or groups of species, were chosen to help determine the effects of management activities on fish habitat. The habitat requirements of MIS are assumed to be similar for other fish species. If a selected species and its habitat are influenced significantly by management activities, like effects can be expected on other fish species with similar habitat requirements. Redband trout, brook trout, and steelhead trout were selected as an indicator group because salmonids have a broad distribution across the Forest and Grassland and are of economic importance resulting from commercial and recreational harvest. The group generally has similar habitat requirements which are narrow enough to ensure viability of most other game fish. The habitat requirements make the group a good indicator of riparian habitat and aquatic habitat condition for both the Ochoco National Forest and the Crooked River National Grassland. The LRMP s state that management of these species will occur through providing habitat by managing per riparian prescriptions (Management Area F-15 Riparian). Within the MA-15 Riparian description the LRMP states that Fully functional riparian areas are essential for the maintenance of viable fish populations on the Forest. Riparian areas provide food, cover, and a source of large woody material for aquatic insects, fish and land animals. The vegetation of streamside areas filter sediment and shade the water surface to help maintain stable stream temperatures. Attributes of a healthy aquatic ecosystem includes: cold and clean water; clean channel substrates; stable streambanks; healthy streamside vegetation; complex channel habitat created by large wood, cobles, boulders, streamside vegetation, and undercut banks; deep pools; and waterways free of barriers. Healthy riparian areas maintain adequate temperature regulation, nutrient cycles, natural erosion rates, and provide for instream wood recruitment. 3

4 Implementation of the LRMP s includes monitoring of the following to determine viability of the management indicator species: Monitoring Item Fisheries: Habitat capability and productivity, species and size composition Actions/Effects Monitored Determine if habitat meets management objectives for John Day River Tributaries and Trout Creek Units of Measure 1. Sedimentation 2. Temperature, 3. Channel morphology 4. Riparian community composition 5. Large woody material 6. Smolt numbers Variability Threshold Loss in habitat capability, objectives not being met Suggested Methods 1. Bucket or ocular 2. Thermograph 3. Cross section 4. Line transects 5. Riparian plant survey 6. Electrofishing There has been no monitoring of smolt numbers on Forest, therefore redd counts will be used as a substitute for determining population trend. 4

5 II. CONSERVATION STATUS Table 1 Status Summary of Steelhead Trout (Oncorhynchus mykiss) Species Federal State Forest (Ochoco LRMP) Steelhead (Oncorhynchus mykiss) Threatened Not listed MIS Federal The Middle Columbia River steelhead distinct population segment (DPS) was listed as threatened under the Endangered Species Act of 1973 (ESA) on January 5, 2006 (71 FR 834). ESA STATUS - THREATENED (unless otherwise cites the following population information was obtained from the Middle Columbia River Recovery Plan available at: Planning/Recovery-Domains/Interior-Columbia/Mid-Columbia/Mid-Col-Plan.cfm The Mid-Columbia River (MCR) Steelhead Distinct Population Segment (DPS) were listed as threatened under the ESA on March 25, 1999 (64 FR 14517) and NMFS reaffirmed its threatened status on January 5, 2006 (71 FR 834). The MCR steelhead DPS includes all naturally-spawned populations in streams within the Columbia River Basin from above the Wind River in Washington and the Hood River in Oregon (exclusive), upstream to and including the Yakima River in Washington, excluding steelhead from the Snake River Basin (71 FR 834 January 5, 2006; 64 FR March 25, 1999). MCR steelhead do not include resident forms of O.mykiss (redband or rainbow trout) co-occurring with these steelhead. Seven steelhead hatchery programs including the Round Butte Hatchery within the Action area are considered are considered part of the MCR steelhead DPS, Four Major Population Groups (MPG) have been identified within the DPS: Cascades Eastern Slope tributaries, Yakima River, John Day River Umatilla/WallaWalla Rivers The ONF includes portions of the John Day River MPG and Cascades Eastern Slope tributaries MPG, either directly inhabited by steelhead or designated as critical habitat. Within the Cascade Eastern Slope MPG, the Deschutes River Eastside population is included within the analysis area covered by this assessment. Figure 1 below shows designated critical steelhead habitat in the area covered by this analysis. Critical Habitat Critical habitat was designated on February 16, 2000 [65 FR 7764], but vacated (undesignated) by court order on April 30, On September 2, 2005, NMFS published a final rule (70 FR 52630) to designate critical habitat for Mid-C steelhead and 12 other ESUs/DPSs of salmon and steelhead. The final rule took effect on January 2, The Critical Habitat Assessment Review Team (CHART) (NMFS 2004c) rated the conservation value of all 5th-field HUCs supporting populations of Mid-C steelhead. Essential features of designated critical habitat include substrate, water quality, water quantity, water temperature, food, riparian 5

6 vegetation, access, water, velocity, space, and safe passage. These features also describe the habitat factors associated with viability for all ESUs and DPSs. The specific habitat requirements for each ESU or DPS differ by life history type and life stage. Critical Habitat is further discussed below in Section III (Species Distribution). 6

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9 NatureServe (Oncorhynchus mykiss) Steelhead Trout Global Status: G5T4 Global Status Last Reviewed: 10Feb2003 Global Status Last Changed: 10May2001 Rounded Global Status: T4 - Apparently Secure Nation: United States National Status: N4 Nation: Canada National Status: NNR U.S. & Canada State/Province Status United States Colorado (SNA), Idaho (S2S3), Montana (S1), Nevada (S2), Oregon (S3) Canada British Columbia (S4), Manitoba (SNA) Interpreting NatureServe Conservation Status Ranks The conservation status of a species or ecosystem is designated by a number from 1 to 5, preceded by a letter reflecting the appropriate geographic scale of the assessment (G = Global), N = National, and S = Subnational). The numbers have the following meaning: Refer the map below in the Species Distribution section page = critically imperiled 2 = imperiled 3 = vulnerable 4 = apparently secure 5 = secure. For example, G1 would indicate that a species is critically imperiled across its entire range (i.e., globally). In this sense the species as a whole is regarded as being at very high risk of extinction. A rank of S3 would indicate the species is vulnerable and at moderate risk within a particular state or province, even though it may be more secure elsewhere. State of Oregon Middle Columbia River steelhead are not listed by the State of Oregon as Threatened or Endangered Ochoco National Forest Steelhead (Oncorhynchus mykiss) are listed as a Management Indicator Species in the Ochoco National Forest LRMP. Other Organizations American Fisheries Society-designated as vulnerable. 9

10 III. BROADVIEW DESCRIPTION OF ANALYSIS AREA The Analysis Area includes lands within the Deschutes and John Day River Basins managed by the Ochoco NF. Figure 1 above displays steelhead habitat (same as critical habitat) within the boundaries of the Ochoco NF. The Deschutes River Basin is located in the north central part of Oregon and drains an area of approximately 10,400 square miles. The John Day River Basin is located east of the Deschutes basin and drains an area of 8,100 square miles. The ONF is 1,330 square miles. The analysis area is predominantly forested ponderosa pine, mixed conifer, juniper woodlands, and high elevation mountain hemlock plant associations. The Deschutes and John Day River Basins are primary watersheds (as defined in PACFISH and INFISH). This analysis includes portions of three 4th field subbasins of the Deschutes (Trout) and John Day Rivers (Lower and Upper John Day River). Brief descriptions of these 4 th field HUCs are included below. This assessment focuses in 5th field HUC s, within the boundary of the Ochoco NF. Table 2 lists river basins and watersheds within the area covered by this analysis. Federal lands are generally contiguous with some intermingled private lands. The following are brief descriptions of the sub-basins within or adjacent to the analysis area. Table 2 MIS Analysis Area by Watershed. MPGs Populations 3 rd Field WA 4 th Field WA 5th Field WA Cascades Deschutes Basin Trout Eastern Slope Tributaries Deschutes River Eastside Upper Trout John Day River MPG John Day Basin Lower John Day John Day River lower mainstem tributaries South Fork John Day River Bridge John Day Basin Upper John Day Mountain John Day Basin Upper John Day Rock John Day Basin Upper John Day Upper Middle John Day John Day Basin Upper John Day Lower South Fork John Day River Deschutes Basin TROUT CREEK WATERSHED (4th Field HUC) The Trout Creek Watershed comprises 446,080 acres; the Ochoco NF manages almost 35,000 acres (5%). Predominant management actions in this watershed include timber management, recreation, agriculture, and livestock. Much of the agriculture is irrigated with water diverted from Trout Creek or one of its tributaries. Push-up dams are still in use on lower Trout Creek to divert water for irrigation. By August, the water withdrawals in Trout Creek have essentially diverted all the water from the stream at Willowdale. However perennial streams on the Forest are important refugia habitats. On the ONF, the upper Trout Creek 5th Field watershed functions as important refugia habitat for steelhead. John Day Basin LOWER JOHN DAY SUBBASIN (4th Field HUC) 10

11 The John Day River drains nearly 8,100 square miles in east-central Oregon, the longest free-flowing river with wild anadromous salmon and steelhead in the Columbia River Basin. The basin includes a major part of Gilliam, Grant, and Wheeler Counties; and portions of Crook, Harney, Jefferson, Morrow, Sherman, Umatilla, Union, and Wasco Counties. The Columbia River bounds the basin to the north, the Blue Mountains to the east, the Aldrich Mountains and Strawberry Range to the south, and the Ochoco Mountains to the west. The lower basin is a plateau of nearly level to rolling Columbia River basalt deeply dissected by the John Day River and its tributaries. The lower basin s vegetation was essentially a bunchgrass climax community with some timber at higher elevations, but the introduction of livestock grazing and farming altered its character. The mainstem John Day River flows 284 miles from its source at an elevation near 9,000 feet in the Strawberry Mountains to its mouth at River Mile (RM) 218 on the Columbia River (EPA Reach ). The upper mainstem down to Picture Gorge near Dayville constitutes the Upper John Day Valley. Picture Gorge extends about 20 miles along the mainstem to Kimberly and creates a natural divide between the upper and lower basin. The lower John Day River from Service Creek (RM 185) downstream to Tumwater Falls (RM 10) is included in the federal and Oregon Scenic Waterways System. The climate of the John Day Basin is semiarid characterized by low winter and high summer temperatures, low average annual precipitation, and dry summers. Most precipitation occurs between late fall and spring. Summertime temperatures reflect hot days and cool nights. Precipitation is low over the whole plateau with much of the moisture falling on the Coast Range and Cascade Mountains before reaching the lower John Day Basin. The Blue Mountains exhibit a great range of climates because of the diversity of the region. Low elevation areas are generally warmer and receive less precipitation than higher elevations. As part of this assessment, the Bridge Creek 5th field Watershed contains important headwater streams on the Ochoco National Forest. UPPER JOHN DAY SUBBASIN (4th Field HUC) Though similar to the lower basin, the upper basin is one of Oregon s most diverse regions comprised of mountains, rugged hills, plateaus cut by streams, alluvial basins, and valleys. Soils are equally diverse and support a number of vegetation types. Coniferous forests and meadows are prevalent above 4,000 feet; the plant communities include grasses, sagebrush, and juniper trees, except on north facing slopes where higher moisture levels support vigorous perennial grasses. The lower basin is a plateau of nearly level to rolling Columbia River basalt deeply dissected by the John Day River and its tributaries. The lower basin s vegetation was essentially a bunchgrass climax community with some timber at higher elevations, but the introduction of livestock grazing and farming altered its character. This assessment includes sections of the following 5th field sub watersheds within the Ochoco National Forest: Mountain, Rock, Upper Middle John Day and Lower South Fork John Day River. 11

12 IV. SPECIES DISTRIBUTION Global Distribution (from NaturServe) Figure 2 U.S. States and Canadian Provinces Global Range: >2,500,000 square km (greater than 1,000,000 square miles) Global Range Comments: Native to streams along the Pacific coast of North America from the Kuskokwim River, Alaska, south to northern Baja California; also the upper Mackenzie River drainage (Arctic basin), Alberta and British Columbia, and endorheic (i.e. having no outflow of water) basins of southern Oregon (Page and Burr 1991). The species has been widely introduced and established in suitable habitats all over the world (Lee et al. 1980). At sea, O. mykiss occurs hroughout the North Pacific above 40 N from the North American coast to the Sea of Okhotsk (Burgner et al. 1992); it is most abundant in the Gulf of Alaska and eastern part of the North Pacific, conforming to the 5 C isotherm in the north and 15 C isotherm in the south. Seasonal shifts in distribution are correlated with changes in water temperature (Sutherland 1973). 12

13 Global Short Term Trend Comments: Of 867 steelhead stocks in British Columbia and the Yukon, Slaney et al. (1996) categorized 9 as extirpated, 8 as high risk, 10 as moderate risk, 143 as special concern, 282 as unthreatened, and 415 as of unknown status. Many winter steelhead populations are at very low levels; populations have declined in nearly all streams in central and southern California (see Nehlsen et al for further details). Winter steelhead stocks from Siuslaw River north to Tillamook Bay, Oregon, have been declining since 1990 (Nehlsen et al. 1991). In the Illinois River (tributary to the Rogue River), Oregon, winter steelhead catches have declined since the mid-1970s (Nehlsen et al. 1991). Several winter populations in the Puget Sound area of Washington have also experienced declines (Nehlsen et al. 1991). Global Protection: Very many (>40) occurrences appropriately protected and managed Global Protection Comments: Many occurrences are in protected areas. Threats: On a range-wide scale, this species is not significantly threatened. However, many subspecies and populations face serious threats (see separate accounts). Declines in winter steelhead stocks from the Siuslaw River north to Tillamook Bay, Oregon, may have resulted from deterioration of ocean feeding conditions, widespread use of hatchery stock, predation by marine mammals, and ocean drift-net fishing (Nehlsen et al. 1991). Declining winter catches on the Illinois River (tributary to the Rogue River), Oregon, since the mid-1970s have been attributed to water withdrawal for irrigation (Nehlsen et al. 1991). In the Columbia River basin, winter stocks are threatened by habitat degradation, main stem passage problems, and interactions with hatchery fish (Nehlson et al. 1991). Declines in several winter populations in the Puget Sound area of Washington have resulted from habitat degradation (e.g., water quality problems, siltation, and sedimentation); predation by sea lions has been reported as a problem for the Lake Washington population (Nehlsen et al. 1991). Whirling disease has caused population declines in some areas. The disease is caused by a protozoan pathogen (inadvertently introduced from Europe) and involves tubifex worms as an alternate host. Brown trout (Salmo trutta) are unaffected by the protozoan and serve as a reservoir. Regional and State of Oregon Distribution The spawning range of the Middle Columbia River steelhead DPS extends over an area of approximately 35,000 square miles in the Columbia plateau of eastern Washington and eastern Oregon. The DPS includes all naturally spawned populations of steelhead in drainages upstream of the Wind River, Washington, and the Hood River, Oregon (exclusive), up to, and including, the Yakima River, Washington, excluding steelhead from the Snake River Basin (64 FR 14517; 71 FR 849). Major drainages in this DPS are the Deschutes, John Day, Umatilla, Walla Walla, Yakima, and Klickitat river systems. The Cascade Mountains form the western border of the plateau in both Oregon and Washington, while the Blue Mountains form the eastern edge. The southern border is marked by the divides that separate the upper Deschutes and John Day basins from the Oregon High Desert and drainages to the south. The Wenatchee Mountains and Palouse areas of eastern Washington border the Middle Columbia on the north. 13

14 Figure 3 Mid-Columbia ESU As referenced in Section II Conservation Status, Four Major Population Groups (MPG) have been identified within the DPS: 14

15 Cascades Eastern Slope tributaries, Yakima River, John Day River Umatilla/WallaWalla Rivers The analysis area covered by this assessment includes portions of the John Day River MPG and Cascades Eastern Slope tributaries MPG, either directly inhabited by steelhead or designated as critical habitat. Within the Cascade Eastern Slope MPG, two populations (Deschutes River Eastside and Deschutes Crooked River), are included, however only the Deschutes River Eastside population is within the analysis area covered by this assessment (ONF Forest Plan). Within the John Day River MPG, two populations (John Day River Lower Mainstem Tributaries and South Fork John Day River), are included within the anlaysis area covered by this assessment. Figure 1 above shows designated critical steelhead habitat in the area covered by this analysis. MID COLUMBIA ESU STEELHEAD TROUT, Deschutes River Basin DPS DESCHUTES BASIN The Deschutes subbasin stretches over 10,700 square miles of land in central Oregon and covers 11 percent of Oregon s land area. The Confederated Tribes of Warm Springs Indian Reservation of Oregon covers approximately 641,000 acres, includes several tributaries of the Deschutes, and is bordered to the south and east by the mainstem Deschutes and the Round Butte dam complex. Summer steelhead occur throughout the mainstem lower Deschutes River below Pelton Reregulating Dam (RM 100) and in most tributaries below the dam. Before construction of the Pelton Round Butte hydroelectric complex, summer steelhead were also found in the Deschutes River upstream to Big Falls (RM 128), in Whychus Creek, and in the Crooked River (Nehlsen 1995). Historic summer steelhead presence in the Metolius River is uncertain (Nehlsen 1995). Construction of Pelton and Round Butte dams, completed in 1958 and 1964, respectively, included upstream passage facilities for adult chinook salmon and steelhead and downstream facilities for migrating juveniles. By the late 1960 s, it became apparent that the upriver runs could not be sustained naturally with these facilities, due primarily to inadequate downstream passage of juveniles through the complex, and summer steelhead production upstream of the dam complex was lost. With the new FERC license, passage at the complex is being restored and started with releases in 2008 of juveniles. Some juvenile MCR steelhead were released above Round Butte Dam in 2006 for monitoring purposes. Metolius River, Whychus Creek, Crooked River and McKay Creek are part of the implementation of this reintroduction. Summer steelhead enter the Deschutes subbasin, primarily from June through March, with peak movement in September or early October. Wild females consistently outnumber males in a run year. Information on sex:age ratio at age of return, and length:weight ratio of wild summer steelhead is not available. Spawning in the lower Deschutes River and westside tributaries usually begins in March and continues through June. Spawning in eastside tributaries occurs from January through mid-april, and may have evolved to an earlier time than westside tributaries or the mainstem because stream flow tends to decrease earlier in the more arid eastside streams (Olsen et al. 1991). 15

16 Fry emerge in spring or early summer depending on time of spawning and water temperature during incubation. Zimmerman and Reeves (1996) documented summer steelhead emergence in late May through June. Juvenile summer steelhead emigrate from the tributaries in spring at age 0 to age 3. Many of the juveniles that migrate from the tributaries continue to rear in the mainstem lower Deschutes River before smolting. Wild summer steelhead juveniles rear in the lower Deschutes River for 1 to 4 years before migrating to the ocean. Lower Deschutes River origin wild summer steelhead typically return after 1 or 2 years in the Pacific Ocean. A total of eight life history patterns were identified on scales collected from a sample of lower Deschutes River origin wild adult summer steelhead (Olsen et al. 1991). Typical of other summer steelhead stocks, very few steelhead return to spawn multiple times Wild summer steelhead spawn in the lower Deschutes River, Warm Springs River system, White River, Shitike Creek, Wapinitia Creek, Eagle Creek, Nena Creek, the Trout Creek system, the Bakeoven system, the Buck Hollow Creek system and other small tributaries with adequate flow and a lack of barriers to fish migration. Spawning in White River is limited to the 2 miles below White River Falls, an impassable barrier. A natural barrier also limits spawning opportunities in Nena Creek. The relative proportion of mainstem and tributary spawning is unknown. Based on limited spawning ground counts in the mainstem and tributaries, managers believe that mainstem spawning accounts for 30% to 60% of natural production (ODFW 1987, 1994). A residualized population of landlocked summer steelhead may persist in Lake Billy Chinook and spawn in tributaries formerly occupied by steelhead (e.g. Whychus Creek and the Crooked River). Groves (2002) noted substantial portion of redband trout in the littoral areas of Lake Billy Chinook exhibited smolt like characteristics. A large number of wild and hatchery steelhead from other Columbia Basin production areas stray into the lower Deschutes River. An unknown number of these stray steelhead leave the lower Deschutes River and continue their migration up the Columbia River. Others are harvested in fisheries in the lower Deschutes River and some remain in the subbasin to spawn. The amount of genetic interchange between out of basin and lower Deschutes River origin wild summer steelhead is unknown. The Warm Springs River system is believed to contribute a large portion of the tributary-spawned wild summer steelhead in the lower Deschutes River. Tributary spawning ground counts are incomplete most years because many tributaries are inaccessible during spawning. The Warm Springs system is particularly valuable as a refuge for wild summer steelhead since all hatchery marked or suspected hatchery origin summer steelhead are not allowed to pass the barrier dam at Warm Springs National Fish Hatchery (WSNFH Operational Plan ). This effectively excludes all non-deschutes River origin summer steelhead except stray wild summer steelhead. The number of stray wild summer steelhead being passed above the barrier dam is unknown. The most recent 5 year geometric mean population estimate for the Deschutes steelhead in aggregate is 5113 natural spawners, slightly below the recovery target of 5,400 with a population growth rate between, about 0.8 to just over 1 depending upon assumptions around the reproductive success of hatchery spawners (Good et al 2005). Threats and Limiting Factors 16

17 The Mid Columbia River Steelhead ESA Recovery Plan identified limiting factors for Trout Creek. One of the primary limiting factors is tributary habitat that has degraded riparian condition, low flows, high water temperatures, degraded channel structure/complexity and floodplain connectivity, and impaired fish passage. Additionally threats that were identified included current land use practices (grazing, roads, residences, forestry and agricultural practices that simplify habitats and irrigation withdrawals. The Deschutes River Eastside population as it relates to habitat on the ONF will be further addressed in Section VI (Population Status and Trend) and Section VII (Habitat and Trend) within the Upper Trout Creek 5 th Field WA. Limiting Factors and Threats will also be further addressed. Figure 4. (Figure ES-3. Management Units and Populations for the Middle Columbia River Steelhead DPS. P. 9 (MCR Plan Summary Document)) Segments within the ONF are included in the Deschutes River Eastside, John Day lower mainstem tributaries, and South Fork John Day River populations. 17

18 MID COLUMBIA ESU STEELHEAD TROUT, John Day River Basin DPS ESA STATUS -- THREATENED The John Day River is the longest free flowing river with wild steelhead in the Columbia River Basin. The John Day Basin has the distinction of being one of the few large basins in Oregon with no steelhead hatchery program. In the early 1960 s, managers released approximately 500,000 hatchery winter steelhead fry and limited numbers of pre-smolts used for experimental purposes. Few likely survived due to the use of improper stocks and hauling mortality (90% of the fish were dead on arrival to the release site). No production releases of hatchery steelhead pre-smolts were ever made in the John Day Basin. Hatchery releases for any purpose ceased in 1966 in favor of wild stocks. The John Day River steelhead populations are currently managed entirely as wild populations. There are five populations of John Day steelhead: Lower Main stem (below Picture Gorge), Upper Main stem (above Picture Gorge), North Fork, Middle Fork, and South Fork. Wild summer steelhead juveniles rear in the lower John Day River for 1-4 years before migrating to the ocean. John Day River-origin wild summer steelhead typically returns after 1 or 2 years in the Pacific Ocean. Typical of other summer steelhead stocks, very few steelhead return to spawn multiple times. Although stray hatchery steelhead are caught in the Lower Mainstem John Day River, especially below Cottonwood Bridge, they have been rare in the upper John Day basin. Stray rates have been estimated at 4-8% or less. A rate accepted by experts to be normal and necessary to maintain genetic diversity of the wild stock. Summer steelhead enter the John Day River Basin in late August and or September when stream temperatures drop and stream flows increase. Steelhead reach spawning areas from March through mid-may while stream flows are suitable. They spawn from March through mid-june. Fry emergence is usually from May through mid-july depending on time of spawning and water temperature during incubation. Fry emergence has been noted as late as August. Rearing is from 1-4 years and juvenile summer steelhead emigrate from April to July. The Mid-Columbia River Steelhead Recovery Plan indicates that survival of egg to smolts typically ranges from %. Survival of smolts to adults range from 2-5%. In the John Day River Basin, summer steelhead production is limited primarily by existing rearing conditions. Livestock overgrazing, water withdrawals for irrigation, clearing of land, road building, logging, and channelization degrade fish habitat by disturbing or destroying riparian vegetation and destabilizing streambanks and watersheds. The results are wide, shallow channels, low, warm summer flows; high turbid spring flows; high sediment loads; and decreased fish production. Passage conditions for both juvenile and adult anadromous fish at Columbia River mainstem dams contribute to declines in wild summer steelhead. The Dalles Dam, which all John Day River migrants must pass, has one of the lower rates of juvenile salmonid passage efficiency for mainstem Columbia River dams due to a lack of turbine screening and effective juvenile bypass facilities. Bonneville Dam, particularly Powerhouse 2, does not have an effective juvenile turbine screening. Increased spill of water at both The Dalles and Bonneville dams, to increase survival of federally listed Snake River salmon, should result in better survival of wild John Day River summer steelhead at these dams. Longer travel time for juveniles through dam- 18

19 created reservoirs in the Columbia River, increased water temperature in the reservoir environment, and increased predation near mainstem dams all contribute to increased losses of juvenile and adult wild summer steelhead. The Columbia River Fish Management Plan governs harvest of wild summer steelhead by treaty tribal fisheries in the mainstem Columbia River. This plan, agreed to by the four treaty tribes, the United States of America, and the states of Oregon, Washington, and Idaho, directs mainstem harvest decisions on wild summer steelhead using run sizes at Bonneville Dam. Treaty tribal impacts to wild summer steelhead are not to exceed 15% of the Group A (those crossing Bonneville Dam April 1 to August 25) wild escapement and 32% of the Group B (those crossing Bonneville Dam August 26 to October 31) wild escapement during fall treaty seasons. Harvest of wild summer steelhead by treaty tribal fisheries in the mainstem Columbia River has been and will continue to be a source of mortality to lower Deschutes River and John Day River wild summer steelhead. Limiting Factors and Threats pertaining to the John Day River tributaries (From the Mid-Columbia Recovery Plan) Within the Mid-Columbia River steelhead recovery plan are identified limiting factors and threats and then management strategies and actions that are recommended to address these limiting factors or threats. While many of these factors and strategies apply basin wide these are specific ones that have been identified for various tributaries to the John Day that originate on the Ochoco National Forest. One of the primary limiting factors is tributary habitat that has degraded riparian condition, low flows, high water temperatures, degraded channel structure/complexity and floodplain connectivity, and impaired fish passage. Additionally threats that were identified included current land use practices (grazing, roads, residences, forestry and agricultural practices that simplify habitats and irrigation withdrawals. The ONF supports habitat for two of the populations within the John Day River Basin MPG; Lower Mainstem Tributaries and South Fork (Figure 4 above). These populations as they relate to habitat on the ONF, will be further addressed in Section VI (Population Status and Trend) and Section VII (Habitat and Trend) within the various 5 th field watersheds: Bridge, Mountain, Rock, Upper Middle John Day, and Lower South Fork John Day. Limiting Factors and Threats will also be further addressed. Limiting Factors and Threats common to all steelhead populations (Deschutes and JohnDay MPGs) on the ONF Section 8 of the MCR plan describes limiting factors and threats to the viability of Mid-C steelhead in Oregon. The findings were identified based on many sources of information, including the Mid-Csteelhead Expert Panel s report, subbasin plans, ODEQ reports, ICTRT reports, NOAA s limiting factors modules, ODFW reports, hydrosystem biological opinion remand documents, and numerous other sources. The limiting factors and threats analyses referenced above are specific to individual populations under their respective MPGs (Deschutes and John Day). In addition, climate change, is anticipated to affect all populations to some degree within the MCR DPS. The following is also form Section 8 of the MCR Plan: Climate change is expected to increase the loss and degradation of steelhead habitat. Many of the environmental attributes that will be influenced by climate change (temperature and hydrograph) are those that have already been influenced significantly by past land use and are currently considered key limiting factors. Environmental changes associated with climate change that pose particular threats to salmonid 19

20 viability include: increased air and stream temperatures; reduced snow pack and a shift in precipitation from snow to rain; altered hydrographs with earlier and higher peak flows, and lower summer-fall flows; more frequent extreme storm events; increased periods of drought; changing ocean temperatures and current patterns; and more frequent and severe fire events (O Neal 2002; Mote et al. 2003; ISAB 2007a; Michael and O Brien 2008). Such environmental changes will impact all life stages of Oregon s Mid- Columbia River steelhead. The magnitude of environmental change will vary considerable across ecoregions; however, habitats at lower elevations east of the Cascade Mountains in the southern portion of the Columbia River basin will generally experience the greatest level of change (ISAB 2007a). 20

21 Critical Habitat Critical habitat was designated on February 16, 2000 [65 FR 7764], but vacated (undesignated)by court order on April 30, On September 2, 2005, NMFS published a final rule (70 FR 52630) to designate critical habitat for Mid-C steelhead and 12 other ESUs/DPSs of salmon and steelhead. The final rule took effect on January 2, The Critical Habitat Assessment Review Team (CHART) (NMFS 2004c) rated the conservation value of all 5th-field HUCs supporting populations of Mid-C steelhead. Essential features of designated critical habitat include substrate, water quality, water quantity, water temperature, food, riparian vegetation, access, water, velocity, space, and safe passage. These features also describe the habitat factors associated with viability for all ESUs and DPSs. The specific habitat requirements for each ESU or DPS differ by life history type and life stage. Primary constituent elements (PCEs) consist of the physical and biological elements identified as essential to the conservation of the species in the documents identifying critical habitat (Table 3-1). Figure 5 (MCR plan 3-4) depicts those streams designated critical habitat for Mid-C steelhead. Figure 5 (3-4 in MCR Plan) Critical habitat designated for salmon and steelhead in Oregon. See also Figure 1 for a more detail for the ONF. 21

22 Ochoco National Forest Distribution On the Ochoco National Forest, a total of 77.4 miles of stream (Critical Habitat) have habitat for steelhead trout. Critical habitat was mapped as known steelhead distribution. Table 3 below shows miles of steelhead trout by stream by 5 th field watershed. Additional information is included within 5 th field watershed discussions below. Habitat availability for MCR steelhead is fairly limited on the ONF. Habitat primarily consists of smaller (stream order) headwater streams on the north and east slope of the Forest, including tributaries to the Deschutes and John Day Rivers. Table 3 Ochoco National Forest Critical Habitat (miles) 5th Field WA Critical Habitat (Miles) UPPER TROUT CREEK 13.7 BRIDGE CREEK 3.9 MOUNTAIN CREEK 9.3 ROCK CREEK 9.5 UPPER MIDDLE JOHN DAY 10.0 LOWER SOUTH FORK JOHN DAY 31.0 Total

23 V. LIFE HISTORY Life History from (3.4, p. 110 of Appendix A-MCR plan) Steelhead is the name commonly applied to the anadromous form of the biological species O. mykiss. The present distribution of steelhead extends from Kamchatka in Asia, east to Alaska, and down to southern California (NMFS 1999c), although the historical range of O. mykiss extended at least to the Mexico border (Busby et al. 1996). O. mykiss exhibit perhaps the most complex suite of life history traits of any species of Pacific salmonid. They can be anadromous or freshwater residents (and under some circumstances, yield offspring of the opposite form). Those that are anadromous can spend up to seven years in fresh water before smoltification, and then spend up to three years in salt water before first spawning. This species can also spawn more than once (iteroparous), whereas all other species of Oncorhynchus except cutthroat trout (O. clarki) spawn once and then die (semelparous). The anadromous form of O. mykiss is presently under NMFS jurisdiction, while the resident freshwater forms, usually called rainbow or redband trout, are under the jurisdiction of the U.S. Fish and Wildlife Service. Within the range of West Coast steelhead, spawning migrations occur throughout the year, with seasonal peaks of activity. In a given river basin there may be one or more peaks in migration activity; since these runs are usually named for the season in which the peak occurs, some rivers may have runs known as winter, spring, summer, or fall steelhead. For example, large rivers, such as the Columbia, Rogue, and Klamath rivers, have migrating adult steelhead at all times of the year. There are local variations in the names used to identify the seasonal runs of steelhead; in Northern California, some biologists have retained the use of the terms spring and fall steelhead to describe what others would call summer steelhead. Steelhead can be divided into two basic reproductive ecotypes, based on the state of sexual maturity at the time of river entry, and duration of spawning migration (Burgner et al. 1992). The stream-maturing type (summer steelhead in the Pacific Northwest and Northern California) enters fresh water in a sexually immature condition between May and October and requires several months to mature and spawn. The ocean-maturing type (winter steelhead in the Pacific Northwest and Northern California) enters fresh water between November and April with well-developed gonads and spawns shortly thereafter. In basins with both summer and winter steelhead runs, it appears that the summer run occurs where habitat is not fully utilized by the winter run or a seasonal hydrologic barrier, such as a waterfall, separates them. Summer steelhead usually spawn farther upstream than winter steelhead (Withler 1966, Roelofs 1983, Behnke 1992). Coastal streams are dominated by winter steelhead, whereas inland steelhead of the Columbia River Basin are almost exclusively summer steelhead. Winter steelhead may have been excluded from inland areas of the Columbia River Basin by Celilo Falls or by the considerable migration distance from the ocean. The Sacramento-San Joaquin River Basin may have historically had multiple runs of steelhead that probably included both ocean-maturing and stream-maturing stocks (CDFG 1995, McEwan and Jackson 1996). These steelhead are referred to as winter steelhead by the California Department of Fish and Game (CDFG); however, some biologists call them fall steelhead (Cramer et. al 1995). Fifteenmile Creek and the Klickitat River support the populations of winter steelhead that are furthest inland in the Columbia Basin. Inland summer steelhead of the Columbia River Basin, especially the Snake River Subbasin, are commonly referred to as either A-run or B-run. These designations are based on a bimodal migration of adult steelhead at Bonneville Dam (235 km from the mouth of the Columbia River), and differences in age (1 versus 2 years in the ocean) and adult size observed among Snake River steelhead. It is unclear, however, to what degree the life history and body size differences observed upstream are correlated back to the groups forming the bimodal migration observed at Bonneville Dam. A-run steelhead are believed to occur throughout the steelhead-bearing streams of the Snake River Basin and the inland Columbia River. B-run steelhead are thought to be produced only in the Clearwater, Middle Fork Salmon, and South Fork Salmon rivers (IDFG 23

24 1994). Life history characteristics for Mid-C steelhead are similar to those of other inland steelhead DPSs. Most fish smolt at two years and spend one to two years in salt water before reentering freshwater, where they may remain up to a year before spawning. All steelhead upstream of The Dalles Dam are summer-run fish that enter the Columbia River from June to August. Adult steelhead ascend mainstem rivers and their tributaries throughout the winter, spawning in the late winter and early spring. Fry emergence typically occurs between May and the end of June. A nonanadromous form of O. mykiss co-occurs with the anadromous form in this DPS; information suggests that the two forms may not be isolated reproductively. Additional information on Life Histories of individual populations (Deschutes River Eastside, John Day River Lower Mainstem Tributaries and South Fork John Day River) of Mid-C steelhead is included in Section IV (Species Distribution) and Section VI (Population Status Trend). Species Biology (Natureserve) Basic Description: A partially anadromous salmonid. Diagnostic Characteristics: Montana: both pure and moderately hybridized populations of westslope cutthroat trout have a high incidence of basibranchial teeth, whereas pure rainbow trout lack these teeth; presence of basibranchial teeth in some individuals of a rainbow trout population indicates hybridization with westslope cutthroat trout (Leary et al. 1996). Reproduction Comments: Spawns usually in spring (February-June), or later depending on water temperature and location. Lays eggs (Wydoski and Whitney 1979), which hatch in 3-4 weeks at C. Fry emerge from gravel 2-3 weeks after hatching. Many are sexually mature in 2-3 years. See Stearley (1992) for a discussion of the historical ecology and life history evolution of Pacific salmons and trouts (Oncorhynchus). Ecology Comments: Normal life span 5-6 years (Simpson and Wallace 1982). Predation by Caspian terns and double-crested cormorants causes significant mortality of juvenile steelhead in the Columbia River estuary (Ryan et al. 2003). Aggressively defends feeding territories in streams and has caused contraction of range of native brook trout in southern Appalachian Mountains region (Larson and Moore 1985). Habitat Type: Freshwater Non-Migrant: Y Locally Migrant: Y Long Distance Migrant: Y Mobility and Migration Comments: Anadromous forms migrate up to at least hundreds of miles between spawning streams and nonspawning marine waters. Stream-dwelling trout may spend an entire life in few hundred meters of stream (Moyle 1976). Lake-dwelling trout typically migrate to tributaries to spawn. Habitat Comments: Capable of surviving in a wide range of temperature conditions. Does best where dissolved oxygen concentration is at least 7 ppm. Anadromous populations occur in coastal rivers. Resident populations now inhabit small headwater streams, large rivers, lakes, or reservoirs; often in cool clear lakes and cool swift streams with silt-free substrate. In streams, deep low velocity pools are important wintering habitats (Sublette et al. 1990). Usually requires a gravel stream riffle for successful spawning. Lake populations move to tributaries to spawn. Eggs are laid in gravel in a depression made by the female. Salinity of 8 ppt is the upper limit for normal development of eggs and alevins (Morgan et al. 1992). 24

25 Food Comments: In lakes, feeds mostly on bottom-dwelling invertebrates (e.g., aquatic insects, amphipods, worms, fish eggs, sometimes small fish) and plankton. In streams, feeds primarily on drift organisms. May ingest aquatic vegetation (probably for attached invertebrates). Diet changes seasonally. In the ocean, the diet consists of fishes and crustaceans. Phenology Comments: May feed at any time throughout a 24-hour period, but usually feeds most actively around dusk. Additional Information is available on the NOAA website and others, including: and Recovery-Planning/Recovery-Domains/Interior-Columbia/Mid-Columbia/Mid-Col-Plan.cfm and Habitat requirements As previously discussed, critical habitat for Mid-Columbia steelhead trout occurs in most all of the tributaries along the north and east facing slopes of the Ochoco National Forest that flow into the John Day River or South Fork of the John Day River (Figures 1 and 5). Primary constituent elements (PCEs) were developed with the critical habitat designation. For anadromous fish, the essential features of designated critical habitat include substrate, water quality, water quantity, water temperature, food, riparian vegetation, access, water, velocity, space, and safe passage. Primary constituent elements of critical habitat for steelhead, i.e., the physical and biological elements that support one or more life stages and are considered essential to the conservation of the species were identified (Table 4). Table 4 (section 3-13 MCR Plan) Types of sites and essential physical and biological features designated as PCEs for steelhead, and the life stage each PCE supports.l andbiological Features ESU/DPS Life Stage Freshwater spawning Water quality, water quantity, and substrate, Spawning, incubation, and larval development, Freshwater rearing Freshwater migration Estuarine areas freshwater, Water quantity and floodplain, connectivity Water quality and forage Natural cover Free of artificial obstructions, water quality and quantity, and natural cover Free of obstruction, water quality and quantity, and salinity Natural cover, forage, and, water quantity Juvenile growth and mobility, Juvenile development, Juvenile mobility and survival Juvenile and adult mobility and, survival Juvenile and adult physiological, transitions between salt and freshwater Growth and maturation, 25

26 Nearshore marine areas Free of obstruction, water quality, and quantity, natural cover, and forage, Growth and maturation, survival, Offshore marine areas Water quality and forage Growth and maturation 26

27 VI. POPULATION STATUS AND TREND As discussed above under the Species Distribution section, the analysis area (ONF) covered by this assessment includes portions of the John Day River MPG and Cascades Eastern Slope tributaries MPG, either directly inhabited by steelhead or designated as critical habitat. Within the Cascade Eastern Slope MPG, two populations (Deschutes River Eastside and Deschutes-Crooked River), are included within the ONF boundary. However, this analysis only addresses the Deschutes River Eastside population as directed in the ONFLRMP. The Deschutes-Crooked River population is technically listed as extinct in the MCR Plan. However, significant efforts are underway to reestablish the population. Within the John Day River MPG, two populations (John Day River Lower Mainstem Tributaries and South Fork John Day River), are included in this analysis. This section addresses population status and trend of the steelhead trout. This section also includes a discussion at the 5th field watershed level on the segments of these populations that are within lands administered by the ONF, e.g, the Deschutes River Eastside population within the Upper Trout Creek 5th field watershed. Additional information from ODFW, USFS and others is integrated into the analysis including a recent Biological Assessment on grazing in anadromous watersheds within the ONF (ONF, 2011). The following information is summarized from the 2009 MCR plan (Current Population Status (MCR plan 1.6): The status of a salmon or steelhead species is expressed in terms of likelihood of persistence over 100 years, or in terms of risk of extinction within 100 years. The ICTRT defined viability at two levels: less than 5 percent risk of extinction within 100 years (viable) and less than 1 percent risk of extinction within 100 years (highly viable). A third category, maintained, represents a less than 25 percent risk. The risk level of the DPS as a whole is built up from the aggregate risk levels of the populations and MPGs. The abundance, productivity, spatial structure, and diversity of the component populations (the viable salmonid population, or VSP, parameters) must be taken into account to determine the risk level. Assessing the current status of the populations according to the viability criteria is a critical first step in determining a path towards MPG and DPS viability. Following ICTRT guidelines, we completed viability assessments for Oregon s ten extant Mid-C steelhead populations. The assessments describe the current status of the populations relative to the abundance/productivity and spatial structure/diversity viability criteria. Overall, the viability assessments show that only three of Oregon s Mid-C steelhead populations currently meet the viability criteria. The North Fork John Day population is highly viable and the Fifteenmile Creek and Deschutes River Eastside populations are viable. The remaining populations rated as either maintained or extinct. Assessment findings are provided for each of the ten populations in the population summaries (later in this section-1.14) and in Section 6 of the recovery plan. Appendix B contains the detailed individual population viability assessments, including population-specific data sources and methods used to estimate abundance. We also completed viability assessments for the three MPGs containing the Oregon populations. The assessment findings indicate that the three MPGs are currently below viable status based on the status of the constituent populations. These findings are shown below in Tables 5 and 8 below. 27